Query 017706
Match_columns 367
No_of_seqs 361 out of 504
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 02:43:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017706.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017706hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0944 Ubiquitin-specific pro 100.0 2.9E-31 6.2E-36 274.8 7.1 158 3-170 438-627 (763)
2 KOG2689 Predicted ubiquitin re 100.0 2.5E-28 5.4E-33 231.7 16.6 207 118-325 4-237 (290)
3 COG5207 UBP14 Isopeptidase T [ 99.9 1.8E-27 4E-32 240.7 8.3 156 3-169 429-613 (749)
4 KOG2507 Ubiquitin regulatory p 99.7 1.2E-17 2.6E-22 166.8 6.7 162 175-338 190-354 (506)
5 KOG2699 Predicted ubiquitin re 99.6 2.4E-15 5.2E-20 150.8 5.2 324 21-361 5-347 (407)
6 PF09409 PUB: PUB domain; Int 99.0 1.2E-10 2.5E-15 94.2 2.8 45 319-363 4-48 (87)
7 PF00627 UBA: UBA/TS-N domain; 98.9 9.1E-10 2E-14 75.7 4.2 37 113-150 1-37 (37)
8 cd00194 UBA Ubiquitin Associat 98.8 1.4E-08 3.1E-13 69.6 5.3 38 114-152 1-38 (38)
9 smart00165 UBA Ubiquitin assoc 98.8 1.3E-08 2.8E-13 69.5 4.9 37 114-151 1-37 (37)
10 KOG0944 Ubiquitin-specific pro 98.5 1.5E-07 3.2E-12 99.6 5.1 46 112-158 633-678 (763)
11 smart00580 PUG domain in prote 97.9 4.6E-06 1E-10 63.2 1.4 35 323-363 1-35 (58)
12 cd02664 Peptidase_C19H A subfa 97.8 6.3E-06 1.4E-10 81.1 1.2 53 42-101 154-213 (327)
13 cd02668 Peptidase_C19L A subfa 97.8 6.4E-06 1.4E-10 80.7 0.6 53 42-101 176-235 (324)
14 cd02667 Peptidase_C19K A subfa 97.7 9.5E-06 2.1E-10 78.0 0.9 49 43-101 132-186 (279)
15 cd02660 Peptidase_C19D A subfa 97.7 9.9E-06 2.1E-10 78.7 0.7 52 43-101 196-253 (328)
16 cd02663 Peptidase_C19G A subfa 97.5 2.6E-05 5.6E-10 75.6 1.1 52 42-100 167-225 (300)
17 cd02657 Peptidase_C19A A subfa 97.5 4.1E-05 9E-10 73.8 1.6 52 42-100 175-233 (305)
18 cd02658 Peptidase_C19B A subfa 97.5 3.4E-05 7.3E-10 74.7 0.6 50 40-96 192-247 (311)
19 cd02661 Peptidase_C19E A subfa 97.4 4.1E-05 8.9E-10 72.9 1.1 52 43-101 183-237 (304)
20 cd02659 peptidase_C19C A subfa 97.4 4.4E-05 9.6E-10 74.4 0.6 53 42-101 171-230 (334)
21 cd02674 Peptidase_C19R A subfa 97.3 9.4E-05 2E-09 68.0 1.2 53 41-100 103-161 (230)
22 cd02673 Peptidase_C19Q A subfa 97.1 0.00017 3.7E-09 68.9 1.4 38 40-85 124-161 (245)
23 TIGR00601 rad23 UV excision re 97.0 0.00084 1.8E-08 68.3 5.2 41 114-155 156-196 (378)
24 KOG1865 Ubiquitin carboxyl-ter 96.8 0.00054 1.2E-08 71.9 2.2 90 5-101 239-341 (545)
25 COG5207 UBP14 Isopeptidase T [ 96.7 0.00074 1.6E-08 70.5 1.8 53 111-165 618-670 (749)
26 cd02671 Peptidase_C19O A subfa 96.6 0.00083 1.8E-08 66.9 1.8 53 42-101 200-263 (332)
27 KOG4598 Putative ubiquitin-spe 95.9 0.0017 3.6E-08 70.0 -0.7 54 41-101 233-293 (1203)
28 COG5533 UBP5 Ubiquitin C-termi 95.9 0.0015 3.2E-08 64.9 -1.3 41 42-89 284-326 (415)
29 cd02662 Peptidase_C19F A subfa 95.8 0.0018 3.9E-08 61.1 -1.0 43 39-96 110-158 (240)
30 KOG2561 Adaptor protein NUB1, 95.5 0.034 7.3E-07 57.7 6.7 48 110-158 425-472 (568)
31 TIGR00601 rad23 UV excision re 95.4 0.024 5.3E-07 57.8 5.4 45 111-156 334-378 (378)
32 KOG0011 Nucleotide excision re 94.7 0.046 9.9E-07 54.6 4.9 40 114-154 298-337 (340)
33 cd02257 Peptidase_C19 Peptidas 94.6 0.018 3.9E-07 51.4 1.8 55 38-99 112-174 (255)
34 cd02672 Peptidase_C19P A subfa 94.5 0.013 2.7E-07 56.9 0.7 40 38-84 130-173 (268)
35 KOG0011 Nucleotide excision re 94.5 0.045 9.8E-07 54.7 4.5 41 113-154 134-174 (340)
36 KOG1866 Ubiquitin carboxyl-ter 93.5 0.017 3.7E-07 62.8 -0.7 53 42-101 266-325 (944)
37 PF09288 UBA_3: Fungal ubiquit 93.4 0.079 1.7E-06 40.0 2.9 30 111-140 6-35 (55)
38 cd02669 Peptidase_C19M A subfa 93.4 0.03 6.5E-07 57.8 1.0 57 38-101 307-369 (440)
39 KOG0163 Myosin class VI heavy 92.4 2.1 4.6E-05 47.4 12.9 84 182-268 924-1014(1259)
40 PTZ00266 NIMA-related protein 91.9 2.4 5.1E-05 48.7 13.4 17 249-266 508-524 (1021)
41 smart00546 CUE Domain that may 91.2 0.42 9E-06 33.5 4.3 37 114-152 2-41 (43)
42 COG1773 Rubredoxin [Energy pro 90.3 0.079 1.7E-06 40.0 -0.1 42 5-50 3-44 (55)
43 KOG2561 Adaptor protein NUB1, 90.1 0.34 7.4E-06 50.5 4.2 45 112-157 373-417 (568)
44 COG5560 UBP12 Ubiquitin C-term 90.0 0.088 1.9E-06 56.8 -0.1 54 41-101 694-753 (823)
45 PF08882 Acetone_carb_G: Aceto 89.9 0.14 3.1E-06 43.7 1.1 46 5-51 24-83 (112)
46 PF00443 UCH: Ubiquitin carbox 89.8 0.078 1.7E-06 48.3 -0.6 49 41-101 141-197 (269)
47 PF02845 CUE: CUE domain; Int 89.1 1.2 2.6E-05 31.1 5.2 38 115-153 2-41 (42)
48 PF14555 UBA_4: UBA-like domai 88.2 1.4 3.1E-05 31.0 5.1 40 117-157 3-43 (43)
49 PF12756 zf-C2H2_2: C2H2 type 88.0 0.1 2.3E-06 41.4 -1.0 66 7-72 1-80 (100)
50 cd00730 rubredoxin Rubredoxin; 87.6 0.13 2.9E-06 37.9 -0.5 42 6-51 2-43 (50)
51 KOG1029 Endocytic adaptor prot 87.3 11 0.00023 42.3 13.2 31 126-156 212-242 (1118)
52 KOG0163 Myosin class VI heavy 87.2 7 0.00015 43.6 11.8 55 208-263 941-995 (1259)
53 PF05672 MAP7: MAP7 (E-MAP-115 87.2 24 0.00053 32.5 15.7 25 177-201 18-42 (171)
54 KOG1868 Ubiquitin C-terminal h 86.5 0.17 3.6E-06 55.1 -0.7 38 43-85 518-555 (653)
55 KOG0418 Ubiquitin-protein liga 86.1 0.79 1.7E-05 42.7 3.5 39 113-152 161-199 (200)
56 cd00350 rubredoxin_like Rubred 85.9 0.37 8E-06 32.3 1.0 25 6-51 2-26 (33)
57 KOG2699 Predicted ubiquitin re 85.8 0.49 1.1E-05 48.7 2.2 54 305-360 153-206 (407)
58 KOG1029 Endocytic adaptor prot 85.5 10 0.00022 42.4 11.9 19 113-131 213-231 (1118)
59 cd02670 Peptidase_C19N A subfa 85.2 0.34 7.3E-06 46.6 0.7 42 60-101 88-134 (241)
60 PF07499 RuvA_C: RuvA, C-termi 85.2 2.2 4.8E-05 30.7 4.8 32 114-145 3-37 (47)
61 PF00301 Rubredoxin: Rubredoxi 84.5 0.32 6.9E-06 35.5 0.1 43 5-51 1-43 (47)
62 PRK03824 hypA hydrogenase nick 80.2 0.82 1.8E-05 40.2 1.1 47 4-51 69-116 (135)
63 PRK12332 tsf elongation factor 79.9 3.8 8.2E-05 38.5 5.5 41 113-154 3-44 (198)
64 PF02148 zf-UBP: Zn-finger in 79.3 0.96 2.1E-05 34.3 1.1 44 5-50 11-57 (63)
65 KOG1144 Translation initiation 79.2 16 0.00035 40.9 10.6 28 187-214 216-243 (1064)
66 PRK09377 tsf elongation factor 78.8 3.9 8.4E-05 40.6 5.5 41 113-154 4-45 (290)
67 KOG0010 Ubiquitin-like protein 78.7 2.8 6.1E-05 44.2 4.6 36 116-152 456-492 (493)
68 TIGR00116 tsf translation elon 78.1 4.2 9.1E-05 40.3 5.5 41 113-154 3-44 (290)
69 cd02665 Peptidase_C19I A subfa 75.3 0.99 2.1E-05 43.0 0.2 37 60-96 118-159 (228)
70 PRK06369 nac nascent polypepti 74.7 7 0.00015 33.8 5.2 41 111-152 73-114 (115)
71 CHL00098 tsf elongation factor 74.3 6.5 0.00014 37.0 5.4 38 116-154 3-41 (200)
72 PF09862 DUF2089: Protein of u 74.2 3.1 6.7E-05 35.9 2.9 12 40-51 10-21 (113)
73 KOG4364 Chromatin assembly fac 74.1 1.4E+02 0.003 33.3 15.7 18 229-246 307-324 (811)
74 PHA00732 hypothetical protein 74.0 3.6 7.8E-05 33.0 3.1 36 6-52 2-37 (79)
75 KOG1870 Ubiquitin C-terminal h 73.7 0.7 1.5E-05 51.9 -1.4 53 42-101 716-774 (842)
76 PTZ00121 MAEBL; Provisional 73.0 55 0.0012 39.4 13.0 15 71-85 904-918 (2084)
77 PHA02768 hypothetical protein; 72.8 3.3 7.2E-05 31.3 2.4 37 4-51 4-40 (55)
78 PF07227 DUF1423: Protein of u 72.4 97 0.0021 32.7 13.7 46 6-51 147-192 (446)
79 smart00531 TFIIE Transcription 71.9 3.1 6.8E-05 36.8 2.6 37 2-51 96-132 (147)
80 KOG2412 Nuclear-export-signal 71.7 36 0.00079 36.7 10.6 16 63-78 19-34 (591)
81 PF14599 zinc_ribbon_6: Zinc-r 71.4 1.8 3.9E-05 33.4 0.8 28 4-50 29-56 (61)
82 PF15236 CCDC66: Coiled-coil d 69.9 88 0.0019 28.5 12.3 24 235-258 115-138 (157)
83 PF07946 DUF1682: Protein of u 69.7 13 0.00028 37.1 6.6 8 71-78 110-117 (321)
84 PF12171 zf-C2H2_jaz: Zinc-fin 69.7 1.1 2.3E-05 28.3 -0.7 20 7-26 3-22 (27)
85 cd00729 rubredoxin_SM Rubredox 69.3 2.5 5.4E-05 28.6 1.0 26 5-51 2-27 (34)
86 PTZ00121 MAEBL; Provisional 68.8 81 0.0018 38.1 13.2 10 258-267 1259-1268(2084)
87 KOG1863 Ubiquitin carboxyl-ter 68.8 1.8 3.9E-05 50.1 0.4 67 28-101 323-396 (1093)
88 PF07946 DUF1682: Protein of u 67.2 27 0.00058 34.8 8.3 9 28-36 42-50 (321)
89 PRK12380 hydrogenase nickel in 66.9 3.1 6.7E-05 35.5 1.4 12 4-15 69-80 (113)
90 PF15236 CCDC66: Coiled-coil d 65.9 1.1E+02 0.0023 28.0 13.0 6 177-182 40-45 (157)
91 PF14353 CpXC: CpXC protein 65.3 4.3 9.4E-05 34.7 2.0 12 40-51 36-47 (128)
92 PF09723 Zn-ribbon_8: Zinc rib 64.1 5.1 0.00011 28.2 1.8 34 1-50 1-34 (42)
93 PF11626 Rap1_C: TRF2-interact 63.5 11 0.00023 30.5 3.9 37 119-156 2-38 (87)
94 TIGR00100 hypA hydrogenase nic 63.4 3.8 8.3E-05 35.0 1.3 27 4-51 69-95 (115)
95 TIGR00264 alpha-NAC-related pr 63.0 16 0.00035 31.6 5.0 39 112-151 76-115 (116)
96 PF05835 Synaphin: Synaphin pr 62.4 18 0.0004 32.2 5.4 21 247-274 58-78 (139)
97 smart00834 CxxC_CXXC_SSSS Puta 62.2 6.5 0.00014 26.6 2.1 16 1-16 1-16 (41)
98 PF12756 zf-C2H2_2: C2H2 type 62.1 8.5 0.00018 30.2 3.1 32 5-36 50-81 (100)
99 smart00290 ZnF_UBP Ubiquitin C 61.8 4.7 0.0001 28.7 1.4 31 5-35 11-44 (50)
100 PRK00398 rpoP DNA-directed RNA 61.5 6 0.00013 28.1 1.8 28 5-51 3-30 (46)
101 PRK03681 hypA hydrogenase nick 61.5 4.7 0.0001 34.4 1.5 10 4-13 69-78 (114)
102 PF00096 zf-C2H2: Zinc finger, 61.0 7 0.00015 23.1 1.8 20 7-26 2-21 (23)
103 COG5077 Ubiquitin carboxyl-ter 60.5 3.5 7.6E-05 45.9 0.7 43 59-101 367-416 (1089)
104 TIGR00310 ZPR1_znf ZPR1 zinc f 59.3 2.3 4.9E-05 39.8 -0.9 38 6-51 1-39 (192)
105 PRK00409 recombination and DNA 58.6 2.3E+02 0.005 31.9 14.4 27 114-140 487-513 (782)
106 TIGR00373 conserved hypothetic 58.1 8.8 0.00019 34.5 2.8 30 4-51 108-137 (158)
107 PF10122 Mu-like_Com: Mu-like 56.9 5.9 0.00013 29.5 1.1 29 5-50 4-32 (51)
108 TIGR02605 CxxC_CxxC_SSSS putat 56.8 8.5 0.00018 27.7 2.0 16 1-16 1-16 (52)
109 PRK00564 hypA hydrogenase nick 56.7 5.7 0.00012 34.1 1.2 12 4-15 70-81 (117)
110 PF07754 DUF1610: Domain of un 54.9 5.3 0.00012 25.3 0.5 11 40-50 14-24 (24)
111 smart00709 Zpr1 Duplicated dom 53.1 3.7 8.1E-05 37.2 -0.5 37 7-51 2-38 (160)
112 PRK06266 transcription initiat 52.6 12 0.00026 34.4 2.7 30 4-51 116-145 (178)
113 PHA00733 hypothetical protein 51.2 16 0.00035 31.8 3.1 36 6-52 74-109 (128)
114 TIGR01069 mutS2 MutS2 family p 50.5 3.1E+02 0.0066 31.0 13.7 36 115-152 483-518 (771)
115 KOG1363 Predicted regulator of 50.4 61 0.0013 34.4 7.8 40 300-343 385-424 (460)
116 KOG3634 Troponin [Cytoskeleton 50.4 92 0.002 31.7 8.6 10 321-330 239-248 (361)
117 COG5134 Uncharacterized conser 49.8 8 0.00017 37.0 1.1 51 1-51 38-88 (272)
118 PF13423 UCH_1: Ubiquitin carb 49.6 9.5 0.00021 36.9 1.6 56 39-101 177-237 (295)
119 PRK00247 putative inner membra 49.2 3.4E+02 0.0074 28.6 14.2 8 29-36 99-106 (429)
120 PF01155 HypA: Hydrogenase exp 49.2 9.8 0.00021 32.3 1.5 12 4-15 69-80 (113)
121 PF13894 zf-C2H2_4: C2H2-type 48.3 17 0.00036 21.0 2.0 20 7-26 2-21 (24)
122 KOG1864 Ubiquitin-specific pro 47.9 8.8 0.00019 41.7 1.2 52 41-99 440-498 (587)
123 KOG1144 Translation initiation 47.8 2.2E+02 0.0047 32.6 11.5 8 208-215 244-251 (1064)
124 PF11547 E3_UbLigase_EDD: E3 u 47.5 77 0.0017 23.6 5.6 46 110-156 5-52 (53)
125 KOG3654 Uncharacterized CH dom 47.5 1.4E+02 0.0031 32.2 9.8 38 221-258 414-451 (708)
126 COG1656 Uncharacterized conser 47.1 11 0.00024 34.6 1.5 40 6-51 98-139 (165)
127 KOG3080 Nucleolar protein-like 47.0 1.3E+02 0.0028 30.4 8.9 55 187-241 182-236 (328)
128 PF01927 Mut7-C: Mut7-C RNAse 46.8 8.8 0.00019 33.9 0.8 43 5-51 91-133 (147)
129 PF12874 zf-met: Zinc-finger o 46.3 15 0.00033 22.1 1.7 21 6-26 1-21 (25)
130 PF11372 DUF3173: Domain of un 46.2 22 0.00048 27.3 2.8 19 119-137 7-25 (59)
131 PRK14605 ruvA Holliday junctio 46.1 46 0.001 31.0 5.5 39 114-152 148-189 (194)
132 COG0375 HybF Zn finger protein 46.0 12 0.00026 32.3 1.5 12 40-51 84-95 (115)
133 COG0264 Tsf Translation elonga 45.4 40 0.00086 33.7 5.2 40 113-153 4-44 (296)
134 PRK14601 ruvA Holliday junctio 45.2 50 0.0011 30.6 5.6 32 114-145 142-173 (183)
135 COG4416 Com Mu-like prophage p 45.1 7.1 0.00015 29.6 -0.0 30 4-50 3-32 (60)
136 PF04615 Utp14: Utp14 protein; 44.9 1.4E+02 0.0031 33.1 10.1 19 175-193 194-212 (735)
137 PF05262 Borrelia_P83: Borreli 44.6 2.6E+02 0.0056 30.0 11.4 16 123-138 95-111 (489)
138 PRK00762 hypA hydrogenase nick 43.3 14 0.0003 32.0 1.5 9 43-51 93-101 (124)
139 PRK05978 hypothetical protein; 43.1 13 0.00028 33.4 1.4 48 3-78 31-78 (148)
140 KOG1074 Transcriptional repres 43.0 14 0.00031 41.5 1.9 54 3-65 351-404 (958)
141 KOG2462 C2H2-type Zn-finger pr 42.9 15 0.00033 36.2 1.9 14 3-16 185-198 (279)
142 KOG2412 Nuclear-export-signal 42.7 4.5E+02 0.0099 28.7 12.7 14 301-314 329-342 (591)
143 TIGR00084 ruvA Holliday juncti 41.8 33 0.00072 31.8 3.9 25 114-138 147-171 (191)
144 KOG3993 Transcription factor ( 41.4 7.3 0.00016 40.6 -0.5 20 121-140 454-473 (500)
145 KOG2072 Translation initiation 41.4 3.3E+02 0.0071 31.3 11.8 23 233-255 832-854 (988)
146 PRK11546 zraP zinc resistance 41.4 1.8E+02 0.0039 26.1 8.3 61 176-236 42-114 (143)
147 COG4008 Predicted metal-bindin 41.2 75 0.0016 28.2 5.7 41 110-152 110-150 (153)
148 KOG0435 Leucyl-tRNA synthetase 40.9 22 0.00048 39.4 2.9 74 5-89 436-516 (876)
149 PF05907 DUF866: Eukaryotic pr 40.8 6.1 0.00013 35.8 -1.1 41 3-51 28-73 (161)
150 COG1996 RPC10 DNA-directed RNA 40.6 15 0.00033 27.2 1.1 30 3-51 4-33 (49)
151 PF06107 DUF951: Bacterial pro 40.2 15 0.00033 28.0 1.1 14 2-15 28-41 (57)
152 PRK14606 ruvA Holliday junctio 39.1 73 0.0016 29.6 5.7 24 115-138 144-167 (188)
153 PRK14600 ruvA Holliday junctio 38.7 73 0.0016 29.6 5.6 36 114-149 145-181 (186)
154 PRK00116 ruvA Holliday junctio 38.1 56 0.0012 30.2 4.8 26 115-140 150-175 (192)
155 PF09845 DUF2072: Zn-ribbon co 38.0 16 0.00036 32.2 1.2 10 7-16 3-12 (131)
156 KOG0608 Warts/lats-like serine 37.9 20 0.00043 39.9 1.9 43 109-151 84-126 (1034)
157 PF05191 ADK_lid: Adenylate ki 37.9 24 0.00052 24.2 1.7 30 5-51 1-30 (36)
158 PF10083 DUF2321: Uncharacteri 37.9 5.9 0.00013 36.0 -1.6 39 6-52 40-78 (158)
159 PRK14602 ruvA Holliday junctio 37.9 76 0.0017 29.7 5.7 25 114-138 155-179 (203)
160 KOG4722 Zn-finger protein [Gen 37.8 2.7E+02 0.0058 29.6 9.9 20 180-199 249-268 (672)
161 KOG2462 C2H2-type Zn-finger pr 37.0 17 0.00036 36.0 1.1 69 4-81 129-197 (279)
162 PF10827 DUF2552: Protein of u 37.0 23 0.0005 28.3 1.7 17 141-157 59-75 (79)
163 PF14690 zf-ISL3: zinc-finger 37.0 17 0.00036 25.4 0.9 40 43-82 3-43 (47)
164 PF14205 Cys_rich_KTR: Cystein 36.2 19 0.00041 27.3 1.1 26 43-73 5-30 (55)
165 PRK06231 F0F1 ATP synthase sub 36.1 3.7E+02 0.0079 25.1 12.8 15 181-195 78-92 (205)
166 KOG0804 Cytoplasmic Zn-finger 36.1 17 0.00037 38.2 1.1 31 6-36 241-274 (493)
167 KOG2907 RNA polymerase I trans 35.7 11 0.00025 32.5 -0.2 24 38-66 70-93 (116)
168 cd02669 Peptidase_C19M A subfa 35.6 16 0.00035 37.8 0.9 42 7-50 30-74 (440)
169 PRK06568 F0F1 ATP synthase sub 35.6 3.3E+02 0.0073 24.5 12.5 14 181-194 34-47 (154)
170 COG1308 EGD2 Transcription fac 35.4 47 0.001 29.1 3.6 39 111-150 81-120 (122)
171 PF06676 DUF1178: Protein of u 35.0 40 0.00086 30.4 3.1 14 1-15 1-14 (148)
172 PLN03086 PRLI-interacting fact 34.9 2.1E+02 0.0045 31.3 9.0 9 253-261 56-64 (567)
173 PRK14603 ruvA Holliday junctio 34.9 86 0.0019 29.3 5.5 24 115-138 153-176 (197)
174 PF06936 Selenoprotein_S: Sele 34.6 1.4E+02 0.003 28.0 6.7 29 222-250 87-115 (190)
175 PRK14604 ruvA Holliday junctio 34.1 1.1E+02 0.0023 28.6 6.0 24 115-138 150-173 (195)
176 COG1594 RPB9 DNA-directed RNA 33.9 16 0.00034 31.3 0.4 29 42-75 72-100 (113)
177 COG3937 Uncharacterized conser 33.4 2.8E+02 0.0061 23.8 7.8 29 175-203 36-64 (108)
178 COG4049 Uncharacterized protei 33.0 23 0.00049 27.2 1.1 28 4-32 16-43 (65)
179 KOG2703 C4-type Zn-finger prot 33.0 17 0.00037 37.7 0.5 27 8-51 42-77 (460)
180 COG1675 TFA1 Transcription ini 32.6 37 0.0008 31.4 2.6 11 41-51 131-141 (176)
181 PF13717 zinc_ribbon_4: zinc-r 32.4 27 0.00058 23.8 1.3 13 3-15 23-35 (36)
182 PF05890 Ebp2: Eukaryotic rRNA 32.4 3.4E+02 0.0074 26.7 9.4 53 188-240 121-173 (271)
183 smart00659 RPOLCX RNA polymera 32.2 31 0.00068 24.7 1.6 17 43-66 20-36 (44)
184 PF10058 DUF2296: Predicted in 31.7 29 0.00063 26.0 1.5 34 2-50 19-52 (54)
185 PRK00247 putative inner membra 31.7 6.4E+02 0.014 26.6 12.1 8 257-264 373-380 (429)
186 PRK14890 putative Zn-ribbon RN 31.6 10 0.00022 29.1 -1.0 13 6-18 8-20 (59)
187 TIGR01069 mutS2 MutS2 family p 31.3 7.5E+02 0.016 27.9 13.0 18 320-337 702-719 (771)
188 COG1545 Predicted nucleic-acid 31.2 31 0.00068 30.4 1.8 17 29-51 36-52 (140)
189 PF02146 SIR2: Sir2 family; I 31.2 48 0.0011 29.7 3.1 14 4-17 104-117 (178)
190 PF08938 HBS1_N: HBS1 N-termin 30.8 26 0.00057 27.8 1.2 27 127-154 45-71 (79)
191 PF10367 Vps39_2: Vacuolar sor 30.7 22 0.00047 28.6 0.7 27 42-78 78-104 (109)
192 PRK14474 F0F1 ATP synthase sub 30.6 5E+02 0.011 25.0 12.5 14 181-194 35-48 (250)
193 PTZ00172 40S ribosomal protein 30.2 39 0.00084 29.0 2.1 45 5-49 20-78 (108)
194 smart00355 ZnF_C2H2 zinc finge 30.0 43 0.00093 19.2 1.8 20 7-26 2-21 (26)
195 KOG2891 Surface glycoprotein [ 29.8 6E+02 0.013 25.7 10.6 73 183-255 324-398 (445)
196 PF04641 Rtf2: Rtf2 RING-finge 29.3 12 0.00027 36.1 -1.1 49 3-52 111-160 (260)
197 KOG0971 Microtubule-associated 29.2 9.9E+02 0.022 28.1 14.2 80 177-257 223-306 (1243)
198 PF05605 zf-Di19: Drought indu 28.8 62 0.0013 23.6 2.8 38 5-50 2-39 (54)
199 PRK13901 ruvA Holliday junctio 28.4 66 0.0014 30.3 3.5 24 115-138 145-168 (196)
200 PF05262 Borrelia_P83: Borreli 27.5 7E+02 0.015 26.8 11.3 8 71-78 49-56 (489)
201 PHA00616 hypothetical protein 27.4 32 0.0007 24.9 1.0 21 6-26 2-22 (44)
202 COG4481 Uncharacterized protei 27.1 34 0.00074 26.1 1.1 14 2-15 31-44 (60)
203 KOG2357 Uncharacterized conser 27.0 1.8E+02 0.0038 30.6 6.6 9 93-101 242-250 (440)
204 PF13451 zf-trcl: Probable zin 26.9 40 0.00088 24.9 1.5 39 3-50 2-41 (49)
205 KOG2505 Ankyrin repeat protein 26.7 5.2E+02 0.011 28.1 10.0 46 114-159 403-458 (591)
206 CHL00118 atpG ATP synthase CF0 26.7 4.5E+02 0.0097 23.2 12.8 17 181-197 52-68 (156)
207 PF04361 DUF494: Protein of un 26.6 1.8E+02 0.0038 26.3 5.9 55 115-185 24-78 (155)
208 TIGR00340 zpr1_rel ZPR1-relate 26.3 15 0.00032 33.6 -1.1 37 8-51 1-37 (163)
209 PRK09173 F0F1 ATP synthase sub 26.1 4.5E+02 0.0098 23.1 12.5 14 181-194 32-45 (159)
210 PRK09335 30S ribosomal protein 25.9 51 0.0011 27.7 2.1 41 5-49 20-74 (95)
211 PF13912 zf-C2H2_6: C2H2-type 25.9 58 0.0013 19.9 1.9 21 6-26 2-22 (27)
212 PLN00186 ribosomal protein S26 25.8 58 0.0013 28.0 2.5 42 5-49 20-78 (109)
213 KOG2002 TPR-containing nuclear 25.3 8.5E+02 0.018 28.5 11.9 23 133-157 724-746 (1018)
214 PRK07352 F0F1 ATP synthase sub 25.2 5E+02 0.011 23.2 12.5 16 181-196 49-64 (174)
215 PRK13428 F0F1 ATP synthase sub 25.2 8.1E+02 0.018 25.7 14.1 22 334-355 311-332 (445)
216 COG0423 GRS1 Glycyl-tRNA synth 24.9 80 0.0017 34.1 3.8 49 4-53 87-140 (558)
217 PRK07353 F0F1 ATP synthase sub 24.9 4.4E+02 0.0094 22.4 12.5 17 181-197 35-51 (140)
218 PF01283 Ribosomal_S26e: Ribos 24.7 22 0.00048 30.7 -0.3 46 4-49 19-78 (113)
219 COG3024 Uncharacterized protei 24.6 42 0.00092 26.2 1.3 11 41-51 6-16 (65)
220 PRK13460 F0F1 ATP synthase sub 24.1 5.2E+02 0.011 23.1 12.5 14 181-194 46-59 (173)
221 PF03879 Cgr1: Cgr1 family; I 24.1 4.6E+02 0.01 22.5 10.4 12 175-186 27-38 (108)
222 PF03811 Zn_Tnp_IS1: InsA N-te 24.0 39 0.00084 23.3 0.9 12 40-51 3-14 (36)
223 KOG2989 Uncharacterized conser 24.0 34 0.00073 33.3 0.8 16 1-16 36-51 (253)
224 COG1645 Uncharacterized Zn-fin 23.8 37 0.0008 30.1 0.9 13 39-51 25-37 (131)
225 COG2888 Predicted Zn-ribbon RN 23.5 55 0.0012 25.3 1.7 10 6-15 10-19 (61)
226 PF03801 Ndc80_HEC: HEC/Ndc80p 23.4 89 0.0019 28.1 3.3 41 112-152 92-137 (157)
227 PF07223 DUF1421: Protein of u 23.4 71 0.0015 32.8 3.0 19 115-133 322-340 (358)
228 KOG3623 Homeobox transcription 23.2 57 0.0012 36.6 2.4 39 5-52 281-319 (1007)
229 PRK02292 V-type ATP synthase s 23.0 5.6E+02 0.012 23.0 13.1 19 181-199 12-30 (188)
230 KOG0681 Actin-related protein 22.9 1.1E+03 0.023 26.2 11.6 42 115-158 206-257 (645)
231 PF09831 DUF2058: Uncharacteri 22.6 6.1E+02 0.013 23.5 8.7 41 224-264 48-88 (177)
232 KOG4571 Activating transcripti 22.6 8E+02 0.017 24.7 10.3 8 207-214 262-269 (294)
233 PRK00418 DNA gyrase inhibitor; 22.6 52 0.0011 25.5 1.4 9 43-51 7-15 (62)
234 COG5222 Uncharacterized conser 22.4 24 0.00051 35.5 -0.6 45 3-51 272-319 (427)
235 PRK08222 hydrogenase 4 subunit 22.4 60 0.0013 29.7 2.1 46 6-51 115-163 (181)
236 PRK09174 F0F1 ATP synthase sub 22.4 6.5E+02 0.014 23.5 13.3 18 181-198 83-100 (204)
237 PF09963 DUF2197: Uncharacteri 22.3 58 0.0013 24.8 1.6 36 4-50 1-39 (56)
238 PRK14472 F0F1 ATP synthase sub 22.1 5.8E+02 0.012 22.8 14.1 14 181-194 48-61 (175)
239 TIGR03831 YgiT_finger YgiT-typ 22.0 8.2 0.00018 26.6 -2.9 14 38-51 28-41 (46)
240 PF14490 HHH_4: Helix-hairpin- 22.0 1.7E+02 0.0037 23.6 4.5 38 115-156 9-46 (94)
241 KOG1071 Mitochondrial translat 21.8 1.7E+02 0.0037 29.8 5.2 40 113-153 45-85 (340)
242 PF00789 UBX: UBX domain; Int 21.6 4.4 9.6E-05 31.7 -4.8 45 297-345 5-49 (82)
243 PF07553 Lipoprotein_Ltp: Host 21.5 1.2E+02 0.0026 22.2 3.1 22 115-136 22-46 (48)
244 PF13465 zf-H2C2_2: Zinc-finge 21.0 27 0.00058 21.9 -0.4 9 43-51 15-23 (26)
245 COG5415 Predicted integral mem 21.0 45 0.00098 32.0 0.9 32 5-51 192-223 (251)
246 PRK08475 F0F1 ATP synthase sub 20.9 6.1E+02 0.013 22.7 14.1 16 247-262 132-147 (167)
247 PF12898 Stc1: Stc1 domain; I 20.6 78 0.0017 25.6 2.2 27 38-68 46-72 (84)
248 KOG1265 Phospholipase C [Lipid 20.5 5.9E+02 0.013 29.7 9.4 9 252-260 1157-1165(1189)
249 KOG3054 Uncharacterized conser 20.4 8.5E+02 0.018 24.2 9.9 69 183-251 107-181 (299)
250 COG2331 Uncharacterized protei 20.4 25 0.00054 28.5 -0.8 16 1-16 8-23 (82)
251 PF09538 FYDLN_acid: Protein o 20.3 42 0.0009 28.6 0.5 10 43-52 10-19 (108)
252 COG0846 SIR2 NAD-dependent pro 20.3 63 0.0014 31.4 1.8 34 4-50 121-154 (250)
253 PF15288 zf-CCHC_6: Zinc knuck 20.2 38 0.00083 24.1 0.2 10 5-14 1-10 (40)
254 PF09567 RE_MamI: MamI restric 20.1 56 0.0012 32.2 1.4 11 41-51 95-105 (314)
255 PRK00409 recombination and DNA 20.1 1.3E+03 0.028 26.1 12.7 19 320-338 713-731 (782)
256 COG0735 Fur Fe2+/Zn2+ uptake r 20.0 53 0.0012 29.0 1.2 45 5-51 93-142 (145)
257 PRK13453 F0F1 ATP synthase sub 20.0 6.4E+02 0.014 22.6 12.8 17 181-197 48-64 (173)
No 1
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=2.9e-31 Score=274.81 Aligned_cols=158 Identities=29% Similarity=0.431 Sum_probs=131.7
Q ss_pred CceeecCCCcccccchHHHHH---------------HHhhhccCCCCcchhhhhhcccccCCCCCCCccccccccccccc
Q 017706 3 GVSLKCGDCGALLRSVQEAQE---------------HAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGH 67 (367)
Q Consensus 3 ~~~l~C~~C~~v~~g~~~aq~---------------h~~~tgh~~F~e~~e~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f 67 (367)
.-|++|..|+.|.+....-.- -..+...++|.. .+.+|+|++||.+ +.|+|+|+|
T Consensus 438 e~Rv~C~~c~kVrYs~~~~~~i~lpv~~~~~v~~~v~~~~cleaff~p---q~~df~s~ac~~K-------~~a~kt~~~ 507 (763)
T KOG0944|consen 438 EDRVSCLGCRKVRYSYESEYLIQLPVPMTNEVREKVPISACLEAFFEP---QVDDFWSTACGEK-------KGATKTTRF 507 (763)
T ss_pred hhhhhhhccccccccchhheeeEeeccccccccccCCHHHHHHHhcCC---cchhhhhHhhcCc-------ccccccccc
Confidence 348999999999955443211 011122334444 3789999999988 899999999
Q ss_pred cccccchhcccccccccc--Cccc---cCCccccccCCC---CC-CCCcc--------cccccCHHHHHHHHhCCCCHHH
Q 017706 68 TDFVDKTSEAAKPISLEV--PKAT---ADSEEAIDVDMS---GS-QPEEM--------VEPEVDKELLKELEAMGFPVAR 130 (367)
Q Consensus 68 ~tFP~~L~v~~~r~~l~~--p~K~---~~~~~~ldl~~~---g~-~~ee~--------~~~~~d~~~l~~L~~MGF~~~~ 130 (367)
+|||+||+||+.||.|.+ |+|+ +.||+.|||+.| |+ |+|+. +.+.+|+.++.+|++||||.++
T Consensus 508 ksfP~yLiiqv~rf~~~dw~pkKld~~iempe~ldls~~rs~g~~p~ee~lpde~~~~~~~~~d~s~i~qL~~MGFp~ea 587 (763)
T KOG0944|consen 508 KSFPDYLIIQVGRFTLQDWVPKKLDVSIEMPEELDLSSYRSKGLQPGEEALPDEAPETSEFAADRSVISQLVEMGFPEEA 587 (763)
T ss_pred ccCCceEEEEeeEEEecCceeeeeccceecchhhchhhhhhcCCCCcccccCCcCcccCccchhHHHHHHHHHcCCCHHH
Confidence 999999999999999986 9999 779999999987 65 66642 4455899999999999999999
Q ss_pred HHHHHHHhCCCCHHHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 017706 131 ATRALHYSGNANVEAAVNWVVEHENDPDIDEMPMVPVSGG 170 (367)
Q Consensus 131 a~kAL~~tgn~~~E~A~~Wl~~h~dd~d~dep~~~~~~~~ 170 (367)
|.|||++|||+++|+|++||++||+|||+++|+.+|+++.
T Consensus 588 c~rAly~tgN~~aEaA~NWl~~HMdDpd~~~p~vvp~~~~ 627 (763)
T KOG0944|consen 588 CRRALYYTGNSGAEAASNWLMEHMDDPDIDDPFVVPGNSP 627 (763)
T ss_pred HHHHHhhhcCccHHHHHHHHHHhccCcccCCceecCCCCC
Confidence 9999999999999999999999999999999999988653
No 2
>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=2.5e-28 Score=231.71 Aligned_cols=207 Identities=29% Similarity=0.414 Sum_probs=161.8
Q ss_pred HHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHH-HHhcCCCCCCCCCCCCCCC--------------------CCCCCCC
Q 017706 118 LKELEAMGFPVARATRALHYSGNANVEAAVNWV-VEHENDPDIDEMPMVPVSG--------------------GGGASKS 176 (367)
Q Consensus 118 l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl-~~h~dd~d~dep~~~~~~~--------------------~~~~~k~ 176 (367)
+++|++|||+..++.+||..|||.|+|.||+|| .+|.+||. |.|...|... ..+..++
T Consensus 4 ~~~l~~mgfps~k~e~al~~~~n~~~e~al~wl~~d~~~d~~-~ap~~~p~~~~~~~~~~~~~sg~~~~s~~se~~e~ik 82 (290)
T KOG2689|consen 4 AQSLEEMGFPSGKAEKALAVYGNRGIEQALDWLEMDHAGDPI-DAPLSTPLAADLGRLPTSFESGKLSDSGYSESEEEIK 82 (290)
T ss_pred HHHHHHhcCchhhhhhHhhhhccccHHHHHHHHHhcccCCCc-cccccccchhhhhcccchhcCCCcCCchhhhhhhhcc
Confidence 489999999999999999999999999999999 89999985 6666554310 1123689
Q ss_pred CCCHHHHHHHHHHHHHHHHHh---hHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 017706 177 SLTPEEIKLKAQELRERARKK---KEEEEKRMEREREKERIRIGKELLEAKRIEEENERKRILALRKAEKEEEKRAREKI 253 (367)
Q Consensus 177 ~lT~EEk~~k~~el~~k~r~k---r~eeek~~~~e~E~~Rr~~gKe~~~~k~~~ee~e~k~~~e~rrrEK~ee~~ar~ri 253 (367)
.||+||+.++...|++++..+ +++-+.++..++++.|+++|++|..+++.+++.++.+++++||++|.++..+|+||
T Consensus 83 ~ls~eE~~~~~~~i~ekik~k~~k~~e~e~~E~~~~~k~~~ks~~~~~~a~~r~q~~e~~~~~qkRrreK~e~~eaRqRV 162 (290)
T KOG2689|consen 83 LLSEEEKKAQTKRILEKIKQKQIKREELELREALEREKQRRKSGDEMSAAKRRLQDDEMRRAAQKRRREKAEDEEARQRV 162 (290)
T ss_pred ccChHHHHHHHHHHHHHhcchhHHHHHHHHHHhhhhHHhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHH
Confidence 999999999999999998555 45667888889999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHhcCCCCC--CCcccCCC-cchhhhhhccCCCCCccchHHHHHHHHhhhhhcCCChHHHHHHH
Q 017706 254 RQKLEEDKAERRRRLGLPPE--DPATTKSS-APVVEEKKSMLPIRPATKVEQMRECLRSLKQNHKDDDAKVKRAF 325 (367)
Q Consensus 254 r~qIe~Dk~eR~~k~~~~~~--~~~~~~~~-~~~~ee~~~~~~~~~~~~~~QlR~~l~sLk~~~~~~~a~~~~a~ 325 (367)
++||++||++|+++++.... .+.+.++. ++......+..|.--..+++|||+++|+.-++.|+..+.|....
T Consensus 163 ~~~Ie~DKaeRka~~e~~~~~~q~~P~~~~~~~s~s~~~~spp~~ys~crlQiRl~DG~Tl~~tF~a~E~L~~VR 237 (290)
T KOG2689|consen 163 LRQIERDKAERKAKYENSVGDSQPKPVKPEPVPSPSAPSQSPPTDYSQCRLQIRLPDGQTLTQTFNARETLAAVR 237 (290)
T ss_pred HHHHHHhHHHHHHHhccccCCCCCCCCCCcCCCCCCccccCCCCcccceEEEEEcCCCCeeeeecCchhhHHHHH
Confidence 99999999999999975222 11111100 00000000011111245889999999999999999876655333
No 3
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=1.8e-27 Score=240.74 Aligned_cols=156 Identities=22% Similarity=0.363 Sum_probs=133.9
Q ss_pred CceeecCCCcccc-------------cchHHHHHHHhhhccCCCCcchhhhhhcccccCCCCCCCccccccccccccccc
Q 017706 3 GVSLKCGDCGALL-------------RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTD 69 (367)
Q Consensus 3 ~~~l~C~~C~~v~-------------~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~t 69 (367)
.-+|+|+.|+.|. .|+.++|+.-+ ...++|... .++|+|.+|+.+ ..|+++++|+|
T Consensus 429 e~rlsC~~C~~v~ySye~~~~i~i~le~n~E~~di~~-~v~a~f~pd---tiE~~CenCk~K-------~~a~~k~~~ks 497 (749)
T COG5207 429 ERRLSCSGCMDVSYSYESMLMICIFLEGNDEPQDIRK-SVEAFFLPD---TIEWSCENCKGK-------KKASRKPFIKS 497 (749)
T ss_pred cceecccccccccccccceEEEEeecccCcchhhHHH-HHHheECcc---ceeeehhhhcCc-------ccccccchhhc
Confidence 5689999999997 67778888877 788888887 578999999877 79999999999
Q ss_pred cccchhcccccccccc--Cccc-----cCCccccccCCC-C--CCCCcc------cccccCHHHHHHHHhCCCCHHHHHH
Q 017706 70 FVDKTSEAAKPISLEV--PKAT-----ADSEEAIDVDMS-G--SQPEEM------VEPEVDKELLKELEAMGFPVARATR 133 (367)
Q Consensus 70 FP~~L~v~~~r~~l~~--p~K~-----~~~~~~ldl~~~-g--~~~ee~------~~~~~d~~~l~~L~~MGF~~~~a~k 133 (367)
||.||++|+.||.|.| ..|+ ++.++-++++.| . +|..|. ...+.|+.++.||++||||.++|.+
T Consensus 498 lPk~LIlq~~R~~lqny~v~kls~pi~~~~D~m~~~~s~msk~~PqtEn~LPdedE~~t~Nqs~I~qL~~mGfp~~~~~r 577 (749)
T COG5207 498 LPKYLILQVGRYSLQNYKVEKLSDPIEMRSDDMIKLGSFMSKFDPQTENLLPDEDEAFTDNQSLIRQLVDMGFPEEDAAR 577 (749)
T ss_pred cCceeEEecceeeccceeehhccCceEEccccccchhhHhhccCCcccccCCccccccCchHHHHHHHHHcCCCHHHHHH
Confidence 9999999999999998 5565 445677888876 2 133322 2356789999999999999999999
Q ss_pred HHHHhCCCCHHHHHHHHHHhcCCCCCCCCCCCCCCC
Q 017706 134 ALHYSGNANVEAAVNWVVEHENDPDIDEMPMVPVSG 169 (367)
Q Consensus 134 AL~~tgn~~~E~A~~Wl~~h~dd~d~dep~~~~~~~ 169 (367)
||..|||++.|.||||||+||||||+++|+.+|++.
T Consensus 578 AL~~tgNqDaEsAMNWLFqHMdDPdlndP~~~~~~v 613 (749)
T COG5207 578 ALGITGNQDAESAMNWLFQHMDDPDLNDPFVPPPNV 613 (749)
T ss_pred HHhhccCcchHHHHHHHHhhccCcccCCCCCCCCCC
Confidence 999999999999999999999999999999887754
No 4
>KOG2507 consensus Ubiquitin regulatory protein UBXD2, contains UAS and UBX domains [General function prediction only]
Probab=99.70 E-value=1.2e-17 Score=166.82 Aligned_cols=162 Identities=23% Similarity=0.211 Sum_probs=128.9
Q ss_pred CCCCCHHHHHHHHHHHHHH---HHHhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 017706 175 KSSLTPEEIKLKAQELRER---ARKKKEEEEKRMEREREKERIRIGKELLEAKRIEEENERKRILALRKAEKEEEKRARE 251 (367)
Q Consensus 175 k~~lT~EEk~~k~~el~~k---~r~kr~eeek~~~~e~E~~Rr~~gKe~~~~k~~~ee~e~k~~~e~rrrEK~ee~~ar~ 251 (367)
+.||..+ -.++.+|.++ .+.++-+++.+.++++|..||+.|||++..+...+++..++++++++|||.++..+|+
T Consensus 190 qrplea~--~~rl~~ltk~leqkr~Ek~kee~~hekeee~~rr~agkE~~~~~a~~~ee~tkrm~eqrkrer~e~~aare 267 (506)
T KOG2507|consen 190 QRPLEAE--PSRLCDLTKNLEQKRVEKTKEEVEHEKEEEPLRRQAGKEPIRPTAPGTEENTKRMREQRKRERKEGTAARE 267 (506)
T ss_pred ccchhhh--hhHHHHHHhhccccchhhhHHHHHHHhhhhhHhhhhcccccccccccchHHHHHHHHHHHHHHHhhHHHHH
Confidence 3455433 3455555555 4555667788888999999999999999999999999999999999999999999999
Q ss_pred HHHHhHHHHHHHHHHhcCCCCCCCcccCCCcchhhhhhccCCCCCccchHHHHHHHHhhhhhcCCChHHHHHHHHHHHHH
Q 017706 252 KIRQKLEEDKAERRRRLGLPPEDPATTKSSAPVVEEKKSMLPIRPATKVEQMRECLRSLKQNHKDDDAKVKRAFQTLLTY 331 (367)
Q Consensus 252 rir~qIe~Dk~eR~~k~~~~~~~~~~~~~~~~~~ee~~~~~~~~~~~~~~QlR~~l~sLk~~~~~~~a~~~~a~~tL~ky 331 (367)
||++||.+||++|+.+|+.+....++.+++....++..-........+++|||+|+|+.+++.||+++.|..+.+++...
T Consensus 268 RI~aqiaadraera~rf~k~v~t~et~k~aa~~ae~~~ge~~~~~d~~rLqiRLPdGssfte~Fps~~vL~~vr~yvrq~ 347 (506)
T KOG2507|consen 268 RILAQIAADRAERAIRFTKSVDTKETMKPAAEGAEEEDGEKSKKADDVRLQIRLPDGSSFTEKFPSTSVLRMVRDYVRQN 347 (506)
T ss_pred HHHHHhhccHHHHHhhhcCccchhhhcchhhhhccccccccccccceeEEEEecCCccchhhcCCcchHHHHHHHHHHhc
Confidence 99999999999999999998887776665544433322111122355789999999999999999999999888888877
Q ss_pred HhhhccC
Q 017706 332 IGNVAKN 338 (367)
Q Consensus 332 l~Ni~~~ 338 (367)
.+|-+.+
T Consensus 348 ~~i~~g~ 354 (506)
T KOG2507|consen 348 QTIGLGA 354 (506)
T ss_pred ccccccc
Confidence 7776654
No 5
>KOG2699 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.56 E-value=2.4e-15 Score=150.85 Aligned_cols=324 Identities=32% Similarity=0.372 Sum_probs=232.7
Q ss_pred HHHHHhhhccCCCCcchhhhhhcccccCCCCCCCccccccccccccccccccchhccccccccccCccccCCc--ccccc
Q 017706 21 AQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEVPKATADSE--EAIDV 98 (367)
Q Consensus 21 aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~p~K~~~~~--~~ldl 98 (367)
.+.|.+-+-|.+|... .|+.++ .+++++...++.+.|+.-.- .....+ |..+.+.+ ..+-+
T Consensus 5 k~~~~ef~~~~~~~ss----------~~~~~~---~e~~~~~~~~s~~~~~~~~~--~~~~~~--~~~~~~~~~~~~~~~ 67 (407)
T KOG2699|consen 5 KYNFQEFKCKVNLASS----------LNDVKH---QESVGEQAHTSSTDQSLPHL--PVTLDT--PWPLLNPAPKVNLLL 67 (407)
T ss_pred HHHHHHHhhccccccc----------ccchhh---hHHHHHHhhccCCCCCCCCC--Cccccc--chhhhccCCCCcccc
Confidence 4566666777777766 344332 25678888888888776444 222222 33221100 01111
Q ss_pred C---CCCCCCCcccccccCHHHHHHHHhCCCCH-HHHHHHHHHhCCCCHHH-HHHHHHHhcCCCCCCCCCCCCCCC---C
Q 017706 99 D---MSGSQPEEMVEPEVDKELLKELEAMGFPV-ARATRALHYSGNANVEA-AVNWVVEHENDPDIDEMPMVPVSG---G 170 (367)
Q Consensus 99 ~---~~g~~~ee~~~~~~d~~~l~~L~~MGF~~-~~a~kAL~~tgn~~~E~-A~~Wl~~h~dd~d~dep~~~~~~~---~ 170 (367)
+ .+|.....+..+.+....+.-...|||+. .+...+++..|+...++ |.+|...|..+......+..+.+. +
T Consensus 68 ~k~~s~gqa~~~~~~~~~~~~i~~~~~~~g~~e~~~t~~~~~~~g~a~~~a~~~~~~~p~~~~~~~~~~~~~e~~~l~~s 147 (407)
T KOG2699|consen 68 SKSSSSGQAAKTNRRNIVFNTILARFDIMGRPEAARTSPALHPSGNQSLEAPAVNFKIPFTSEIQRFKMPKGETNTLESS 147 (407)
T ss_pred ccccccchhhhcccCCcccchhhccccccCCccccccccCcccchhhhhcCCCCcccccccccchhhccccCCccccccc
Confidence 1 12332223444556666777788899999 77788899999988888 999999999887655544444332 2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHhhHHHHHHHHH--HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 017706 171 GGASKSSLTPEEIKLKAQELRERARKKKEEEEKRMER--EREKERIRIGKELLEAKRIEEENERKRILALRKAEKEEEKR 248 (367)
Q Consensus 171 ~~~~k~~lT~EEk~~k~~el~~k~r~kr~eeek~~~~--e~E~~Rr~~gKe~~~~k~~~ee~e~k~~~e~rrrEK~ee~~ 248 (367)
....++.+|...-..+.++|.+..+..+.++++..++ ++|++|.++|+++.+.+..-....++..+..+..|++|+..
T Consensus 148 ~~~~~ss~~~~~~~~k~~e~se~~~d~~~kqe~~~~~~pE~ek~R~rl~~el~~~~v~g~he~le~v~~~~~ae~eEe~~ 227 (407)
T KOG2699|consen 148 GDPEPSSLTKIFVNTKAKELSESGRDIRQKQEQNTERNPEREKERKRLGNELLKEKVLGCHEPLEAVLVLRPAEDEEEYE 227 (407)
T ss_pred CCcCchhhhhccccccchhhhhhhhhhHHHhhhhhccchhhhhhhhccccchhhcccccccchHHHHHHhcccccHHHHH
Confidence 2345677888888889999999999999999988888 99999999999999988866667777778899999999999
Q ss_pred HHHHHHHhHHHHHHHHHHhcCCCCCCCcc----cCCCcchhhhhh--ccCCCCCccchHHHHHHHHhhhhhcCCChHHHH
Q 017706 249 AREKIRQKLEEDKAERRRRLGLPPEDPAT----TKSSAPVVEEKK--SMLPIRPATKVEQMRECLRSLKQNHKDDDAKVK 322 (367)
Q Consensus 249 ar~rir~qIe~Dk~eR~~k~~~~~~~~~~----~~~~~~~~ee~~--~~~~~~~~~~~~QlR~~l~sLk~~~~~~~a~~~ 322 (367)
+++.++.+...++.+|++.+|.|..+... ..++.+...... ...+.+++.....+|.++..+..++.+++..-.
T Consensus 228 ~~e~~l~k~~s~~ser~~~l~~P~~tk~~Re~~~~~~~~la~~~~l~v~f~~~~i~~~~~~r~e~i~~~q~l~~~~~~~k 307 (407)
T KOG2699|consen 228 LVEKTLRKLQSLKSERKRLLGAPPVTKADRESAANPSLPLAPAIELPVKFPDREIKQEAFLRSELIELLQNLVSSDLKEK 307 (407)
T ss_pred HHHHHHHHHHHHhhhhhhhhcCCccchhHHHHhhccCccccccceeeeecChHHHHHHHHhhHHHHHHHHHhhhhhhcch
Confidence 99999999999999999999988874322 111111111111 122233333447799999999999988886544
Q ss_pred H-HHHHHHHHHhhhccCCChhhhhhhhccccccccccccc
Q 017706 323 R-AFQTLLTYIGNVAKNPNEEKFRKIRLSNQTFQVWNFFT 361 (367)
Q Consensus 323 ~-a~~tL~kyl~Ni~~~P~eeK~rkIr~~N~~f~~~~~~~ 361 (367)
. ++.++.+|..|++++|+.+.|+.|++.|..|..++-++
T Consensus 308 ~~~~~~~~~~~~~~ak~pd~~l~q~~f~~~~~~~~~~g~~ 347 (407)
T KOG2699|consen 308 EMAFLTLYTPFKNVAKDPDGELLQGIFLPNELLLARYGFV 347 (407)
T ss_pred HHHHHHhhcccchhccCcchhhhhhhhchhHHHHHHHhcc
Confidence 4 99999999999999999999999999999998877543
No 6
>PF09409 PUB: PUB domain; InterPro: IPR018997 The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain []. This domain is also found on other proteins linked to the ubiquitin-proteasome system. ; PDB: 2CM0_A 2CCQ_A 2D5U_A 2HPL_A 2HPJ_A.
Probab=99.03 E-value=1.2e-10 Score=94.24 Aligned_cols=45 Identities=42% Similarity=0.594 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHhhhccCCChhhhhhhhccccccccccccccC
Q 017706 319 AKVKRAFQTLLTYIGNVAKNPNEEKFRKIRLSNQTFQVWNFFTID 363 (367)
Q Consensus 319 a~~~~a~~tL~kyl~Ni~~~P~eeK~rkIr~~N~~f~~~~~~~~~ 363 (367)
+.+.+|++||.+|+.||+.||.++|||+||++|++|+++|+..-|
T Consensus 4 ~~~~~al~~L~~il~NI~~~P~~~kyR~Ir~~N~~f~~~i~~~~g 48 (87)
T PF09409_consen 4 EAFQKALETLEKILSNILSNPNEEKYRRIRLSNKTFQEKILPVPG 48 (87)
T ss_dssp HHHHHHHHHHHHHHHHHHHSTT-CGGGEEETTSHHHHHHTTTSTT
T ss_pred HHHHHHHHHHHHHHHHHccCCCcccceEeecCcchHHHHhcCChh
Confidence 468999999999999999999999999999999999999987644
No 7
>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=98.94 E-value=9.1e-10 Score=75.71 Aligned_cols=37 Identities=41% Similarity=0.701 Sum_probs=34.2
Q ss_pred cCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHH
Q 017706 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWV 150 (367)
Q Consensus 113 ~d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl 150 (367)
+|++.|.+|++|||+++.|++||..+|| |++.|++||
T Consensus 1 i~~~~v~~L~~mGf~~~~~~~AL~~~~~-nve~A~~~L 37 (37)
T PF00627_consen 1 IDEEKVQQLMEMGFSREQAREALRACNG-NVERAVDWL 37 (37)
T ss_dssp SHHHHHHHHHHHTS-HHHHHHHHHHTTT-SHHHHHHHH
T ss_pred CCHHHHHHHHHcCCCHHHHHHHHHHcCC-CHHHHHHhC
Confidence 4688999999999999999999999999 999999998
No 8
>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=98.77 E-value=1.4e-08 Score=69.57 Aligned_cols=38 Identities=47% Similarity=0.754 Sum_probs=35.3
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Q 017706 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVE 152 (367)
Q Consensus 114 d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~ 152 (367)
+++.+++|++|||+++.|..||..++| |++.|++|||+
T Consensus 1 ~~~~v~~L~~mGf~~~~~~~AL~~~~~-d~~~A~~~L~~ 38 (38)
T cd00194 1 DEEKLEQLLEMGFSREEARKALRATNN-NVERAVEWLLE 38 (38)
T ss_pred CHHHHHHHHHcCCCHHHHHHHHHHhCC-CHHHHHHHHhC
Confidence 357899999999999999999999998 99999999984
No 9
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=98.76 E-value=1.3e-08 Score=69.51 Aligned_cols=37 Identities=35% Similarity=0.560 Sum_probs=34.5
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Q 017706 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVV 151 (367)
Q Consensus 114 d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~ 151 (367)
+++.+++|++|||+++.|..||+.++| +++.|++|||
T Consensus 1 ~~~~v~~L~~mGf~~~~a~~aL~~~~~-d~~~A~~~L~ 37 (37)
T smart00165 1 DEEKIDQLLEMGFSREEALKALRAANG-NVERAAEYLL 37 (37)
T ss_pred CHHHHHHHHHcCCCHHHHHHHHHHhCC-CHHHHHHHHC
Confidence 357899999999999999999999998 8999999996
No 10
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=98.46 E-value=1.5e-07 Score=99.62 Aligned_cols=46 Identities=41% Similarity=0.677 Sum_probs=43.6
Q ss_pred ccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCCCC
Q 017706 112 EVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHENDPD 158 (367)
Q Consensus 112 ~~d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~dd~d 158 (367)
+++++.|.++++|||+++.|.+||..|+| +||.|+||||+|+|++-
T Consensus 633 ~~~e~~v~si~smGf~~~qa~~aL~~~n~-nveravDWif~h~d~~~ 678 (763)
T KOG0944|consen 633 EVDEESVASIVSMGFSRNQAIKALKATNN-NVERAVDWIFSHMDIPV 678 (763)
T ss_pred CCChhHheeeeeecCcHHHHHHHHHhcCc-cHHHHHHHHHhcccccc
Confidence 68999999999999999999999999998 99999999999999663
No 11
>smart00580 PUG domain in protein kinases, N-glycanases and other nuclear proteins.
Probab=97.89 E-value=4.6e-06 Score=63.23 Aligned_cols=35 Identities=23% Similarity=0.237 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhhhccCCChhhhhhhhccccccccccccccC
Q 017706 323 RAFQTLLTYIGNVAKNPNEEKFRKIRLSNQTFQVWNFFTID 363 (367)
Q Consensus 323 ~a~~tL~kyl~Ni~~~P~eeK~rkIr~~N~~f~~~~~~~~~ 363 (367)
+|+.+|++|++||+.||+|+| +|++||++|...-|
T Consensus 1 ~sv~dLLr~irNi~~hp~e~k------~n~~~~~~l~~~pg 35 (58)
T smart00580 1 ESVRDLLRALRNILHHPREEK------GNPAIKERLGDVPG 35 (58)
T ss_pred CcHHHHHHHHHHHhhCcchhh------cCHHHHHHhcCCCc
Confidence 378899999999999999999 99999999988655
No 12
>cd02664 Peptidase_C19H A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.81 E-value=6.3e-06 Score=81.12 Aligned_cols=53 Identities=11% Similarity=0.127 Sum_probs=46.1
Q ss_pred hcccccCCCCCCCccccccccccccccccccchhcccccccccc----Cccc---cCCccccccCCC
Q 017706 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~----p~K~---~~~~~~ldl~~~ 101 (367)
.|.|+.||++ ..+.|++.|.++|++|+|+++||.++. ..|+ +..|..|||+.+
T Consensus 154 ~~~C~~C~~~-------~~a~k~~~i~~lP~vLii~LkRF~~~~~~~~~~Ki~~~v~fp~~ldl~~~ 213 (327)
T cd02664 154 QYYCEKCASL-------QDAEKEMKVTGAPEYLILTLLRFSYDQKTHVREKIMDNVSINEVLSLPVR 213 (327)
T ss_pred ceeCCccCCc-------cceeEEEEcccCChhhEEEeeeeEEccccCcceecCceEecCCEEecCcc
Confidence 4999999986 689999999999999999999999874 5677 667888998755
No 13
>cd02668 Peptidase_C19L A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.77 E-value=6.4e-06 Score=80.69 Aligned_cols=53 Identities=13% Similarity=0.163 Sum_probs=46.4
Q ss_pred hcccccCCCCCCCccccccccccccccccccchhcccccccccc----Cccc---cCCccccccCCC
Q 017706 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~----p~K~---~~~~~~ldl~~~ 101 (367)
.|.|+.|+++ ..+.|++.|.++|++|+|+.+||.++. +.|+ +..|..|||+.|
T Consensus 176 ~~~C~~C~~~-------~~a~k~~~i~~lP~iLii~LkRf~~d~~~~~~~Ki~~~v~fp~~Ldl~~~ 235 (324)
T cd02668 176 QYFCESCNSK-------TDATRRIRLTTLPPTLNFQLLRFVFDRKTGAKKKLNASISFPEILDMGEY 235 (324)
T ss_pred cccCCCCCce-------eeeEEEEEecCCCCeEEEEEEcceeecccCcceeCCcEEECCCeEechhh
Confidence 3899999987 688999999999999999999999873 6777 667889999866
No 14
>cd02667 Peptidase_C19K A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.72 E-value=9.5e-06 Score=77.97 Aligned_cols=49 Identities=14% Similarity=0.151 Sum_probs=43.6
Q ss_pred cccccCCCCCCCccccccccccccccccccchhcccccccccc---Cccc---cCCccccccCCC
Q 017706 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV---PKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 43 ~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~---p~K~---~~~~~~ldl~~~ 101 (367)
|.|+.|++ ++|++.|.++|++|+|+.+||.++. +.|+ +..|..|||+.|
T Consensus 132 ~~C~~C~~----------a~k~~~i~~~P~~Lii~LkRF~~~~~~~~~Ki~~~v~fP~~Ldl~~~ 186 (279)
T cd02667 132 FACENCTK----------AKKQYLISKLPPVLVIHLKRFQQPRSANLRKVSRHVSFPEILDLAPF 186 (279)
T ss_pred ccCCccCc----------eeeEeEhhhCCCeEEEEEeccccCcccCceecCceEeCCCccchhhc
Confidence 89999985 6889999999999999999999994 6787 668899999876
No 15
>cd02660 Peptidase_C19D A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.70 E-value=9.9e-06 Score=78.72 Aligned_cols=52 Identities=10% Similarity=0.141 Sum_probs=45.9
Q ss_pred cccccCCCCCCCccccccccccccccccccchhcccccccccc---Cccc---cCCccccccCCC
Q 017706 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV---PKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 43 ~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~---p~K~---~~~~~~ldl~~~ 101 (367)
|.|+.||.+ ..+.|++.|.++|++|+|+++||..+. +.|+ +..|..|||+.|
T Consensus 196 ~~C~~C~~~-------~~~~~~~~i~~lP~~Lii~lkRf~~~~~~~~~K~~~~v~fp~~Ldl~~~ 253 (328)
T cd02660 196 YKCSGCGST-------QEATKQLSIKKLPPVLCFQLKRFEHSLNKTSRKIDTYVQFPLELNMTPY 253 (328)
T ss_pred ccCCCCCCc-------cceEEEEEecCCCceeEEEEEeEEecCCCCCcCCCcEEeCCCEechhhh
Confidence 689999986 688999999999999999999999985 6777 667888999865
No 16
>cd02663 Peptidase_C19G A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.54 E-value=2.6e-05 Score=75.60 Aligned_cols=52 Identities=10% Similarity=0.015 Sum_probs=44.6
Q ss_pred hcccccCCCCCCCccccccccccccccccccchhcccccccccc----Cccc---cCCccccccCC
Q 017706 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (367)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~----p~K~---~~~~~~ldl~~ 100 (367)
.|.|+.|+++ ..++|+..|..+|++|+|+.+||.++. ..|+ +..|..||+..
T Consensus 167 ~~~C~~C~~~-------~~a~k~~~i~~lP~vLii~LkRF~~~~~~~~~~Ki~~~v~fp~~L~~~~ 225 (300)
T cd02663 167 KFYCDECCSL-------QEAEKRMKIKKLPKILALHLKRFKYDEQLNRYIKLFYRVVFPLELRLFN 225 (300)
T ss_pred cEECCCCCCc-------eeEEEEEEeccCCceeEEEEEeEEeecccCCceecCceEecCcEEeccc
Confidence 4899999986 688999999999999999999999884 5676 66788888864
No 17
>cd02657 Peptidase_C19A A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.49 E-value=4.1e-05 Score=73.75 Aligned_cols=52 Identities=8% Similarity=-0.037 Sum_probs=42.9
Q ss_pred hcccccCCCCCCCccccccccccccccccccchhcccccccccc----Cccc---cCCccccccCC
Q 017706 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (367)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~----p~K~---~~~~~~ldl~~ 100 (367)
...|+.||.. ..++|++.|.++|++|+|+.+||.++. ..|+ +..|..||++.
T Consensus 175 ~~~~~~~~~~-------~~~~k~~~i~~lP~vLii~LkRF~~~~~~~~~~Ki~~~v~fP~~Ldl~~ 233 (305)
T cd02657 175 EKHSPTLGRD-------AIYTKTSRISRLPKYLTVQFVRFFWKRDIQKKAKILRKVKFPFELDLYE 233 (305)
T ss_pred hhcCcccCCC-------ceEEEEEEeccCCcEEEEEEECCccccccCceeecCcEEECCceEeccc
Confidence 3589999875 678999999999999999999999874 3455 66788898864
No 18
>cd02658 Peptidase_C19B A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.46 E-value=3.4e-05 Score=74.67 Aligned_cols=50 Identities=28% Similarity=0.387 Sum_probs=41.5
Q ss_pred hhhcccccCCCCCCCccccccccccccccccccchhccccccccc-c--Cccc---cCCcccc
Q 017706 40 VLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLE-V--PKAT---ADSEEAI 96 (367)
Q Consensus 40 v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~-~--p~K~---~~~~~~l 96 (367)
.+++.|+.||++ ..+.|++.+.++|++|+|+++||... + |+|+ +..|..+
T Consensus 192 ~i~~~C~~C~~~-------~~a~k~~~i~~lP~vLii~LkRF~~~~~~~~~Ki~~~v~~p~~l 247 (311)
T cd02658 192 TIEDFCSTCKEK-------TTATKTTGFKTFPDYLVINMKRFQLLENWVPKKLDVPIDVPEEL 247 (311)
T ss_pred cccccccCCCCc-------ccEEEEEEeecCCceEEEEeEEEEecCCCceEeeccccccCCcC
Confidence 567899999987 78999999999999999999999995 3 8887 4445444
No 19
>cd02661 Peptidase_C19E A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.45 E-value=4.1e-05 Score=72.87 Aligned_cols=52 Identities=15% Similarity=0.047 Sum_probs=44.3
Q ss_pred cccccCCCCCCCccccccccccccccccccchhccccccccccCccc---cCCccccccCCC
Q 017706 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEVPKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 43 ~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~p~K~---~~~~~~ldl~~~ 101 (367)
|.|+.||++ ..+.++..|.++|++|+|+++||.++...|+ +..|..|||+.+
T Consensus 183 ~~C~~C~~~-------~~~~~~~~i~~~P~iL~i~l~Rf~~~~~~Ki~~~v~f~~~L~l~~~ 237 (304)
T cd02661 183 YKCERCKKK-------VKASKQLTIHRAPNVLTIHLKRFSNFRGGKINKQISFPETLDLSPY 237 (304)
T ss_pred eeCCCCCCc-------cceEEEEEEecCCcEEEEEEeccccCCccccCCeEecCCeechhhc
Confidence 899999986 6788999999999999999999999855555 556778888754
No 20
>cd02659 peptidase_C19C A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.40 E-value=4.4e-05 Score=74.37 Aligned_cols=53 Identities=13% Similarity=0.169 Sum_probs=45.4
Q ss_pred hcccccCCCCCCCccccccccccccccccccchhcccccccccc----Cccc---cCCccccccCCC
Q 017706 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~----p~K~---~~~~~~ldl~~~ 101 (367)
.|.|+.||++ ..+.|+..|.++|++|+|+.+||.++. ..|+ +..|..||++.+
T Consensus 171 ~~~C~~C~~~-------~~~~k~~~i~~lP~vLii~l~Rf~~~~~~~~~~K~~~~v~fp~~Ldl~~~ 230 (334)
T cd02659 171 KYFCEKCGKK-------VDAEKGVCFKKLPPVLTLQLKRFEFDFETMMRIKINDRFEFPLELDMEPY 230 (334)
T ss_pred cEecCcCCCc-------ccEEEEEEeecCCCEEEEEeeeeEEccccCcceeCCceEeCCceecCccc
Confidence 3999999986 688999999999999999999999873 5665 667888998765
No 21
>cd02674 Peptidase_C19R A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.27 E-value=9.4e-05 Score=67.96 Aligned_cols=53 Identities=13% Similarity=0.132 Sum_probs=43.0
Q ss_pred hhcccccCCCCCCCccccccccccccccccccchhcccccccccc--Cccc---cCCc-cccccCC
Q 017706 41 LNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSE-EAIDVDM 100 (367)
Q Consensus 41 ~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~--p~K~---~~~~-~~ldl~~ 100 (367)
..+.|+.||.. ..+.++..|.++|++|+|+++||...+ ..|+ +..| +.||++.
T Consensus 103 ~~~~C~~C~~~-------~~~~~~~~i~~lP~iLii~l~R~~~~~~~~~K~~~~v~~~~~~l~l~~ 161 (230)
T cd02674 103 NAWKCPKCKKK-------RKATKKLTISRLPKVLIIHLKRFSFSRGSTRKLTTPVTFPLNDLDLTP 161 (230)
T ss_pred CceeCCCCCCc-------cceEEEEEEecCChhhEeEhhheecCCCCcccCCceEecccccccccc
Confidence 35899999986 778899999999999999999999985 6665 4344 4577654
No 22
>cd02673 Peptidase_C19Q A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.13 E-value=0.00017 Score=68.93 Aligned_cols=38 Identities=16% Similarity=0.176 Sum_probs=33.2
Q ss_pred hhhcccccCCCCCCCccccccccccccccccccchhcccccccccc
Q 017706 40 VLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV 85 (367)
Q Consensus 40 v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~ 85 (367)
.+++.|+.|+.. .++|+++|.+||++|+|+.+||.+..
T Consensus 124 ~~e~~C~~C~~~--------~a~k~~~i~~~P~vL~i~lkRf~~~~ 161 (245)
T cd02673 124 PIEKDCSSCKCE--------SAISSERIMTFPECLSINLKRYKLRI 161 (245)
T ss_pred ccCccCCCCCCc--------cceeechhhhCChhhEEeeEeeeecc
Confidence 457999999874 67888999999999999999998764
No 23
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.01 E-value=0.00084 Score=68.34 Aligned_cols=41 Identities=24% Similarity=0.362 Sum_probs=37.6
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcC
Q 017706 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHEN 155 (367)
Q Consensus 114 d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~d 155 (367)
-+..|+.|++|||+++.+.+||++.-| |.++|++||+...-
T Consensus 156 ~e~~I~~i~eMGf~R~qV~~ALRAafN-NPdRAVEYL~tGIP 196 (378)
T TIGR00601 156 RETTIEEIMEMGYEREEVERALRAAFN-NPDRAVEYLLTGIP 196 (378)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHhC-CHHHHHHHHHhCCC
Confidence 477899999999999999999999998 99999999998743
No 24
>KOG1865 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=96.84 E-value=0.00054 Score=71.95 Aligned_cols=90 Identities=14% Similarity=0.146 Sum_probs=66.2
Q ss_pred eeecCCCcccc----------cchHHHHHHHhhhccCCCCcchhhhhhcccccCCCCCCCccccccccccccccccccch
Q 017706 5 SLKCGDCGALL----------RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKT 74 (367)
Q Consensus 5 ~l~C~~C~~v~----------~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L 74 (367)
.|+|..|..+= .+-.+|+.+.+.--+-.=.|.-+-..-|.|..|.++ +.|.|+..+..-|.+|
T Consensus 239 ~vkC~~C~~vS~tyE~~~dltvei~d~~sl~~AL~qFt~~E~L~gen~Y~C~~Ck~~-------v~A~K~lti~raPnVL 311 (545)
T KOG1865|consen 239 QIKCLHCKGVSDTYEPYLDLTLEIQDASSLQQALEQFTKPEKLDGENAYHCGRCKQK-------VPASKQLTIHRAPNVL 311 (545)
T ss_pred ceecccCCCcccccccccceEEEeccchhHHHHHHHhhhHHhhCCccccccchhhhh-------CcccceeeeecCCceE
Confidence 58999999886 222355554442222111222121234999999987 8999999999999999
Q ss_pred hccccccccccCccc---cCCccccccCCC
Q 017706 75 SEAAKPISLEVPKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 75 ~v~~~r~~l~~p~K~---~~~~~~ldl~~~ 101 (367)
.|+.+||+.+.--|+ |..|+.|||..|
T Consensus 312 Ti~LKRF~~~~~gKI~K~I~fPE~LDl~Py 341 (545)
T KOG1865|consen 312 TLHLKRFSNGTGGKISKPVSFPETLDLQPY 341 (545)
T ss_pred EEeeehhccCcccccccccCCccccccccc
Confidence 999999999876666 778999999987
No 25
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=96.69 E-value=0.00074 Score=70.50 Aligned_cols=53 Identities=19% Similarity=0.292 Sum_probs=45.4
Q ss_pred cccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCCCCCCCCCCC
Q 017706 111 PEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHENDPDIDEMPMV 165 (367)
Q Consensus 111 ~~~d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~dd~d~dep~~~ 165 (367)
.+||+..+..|.+|||..+.|++||.-+++ +++.+++|++.|.|.. +++|..+
T Consensus 618 keVdE~~~~Slle~Gln~n~~Rkal~~~n~-d~~r~V~w~~N~~D~t-F~EP~v~ 670 (749)
T COG5207 618 KEVDESKARSLLENGLNPNLCRKALMDMNT-DSKRRVVWCINDDDGT-FPEPEVP 670 (749)
T ss_pred ccccHHHHHHHHHcCCCHHHHHHHHHHccC-CchheEEEEEeCCCCC-CCCCCCC
Confidence 468999999999999999999999988776 9999999999965544 7777544
No 26
>cd02671 Peptidase_C19O A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=96.64 E-value=0.00083 Score=66.89 Aligned_cols=53 Identities=6% Similarity=0.021 Sum_probs=42.5
Q ss_pred hcccccCCCCCCCccccccccccccccccccchhcccccccccc--------Cccc---cCCccccccCCC
Q 017706 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--------PKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~--------p~K~---~~~~~~ldl~~~ 101 (367)
.|.|+.|+++ +.|+|++.|.++|++|+|+++||.+.. ..|+ +..|..||+..+
T Consensus 200 ~y~C~~C~~~-------~~a~k~~~~~~~P~vL~i~LkRF~~~~~~~~~~~~~~Ki~~~v~fp~~L~~~~~ 263 (332)
T cd02671 200 KYFCENCHHY-------TEAERSLLFDKLPEVITIHLKCFAANGSEFDCYGGLSKVNTPLLTPLKLSLEEW 263 (332)
T ss_pred CeeCCCCCCc-------eeEEEEEEEecCCCEEEEEeeeeccccccccccCCceecCccccCccccccccc
Confidence 4999999986 789999999999999999999999752 3455 445666776543
No 27
>KOG4598 consensus Putative ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=95.90 E-value=0.0017 Score=69.97 Aligned_cols=54 Identities=13% Similarity=0.120 Sum_probs=46.6
Q ss_pred hhcccccCCCCCCCccccccccccccccccccchhccccccccc-c---Cccc---cCCccccccCCC
Q 017706 41 LNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLE-V---PKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 41 ~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~-~---p~K~---~~~~~~ldl~~~ 101 (367)
..|-|..|+++| -|.|--+|++||=.|-++.+||.|+ + -+|| +-.|+.|||..|
T Consensus 233 nqy~ce~ck~k~-------dahkgl~~~~fpy~lt~~lkrfdfdy~tmhriklnd~~tfp~~l~ln~~ 293 (1203)
T KOG4598|consen 233 NQYMCENCKSKQ-------DAHKGLRITQFPYLLTIQLKRFDFDYNTMHRIKLNDKMTFPDVLDLNDY 293 (1203)
T ss_pred cHHHHhhhhhhh-------hhhcCceeeccceeeEEeeecccccchheeeeeecccccCcccccHHHh
Confidence 359999999985 6789999999999999999999999 3 6777 558999999744
No 28
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=95.85 E-value=0.0015 Score=64.87 Aligned_cols=41 Identities=22% Similarity=0.309 Sum_probs=35.9
Q ss_pred hcccccCCCCCCCccccccccccccccccccchhcccccccccc--Cccc
Q 017706 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT 89 (367)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~--p~K~ 89 (367)
...||.||++ ..+.|+....-.|++|+||++||++-. |+|+
T Consensus 284 ~W~CpkC~~k-------~ss~K~~~I~~lP~~LII~i~RF~i~V~~~~ki 326 (415)
T COG5533 284 AWRCPKCGRK-------ESSRKRMEILVLPDVLIIHISRFHISVMGRKKI 326 (415)
T ss_pred cccCchhccc-------ccchheEEEEecCceEEEEeeeeeEEeeccccc
Confidence 4799999997 678899999999999999999999665 6665
No 29
>cd02662 Peptidase_C19F A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=95.77 E-value=0.0018 Score=61.06 Aligned_cols=43 Identities=9% Similarity=0.111 Sum_probs=33.8
Q ss_pred hhhhcccccCCCCCCCccccccccccccccccccchhcccccccccc---Cccc---cCCcccc
Q 017706 39 AVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV---PKAT---ADSEEAI 96 (367)
Q Consensus 39 ~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~---p~K~---~~~~~~l 96 (367)
.+.++.|+.| ++.|.++|++|+|+.+||.++. +.|+ +..|+.|
T Consensus 110 ~l~~~~C~~C---------------~~~i~~lP~vLii~LkRF~~~~~~~~~K~~~~v~fp~~l 158 (240)
T cd02662 110 IIDDYKCDRC---------------QTVIVRLPQILCIHLSRSVFDGRGTSTKNSCKVSFPERL 158 (240)
T ss_pred cccCcCCCCC---------------eEEeecCCcEEEEEEEEEEEcCCCceeeeccEEECCCcc
Confidence 3446999999 4469999999999999999885 6676 5556555
No 30
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.45 E-value=0.034 Score=57.68 Aligned_cols=48 Identities=31% Similarity=0.385 Sum_probs=42.3
Q ss_pred ccccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCCCC
Q 017706 110 EPEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHENDPD 158 (367)
Q Consensus 110 ~~~~d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~dd~d 158 (367)
.+.||...|.+|+.|||++..|.-||..+|| +.+.|+..|......+.
T Consensus 425 p~~vd~~~la~Lv~mGF~e~~A~~ALe~~gn-n~~~a~~~L~~s~~n~~ 472 (568)
T KOG2561|consen 425 PEQVDGISLAELVSMGFEEGKARSALEAGGN-NEDTAQRLLSASVANEG 472 (568)
T ss_pred CcccchhhHHHHHHhccccchHHHHHHhcCC-cHHHHHHHHHHhCCCCc
Confidence 3458999999999999999999999999988 99999999987766653
No 31
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.35 E-value=0.024 Score=57.83 Aligned_cols=45 Identities=27% Similarity=0.372 Sum_probs=40.1
Q ss_pred cccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCC
Q 017706 111 PEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHEND 156 (367)
Q Consensus 111 ~~~d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~dd 156 (367)
..-+.++++-|.+|||++..+.-|-++++- |.|.|.||||+|..|
T Consensus 334 T~eE~~AIeRL~~LGF~r~~viqaY~ACdK-NEelAAn~Lf~~~~~ 378 (378)
T TIGR00601 334 TPEEKEAIERLCALGFDRGLVIQAYFACDK-NEELAANYLLSQNFD 378 (378)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHHhcCC-cHHHHHHHHHhhcCC
Confidence 334789999999999999999999988774 999999999999876
No 32
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=94.68 E-value=0.046 Score=54.64 Aligned_cols=40 Identities=38% Similarity=0.588 Sum_probs=36.8
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 017706 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (367)
Q Consensus 114 d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~ 154 (367)
+.++++-|..|||++..+.-|.++.. +|-|.|.||||+|+
T Consensus 298 e~eAIeRL~alGF~ralViqayfACd-KNEelAAN~Ll~~~ 337 (340)
T KOG0011|consen 298 EKEAIERLEALGFPRALVIQAYFACD-KNEELAANYLLSHS 337 (340)
T ss_pred HHHHHHHHHHhCCcHHHHHHHHHhcC-ccHHHHHHHHHhhc
Confidence 67899999999999999999988865 58999999999999
No 33
>cd02257 Peptidase_C19 Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=94.58 E-value=0.018 Score=51.36 Aligned_cols=55 Identities=16% Similarity=0.120 Sum_probs=43.7
Q ss_pred hhhhhcccccCC--CCCCCccccccccccccccccccchhcccccccccc---Cccc---cCCccccccC
Q 017706 38 EAVLNLVCATCG--KPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV---PKAT---ADSEEAIDVD 99 (367)
Q Consensus 38 e~v~~~~C~~Cg--~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~---p~K~---~~~~~~ldl~ 99 (367)
+.+..+.|..|+ +. ..+.++..|.++|++|+|+++||..+. +.|+ +..++.+++.
T Consensus 112 e~~~~~~~~~c~~~~~-------~~~~~~~~i~~lP~~L~i~l~R~~~~~~~~~~k~~~~v~~~~~l~~~ 174 (255)
T cd02257 112 EILEGDNCYKCEKKKK-------QEATKRLKIKKLPPVLIIHLKRFSFNEDGTKEKLNTKVSFPLELDLS 174 (255)
T ss_pred hccCCCCcccCCCCcc-------cceeEEEecccCCceeEEEeeceeeccccccccCCCeEeCCCcccCc
Confidence 446668899997 33 678899999999999999999999875 6666 5566677764
No 34
>cd02672 Peptidase_C19P A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=94.55 E-value=0.013 Score=56.88 Aligned_cols=40 Identities=23% Similarity=0.164 Sum_probs=35.4
Q ss_pred hhhhhcccccCCCCCCCcccccccccccccccccc----chhccccccccc
Q 017706 38 EAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVD----KTSEAAKPISLE 84 (367)
Q Consensus 38 e~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~----~L~v~~~r~~l~ 84 (367)
|.+..+.|+.|+++ ..++|++.+.+||+ +|+||.+||..+
T Consensus 130 E~~~~~~C~~C~~~-------~~a~k~~~i~~lP~~L~~VL~i~lkrf~~~ 173 (268)
T cd02672 130 EKVTKAWCDTCCKY-------QPLEQTTSIRHLPDILLLVLVINLSVTNGE 173 (268)
T ss_pred hhcccccccccCcc-------cccEEEEEeecCCCcccceEEEEEeccChh
Confidence 44557999999987 78999999999999 999999999864
No 35
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=94.50 E-value=0.045 Score=54.67 Aligned_cols=41 Identities=24% Similarity=0.341 Sum_probs=37.4
Q ss_pred cCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 017706 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (367)
Q Consensus 113 ~d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~ 154 (367)
..+..+.+|++|||.+....+||++.-| +.++|++||+...
T Consensus 134 ~~e~~V~~Im~MGy~re~V~~AlRAafN-NPeRAVEYLl~GI 174 (340)
T KOG0011|consen 134 EYEQTVQQIMEMGYDREEVERALRAAFN-NPERAVEYLLNGI 174 (340)
T ss_pred hhHHHHHHHHHhCccHHHHHHHHHHhhC-ChhhhHHHHhcCC
Confidence 4678899999999999999999999998 8999999999754
No 36
>KOG1866 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=93.50 E-value=0.017 Score=62.82 Aligned_cols=53 Identities=13% Similarity=0.102 Sum_probs=45.6
Q ss_pred hcccccCCCCCCCccccccccccccccccccchhccccccccc--c--Cccc---cCCccccccCCC
Q 017706 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLE--V--PKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~--~--p~K~---~~~~~~ldl~~~ 101 (367)
-|.|..|.++ +.-.|+|.|+..|.+|+||.+||.++ + -.|- +..|-.||++.|
T Consensus 266 AYhCeKCdeK-------~~TvkRt~ik~LPsvl~IqLkRF~yD~e~~~~iK~n~~frFP~~ldMePY 325 (944)
T KOG1866|consen 266 AYHCEKCDEK-------VDTVKRTCIKKLPSVLAIQLKRFDYDWERECAIKFNDYFRFPRELDMEPY 325 (944)
T ss_pred hhhhhhhhhh-------hHhHHHHHHhhCChhheehhhhccchhhhccccccchhcccchhhcCCce
Confidence 4999999987 78899999999999999999999999 2 6665 557888888855
No 37
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=93.41 E-value=0.079 Score=39.96 Aligned_cols=30 Identities=30% Similarity=0.512 Sum_probs=22.2
Q ss_pred cccCHHHHHHHHhCCCCHHHHHHHHHHhCC
Q 017706 111 PEVDKELLKELEAMGFPVARATRALHYSGN 140 (367)
Q Consensus 111 ~~~d~~~l~~L~~MGF~~~~a~kAL~~tgn 140 (367)
.-+|.++|+++.+|||+.+++..||+..|=
T Consensus 6 ~Gi~~~lVd~F~~mGF~~dkVvevlrrlgi 35 (55)
T PF09288_consen 6 YGIDKDLVDQFENMGFERDKVVEVLRRLGI 35 (55)
T ss_dssp ---SHHHHHHHHHHT--HHHHHHHHHHS--
T ss_pred cCCCHHHHHHHHHcCCcHHHHHHHHHHhCC
Confidence 457999999999999999999999998763
No 38
>cd02669 Peptidase_C19M A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=93.40 E-value=0.03 Score=57.81 Aligned_cols=57 Identities=11% Similarity=-0.106 Sum_probs=44.4
Q ss_pred hhhhhcccccCCCCCCCccccccccccccccccccchhcccccccccc--Cccc---cCCccc-cccCCC
Q 017706 38 EAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSEEA-IDVDMS 101 (367)
Q Consensus 38 e~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~--p~K~---~~~~~~-ldl~~~ 101 (367)
|-...|.|+.|... ..++|+..+...|++|+|+.+||...+ ..|. |..|.. |||+.|
T Consensus 307 e~L~ky~~~~c~~~-------~~a~k~~~I~~LP~vLiihLKRF~~~~~~~~K~~t~V~FP~~~LDm~~y 369 (440)
T cd02669 307 QLLKKYDGKTETEL-------KDSLKRYLISRLPKYLIFHIKRFSKNNFFKEKNPTIVNFPIKNLDLSDY 369 (440)
T ss_pred HHHHhcCCccceec-------ccceEEEEEeeCCcEEEEEEecccCCCCccccCCCEEECCCCccchhhh
Confidence 33456899999875 567999999999999999999999875 3344 556664 788765
No 39
>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]
Probab=92.36 E-value=2.1 Score=47.42 Aligned_cols=84 Identities=36% Similarity=0.452 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH------hHHHHHHHH-HHHH
Q 017706 182 EIKLKAQELRERARKKKEEEEKRMEREREKERIRIGKELLEAKRIEEENERKRILALRKA------EKEEEKRAR-EKIR 254 (367)
Q Consensus 182 Ek~~k~~el~~k~r~kr~eeek~~~~e~E~~Rr~~gKe~~~~k~~~ee~e~k~~~e~rrr------EK~ee~~ar-~rir 254 (367)
|+..+++||.+.-|+.|+.+|++...+-|+.| .+.-+++|++++|.++++.-+.-++ ++.+..... .+-+
T Consensus 924 er~rk~qE~~E~ER~rrEaeek~rre~ee~k~---~k~e~e~kRK~eEeqr~~qee~e~~l~~e~q~qla~e~eee~k~q 1000 (1259)
T KOG0163|consen 924 ERLRKIQELAEAERKRREAEEKRRREEEEKKR---AKAEMETKRKAEEEQRKAQEEEERRLALELQEQLAKEAEEEAKRQ 1000 (1259)
T ss_pred HHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666788877777777766654443333333 3444567777777776654332222 111111111 1335
Q ss_pred HhHHHHHHHHHHhc
Q 017706 255 QKLEEDKAERRRRL 268 (367)
Q Consensus 255 ~qIe~Dk~eR~~k~ 268 (367)
.|++.+|..+.-.+
T Consensus 1001 ~~~Eqer~D~~la~ 1014 (1259)
T KOG0163|consen 1001 NQLEQERRDHELAL 1014 (1259)
T ss_pred hHHHHHHHHHHHHH
Confidence 66787777765533
No 40
>PTZ00266 NIMA-related protein kinase; Provisional
Probab=91.94 E-value=2.4 Score=48.72 Aligned_cols=17 Identities=41% Similarity=0.806 Sum_probs=7.5
Q ss_pred HHHHHHHhHHHHHHHHHH
Q 017706 249 AREKIRQKLEEDKAERRR 266 (367)
Q Consensus 249 ar~rir~qIe~Dk~eR~~ 266 (367)
.++|++ .++.++.+|++
T Consensus 508 e~er~~-r~e~e~~e~~r 524 (1021)
T PTZ00266 508 ERERVD-RLERDRLEKAR 524 (1021)
T ss_pred HHHHHH-HHHHHHHHHHH
Confidence 334433 33455555544
No 41
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=91.20 E-value=0.42 Score=33.52 Aligned_cols=37 Identities=35% Similarity=0.532 Sum_probs=30.5
Q ss_pred CHHHHHHHHhCCCCH---HHHHHHHHHhCCCCHHHHHHHHHH
Q 017706 114 DKELLKELEAMGFPV---ARATRALHYSGNANVEAAVNWVVE 152 (367)
Q Consensus 114 d~~~l~~L~~MGF~~---~~a~kAL~~tgn~~~E~A~~Wl~~ 152 (367)
+++.+.+|.+| ||. ..++..|...+| +++.|++-|++
T Consensus 2 ~~~~v~~L~~m-FP~l~~~~I~~~L~~~~g-~ve~~i~~LL~ 41 (43)
T smart00546 2 NDEALHDLKDM-FPNLDEEVIKAVLEANNG-NVEATINNLLE 41 (43)
T ss_pred hHHHHHHHHHH-CCCCCHHHHHHHHHHcCC-CHHHHHHHHHc
Confidence 46789999999 775 777888887666 89999999875
No 42
>COG1773 Rubredoxin [Energy production and conversion]
Probab=90.35 E-value=0.079 Score=39.98 Aligned_cols=42 Identities=19% Similarity=0.467 Sum_probs=33.4
Q ss_pred eeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCC
Q 017706 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~ 50 (367)
+-+|.+||+|.....+...+.-.-| +-|.+. -.+..||-||-
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~gi~pg-T~fedl---Pd~w~CP~Cg~ 44 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRCGIAPG-TPFEDL---PDDWVCPECGV 44 (55)
T ss_pred ceEecCCceEeccccCCccCCCCCC-CchhhC---CCccCCCCCCC
Confidence 5799999999988888777776334 448887 56799999984
No 43
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=90.15 E-value=0.34 Score=50.50 Aligned_cols=45 Identities=22% Similarity=0.372 Sum_probs=39.2
Q ss_pred ccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCCC
Q 017706 112 EVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHENDP 157 (367)
Q Consensus 112 ~~d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~dd~ 157 (367)
-||+-++.-|++|||+...|.-||.-+.| ++..|+|-|-.|.|..
T Consensus 373 wvn~rs~~rL~~mGyer~la~eaL~r~~N-di~~aldllq~esdel 417 (568)
T KOG2561|consen 373 WVNPRSLERLVSMGYERELAAEALRRNEN-DIQKALDLLQDESDEL 417 (568)
T ss_pred ccCHHHHHHHHhcchHhHHHHHHHHhccC-cHHHHHHhcCCcchhh
Confidence 37999999999999999999999999888 8988888776666653
No 44
>COG5560 UBP12 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=89.97 E-value=0.088 Score=56.75 Aligned_cols=54 Identities=11% Similarity=0.014 Sum_probs=44.5
Q ss_pred hhcccccCCCCCCCccccccccccccccccccchhcccccccccc--Cccc---cC-CccccccCCC
Q 017706 41 LNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---AD-SEEAIDVDMS 101 (367)
Q Consensus 41 ~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~--p~K~---~~-~~~~ldl~~~ 101 (367)
...+||+|+.. -.|+|+.-.-..|++|+||.+||.-++ +.|. |+ +=+.|||+.+
T Consensus 694 DswyCpgCkef-------rqasKqmelwrlP~iLiihLkRFss~rsfrdKiddlVeyPiddldLs~~ 753 (823)
T COG5560 694 DSWYCPGCKEF-------RQASKQMELWRLPMILIIHLKRFSSVRSFRDKIDDLVEYPIDDLDLSGV 753 (823)
T ss_pred ccccCCchHhh-------hhhhhhhhhhcCChheeeehhhhhhcccchhhhhhhhccccccccccce
Confidence 34899999764 789999999999999999999999987 8887 44 3356777744
No 45
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=89.87 E-value=0.14 Score=43.73 Aligned_cols=46 Identities=20% Similarity=0.484 Sum_probs=30.2
Q ss_pred eeecCCCcccccchH------------HHHHHHhhhccCCCCcch--hhhhhcccccCCCC
Q 017706 5 SLKCGDCGALLRSVQ------------EAQEHAELTSHSNFSEST--EAVLNLVCATCGKP 51 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~------------~aq~h~~~tgh~~F~e~~--e~v~~~~C~~Cg~~ 51 (367)
.++| .||..+-+-. ++.+-..+..-..|.... ..+.+|+||.||..
T Consensus 24 ~vkc-~CGh~f~d~r~NwK~~alv~vRd~~E~~~~iYp~~~aPdp~w~~irEyyCP~Cgt~ 83 (112)
T PF08882_consen 24 VVKC-DCGHEFCDARENWKLGALVYVRDPEEIHPEIYPFTMAPDPEWQVIREYYCPGCGTQ 83 (112)
T ss_pred eeec-cCCCeecChhcChhhCcEEEecChHHhhhhhcccccCCCCCcEEEEEEECCCCcce
Confidence 5788 8999993333 333333334555666543 46789999999974
No 46
>PF00443 UCH: Ubiquitin carboxyl-terminal hydrolase; InterPro: IPR001394 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C19 (ubiquitin-specific protease family, clan CA). Families within the CA clan are loosely termed papain-like as protein fold of the peptidase unit resembles that of papain, the type example for clan CA. Predicted active site residues for members of this family and family C1 occur in the same order in the sequence: N/Q, C, H. The type example is human ubiquitin-specific protease 14. Ubiquitin is highly conserved, commonly found conjugated to proteins in eukaryotic cells, where it may act as a marker for rapid degradation, or it may have a chaperone function in protein assembly []. The ubiquitin is released by cleavage from the bound protein by a protease []. A number of deubiquitinising proteases are known: all are activated by thiol compounds [, ], and inhibited by thiol-blocking agents and ubiquitin aldehyde [, ], and as such have the properties of cysteine proteases []. The deubiquitinsing proteases can be split into 2 size ranges (20-30 kDa, IPR001578 from INTERPRO, and 100-200 kDa) []: this family are the 100-200 kDa peptides which includes the Ubp1 ubiquitin peptidase from yeast. Only one conserved cysteine can be identified, along with two conserved histidines. The spacing between the cysteine and the second histidine is thought to be more representative of the cysteine/histidine spacing of a cysteine protease catalytic dyad [].; GO: 0004221 ubiquitin thiolesterase activity, 0006511 ubiquitin-dependent protein catabolic process; PDB: 2LBC_A 3MHH_A 3MHS_A 3M99_A 2Y6E_D 2VHF_A 2HD5_A 3NHE_A 2IBI_A 1NBF_B ....
Probab=89.76 E-value=0.078 Score=48.27 Aligned_cols=49 Identities=12% Similarity=0.253 Sum_probs=36.4
Q ss_pred hhcccccCCCCCCCccccccccccccccccccchhcccccccccc----Cccc---cCCc-cccccCCC
Q 017706 41 LNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSE-EAIDVDMS 101 (367)
Q Consensus 41 ~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~----p~K~---~~~~-~~ldl~~~ 101 (367)
..+.|..|+.. ...|.++|++|+|+.+||.+.. ..|. +..| +.|||+.+
T Consensus 141 ~~~~c~~c~~~------------~~~~~~~P~~L~i~l~R~~~~~~~~~~~K~~~~v~~~~~~l~l~~~ 197 (269)
T PF00443_consen 141 SSIKCSSCKNS------------QSSISSLPPILIIQLKRFEFDQETGRSKKINNPVEFPLEELDLSPY 197 (269)
T ss_dssp EEEEETTTTCE------------EEEEEEBBSEEEEEEE-EEEESTSSEEEE--CEEB--SSEEEGGGG
T ss_pred ccccccccccc------------ccccccccceeeeccccceeccccccccccccccccCchhhhhhhh
Confidence 35789999873 8889999999999999996663 5666 6678 78999865
No 47
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=89.14 E-value=1.2 Score=31.10 Aligned_cols=38 Identities=24% Similarity=0.395 Sum_probs=30.3
Q ss_pred HHHHHHHHhC--CCCHHHHHHHHHHhCCCCHHHHHHHHHHh
Q 017706 115 KELLKELEAM--GFPVARATRALHYSGNANVEAAVNWVVEH 153 (367)
Q Consensus 115 ~~~l~~L~~M--GF~~~~a~kAL~~tgn~~~E~A~~Wl~~h 153 (367)
++.+.+|.+| .++......+|..+++ +++.|++-|++.
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~-~ve~ai~~LL~~ 41 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNG-DVEAAIDALLEM 41 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTT-THHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCC-CHHHHHHHHHcC
Confidence 5678999998 3456888888977776 899999999874
No 48
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=88.17 E-value=1.4 Score=30.96 Aligned_cols=40 Identities=23% Similarity=0.223 Sum_probs=29.4
Q ss_pred HHHHHH-hCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCCC
Q 017706 117 LLKELE-AMGFPVARATRALHYSGNANVEAAVNWVVEHENDP 157 (367)
Q Consensus 117 ~l~~L~-~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~dd~ 157 (367)
+|.+++ -.|.++..|..-|..+++ +++.|++-.|++.++|
T Consensus 3 ~i~~F~~iTg~~~~~A~~~L~~~~w-dle~Av~~y~~~~~~~ 43 (43)
T PF14555_consen 3 KIAQFMSITGADEDVAIQYLEANNW-DLEAAVNAYFDDGEAP 43 (43)
T ss_dssp HHHHHHHHH-SSHHHHHHHHHHTTT--HHHHHHHHHHSS-S-
T ss_pred HHHHHHHHHCcCHHHHHHHHHHcCC-CHHHHHHHHHhCCCCC
Confidence 444444 358999999999999887 9999999999987765
No 49
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=88.02 E-value=0.1 Score=41.37 Aligned_cols=66 Identities=20% Similarity=0.358 Sum_probs=24.3
Q ss_pred ecCCCcccccchHHHHHHHhhhccCCCCcc-------------hhhhhh-cccccCCCCCCCcccccccccccccccccc
Q 017706 7 KCGDCGALLRSVQEAQEHAELTSHSNFSES-------------TEAVLN-LVCATCGKPCRSKTETDLHRKRTGHTDFVD 72 (367)
Q Consensus 7 ~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~-------------~e~v~~-~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~ 72 (367)
+|..|+..+.+...-..|...+-..++... ...+.+ +.|+.|++.|.+......|..+.+|..+..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 699999999999999999984433344421 123334 999999999988888888988888887644
No 50
>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=87.57 E-value=0.13 Score=37.94 Aligned_cols=42 Identities=19% Similarity=0.491 Sum_probs=27.6
Q ss_pred eecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 6 l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
-+|.+||++-....+-..+.-..| +.|.+. ..+++||.||.+
T Consensus 2 y~C~~CgyiYd~~~Gd~~~~i~pG-t~f~~L---p~~w~CP~C~a~ 43 (50)
T cd00730 2 YECRICGYIYDPAEGDPDEGIPPG-TPFEDL---PDDWVCPVCGAG 43 (50)
T ss_pred cCCCCCCeEECCCCCCcccCcCCC-CCHhHC---CCCCCCCCCCCc
Confidence 579999999976654433333223 235444 457999999864
No 51
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=87.30 E-value=11 Score=42.25 Aligned_cols=31 Identities=23% Similarity=0.275 Sum_probs=20.7
Q ss_pred CCHHHHHHHHHHhCCCCHHHHHHHHHHhcCC
Q 017706 126 FPVARATRALHYSGNANVEAAVNWVVEHEND 156 (367)
Q Consensus 126 F~~~~a~kAL~~tgn~~~E~A~~Wl~~h~dd 156 (367)
.+-..|+-||-.+|=....-|-=|-++..|-
T Consensus 212 Lsg~qaR~aL~qS~Lpq~~LA~IW~LsDvd~ 242 (1118)
T KOG1029|consen 212 LSGQQARSALGQSGLPQNQLAHIWTLSDVDG 242 (1118)
T ss_pred cccHHHHHHHHhcCCchhhHhhheeeeccCC
Confidence 4446777788777765667777777765543
No 52
>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]
Probab=87.23 E-value=7 Score=43.57 Aligned_cols=55 Identities=35% Similarity=0.401 Sum_probs=32.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHHH
Q 017706 208 EREKERIRIGKELLEAKRIEEENERKRILALRKAEKEEEKRAREKIRQKLEEDKAE 263 (367)
Q Consensus 208 e~E~~Rr~~gKe~~~~k~~~ee~e~k~~~e~rrrEK~ee~~ar~rir~qIe~Dk~e 263 (367)
|.|..||+.--+-..++.+++ ..||.+-++++++++++...---+.+|++...++
T Consensus 941 Eaeek~rre~ee~k~~k~e~e-~kRK~eEeqr~~qee~e~~l~~e~q~qla~e~ee 995 (1259)
T KOG0163|consen 941 EAEEKRRREEEEKKRAKAEME-TKRKAEEEQRKAQEEEERRLALELQEQLAKEAEE 995 (1259)
T ss_pred hhhHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 334444444444444444433 2344555667777777777777778788777665
No 53
>PF05672 MAP7: MAP7 (E-MAP-115) family; InterPro: IPR008604 The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115 kDa epithelial MAP (E-MAP-115) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin []. The binding of this microtubule associated protein is nucleotide independent [].
Probab=87.20 E-value=24 Score=32.51 Aligned_cols=25 Identities=36% Similarity=0.353 Sum_probs=19.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhHHH
Q 017706 177 SLTPEEIKLKAQELRERARKKKEEE 201 (367)
Q Consensus 177 ~lT~EEk~~k~~el~~k~r~kr~ee 201 (367)
..++||+..-|.+.+..+|+.++.+
T Consensus 18 TtdaEEAtkiLAEkRRlAReQkErE 42 (171)
T PF05672_consen 18 TTDAEEATKILAEKRRLAREQKERE 42 (171)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhhhH
Confidence 5788999988999888887776544
No 54
>KOG1868 consensus Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=86.51 E-value=0.17 Score=55.15 Aligned_cols=38 Identities=18% Similarity=0.143 Sum_probs=31.3
Q ss_pred cccccCCCCCCCccccccccccccccccccchhcccccccccc
Q 017706 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV 85 (367)
Q Consensus 43 ~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~ 85 (367)
+.||.|+.+..+. .+|+.-|-.||++|+|+++||..+.
T Consensus 518 w~Cp~c~~~~~~~-----~lK~~~i~~lp~iLiihL~Rf~~~~ 555 (653)
T KOG1868|consen 518 WLCPRCKHKESSK-----TLKKLTILRLPKILIIHLKRFSSDG 555 (653)
T ss_pred cCCccccCccccc-----ccceeeeecCCHHHHHHHHHhccCc
Confidence 7999999862111 1499999999999999999999994
No 55
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.13 E-value=0.79 Score=42.70 Aligned_cols=39 Identities=28% Similarity=0.273 Sum_probs=33.1
Q ss_pred cCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Q 017706 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVE 152 (367)
Q Consensus 113 ~d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~ 152 (367)
.+...++.|.+|||+++.+..+|.-.+- +++.|.+.+++
T Consensus 161 ~~~~~v~~l~~mGf~~~~~i~~L~~~~w-~~~~a~~~~~s 199 (200)
T KOG0418|consen 161 WDKKKVDSLIEMGFSELEAILVLSGSDW-NLADATEQLLS 199 (200)
T ss_pred hhHHHHHHHHHhcccHHHHHHHhhcccc-chhhhhHhhcc
Confidence 5788899999999999999999976554 78888887765
No 56
>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=85.93 E-value=0.37 Score=32.29 Aligned_cols=25 Identities=32% Similarity=0.821 Sum_probs=19.3
Q ss_pred eecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 6 l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
-+|.+||.+..+.. .+..||.||.+
T Consensus 2 ~~C~~CGy~y~~~~---------------------~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEE---------------------APWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCc---------------------CCCcCcCCCCc
Confidence 47999998876543 45799999975
No 57
>KOG2699 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=85.80 E-value=0.49 Score=48.73 Aligned_cols=54 Identities=22% Similarity=0.169 Sum_probs=44.2
Q ss_pred HHHHhhhhhcCCChHHHHHHHHHHHHHHhhhccCCChhhhhhhhcccccccccccc
Q 017706 305 ECLRSLKQNHKDDDAKVKRAFQTLLTYIGNVAKNPNEEKFRKIRLSNQTFQVWNFF 360 (367)
Q Consensus 305 ~~l~sLk~~~~~~~a~~~~a~~tL~kyl~Ni~~~P~eeK~rkIr~~N~~f~~~~~~ 360 (367)
..+..+..++.+.+ ....+.+++.+|..||..||..+|||++ ++|..|+++|++
T Consensus 153 ss~~~~~~~~k~~e-~se~~~d~~~kqe~~~~~~pE~ek~R~r-l~~el~~~~v~g 206 (407)
T KOG2699|consen 153 SSLTKIFVNTKAKE-LSESGRDIRQKQEQNTERNPEREKERKR-LGNELLKEKVLG 206 (407)
T ss_pred hhhhhccccccchh-hhhhhhhhHHHhhhhhccchhhhhhhhc-cccchhhccccc
Confidence 34445555555554 5688999999999999999999999988 999999999943
No 58
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=85.47 E-value=10 Score=42.40 Aligned_cols=19 Identities=16% Similarity=0.270 Sum_probs=13.3
Q ss_pred cCHHHHHHHHhCCCCHHHH
Q 017706 113 VDKELLKELEAMGFPVARA 131 (367)
Q Consensus 113 ~d~~~l~~L~~MGF~~~~a 131 (367)
-.+.+-..|+--|.|.+.-
T Consensus 213 sg~qaR~aL~qS~Lpq~~L 231 (1118)
T KOG1029|consen 213 SGQQARSALGQSGLPQNQL 231 (1118)
T ss_pred ccHHHHHHHHhcCCchhhH
Confidence 3555677788888887653
No 59
>cd02670 Peptidase_C19N A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=85.23 E-value=0.34 Score=46.60 Aligned_cols=42 Identities=7% Similarity=-0.156 Sum_probs=34.7
Q ss_pred cccccccccccccchhcccccccccc--Cccc---cCCccccccCCC
Q 017706 60 LHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 60 ~a~K~t~f~tFP~~L~v~~~r~~l~~--p~K~---~~~~~~ldl~~~ 101 (367)
.+.+...|..+|++|+|+.+||.... +.|+ |..|..|||+.|
T Consensus 88 ~~~~~e~i~~lP~vLiIhLKRF~~~~~~~~Kl~~~I~fP~~Ldl~~~ 134 (241)
T cd02670 88 QYFNNSVFAKAPSCLIICLKRYGKTEGKAQKMFKKILIPDEIDIPDF 134 (241)
T ss_pred HHhchhhhhhCCCeEEEEEEccccCCCcceeCCcEECCCCcCCchhh
Confidence 34444449999999999999999985 7788 778899999876
No 60
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=85.19 E-value=2.2 Score=30.67 Aligned_cols=32 Identities=25% Similarity=0.361 Sum_probs=23.6
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHh---CCCCHHH
Q 017706 114 DKELLKELEAMGFPVARATRALHYS---GNANVEA 145 (367)
Q Consensus 114 d~~~l~~L~~MGF~~~~a~kAL~~t---gn~~~E~ 145 (367)
-+++++.|+++||++..+.+|+... .+.+++.
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~~~~~~~~~e~ 37 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKLLEKPGMDVEE 37 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHHHHSTTS-HHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhcCCCCCHHH
Confidence 3678999999999999999998776 2345554
No 61
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=84.48 E-value=0.32 Score=35.53 Aligned_cols=43 Identities=23% Similarity=0.551 Sum_probs=24.4
Q ss_pred eeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
+-+|.+||+|-....+=-.+.- .--+-|.+. -.+++||.||..
T Consensus 1 ky~C~~CgyvYd~~~Gd~~~~i-~pGt~F~~L---p~~w~CP~C~a~ 43 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPENGI-PPGTPFEDL---PDDWVCPVCGAP 43 (47)
T ss_dssp EEEETTTSBEEETTTBBGGGTB--TT--GGGS----TT-B-TTTSSB
T ss_pred CcCCCCCCEEEcCCcCCcccCc-CCCCCHHHC---CCCCcCcCCCCc
Confidence 4689999999866554322222 123446665 556999999863
No 62
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=80.17 E-value=0.82 Score=40.20 Aligned_cols=47 Identities=26% Similarity=0.427 Sum_probs=26.8
Q ss_pred ceeecCCCcccccchHHHHHHHhhhccCCCCcchhhh-hhcccccCCCC
Q 017706 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAV-LNLVCATCGKP 51 (367)
Q Consensus 4 ~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v-~~~~C~~Cg~~ 51 (367)
.+..|.+||.........+++.. +-++.+.=..+.. ..+.||.||+.
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDE-EIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccc-cccccccccccccccCcCCcCCCCC
Confidence 56899999988765533333222 3333333332222 23679999974
No 63
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=79.86 E-value=3.8 Score=38.45 Aligned_cols=41 Identities=27% Similarity=0.519 Sum_probs=35.5
Q ss_pred cCHHHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 017706 113 VDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (367)
Q Consensus 113 ~d~~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~ 154 (367)
++..++..|-+ -|.+--.|++||..++| |++.|++||-...
T Consensus 3 i~a~~ik~LR~~tga~~~~ck~AL~~~~g-d~~~A~~~lr~~g 44 (198)
T PRK12332 3 ITAKLVKELREKTGAGMMDCKKALEEANG-DMEKAIEWLREKG 44 (198)
T ss_pred CCHHHHHHHHHHHCCCHHHHHHHHHHcCC-CHHHHHHHHHHhh
Confidence 56678888874 58999999999999998 9999999998754
No 64
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=79.31 E-value=0.96 Score=34.33 Aligned_cols=44 Identities=20% Similarity=0.277 Sum_probs=31.1
Q ss_pred eeecCCCcccccc---hHHHHHHHhhhccCCCCcchhhhhhcccccCCC
Q 017706 5 SLKCGDCGALLRS---VQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (367)
Q Consensus 5 ~l~C~~C~~v~~g---~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~ 50 (367)
..-|..||.++=| ..-|..|++.+||..|-... .....|-.|+.
T Consensus 11 lw~CL~Cg~~~C~~~~~~Ha~~H~~~~~H~l~v~~~--~~~i~C~~C~~ 57 (63)
T PF02148_consen 11 LWLCLTCGYVGCGRYSNGHALKHYKETGHPLAVSLS--TGSIWCYACDD 57 (63)
T ss_dssp EEEETTTS-EEETTTSTSHHHHHHHHHT--EEEETT--TTCEEETTTTE
T ss_pred eEEeCCCCcccccCCcCcHHHHhhcccCCeEEEECC--CCeEEEcCCCc
Confidence 3569999999955 46799999999999998763 22357877764
No 65
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=79.24 E-value=16 Score=40.94 Aligned_cols=28 Identities=32% Similarity=0.504 Sum_probs=11.8
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 017706 187 AQELRERARKKKEEEEKRMEREREKERI 214 (367)
Q Consensus 187 ~~el~~k~r~kr~eeek~~~~e~E~~Rr 214 (367)
+.+|++.+...++++|++...+.|+.||
T Consensus 216 v~~~qe~La~~qe~eE~qkreeEE~~r~ 243 (1064)
T KOG1144|consen 216 VRAMQEALAKRQEEEERQKREEEERLRR 243 (1064)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555544444333333333333333
No 66
>PRK09377 tsf elongation factor Ts; Provisional
Probab=78.82 E-value=3.9 Score=40.59 Aligned_cols=41 Identities=24% Similarity=0.494 Sum_probs=36.0
Q ss_pred cCHHHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 017706 113 VDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (367)
Q Consensus 113 ~d~~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~ 154 (367)
++..++..|-+ -|.+---|++||..++| |++.|++||-.+.
T Consensus 4 is~~~IK~LR~~Tgagm~dCKkAL~e~~g-D~ekAi~~Lrk~G 45 (290)
T PRK09377 4 ITAALVKELRERTGAGMMDCKKALTEADG-DIEKAIEWLRKKG 45 (290)
T ss_pred cCHHHHHHHHHHHCCCHHHHHHHHHHcCC-CHHHHHHHHHHhc
Confidence 56778888874 59999999999999998 9999999998864
No 67
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=78.67 E-value=2.8 Score=44.21 Aligned_cols=36 Identities=31% Similarity=0.487 Sum_probs=31.3
Q ss_pred HHHHHHHhCCCC-HHHHHHHHHHhCCCCHHHHHHHHHH
Q 017706 116 ELLKELEAMGFP-VARATRALHYSGNANVEAAVNWVVE 152 (367)
Q Consensus 116 ~~l~~L~~MGF~-~~~a~kAL~~tgn~~~E~A~~Wl~~ 152 (367)
.-++||.+|||. +++...||.+||+ ++.+|++-|+.
T Consensus 456 ~QLeQL~~MGF~nre~nlqAL~atgG-di~aAverll~ 492 (493)
T KOG0010|consen 456 TQLEQLNDMGFLDREANLQALRATGG-DINAAVERLLG 492 (493)
T ss_pred HHHHHHHhcCCccHHHHHHHHHHhcC-cHHHHHHHHhc
Confidence 448999999985 6888999999998 99999998763
No 68
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=78.13 E-value=4.2 Score=40.35 Aligned_cols=41 Identities=24% Similarity=0.353 Sum_probs=35.9
Q ss_pred cCHHHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 017706 113 VDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (367)
Q Consensus 113 ~d~~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~ 154 (367)
++..++..|-+ -|.+---|++||..++| |++.|++||-.+.
T Consensus 3 isa~~IK~LRe~Tgagm~dCKkAL~e~~g-DiekAi~~LRkkG 44 (290)
T TIGR00116 3 ITAQLVKELRERTGAGMMDCKKALTEANG-DFEKAIKNLRESG 44 (290)
T ss_pred CCHHHHHHHHHHHCCCHHHHHHHHHHcCC-CHHHHHHHHHHhc
Confidence 56778888874 59999999999999998 9999999998864
No 69
>cd02665 Peptidase_C19I A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=75.34 E-value=0.99 Score=43.05 Aligned_cols=37 Identities=8% Similarity=0.048 Sum_probs=28.7
Q ss_pred cccccccccccccchhcccccccccc--Cccc---cCCcccc
Q 017706 60 LHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSEEAI 96 (367)
Q Consensus 60 ~a~K~t~f~tFP~~L~v~~~r~~l~~--p~K~---~~~~~~l 96 (367)
.+.|+..|..+|++|+|+.+||.+.. ..|+ +..|..|
T Consensus 118 ~~~~~~~i~~lP~vL~i~LkRF~~~~~~~~Ki~~~v~FP~~l 159 (228)
T cd02665 118 KSGQERWFTELPPVLTFELSRFEFNQGRPEKIHDKLEFPQII 159 (228)
T ss_pred hhhhhhhhhhCChhhEEEeEeeEEcCCccEECCEEEEeeCcc
Confidence 46778889999999999999999974 5665 4445444
No 70
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=74.72 E-value=7 Score=33.80 Aligned_cols=41 Identities=17% Similarity=0.229 Sum_probs=36.2
Q ss_pred cccCHHHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Q 017706 111 PEVDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVE 152 (367)
Q Consensus 111 ~~~d~~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~ 152 (367)
..++++-++.+++ -|.|++.|.+||..++| ++-.|+-||.+
T Consensus 73 ~~i~~edI~lv~~q~gvs~~~A~~AL~~~~g-Dl~~AI~~L~~ 114 (115)
T PRK06369 73 VEIPEEDIELVAEQTGVSEEEARKALEEANG-DLAEAILKLSS 114 (115)
T ss_pred CCCCHHHHHHHHHHHCcCHHHHHHHHHHcCC-cHHHHHHHHhc
Confidence 5688999988884 79999999999999988 99999999865
No 71
>CHL00098 tsf elongation factor Ts
Probab=74.34 E-value=6.5 Score=37.00 Aligned_cols=38 Identities=26% Similarity=0.367 Sum_probs=32.0
Q ss_pred HHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 017706 116 ELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (367)
Q Consensus 116 ~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~ 154 (367)
.++..|-+ -|.+---|++||..++| |++.|++||-.+.
T Consensus 3 ~~ik~LR~~Tgag~~dck~AL~e~~g-d~~~A~~~Lr~~g 41 (200)
T CHL00098 3 ELVKELRDKTGAGMMDCKKALQEANG-DFEKALESLRQKG 41 (200)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCC-CHHHHHHHHHHhh
Confidence 45666653 58899999999999998 9999999998864
No 72
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=74.22 E-value=3.1 Score=35.85 Aligned_cols=12 Identities=42% Similarity=0.991 Sum_probs=9.2
Q ss_pred hhhcccccCCCC
Q 017706 40 VLNLVCATCGKP 51 (367)
Q Consensus 40 v~~~~C~~Cg~~ 51 (367)
|..+.|++||..
T Consensus 10 vt~l~C~~C~t~ 21 (113)
T PF09862_consen 10 VTRLKCPSCGTE 21 (113)
T ss_pred EEEEEcCCCCCE
Confidence 556899999864
No 73
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=74.09 E-value=1.4e+02 Score=33.27 Aligned_cols=18 Identities=11% Similarity=0.335 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHhHHHH
Q 017706 229 ENERKRILALRKAEKEEE 246 (367)
Q Consensus 229 e~e~k~~~e~rrrEK~ee 246 (367)
+++.+++.+++|+.++++
T Consensus 307 KqqkekEkeEKrrKdE~E 324 (811)
T KOG4364|consen 307 KQQKEKEKEEKRRKDEQE 324 (811)
T ss_pred HHHHHHHHHHHhhhhHHH
Confidence 333333444444444333
No 74
>PHA00732 hypothetical protein
Probab=73.97 E-value=3.6 Score=33.04 Aligned_cols=36 Identities=28% Similarity=0.584 Sum_probs=29.4
Q ss_pred eecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCCC
Q 017706 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (367)
Q Consensus 6 l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~~ 52 (367)
.+|..||..+.....-+.|.. +.|.. +.|+.||+.|
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r-~~H~~----------~~C~~CgKsF 37 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHAR-RNHTL----------TKCPVCNKSY 37 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhh-cccCC----------CccCCCCCEe
Confidence 369999999999999999987 44653 3699999975
No 75
>KOG1870 consensus Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=73.73 E-value=0.7 Score=51.90 Aligned_cols=53 Identities=9% Similarity=0.104 Sum_probs=43.3
Q ss_pred hcccccCCCCCCCccccccccccccccccccchhcccccccccc--Cccc---cC-CccccccCCC
Q 017706 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---AD-SEEAIDVDMS 101 (367)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~--p~K~---~~-~~~~ldl~~~ 101 (367)
.+.||.|.+. ..|+|+.-.-..|++|||+.+||.+.+ ..|+ ++ +...||++.|
T Consensus 716 ~w~C~~Cke~-------~~A~Kk~~lwrlPeiLiihLKrF~~~r~~~~k~~~~v~fPi~~ld~s~~ 774 (842)
T KOG1870|consen 716 RWYCPQCKEL-------RQATKKLDLWRLPEILIIHLKRFQYSRESSSKVKTKVEFPLGSLDLSEF 774 (842)
T ss_pred cccChHHHHH-------HHHhhhhhhhhCCceEEEEeecceeechhhhhhCccccCCCcCCCcchh
Confidence 4899999875 789999999999999999999999997 4444 33 5567887766
No 76
>PTZ00121 MAEBL; Provisional
Probab=73.04 E-value=55 Score=39.40 Aligned_cols=15 Identities=13% Similarity=0.158 Sum_probs=8.2
Q ss_pred ccchhcccccccccc
Q 017706 71 VDKTSEAAKPISLEV 85 (367)
Q Consensus 71 P~~L~v~~~r~~l~~ 85 (367)
|||=-..|-||-|.|
T Consensus 904 PDyEtKCPPR~PLkn 918 (2084)
T PTZ00121 904 PDYEEKCPPRFPLKS 918 (2084)
T ss_pred CcccccCCCCCCCCC
Confidence 555555555555554
No 77
>PHA02768 hypothetical protein; Provisional
Probab=72.77 E-value=3.3 Score=31.31 Aligned_cols=37 Identities=22% Similarity=0.476 Sum_probs=30.3
Q ss_pred ceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 4 ~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
+--+|..||..+.-...=+.|.. -|. ..|+|..||+-
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r--~H~---------k~~kc~~C~k~ 40 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLR--KHN---------TNLKLSNCKRI 40 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHH--hcC---------CcccCCcccce
Confidence 34489999999999888899998 376 14799999985
No 78
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=72.40 E-value=97 Score=32.73 Aligned_cols=46 Identities=20% Similarity=0.291 Sum_probs=24.2
Q ss_pred eecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 6 l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
|.|+.||+.---.=+=+.+.--||.+.=+..+.....|+|-.||++
T Consensus 147 i~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 147 IGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred EeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 5677777654211111111112344444444334456999999985
No 79
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=71.89 E-value=3.1 Score=36.78 Aligned_cols=37 Identities=22% Similarity=0.541 Sum_probs=24.7
Q ss_pred CCceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 2 AGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 2 ~~~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
+.....|..||.... ..+|..+.. +. ..|.||.||..
T Consensus 96 ~~~~Y~Cp~C~~~y~-~~ea~~~~d------~~------~~f~Cp~Cg~~ 132 (147)
T smart00531 96 NNAYYKCPNCQSKYT-FLEANQLLD------MD------GTFTCPRCGEE 132 (147)
T ss_pred CCcEEECcCCCCEee-HHHHHHhcC------CC------CcEECCCCCCE
Confidence 356788999997766 445554432 11 23899999975
No 80
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=71.73 E-value=36 Score=36.66 Aligned_cols=16 Identities=25% Similarity=0.250 Sum_probs=10.3
Q ss_pred ccccccccccchhccc
Q 017706 63 KRTGHTDFVDKTSEAA 78 (367)
Q Consensus 63 K~t~f~tFP~~L~v~~ 78 (367)
-...|-+|||...+++
T Consensus 19 d~epn~~fpdl~a~~a 34 (591)
T KOG2412|consen 19 DPEPNWNFPDLVAEIA 34 (591)
T ss_pred CCCCCCCchhHHHHhh
Confidence 3455667888776654
No 81
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=71.43 E-value=1.8 Score=33.36 Aligned_cols=28 Identities=39% Similarity=0.841 Sum_probs=14.6
Q ss_pred ceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCC
Q 017706 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (367)
Q Consensus 4 ~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~ 50 (367)
..|.||+|+. ++.+.|. ++..+|+.||+
T Consensus 29 v~IlCNDC~~--------------~s~v~fH-----~lg~KC~~C~S 56 (61)
T PF14599_consen 29 VWILCNDCNA--------------KSEVPFH-----FLGHKCSHCGS 56 (61)
T ss_dssp EEEEESSS----------------EEEEE-------TT----TTTS-
T ss_pred EEEECCCCCC--------------ccceeee-----HhhhcCCCCCC
Confidence 4688999986 4666666 45689999996
No 82
>PF15236 CCDC66: Coiled-coil domain-containing protein 66
Probab=69.92 E-value=88 Score=28.52 Aligned_cols=24 Identities=21% Similarity=0.097 Sum_probs=9.9
Q ss_pred HHHHHHHhHHHHHHHHHHHHHhHH
Q 017706 235 ILALRKAEKEEEKRAREKIRQKLE 258 (367)
Q Consensus 235 ~~e~rrrEK~ee~~ar~rir~qIe 258 (367)
++..++-+..-+...+....++.+
T Consensus 115 e~~~~k~~~l~e~~q~Aqe~A~~~ 138 (157)
T PF15236_consen 115 EEQTRKTQELYEAMQRAQEEAQRE 138 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444444433
No 83
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=69.68 E-value=13 Score=37.12 Aligned_cols=8 Identities=13% Similarity=0.156 Sum_probs=4.0
Q ss_pred ccchhccc
Q 017706 71 VDKTSEAA 78 (367)
Q Consensus 71 P~~L~v~~ 78 (367)
+|++.|-+
T Consensus 110 ~D~v~i~i 117 (321)
T PF07946_consen 110 KDRVTIEI 117 (321)
T ss_pred CCeEEEEE
Confidence 55555444
No 84
>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=69.67 E-value=1.1 Score=28.33 Aligned_cols=20 Identities=20% Similarity=0.557 Sum_probs=11.3
Q ss_pred ecCCCcccccchHHHHHHHh
Q 017706 7 KCGDCGALLRSVQEAQEHAE 26 (367)
Q Consensus 7 ~C~~C~~v~~g~~~aq~h~~ 26 (367)
-|..|+..+.++...+.|..
T Consensus 3 ~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 3 YCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp BBTTTTBBBSSHHHHHCCTT
T ss_pred CcccCCCCcCCHHHHHHHHc
Confidence 35556655555555555554
No 85
>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=69.25 E-value=2.5 Score=28.62 Aligned_cols=26 Identities=27% Similarity=0.653 Sum_probs=18.8
Q ss_pred eeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
.-+|.+||.+..|.. .-..||.||.+
T Consensus 2 ~~~C~~CG~i~~g~~---------------------~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGEE---------------------APEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECCc---------------------CCCcCcCCCCc
Confidence 358999998876642 11399999975
No 86
>PTZ00121 MAEBL; Provisional
Probab=68.84 E-value=81 Score=38.09 Aligned_cols=10 Identities=40% Similarity=0.345 Sum_probs=3.9
Q ss_pred HHHHHHHHHh
Q 017706 258 EEDKAERRRR 267 (367)
Q Consensus 258 e~Dk~eR~~k 267 (367)
+++.+++++|
T Consensus 1259 ear~a~~A~r 1268 (2084)
T PTZ00121 1259 EARMAHFARR 1268 (2084)
T ss_pred HHHHHHHHHH
Confidence 3333333333
No 87
>KOG1863 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=68.83 E-value=1.8 Score=50.05 Aligned_cols=67 Identities=13% Similarity=-0.031 Sum_probs=50.3
Q ss_pred hccCCCCcchhhhhhcccccCCCCCCCccccccccccccccccccchhcccccccccc----Cccc---cCCccccccCC
Q 017706 28 TSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (367)
Q Consensus 28 tgh~~F~e~~e~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~----p~K~---~~~~~~ldl~~ 100 (367)
.-|.+|+..+-.-.+-.|..|... ..|.|-..|.+||++|.+++.||.++. +.|+ ...|..||++.
T Consensus 323 sf~~y~~~E~l~gdn~~~~~~~~~-------~~a~k~~~f~~lPpvl~~qL~Rf~~~~~~~~~~Ki~d~~~fp~~i~~d~ 395 (1093)
T KOG1863|consen 323 SLHLYFEAEILLGDNKYDAECHGL-------QDAKKGVLFDSLPPVLFIQLMRFEYDFSTGQKIKINDKFEFPLIIDMDR 395 (1093)
T ss_pred HHHHhhhHHHhcCCccccccccch-------hhhhcceeeccCCchhhhhhhheeeeccCCceeehhhccCCccccccch
Confidence 778888744211112378999775 678888999999999999999999983 8887 34677777776
Q ss_pred C
Q 017706 101 S 101 (367)
Q Consensus 101 ~ 101 (367)
|
T Consensus 396 ~ 396 (1093)
T KOG1863|consen 396 Y 396 (1093)
T ss_pred h
Confidence 5
No 88
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=67.20 E-value=27 Score=34.84 Aligned_cols=9 Identities=33% Similarity=0.272 Sum_probs=4.3
Q ss_pred hccCCCCcc
Q 017706 28 TSHSNFSES 36 (367)
Q Consensus 28 tgh~~F~e~ 36 (367)
.-+.+|+-+
T Consensus 42 ~L~~~Fa~V 50 (321)
T PF07946_consen 42 LLESNFALV 50 (321)
T ss_pred HHHhhcccc
Confidence 444555443
No 89
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=66.91 E-value=3.1 Score=35.45 Aligned_cols=12 Identities=25% Similarity=0.642 Sum_probs=8.8
Q ss_pred ceeecCCCcccc
Q 017706 4 VSLKCGDCGALL 15 (367)
Q Consensus 4 ~~l~C~~C~~v~ 15 (367)
.+.+|..||..+
T Consensus 69 ~~~~C~~Cg~~~ 80 (113)
T PRK12380 69 AQAWCWDCSQVV 80 (113)
T ss_pred cEEEcccCCCEE
Confidence 467899998543
No 90
>PF15236 CCDC66: Coiled-coil domain-containing protein 66
Probab=65.87 E-value=1.1e+02 Score=27.98 Aligned_cols=6 Identities=33% Similarity=0.623 Sum_probs=3.3
Q ss_pred CCCHHH
Q 017706 177 SLTPEE 182 (367)
Q Consensus 177 ~lT~EE 182 (367)
+|+|.+
T Consensus 40 llDpa~ 45 (157)
T PF15236_consen 40 LLDPAQ 45 (157)
T ss_pred cCCHHH
Confidence 555554
No 91
>PF14353 CpXC: CpXC protein
Probab=65.34 E-value=4.3 Score=34.72 Aligned_cols=12 Identities=25% Similarity=1.057 Sum_probs=9.9
Q ss_pred hhhcccccCCCC
Q 017706 40 VLNLVCATCGKP 51 (367)
Q Consensus 40 v~~~~C~~Cg~~ 51 (367)
.-.+.||.||..
T Consensus 36 l~~~~CP~Cg~~ 47 (128)
T PF14353_consen 36 LFSFTCPSCGHK 47 (128)
T ss_pred cCEEECCCCCCc
Confidence 446899999986
No 92
>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=64.06 E-value=5.1 Score=28.18 Aligned_cols=34 Identities=26% Similarity=0.582 Sum_probs=21.9
Q ss_pred CCCceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCC
Q 017706 1 MAGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (367)
Q Consensus 1 ~~~~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~ 50 (367)
|.-+..+|..||..+.- ...+++ .....||.||.
T Consensus 1 MP~Yey~C~~Cg~~fe~------------~~~~~~----~~~~~CP~Cg~ 34 (42)
T PF09723_consen 1 MPIYEYRCEECGHEFEV------------LQSISE----DDPVPCPECGS 34 (42)
T ss_pred CCCEEEEeCCCCCEEEE------------EEEcCC----CCCCcCCCCCC
Confidence 44567899999987632 222333 23368999997
No 93
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=63.45 E-value=11 Score=30.51 Aligned_cols=37 Identities=24% Similarity=0.318 Sum_probs=31.3
Q ss_pred HHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCC
Q 017706 119 KELEAMGFPVARATRALHYSGNANVEAAVNWVVEHEND 156 (367)
Q Consensus 119 ~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~dd 156 (367)
..+.+.||+...+..||++|.+ ++..|..+++.+...
T Consensus 2 ~~~~~~g~~~~~v~~aL~~tSg-d~~~a~~~vl~~l~~ 38 (87)
T PF11626_consen 2 KHYEELGYSREFVTHALYATSG-DPELARRFVLNFLQA 38 (87)
T ss_dssp HHHHHHTB-HHHHHHHHHHTTT-BHHHHHHHHHHCHCH
T ss_pred chHHHhCCCHHHHHHHHHHhCC-CHHHHHHHHHHHHHc
Confidence 3477899999999999999988 899999999888543
No 94
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=63.36 E-value=3.8 Score=34.97 Aligned_cols=27 Identities=22% Similarity=0.437 Sum_probs=18.2
Q ss_pred ceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 4 ~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
.+..|..||..+.-.. ..+.||.||+.
T Consensus 69 ~~~~C~~Cg~~~~~~~---------------------~~~~CP~Cgs~ 95 (115)
T TIGR00100 69 VECECEDCSEEVSPEI---------------------DLYRCPKCHGI 95 (115)
T ss_pred cEEEcccCCCEEecCC---------------------cCccCcCCcCC
Confidence 4678999986542210 13689999985
No 95
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=63.02 E-value=16 Score=31.65 Aligned_cols=39 Identities=18% Similarity=0.240 Sum_probs=34.5
Q ss_pred ccCHHHHHHHH-hCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Q 017706 112 EVDKELLKELE-AMGFPVARATRALHYSGNANVEAAVNWVV 151 (367)
Q Consensus 112 ~~d~~~l~~L~-~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~ 151 (367)
.++++-++.++ .-|.|+..|.+||..++| ++-.|+-||.
T Consensus 76 ~i~~eDI~lV~eq~gvs~e~A~~AL~~~~g-Dl~~AI~~L~ 115 (116)
T TIGR00264 76 EITEDDIELVMKQCNVSKEEARRALEECGG-DLAEAIMKLE 115 (116)
T ss_pred CCCHHHHHHHHHHhCcCHHHHHHHHHHcCC-CHHHHHHHhh
Confidence 58888898887 479999999999999988 8999998885
No 96
>PF05835 Synaphin: Synaphin protein; InterPro: IPR008849 This family consists of several eukaryotic synaphin 1 and 2 proteins. Synaphin/complexin is a cytosolic protein that preferentially binds to syntaxin within the SNARE complex. Synaphin promotes SNAREs to form precomplexes that oligomerise into higher order structures. A peptide from the central, syntaxin binding domain of synaphin competitively inhibits these two proteins from interacting and prevents SNARE complexes from oligomerising. It is thought that oligomerisation of SNARE complexes into a higher order structure creates a SNARE scaffold for efficient, regulated fusion of synaptic vesicles []. Synaphin promotes neuronal exocytosis by promoting interaction between the complementary syntaxin and synaptobrevin transmembrane regions that reside in opposing membranes prior to fusion [].; GO: 0019905 syntaxin binding, 0006836 neurotransmitter transport; PDB: 3RL0_m 3RK3_E 1L4A_E 1KIL_E.
Probab=62.40 E-value=18 Score=32.23 Aligned_cols=21 Identities=38% Similarity=0.727 Sum_probs=11.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCCCC
Q 017706 247 KRAREKIRQKLEEDKAERRRRLGLPPED 274 (367)
Q Consensus 247 ~~ar~rir~qIe~Dk~eR~~k~~~~~~~ 274 (367)
.+.|+++|++| |.|++++..+
T Consensus 58 eaERe~mRq~I-------RdKY~l~k~e 78 (139)
T PF05835_consen 58 EAEREKMRQHI-------RDKYGLKKKE 78 (139)
T ss_dssp HHHHHHHHHHH-------HHHHT-----
T ss_pred HHHHHHHHHHH-------Hhhccccccc
Confidence 35678899999 3567776643
No 97
>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=62.24 E-value=6.5 Score=26.65 Aligned_cols=16 Identities=31% Similarity=0.744 Sum_probs=12.3
Q ss_pred CCCceeecCCCccccc
Q 017706 1 MAGVSLKCGDCGALLR 16 (367)
Q Consensus 1 ~~~~~l~C~~C~~v~~ 16 (367)
|.-+..+|..||..+.
T Consensus 1 Mp~Y~y~C~~Cg~~fe 16 (41)
T smart00834 1 MPIYEYRCEDCGHTFE 16 (41)
T ss_pred CCCEEEEcCCCCCEEE
Confidence 4457789999998774
No 98
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=62.10 E-value=8.5 Score=30.20 Aligned_cols=32 Identities=28% Similarity=0.484 Sum_probs=26.4
Q ss_pred eeecCCCcccccchHHHHHHHhhhccCCCCcc
Q 017706 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSES 36 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~ 36 (367)
.+.|..|+..+.+...-+.|+...||..+...
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~~ 81 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNSE 81 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S--
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCcccc
Confidence 48999999999999999999999999998653
No 99
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=61.83 E-value=4.7 Score=28.66 Aligned_cols=31 Identities=29% Similarity=0.309 Sum_probs=23.6
Q ss_pred eeecCCCcccccch---HHHHHHHhhhccCCCCc
Q 017706 5 SLKCGDCGALLRSV---QEAQEHAELTSHSNFSE 35 (367)
Q Consensus 5 ~l~C~~C~~v~~g~---~~aq~h~~~tgh~~F~e 35 (367)
.--|..|+.++-+. .-++.|...|||..+-.
T Consensus 11 l~~CL~C~~~~c~~~~~~h~~~H~~~t~H~~~~~ 44 (50)
T smart00290 11 LWLCLTCGQVGCGRYQLGHALEHFEETGHPLVVK 44 (50)
T ss_pred eEEecCCCCcccCCCCCcHHHHHhhhhCCCEEEE
Confidence 34688898888533 45999999999987653
No 100
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=61.48 E-value=6 Score=28.13 Aligned_cols=28 Identities=29% Similarity=0.628 Sum_probs=19.0
Q ss_pred eeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
..+|..||..+.- .+. ...+.||.||.+
T Consensus 3 ~y~C~~CG~~~~~----------------~~~---~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVEL----------------DEY---GTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEE----------------CCC---CCceECCCCCCe
Confidence 5689999876532 222 124799999986
No 101
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=61.46 E-value=4.7 Score=34.43 Aligned_cols=10 Identities=20% Similarity=0.544 Sum_probs=8.0
Q ss_pred ceeecCCCcc
Q 017706 4 VSLKCGDCGA 13 (367)
Q Consensus 4 ~~l~C~~C~~ 13 (367)
.+.+|..||.
T Consensus 69 ~~~~C~~Cg~ 78 (114)
T PRK03681 69 AECWCETCQQ 78 (114)
T ss_pred cEEEcccCCC
Confidence 4678999985
No 102
>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=61.01 E-value=7 Score=23.15 Aligned_cols=20 Identities=30% Similarity=0.579 Sum_probs=17.8
Q ss_pred ecCCCcccccchHHHHHHHh
Q 017706 7 KCGDCGALLRSVQEAQEHAE 26 (367)
Q Consensus 7 ~C~~C~~v~~g~~~aq~h~~ 26 (367)
+|..||..+.....=+.|..
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHh
Confidence 69999999999999888887
No 103
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=60.54 E-value=3.5 Score=45.87 Aligned_cols=43 Identities=9% Similarity=-0.107 Sum_probs=35.8
Q ss_pred ccccccccccccccchhcccccccccc----Cccc---cCCccccccCCC
Q 017706 59 DLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 59 ~~a~K~t~f~tFP~~L~v~~~r~~l~~----p~K~---~~~~~~ldl~~~ 101 (367)
.-|.|-.-|.|||++|.++.+||..+- -+|. -..|..+|+..|
T Consensus 367 qdAkKGViFeSlPpVlhlqLKRFeyDfe~d~mvKINDryEFP~eiDl~pf 416 (1089)
T COG5077 367 QDAKKGVIFESLPPVLHLQLKRFEYDFERDMMVKINDRYEFPLEIDLLPF 416 (1089)
T ss_pred hhhccceeeccCchHHHHHHHHhccccccCceeeecccccCcchhccccc
Confidence 468899999999999999999999994 5565 337888998765
No 104
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=59.27 E-value=2.3 Score=39.77 Aligned_cols=38 Identities=24% Similarity=0.566 Sum_probs=25.2
Q ss_pred eecCCCcccccchHHHHHHHhhhc-cCCCCcchhhhhhcccccCCCC
Q 017706 6 LKCGDCGALLRSVQEAQEHAELTS-HSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 6 l~C~~C~~v~~g~~~aq~h~~~tg-h~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
|.|.+||.-+....- .|- =-+|+++- +.-|.|++||-+
T Consensus 1 ~~Cp~C~~~~~~~~~------~~~~IP~F~evi--i~sf~C~~CGyr 39 (192)
T TIGR00310 1 IDCPSCGGECETVMK------TVNDIPYFGEVL--ETSTICEHCGYR 39 (192)
T ss_pred CcCCCCCCCCEEEEE------EEcCCCCcceEE--EEEEECCCCCCc
Confidence 579999975432221 233 45699982 446999999976
No 105
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=58.59 E-value=2.3e+02 Score=31.94 Aligned_cols=27 Identities=15% Similarity=0.257 Sum_probs=21.6
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhCC
Q 017706 114 DKELLKELEAMGFPVARATRALHYSGN 140 (367)
Q Consensus 114 d~~~l~~L~~MGF~~~~a~kAL~~tgn 140 (367)
...++....-+|||.....+|-...+.
T Consensus 487 ~S~a~~iA~~~Glp~~ii~~A~~~~~~ 513 (782)
T PRK00409 487 KSNAFEIAKRLGLPENIIEEAKKLIGE 513 (782)
T ss_pred CcHHHHHHHHhCcCHHHHHHHHHHHhh
Confidence 457888899999999999888766543
No 106
>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=58.15 E-value=8.8 Score=34.52 Aligned_cols=30 Identities=30% Similarity=0.577 Sum_probs=20.5
Q ss_pred ceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 4 ~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
.--.|..|| ......+|.+ .+|.||.||..
T Consensus 108 ~~Y~Cp~c~-~r~tf~eA~~-----------------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICPNMC-VRFTFNEAME-----------------LNFTCPRCGAM 137 (158)
T ss_pred CeEECCCCC-cEeeHHHHHH-----------------cCCcCCCCCCE
Confidence 345688888 4555555554 26999999974
No 107
>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=56.90 E-value=5.9 Score=29.55 Aligned_cols=29 Identities=28% Similarity=0.770 Sum_probs=19.6
Q ss_pred eeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCC
Q 017706 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~ 50 (367)
-++|..|+..|-- .|.+. .++.+||-||.
T Consensus 4 eiRC~~CnklLa~----------~g~~~-------~leIKCpRC~t 32 (51)
T PF10122_consen 4 EIRCGHCNKLLAK----------AGEVI-------ELEIKCPRCKT 32 (51)
T ss_pred ceeccchhHHHhh----------hcCcc-------EEEEECCCCCc
Confidence 4799999987632 13222 24569999997
No 108
>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=56.83 E-value=8.5 Score=27.73 Aligned_cols=16 Identities=25% Similarity=0.615 Sum_probs=12.5
Q ss_pred CCCceeecCCCccccc
Q 017706 1 MAGVSLKCGDCGALLR 16 (367)
Q Consensus 1 ~~~~~l~C~~C~~v~~ 16 (367)
|--+..+|.+||..+.
T Consensus 1 MP~Yey~C~~Cg~~fe 16 (52)
T TIGR02605 1 MPIYEYRCTACGHRFE 16 (52)
T ss_pred CCCEEEEeCCCCCEeE
Confidence 4457789999998775
No 109
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.68 E-value=5.7 Score=34.07 Aligned_cols=12 Identities=42% Similarity=1.077 Sum_probs=8.9
Q ss_pred ceeecCCCcccc
Q 017706 4 VSLKCGDCGALL 15 (367)
Q Consensus 4 ~~l~C~~C~~v~ 15 (367)
.+..|..||..+
T Consensus 70 ~~~~C~~Cg~~~ 81 (117)
T PRK00564 70 VELECKDCSHVF 81 (117)
T ss_pred CEEEhhhCCCcc
Confidence 567899998543
No 110
>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=54.88 E-value=5.3 Score=25.32 Aligned_cols=11 Identities=27% Similarity=0.857 Sum_probs=8.8
Q ss_pred hhhcccccCCC
Q 017706 40 VLNLVCATCGK 50 (367)
Q Consensus 40 v~~~~C~~Cg~ 50 (367)
.+.|.||.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 35699999995
No 111
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=53.06 E-value=3.7 Score=37.22 Aligned_cols=37 Identities=30% Similarity=0.599 Sum_probs=24.6
Q ss_pred ecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 7 KCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 7 ~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
-|.+||+-+. .+...|-=-+|+++- +.-|.|++||-+
T Consensus 2 ~Cp~C~~~~~------~~~~~~~IP~F~evi--i~sf~C~~CGyk 38 (160)
T smart00709 2 DCPSCGGNGT------TRMLLTSIPYFREVI--IMSFECEHCGYR 38 (160)
T ss_pred cCCCCCCCCE------EEEEEecCCCcceEE--EEEEECCCCCCc
Confidence 4999987642 222234445699972 346999999976
No 112
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=52.62 E-value=12 Score=34.42 Aligned_cols=30 Identities=27% Similarity=0.597 Sum_probs=19.7
Q ss_pred ceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 4 ~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
.--.|..||.. ....+|-+ .+|.||.||..
T Consensus 116 ~~Y~Cp~C~~r-ytf~eA~~-----------------~~F~Cp~Cg~~ 145 (178)
T PRK06266 116 MFFFCPNCHIR-FTFDEAME-----------------YGFRCPQCGEM 145 (178)
T ss_pred CEEECCCCCcE-EeHHHHhh-----------------cCCcCCCCCCC
Confidence 34578888843 44444432 26999999985
No 113
>PHA00733 hypothetical protein
Probab=51.18 E-value=16 Score=31.78 Aligned_cols=36 Identities=25% Similarity=0.460 Sum_probs=21.8
Q ss_pred eecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCCC
Q 017706 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (367)
Q Consensus 6 l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~~ 52 (367)
..|..||..+.....-..|... |. ..|.|+.||+.|
T Consensus 74 y~C~~Cgk~Fss~s~L~~H~r~--h~---------~~~~C~~CgK~F 109 (128)
T PHA00733 74 YVCPLCLMPFSSSVSLKQHIRY--TE---------HSKVCPVCGKEF 109 (128)
T ss_pred ccCCCCCCcCCCHHHHHHHHhc--CC---------cCccCCCCCCcc
Confidence 4677777777666666666552 20 126777777654
No 114
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=50.47 E-value=3.1e+02 Score=30.98 Aligned_cols=36 Identities=17% Similarity=0.282 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Q 017706 115 KELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVE 152 (367)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~ 152 (367)
..++....-+|||.....+|-...+. ...-++-|++
T Consensus 483 S~a~~iA~~~Glp~~ii~~A~~~~~~--~~~~~~~li~ 518 (771)
T TIGR01069 483 SYAFEIAQRYGIPHFIIEQAKTFYGE--FKEEINVLIE 518 (771)
T ss_pred cHHHHHHHHhCcCHHHHHHHHHHHHh--hHHHHHHHHH
Confidence 46788888999999999888766553 3333444443
No 115
>KOG1363 consensus Predicted regulator of the ubiquitin pathway (contains UAS and UBX domains) [Signal transduction mechanisms]
Probab=50.36 E-value=61 Score=34.35 Aligned_cols=40 Identities=15% Similarity=0.124 Sum_probs=26.6
Q ss_pred hHHHHHHHHhhhhhcCCChHHHHHHHHHHHHHHhhhccCCChhh
Q 017706 300 VEQMRECLRSLKQNHKDDDAKVKRAFQTLLTYIGNVAKNPNEEK 343 (367)
Q Consensus 300 ~~QlR~~l~sLk~~~~~~~a~~~~a~~tL~kyl~Ni~~~P~eeK 343 (367)
...+|+|.|.-.--.|... ..+++|.-|+.+...+|.+=+
T Consensus 385 ~l~iR~P~G~r~~RrF~~s----~~~q~l~~~v~~~~~~~~e~~ 424 (460)
T KOG1363|consen 385 TVAIRLPSGTRLERRFLKS----DKLQILYDYVDSNGFHPEEYS 424 (460)
T ss_pred eeEEECCCCCeeeeeeecc----cchhHHHHHHHhccCCchhhc
Confidence 4567788888777776654 445568888888775554433
No 116
>KOG3634 consensus Troponin [Cytoskeleton]
Probab=50.35 E-value=92 Score=31.75 Aligned_cols=10 Identities=20% Similarity=0.311 Sum_probs=4.5
Q ss_pred HHHHHHHHHH
Q 017706 321 VKRAFQTLLT 330 (367)
Q Consensus 321 ~~~a~~tL~k 330 (367)
.+.-++.|++
T Consensus 239 iKELhqrI~k 248 (361)
T KOG3634|consen 239 IKELHQRICK 248 (361)
T ss_pred HHHHHHHHHH
Confidence 4444444443
No 117
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=49.82 E-value=8 Score=37.02 Aligned_cols=51 Identities=12% Similarity=0.346 Sum_probs=29.5
Q ss_pred CCCceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 1 MAGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 1 ~~~~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
|.-|.++|..||.-..-...--.--+..|..++-...-.-.-..|+-|+.+
T Consensus 38 ~TPF~~RCL~C~~YI~K~~rfNavkE~~~dK~y~~~kiYRf~I~C~~C~n~ 88 (272)
T COG5134 38 ETPFPVRCLNCENYIQKGTRFNAVKEEIGDKSYYTTKIYRFSIKCHLCSNP 88 (272)
T ss_pred ccCcceeecchhhhhhcccchhHHHHHhcccccceeEEEEEEEEccCCCCc
Confidence 356999999999876433322222233345555443211223589999975
No 118
>PF13423 UCH_1: Ubiquitin carboxyl-terminal hydrolase
Probab=49.62 E-value=9.5 Score=36.89 Aligned_cols=56 Identities=18% Similarity=0.121 Sum_probs=39.6
Q ss_pred hhhhcccccCCCCCCCccccccccccccccccccchhcccccccccc--Cccc---cCCccccccCCC
Q 017706 39 AVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSEEAIDVDMS 101 (367)
Q Consensus 39 ~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~--p~K~---~~~~~~ldl~~~ 101 (367)
......|+.|++. ....-+..+.+.|++|+|++.+...+. +.+. +.+|..++++.+
T Consensus 177 ~~~~a~C~~C~~~-------~~~~~~r~i~~LPpVL~In~~~~~~~~~w~~~~~~~~~ip~~i~~~~~ 237 (295)
T PF13423_consen 177 QQTRAWCEKCNKY-------QPTEQRRTIRSLPPVLSINLNRYSEEEFWPKKNWLKIWIPPSINLPHF 237 (295)
T ss_pred ccccccccccccc-------cceeeeeeccCCCcEEEEEccCCCcccccccccCCceecceeeecccc
Confidence 3444799999985 445556668999999999999988883 4444 444555665543
No 119
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=49.24 E-value=3.4e+02 Score=28.59 Aligned_cols=8 Identities=0% Similarity=0.027 Sum_probs=3.6
Q ss_pred ccCCCCcc
Q 017706 29 SHSNFSES 36 (367)
Q Consensus 29 gh~~F~e~ 36 (367)
|-.-|.+|
T Consensus 99 ginP~~gc 106 (429)
T PRK00247 99 GYNPLAGC 106 (429)
T ss_pred CCCchHHH
Confidence 44444444
No 120
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=49.20 E-value=9.8 Score=32.30 Aligned_cols=12 Identities=33% Similarity=0.919 Sum_probs=8.2
Q ss_pred ceeecCCCcccc
Q 017706 4 VSLKCGDCGALL 15 (367)
Q Consensus 4 ~~l~C~~C~~v~ 15 (367)
.+.+|..||..+
T Consensus 69 ~~~~C~~Cg~~~ 80 (113)
T PF01155_consen 69 ARARCRDCGHEF 80 (113)
T ss_dssp -EEEETTTS-EE
T ss_pred CcEECCCCCCEE
Confidence 467899998765
No 121
>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=48.27 E-value=17 Score=20.97 Aligned_cols=20 Identities=35% Similarity=0.698 Sum_probs=15.2
Q ss_pred ecCCCcccccchHHHHHHHh
Q 017706 7 KCGDCGALLRSVQEAQEHAE 26 (367)
Q Consensus 7 ~C~~C~~v~~g~~~aq~h~~ 26 (367)
+|..||..+....+=..|..
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHH
Confidence 68899999988888888876
No 122
>KOG1864 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=47.87 E-value=8.8 Score=41.68 Aligned_cols=52 Identities=8% Similarity=0.010 Sum_probs=41.3
Q ss_pred hhcccccCCCCCCCccccccccccccccccccchhcccccccccc----Cccc---cCCccccccC
Q 017706 41 LNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVD 99 (367)
Q Consensus 41 ~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~~l~~----p~K~---~~~~~~ldl~ 99 (367)
.-|+|..|... ..|.++.+++..|.+|+++.+||+..- =+|+ +++|..+++-
T Consensus 440 nky~c~~c~s~-------qeae~~l~~k~lp~~L~l~Lkrfk~~~~~~~~~kl~~~v~~plel~l~ 498 (587)
T KOG1864|consen 440 NKYSCENCCSL-------QEAERRLKIKKLPYVLTLHLKRFKYSEQQNRYTKLLYRVVFPLELRLK 498 (587)
T ss_pred CcccccccCch-------hhHHHhccccCCcceeeeehhccccccccccccccccccccccceeec
Confidence 34999999876 689999999999999999999999995 3444 4455555553
No 123
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=47.78 E-value=2.2e+02 Score=32.58 Aligned_cols=8 Identities=63% Similarity=0.808 Sum_probs=3.1
Q ss_pred HHHHHHHH
Q 017706 208 EREKERIR 215 (367)
Q Consensus 208 e~E~~Rr~ 215 (367)
+.|.+|++
T Consensus 244 eeEEer~~ 251 (1064)
T KOG1144|consen 244 EEEEERRR 251 (1064)
T ss_pred HHHHHHHH
Confidence 33333433
No 124
>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.
Probab=47.55 E-value=77 Score=23.57 Aligned_cols=46 Identities=20% Similarity=0.325 Sum_probs=33.9
Q ss_pred ccccCHHHHHHHH--hCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCC
Q 017706 110 EPEVDKELLKELE--AMGFPVARATRALHYSGNANVEAAVNWVVEHEND 156 (367)
Q Consensus 110 ~~~~d~~~l~~L~--~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~dd 156 (367)
.+.+.++++.+.. =-|-|++...+-|..|+= ++..|+|-|++..|+
T Consensus 5 a~~vPedlI~q~q~VLqgksR~vIirELqrTnL-dVN~AvNNlLsRDde 52 (53)
T PF11547_consen 5 ASQVPEDLINQAQVVLQGKSRNVIIRELQRTNL-DVNLAVNNLLSRDDE 52 (53)
T ss_dssp GGGS-HHHHHHHHHHSTTS-HHHHHHHHHHTTT--HHHHHHHHHHHH--
T ss_pred cccCCHHHHHHHHHHHcCCcHHHHHHHHHHhcc-cHHHHHHHHhccccC
Confidence 3456777876654 479999999999999875 999999999987654
No 125
>KOG3654 consensus Uncharacterized CH domain protein [Cytoskeleton]
Probab=47.48 E-value=1.4e+02 Score=32.19 Aligned_cols=38 Identities=42% Similarity=0.501 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhHH
Q 017706 221 LEAKRIEEENERKRILALRKAEKEEEKRAREKIRQKLE 258 (367)
Q Consensus 221 ~~~k~~~ee~e~k~~~e~rrrEK~ee~~ar~rir~qIe 258 (367)
+++.-++...|..|.+++-|.-|+|+...|+=||+..+
T Consensus 414 leae~e~kreearrkaeeer~~keee~arrefirqey~ 451 (708)
T KOG3654|consen 414 LEAEKEQKREEARRKAEEERAPKEEEVARREFIRQEYE 451 (708)
T ss_pred HHHHHHHHHHHHHHhhHhhhcchhhhhhHHHHHHHHHH
Confidence 34444555556666677777778888888877777653
No 126
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=47.06 E-value=11 Score=34.56 Aligned_cols=40 Identities=28% Similarity=0.483 Sum_probs=20.9
Q ss_pred eecCCCcccccchH--HHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 6 LKCGDCGALLRSVQ--EAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 6 l~C~~C~~v~~g~~--~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
-+|..||+.+.-.. ++..-.... |+-+.+. =+.||.||+.
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~-~~~~~~~-----f~~C~~Cgki 139 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEK-VYRNYEE-----FYRCPKCGKI 139 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchh-hhhcccc-----eeECCCCccc
Confidence 47999999983332 222111101 2222211 1679999974
No 127
>KOG3080 consensus Nucleolar protein-like/EBNA1-binding protein [RNA processing and modification]
Probab=47.04 E-value=1.3e+02 Score=30.35 Aligned_cols=55 Identities=29% Similarity=0.420 Sum_probs=33.8
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 017706 187 AQELRERARKKKEEEEKRMEREREKERIRIGKELLEAKRIEEENERKRILALRKA 241 (367)
Q Consensus 187 ~~el~~k~r~kr~eeek~~~~e~E~~Rr~~gKe~~~~k~~~ee~e~k~~~e~rrr 241 (367)
++..+.++-.+....++.++..+-++-++.||.+|.++-.....|.+..++..++
T Consensus 182 MqKVr~~Li~eq~~ke~sE~ark~RelKKfgKqVQ~~~l~~Rq~EKk~~lekiKk 236 (328)
T KOG3080|consen 182 MQKVRQRLIKEQTAKERSEEARKQRELKKFGKQVQKAKLQERQREKKETLEKIKK 236 (328)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444445555555667778899999888766666666555555543
No 128
>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=46.75 E-value=8.8 Score=33.89 Aligned_cols=43 Identities=21% Similarity=0.400 Sum_probs=25.4
Q ss_pred eeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
--+|..||..+.......- ...-....|.... .=+.||.||+-
T Consensus 91 ~sRC~~CN~~L~~v~~~~v-~~~vp~~v~~~~~---~f~~C~~C~ki 133 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEV-KDRVPPYVYETYD---EFWRCPGCGKI 133 (147)
T ss_pred CCccCCCCcEeeechhhcc-ccccCccccccCC---eEEECCCCCCE
Confidence 4589999999866643221 1113344443331 13799999974
No 129
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=46.35 E-value=15 Score=22.11 Aligned_cols=21 Identities=19% Similarity=0.434 Sum_probs=18.7
Q ss_pred eecCCCcccccchHHHHHHHh
Q 017706 6 LKCGDCGALLRSVQEAQEHAE 26 (367)
Q Consensus 6 l~C~~C~~v~~g~~~aq~h~~ 26 (367)
..|..|+..+.+...-+.|..
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 369999999999999999987
No 130
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=46.22 E-value=22 Score=27.29 Aligned_cols=19 Identities=26% Similarity=0.454 Sum_probs=16.2
Q ss_pred HHHHhCCCCHHHHHHHHHH
Q 017706 119 KELEAMGFPVARATRALHY 137 (367)
Q Consensus 119 ~~L~~MGF~~~~a~kAL~~ 137 (367)
..|++|||++..|..-++.
T Consensus 7 ~dLi~lGf~~~tA~~IIrq 25 (59)
T PF11372_consen 7 KDLIELGFSESTARDIIRQ 25 (59)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 5799999999999987654
No 131
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=46.08 E-value=46 Score=30.96 Aligned_cols=39 Identities=21% Similarity=0.490 Sum_probs=29.8
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhC---CCCHHHHHHHHHH
Q 017706 114 DKELLKELEAMGFPVARATRALHYSG---NANVEAAVNWVVE 152 (367)
Q Consensus 114 d~~~l~~L~~MGF~~~~a~kAL~~tg---n~~~E~A~~Wl~~ 152 (367)
..+++..|.++||+...|.+|+...+ +.+++..+-|.+.
T Consensus 148 ~~e~~~aL~~LGy~~~~a~~ai~~~~~~~~~~~~~~ir~aLk 189 (194)
T PRK14605 148 NSDILATLTALGYSSSEAAKAISSLGDNGDLPLEERIKLALN 189 (194)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhccCCCCHHHHHHHHHH
Confidence 46789999999999999999988764 3356665555443
No 132
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=46.00 E-value=12 Score=32.35 Aligned_cols=12 Identities=33% Similarity=0.827 Sum_probs=9.9
Q ss_pred hhhcccccCCCC
Q 017706 40 VLNLVCATCGKP 51 (367)
Q Consensus 40 v~~~~C~~Cg~~ 51 (367)
..+|.||.||+.
T Consensus 84 ~~~~~CP~C~s~ 95 (115)
T COG0375 84 ELDYRCPKCGSI 95 (115)
T ss_pred hheeECCCCCCC
Confidence 567889999975
No 133
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=45.42 E-value=40 Score=33.72 Aligned_cols=40 Identities=28% Similarity=0.541 Sum_probs=31.9
Q ss_pred cCHHHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHHHh
Q 017706 113 VDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEH 153 (367)
Q Consensus 113 ~d~~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h 153 (367)
+...+|..|-+ -|=+---|++||..|++ |+|.|++||-..
T Consensus 4 ita~~VKeLRe~TgAGMmdCKkAL~E~~G-d~EkAie~LR~k 44 (296)
T COG0264 4 ITAALVKELREKTGAGMMDCKKALEEANG-DIEKAIEWLREK 44 (296)
T ss_pred ccHHHHHHHHHHhCCcHHHHHHHHHHcCC-CHHHHHHHHHHh
Confidence 45566666764 36777899999999977 999999999874
No 134
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.17 E-value=50 Score=30.61 Aligned_cols=32 Identities=19% Similarity=0.307 Sum_probs=25.5
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHH
Q 017706 114 DKELLKELEAMGFPVARATRALHYSGNANVEA 145 (367)
Q Consensus 114 d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~ 145 (367)
..++++.|+++||++..|.+|+..-.+.+++.
T Consensus 142 ~~ea~~AL~~LGy~~~ea~~a~~~~~~~~~ee 173 (183)
T PRK14601 142 KSEALAALLTLGFKQEKIIKVLASCQSTGTSE 173 (183)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcccCCHHH
Confidence 36889999999999999999997754334443
No 135
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=45.05 E-value=7.1 Score=29.58 Aligned_cols=30 Identities=23% Similarity=0.628 Sum_probs=20.2
Q ss_pred ceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCC
Q 017706 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (367)
Q Consensus 4 ~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~ 50 (367)
..|+|..||+++.. +.|... ++-+||.|..
T Consensus 3 ~tiRC~~CnKlLa~-------------a~~~~y----le~KCPrCK~ 32 (60)
T COG4416 3 QTIRCAKCNKLLAE-------------AEGQAY----LEKKCPRCKE 32 (60)
T ss_pred eeeehHHHhHHHHh-------------ccccee----eeecCCccce
Confidence 36899999998732 222222 4569999974
No 136
>PF04615 Utp14: Utp14 protein; InterPro: IPR006709 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. This entry contains Utp14, a large ribonuclear protein associated with snoRNA U3 [].; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=44.89 E-value=1.4e+02 Score=33.07 Aligned_cols=19 Identities=26% Similarity=0.270 Sum_probs=14.1
Q ss_pred CCCCCHHHHHHHHHHHHHH
Q 017706 175 KSSLTPEEIKLKAQELRER 193 (367)
Q Consensus 175 k~~lT~EEk~~k~~el~~k 193 (367)
...||.||.+++..+|+.-
T Consensus 194 ~~~ms~eE~~~r~~el~~~ 212 (735)
T PF04615_consen 194 LKKMSLEEAKERRAELAKM 212 (735)
T ss_pred hccCCHHHHHHHHHHHHHH
Confidence 4689999998876666544
No 137
>PF05262 Borrelia_P83: Borrelia P83/100 protein; InterPro: IPR007926 This family consists of several Borrelia P83/P100 antigen proteins.
Probab=44.61 E-value=2.6e+02 Score=30.02 Aligned_cols=16 Identities=31% Similarity=0.326 Sum_probs=9.2
Q ss_pred hCCCCHHHH-HHHHHHh
Q 017706 123 AMGFPVARA-TRALHYS 138 (367)
Q Consensus 123 ~MGF~~~~a-~kAL~~t 138 (367)
..||+..-| .-|.+.|
T Consensus 95 aygY~~~~a~~lA~fit 111 (489)
T PF05262_consen 95 AYGYSDEDAETLATFIT 111 (489)
T ss_pred hcCCChhhHHHHHHHHH
Confidence 678887544 3554443
No 138
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=43.32 E-value=14 Score=32.04 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=7.5
Q ss_pred cccccCCCC
Q 017706 43 LVCATCGKP 51 (367)
Q Consensus 43 ~~C~~Cg~~ 51 (367)
+.||.||+.
T Consensus 93 ~~CP~Cgs~ 101 (124)
T PRK00762 93 IECPVCGNK 101 (124)
T ss_pred CcCcCCCCC
Confidence 579999974
No 139
>PRK05978 hypothetical protein; Provisional
Probab=43.11 E-value=13 Score=33.45 Aligned_cols=48 Identities=23% Similarity=0.366 Sum_probs=27.9
Q ss_pred CceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCCCCCccccccccccccccccccchhccc
Q 017706 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAA 78 (367)
Q Consensus 3 ~~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~ 78 (367)
|++.+|-.||.. |- |...- .+.-.|+.||-.+ ..-+.. .+|-|+++.+
T Consensus 31 Gl~grCP~CG~G---------------~L-F~g~L--kv~~~C~~CG~~~--------~~~~a~--DgpAy~~i~i 78 (148)
T PRK05978 31 GFRGRCPACGEG---------------KL-FRAFL--KPVDHCAACGEDF--------THHRAD--DLPAYLVIVI 78 (148)
T ss_pred HHcCcCCCCCCC---------------cc-ccccc--ccCCCccccCCcc--------ccCCcc--ccCcchhHHH
Confidence 678899999853 32 22221 2335899999752 111222 4777777654
No 140
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=42.95 E-value=14 Score=41.46 Aligned_cols=54 Identities=28% Similarity=0.468 Sum_probs=42.5
Q ss_pred CceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCCCCCccccccccccc
Q 017706 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRT 65 (367)
Q Consensus 3 ~~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~~~~~~e~~~a~K~t 65 (367)
.|+-+|--|++||.....=|-|.. .|+ +|. -|.|..||..|.+..-...|.-+.
T Consensus 351 ~~khkCr~CakvfgS~SaLqiHlR--SHT--GER-----PfqCnvCG~~FSTkGNLKvH~~rH 404 (958)
T KOG1074|consen 351 FFKHKCRFCAKVFGSDSALQIHLR--SHT--GER-----PFQCNVCGNRFSTKGNLKVHFQRH 404 (958)
T ss_pred cccchhhhhHhhcCchhhhhhhhh--ccC--CCC-----Ceeecccccccccccceeeeeeec
Confidence 578899999999999999999987 665 444 289999999987776665555443
No 141
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=42.91 E-value=15 Score=36.20 Aligned_cols=14 Identities=29% Similarity=0.795 Sum_probs=9.0
Q ss_pred CceeecCCCccccc
Q 017706 3 GVSLKCGDCGALLR 16 (367)
Q Consensus 3 ~~~l~C~~C~~v~~ 16 (367)
++...|++||+.|.
T Consensus 185 ~l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 185 TLPCECGICGKAFS 198 (279)
T ss_pred CCCccccccccccc
Confidence 45566777777664
No 142
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=42.69 E-value=4.5e+02 Score=28.69 Aligned_cols=14 Identities=29% Similarity=0.432 Sum_probs=7.2
Q ss_pred HHHHHHHHhhhhhc
Q 017706 301 EQMRECLRSLKQNH 314 (367)
Q Consensus 301 ~QlR~~l~sLk~~~ 314 (367)
++++-+.-++++.-
T Consensus 329 ~~lk~~~~~~kr~i 342 (591)
T KOG2412|consen 329 EELKNYNQSLKRAI 342 (591)
T ss_pred HHHHHHHHHHHhhc
Confidence 44555555555443
No 143
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=41.80 E-value=33 Score=31.80 Aligned_cols=25 Identities=24% Similarity=0.405 Sum_probs=22.0
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHh
Q 017706 114 DKELLKELEAMGFPVARATRALHYS 138 (367)
Q Consensus 114 d~~~l~~L~~MGF~~~~a~kAL~~t 138 (367)
..++++.|.++||++..|.+|+...
T Consensus 147 ~~e~~~aL~~LGy~~~e~~~ai~~~ 171 (191)
T TIGR00084 147 RDELFEALVSLGYKPQEIQQALKKI 171 (191)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4678999999999999999998765
No 144
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=41.45 E-value=7.3 Score=40.63 Aligned_cols=20 Identities=15% Similarity=0.215 Sum_probs=14.6
Q ss_pred HHhCCCCHHHHHHHHHHhCC
Q 017706 121 LEAMGFPVARATRALHYSGN 140 (367)
Q Consensus 121 L~~MGF~~~~a~kAL~~tgn 140 (367)
...-||+...|--+++.+-|
T Consensus 454 ~~~q~f~~ky~~atfyss~~ 473 (500)
T KOG3993|consen 454 IAEQGFTCKYCPATFYSSPG 473 (500)
T ss_pred chhhccccccchHhhhcCcc
Confidence 34578998888888776654
No 145
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=41.45 E-value=3.3e+02 Score=31.26 Aligned_cols=23 Identities=26% Similarity=0.396 Sum_probs=9.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHH
Q 017706 233 KRILALRKAEKEEEKRAREKIRQ 255 (367)
Q Consensus 233 k~~~e~rrrEK~ee~~ar~rir~ 255 (367)
++..++|..+....+..++|-++
T Consensus 832 kr~~~eRe~e~~~ak~ekqr~re 854 (988)
T KOG2072|consen 832 KRTEEEREIENRVAKKEKQRQRE 854 (988)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Confidence 33333333344444444444444
No 146
>PRK11546 zraP zinc resistance protein; Provisional
Probab=41.44 E-value=1.8e+02 Score=26.15 Aligned_cols=61 Identities=20% Similarity=0.218 Sum_probs=33.5
Q ss_pred CCCCHHHHHH----------HHHHHHHHHHHhhHHHHHHHHHHH--HHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 017706 176 SSLTPEEIKL----------KAQELRERARKKKEEEEKRMERER--EKERIRIGKELLEAKRIEEENERKRIL 236 (367)
Q Consensus 176 ~~lT~EEk~~----------k~~el~~k~r~kr~eeek~~~~e~--E~~Rr~~gKe~~~~k~~~ee~e~k~~~ 236 (367)
.+||+|.-.. +...||+++..|+.|-.......+ +..=++.-+|+.+.+.++.++..+..+
T Consensus 42 ~~LT~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~ELnALl~~~~pD~~kI~aL~kEI~~Lr~kL~e~r~~~~~ 114 (143)
T PRK11546 42 APLTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNALLTANPPDSSKINAVAKEMENLRQSLDELRVKRDI 114 (143)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3799885432 356677777766654433222111 233345557777777766665554433
No 147
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=41.20 E-value=75 Score=28.21 Aligned_cols=41 Identities=20% Similarity=0.156 Sum_probs=35.9
Q ss_pred ccccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Q 017706 110 EPEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVE 152 (367)
Q Consensus 110 ~~~~d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~ 152 (367)
.++++.+.+..|.+-|.+++.|++||..+| ++-.||.-|..
T Consensus 110 ~s~~~~e~v~v~a~a~v~~eeAr~aleeag--Dl~~A~k~l~~ 150 (153)
T COG4008 110 HSEPPVEEVEVLADAFVTPEEAREALEEAG--DLRTAMKILRM 150 (153)
T ss_pred cCCCcHHHHHHHHHhcCCHHHHHHHHHHcC--CHHHHHHHHHH
Confidence 356777889999999999999999999998 79999987765
No 148
>KOG0435 consensus Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=40.85 E-value=22 Score=39.44 Aligned_cols=74 Identities=27% Similarity=0.539 Sum_probs=42.9
Q ss_pred eeecCCCcccccchHH-HHHHHhhhccCCCCc------chhhhhhcccccCCCCCCCccccccccccccccccccchhcc
Q 017706 5 SLKCGDCGALLRSVQE-AQEHAELTSHSNFSE------STEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEA 77 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~~-aq~h~~~tgh~~F~e------~~e~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~ 77 (367)
-++|.+||.|=.-..+ +-.+-+. ..|.+ ..++-++..||.||++. . .-+.-..||.|.-.-.
T Consensus 436 ivhc~~cG~vpVpes~LPV~LP~l---~~~~~kG~Pls~~~e~vn~~cP~cg~pA--k------RETDTMDTFvDSsWYY 504 (876)
T KOG0435|consen 436 IVHCDDCGAVPVPESELPVTLPEL---NDFTPKGPPLSKADEWVNVDCPRCGEPA--K------RETDTMDTFVDSSWYY 504 (876)
T ss_pred eEEcCCCCcccCcHHHCCcccccc---cccCCCCCcccchhhheeccCccCCCcc--c------ccccccchhhccceee
Confidence 4799999988765554 2222221 12222 13667789999999872 1 1233367888877666
Q ss_pred ccccccccCccc
Q 017706 78 AKPISLEVPKAT 89 (367)
Q Consensus 78 ~~r~~l~~p~K~ 89 (367)
.|=.+--||-.+
T Consensus 505 lRylDpkN~e~~ 516 (876)
T KOG0435|consen 505 LRYLDPKNPEEP 516 (876)
T ss_pred EeecCCCCcccc
Confidence 653333354444
No 149
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=40.83 E-value=6.1 Score=35.82 Aligned_cols=41 Identities=22% Similarity=0.530 Sum_probs=18.1
Q ss_pred CceeecCCCcccc---cchHHHHHHH--hhhccCCCCcchhhhhhcccccCCCC
Q 017706 3 GVSLKCGDCGALL---RSVQEAQEHA--ELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 3 ~~~l~C~~C~~v~---~g~~~aq~h~--~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
.|.|+|+.||.+- ........|- --+|.+|| -++|..|++.
T Consensus 28 ~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNf--------v~KCk~C~re 73 (161)
T PF05907_consen 28 FFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANF--------VMKCKFCKRE 73 (161)
T ss_dssp EEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESE--------EE--SSSS--
T ss_pred EEEEEECCCCCccCcceEeecceEEecCCCccceEe--------EecCcCcCCc
Confidence 4899999999865 1222221111 11233333 3799999875
No 150
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=40.62 E-value=15 Score=27.15 Aligned_cols=30 Identities=27% Similarity=0.657 Sum_probs=19.7
Q ss_pred CceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 3 ~~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
-+.-+|..||..+ +....-....||.||..
T Consensus 4 ~~~Y~C~~Cg~~~-------------------~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREV-------------------ELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCee-------------------ehhhccCceeCCCCCcE
Confidence 3456899998876 11122345799999975
No 151
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=40.24 E-value=15 Score=27.98 Aligned_cols=14 Identities=36% Similarity=0.895 Sum_probs=12.0
Q ss_pred CCceeecCCCcccc
Q 017706 2 AGVSLKCGDCGALL 15 (367)
Q Consensus 2 ~~~~l~C~~C~~v~ 15 (367)
+.|+|+|..||.+.
T Consensus 28 aDikikC~gCg~~i 41 (57)
T PF06107_consen 28 ADIKIKCLGCGRQI 41 (57)
T ss_pred CcEEEEECCCCCEE
Confidence 57999999999875
No 152
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=39.09 E-value=73 Score=29.57 Aligned_cols=24 Identities=29% Similarity=0.501 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHh
Q 017706 115 KELLKELEAMGFPVARATRALHYS 138 (367)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~t 138 (367)
.++++.|+++||++..|.+|+...
T Consensus 144 ~e~~~AL~~LGy~~~ea~~av~~~ 167 (188)
T PRK14606 144 HESLEALVSLGYPEKQAREAVKHV 167 (188)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 678999999999999999999776
No 153
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=38.69 E-value=73 Score=29.55 Aligned_cols=36 Identities=14% Similarity=0.252 Sum_probs=26.9
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhCC-CCHHHHHHH
Q 017706 114 DKELLKELEAMGFPVARATRALHYSGN-ANVEAAVNW 149 (367)
Q Consensus 114 d~~~l~~L~~MGF~~~~a~kAL~~tgn-~~~E~A~~W 149 (367)
..+++..|+++||++..|.+||..-.. .+++..+-+
T Consensus 145 ~~e~~~aL~~LGy~~~ea~~al~~v~~~~~~eelir~ 181 (186)
T PRK14600 145 NDDALAALISLGYEKTKAFNAIQKIKPNLSTQDIIRK 181 (186)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhcCCCHHHHHHH
Confidence 367899999999999999999876532 255544444
No 154
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=38.14 E-value=56 Score=30.16 Aligned_cols=26 Identities=23% Similarity=0.317 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCC
Q 017706 115 KELLKELEAMGFPVARATRALHYSGN 140 (367)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~tgn 140 (367)
.+++..|.++||+...|.+++...+.
T Consensus 150 ~ev~~aL~~LG~~~~~a~~~~~~~~~ 175 (192)
T PRK00116 150 EEAVSALVALGYKPKEASKAVAKILK 175 (192)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 68999999999999999999988864
No 155
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=38.03 E-value=16 Score=32.25 Aligned_cols=10 Identities=30% Similarity=1.135 Sum_probs=8.6
Q ss_pred ecCCCccccc
Q 017706 7 KCGDCGALLR 16 (367)
Q Consensus 7 ~C~~C~~v~~ 16 (367)
+|+.||.++.
T Consensus 3 ~Ct~Cg~~f~ 12 (131)
T PF09845_consen 3 QCTKCGRVFE 12 (131)
T ss_pred ccCcCCCCcC
Confidence 7999998874
No 156
>KOG0608 consensus Warts/lats-like serine threonine kinases [Cell cycle control, cell division, chromosome partitioning]
Probab=37.94 E-value=20 Score=39.87 Aligned_cols=43 Identities=21% Similarity=0.255 Sum_probs=39.0
Q ss_pred cccccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Q 017706 109 VEPEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVV 151 (367)
Q Consensus 109 ~~~~~d~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~ 151 (367)
...++|..++.-|+.-||.+..+..||..+++.+++.|++++-
T Consensus 84 a~s~sn~qmlq~lv~ag~d~~~a~~al~~pns~sie~sie~~s 126 (1034)
T KOG0608|consen 84 AGSESNSQMLQGLVGAGNDRHMALGALATPNSRSIEASIETIS 126 (1034)
T ss_pred cccccchhhhHhhhhccccchhhhhhhcCCCccccchhhhccc
Confidence 3467889999999999999999999999999999999999873
No 157
>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=37.93 E-value=24 Score=24.23 Aligned_cols=30 Identities=30% Similarity=0.727 Sum_probs=21.2
Q ss_pred eeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
|.-|..||.+ =|..|... ..+-+|+.||..
T Consensus 1 Rr~C~~Cg~~--------------Yh~~~~pP---~~~~~Cd~cg~~ 30 (36)
T PF05191_consen 1 RRICPKCGRI--------------YHIEFNPP---KVEGVCDNCGGE 30 (36)
T ss_dssp EEEETTTTEE--------------EETTTB-----SSTTBCTTTTEB
T ss_pred CcCcCCCCCc--------------cccccCCC---CCCCccCCCCCe
Confidence 4678888875 47778876 566799999863
No 158
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=37.92 E-value=5.9 Score=35.96 Aligned_cols=39 Identities=26% Similarity=0.525 Sum_probs=23.2
Q ss_pred eecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCCC
Q 017706 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (367)
Q Consensus 6 l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~~ 52 (367)
.+|..|+.-..|. -|.+ |-..|+. ....-.+|..||+++
T Consensus 40 ~~Cp~C~~~IrG~----y~v~--gv~~~g~--~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 40 TSCPNCSTPIRGD----YHVE--GVFGLGG--HYEAPSYCHNCGKPY 78 (158)
T ss_pred HHCcCCCCCCCCc----eecC--CeeeeCC--CCCCChhHHhCCCCC
Confidence 3567777776654 3333 4444432 223557999999875
No 159
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.89 E-value=76 Score=29.74 Aligned_cols=25 Identities=20% Similarity=0.267 Sum_probs=22.0
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHh
Q 017706 114 DKELLKELEAMGFPVARATRALHYS 138 (367)
Q Consensus 114 d~~~l~~L~~MGF~~~~a~kAL~~t 138 (367)
-.++++.|+++||++..|.+|+..-
T Consensus 155 ~~ea~~AL~~LGy~~~ea~~av~~~ 179 (203)
T PRK14602 155 FRDALAGLANLGYGEEEARPVLKEV 179 (203)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3678999999999999999998765
No 160
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=37.83 E-value=2.7e+02 Score=29.63 Aligned_cols=20 Identities=40% Similarity=0.518 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHhhH
Q 017706 180 PEEIKLKAQELRERARKKKE 199 (367)
Q Consensus 180 ~EEk~~k~~el~~k~r~kr~ 199 (367)
-|||+..+++||+++++.+.
T Consensus 249 HEeKQ~~AeeLRekLqE~Ka 268 (672)
T KOG4722|consen 249 HEEKQKHAEELREKLQEAKA 268 (672)
T ss_pred hHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999998875
No 161
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=37.02 E-value=17 Score=35.97 Aligned_cols=69 Identities=19% Similarity=0.343 Sum_probs=46.1
Q ss_pred ceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCCCCCccccccccccccccccccchhcccccc
Q 017706 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPI 81 (367)
Q Consensus 4 ~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~~r~ 81 (367)
-+-+|..||+.......=. -|..|.=..++..-+.|+.|||.+.|.++...|+.+.. .|=.-.|--++|
T Consensus 129 ~r~~c~eCgk~ysT~snLs------rHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~---l~c~C~iCGKaF 197 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLS------RHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT---LPCECGICGKAF 197 (279)
T ss_pred Cceeccccccccccccccc------hhhcccccccccccccCCCCCceeeehHHHhhHhhccC---CCcccccccccc
Confidence 4678999999986654433 35555555455667999999998888877777766543 444445555443
No 162
>PF10827 DUF2552: Protein of unknown function (DUF2552) ; InterPro: IPR020157 This entry contains proteins with no known function.
Probab=36.98 E-value=23 Score=28.26 Aligned_cols=17 Identities=24% Similarity=0.546 Sum_probs=14.8
Q ss_pred CCHHHHHHHHHHhcCCC
Q 017706 141 ANVEAAVNWVVEHENDP 157 (367)
Q Consensus 141 ~~~E~A~~Wl~~h~dd~ 157 (367)
..++.|++||-+||++-
T Consensus 59 ~tld~Ai~Wi~e~M~~i 75 (79)
T PF10827_consen 59 PTLDLAIAWIGEHMPHI 75 (79)
T ss_pred ccHHHHHHHHHhcccch
Confidence 37999999999999873
No 163
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=36.97 E-value=17 Score=25.43 Aligned_cols=40 Identities=10% Similarity=0.076 Sum_probs=20.8
Q ss_pred cccccCCCCCCCc-cccccccccccccccccchhccccccc
Q 017706 43 LVCATCGKPCRSK-TETDLHRKRTGHTDFVDKTSEAAKPIS 82 (367)
Q Consensus 43 ~~C~~Cg~~~~~~-~e~~~a~K~t~f~tFP~~L~v~~~r~~ 82 (367)
..||.||....-. .-...-.....+..+|=+|.+..+||.
T Consensus 3 ~~Cp~Cg~~~~~~~g~~~r~i~~l~~~~~~~~L~i~~~R~~ 43 (47)
T PF14690_consen 3 PRCPHCGSPSVHRHGYKTRRIRHLPIGGRPVYLRIRKRRYR 43 (47)
T ss_pred ccCCCcCCCceECCceEEEEEeecccCCEEEEEEEEeEEEE
Confidence 4799999762000 001122223445556666777666653
No 164
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=36.16 E-value=19 Score=27.27 Aligned_cols=26 Identities=23% Similarity=0.378 Sum_probs=17.4
Q ss_pred cccccCCCCCCCccccccccccccccccccc
Q 017706 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDK 73 (367)
Q Consensus 43 ~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~ 73 (367)
+.||.||.+- .......|..+.||=|
T Consensus 5 i~CP~CgnKT-----R~kir~DT~LkNfPly 30 (55)
T PF14205_consen 5 ILCPICGNKT-----RLKIREDTVLKNFPLY 30 (55)
T ss_pred EECCCCCCcc-----ceeeecCceecccccc
Confidence 5799998651 2445667777788754
No 165
>PRK06231 F0F1 ATP synthase subunit B; Validated
Probab=36.14 E-value=3.7e+02 Score=25.14 Aligned_cols=15 Identities=13% Similarity=-0.024 Sum_probs=6.6
Q ss_pred HHHHHHHHHHHHHHH
Q 017706 181 EEIKLKAQELRERAR 195 (367)
Q Consensus 181 EEk~~k~~el~~k~r 195 (367)
++|+..+..-...+.
T Consensus 78 ~~R~~~I~~~L~~Ae 92 (205)
T PRK06231 78 NKRKELIEAEINQAN 92 (205)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344444444444443
No 166
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=36.10 E-value=17 Score=38.22 Aligned_cols=31 Identities=29% Similarity=0.257 Sum_probs=25.0
Q ss_pred eecCCCcccc---cchHHHHHHHhhhccCCCCcc
Q 017706 6 LKCGDCGALL---RSVQEAQEHAELTSHSNFSES 36 (367)
Q Consensus 6 l~C~~C~~v~---~g~~~aq~h~~~tgh~~F~e~ 36 (367)
..|..||.|+ +-..-|+.|=++|||.+-=+-
T Consensus 241 wicliCg~vgcgrY~eghA~rHweet~H~yalel 274 (493)
T KOG0804|consen 241 WICLICGNVGCGRYKEGHARRHWEETGHCYALEL 274 (493)
T ss_pred EEEEEccceecccccchhHHHHHHhhcceEEEee
Confidence 4677788887 566779999999999987663
No 167
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=35.66 E-value=11 Score=32.46 Aligned_cols=24 Identities=29% Similarity=0.577 Sum_probs=16.5
Q ss_pred hhhhhcccccCCCCCCCcccccccccccc
Q 017706 38 EAVLNLVCATCGKPCRSKTETDLHRKRTG 66 (367)
Q Consensus 38 e~v~~~~C~~Cg~~~~~~~e~~~a~K~t~ 66 (367)
..+++-+||.||-. +++.|+-+++
T Consensus 70 ga~I~~kCpkCghe-----~m~Y~T~QlR 93 (116)
T KOG2907|consen 70 GAVIKHKCPKCGHE-----EMSYHTLQLR 93 (116)
T ss_pred ccchhccCcccCCc-----hhhhhhhhcc
Confidence 46788899999964 4555555544
No 168
>cd02669 Peptidase_C19M A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=35.64 E-value=16 Score=37.79 Aligned_cols=42 Identities=21% Similarity=0.349 Sum_probs=32.6
Q ss_pred ecCCCccccc---chHHHHHHHhhhccCCCCcchhhhhhcccccCCC
Q 017706 7 KCGDCGALLR---SVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (367)
Q Consensus 7 ~C~~C~~v~~---g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~ 50 (367)
-|.+||+++. ++.-|-.|+.++||..|-... ....+|=.|+-
T Consensus 30 ~CL~cg~~~~g~~~~~ha~~H~~~~~H~~~v~l~--t~~~yc~~~~~ 74 (440)
T cd02669 30 ACLVCGKYFQGRGKGSHAYTHSLEDNHHVFLNLE--TLKFYCLPDNY 74 (440)
T ss_pred EEcccCCeecCCCCCcHHHHHhhccCCCEEEECC--CCCEEEeCCCC
Confidence 7999996653 445699999999999887653 24579999986
No 169
>PRK06568 F0F1 ATP synthase subunit B; Validated
Probab=35.62 E-value=3.3e+02 Score=24.54 Aligned_cols=14 Identities=29% Similarity=0.200 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHHHH
Q 017706 181 EEIKLKAQELRERA 194 (367)
Q Consensus 181 EEk~~k~~el~~k~ 194 (367)
+++..++..=...+
T Consensus 34 eeR~~~I~~~Ld~A 47 (154)
T PRK06568 34 DAKILEVQEKVLKA 47 (154)
T ss_pred HHHHHHHHHHHHHH
Confidence 44555444444333
No 170
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=35.45 E-value=47 Score=29.06 Aligned_cols=39 Identities=21% Similarity=0.321 Sum_probs=31.1
Q ss_pred cccCHHHHHHHH-hCCCCHHHHHHHHHHhCCCCHHHHHHHH
Q 017706 111 PEVDKELLKELE-AMGFPVARATRALHYSGNANVEAAVNWV 150 (367)
Q Consensus 111 ~~~d~~~l~~L~-~MGF~~~~a~kAL~~tgn~~~E~A~~Wl 150 (367)
..++++-+...+ .-|-|++.|.+||..+|+ ++-.|+--|
T Consensus 81 ~~i~eeDIkLV~eQa~VsreeA~kAL~e~~G-DlaeAIm~L 120 (122)
T COG1308 81 SDISEEDIKLVMEQAGVSREEAIKALEEAGG-DLAEAIMKL 120 (122)
T ss_pred CCCCHHHHHHHHHHhCCCHHHHHHHHHHcCC-cHHHHHHHh
Confidence 347777777666 479999999999999998 787777654
No 171
>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=35.03 E-value=40 Score=30.40 Aligned_cols=14 Identities=29% Similarity=0.482 Sum_probs=10.5
Q ss_pred CCCceeecCCCcccc
Q 017706 1 MAGVSLKCGDCGALL 15 (367)
Q Consensus 1 ~~~~~l~C~~C~~v~ 15 (367)
|=.|.|+|. ||+.|
T Consensus 1 MI~y~L~C~-~gH~F 14 (148)
T PF06676_consen 1 MIVYDLRCE-NGHEF 14 (148)
T ss_pred CeeEEEecC-CCCcc
Confidence 346899998 77776
No 172
>PLN03086 PRLI-interacting factor K; Provisional
Probab=34.94 E-value=2.1e+02 Score=31.26 Aligned_cols=9 Identities=22% Similarity=0.589 Sum_probs=4.1
Q ss_pred HHHhHHHHH
Q 017706 253 IRQKLEEDK 261 (367)
Q Consensus 253 ir~qIe~Dk 261 (367)
|.+|+++|.
T Consensus 56 ~~~~~~~~~ 64 (567)
T PLN03086 56 IEAQIKADQ 64 (567)
T ss_pred HHHHHHHHH
Confidence 344454443
No 173
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.85 E-value=86 Score=29.27 Aligned_cols=24 Identities=21% Similarity=0.272 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHh
Q 017706 115 KELLKELEAMGFPVARATRALHYS 138 (367)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~t 138 (367)
.++++.|+++||++..|.+||...
T Consensus 153 ~ea~~AL~~LGy~~~ea~~al~~i 176 (197)
T PRK14603 153 EDAVLALLALGFREAQVRSVVAEL 176 (197)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 578999999999999999999764
No 174
>PF06936 Selenoprotein_S: Selenoprotein S (SelS); InterPro: IPR009703 This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. These proteins are involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins which participate in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner []. They probably serve as a linker between DER1, which mediates the retro-translocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination.; GO: 0008430 selenium binding, 0006886 intracellular protein transport, 0030176 integral to endoplasmic reticulum membrane; PDB: 2Q2F_A.
Probab=34.63 E-value=1.4e+02 Score=28.03 Aligned_cols=29 Identities=24% Similarity=0.351 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 017706 222 EAKRIEEENERKRILALRKAEKEEEKRAR 250 (367)
Q Consensus 222 ~~k~~~ee~e~k~~~e~rrrEK~ee~~ar 250 (367)
.++++|++..-++..+.+.++++++...|
T Consensus 87 aAR~RmQEE~dakA~~~kEKq~q~EEEKR 115 (190)
T PF06936_consen 87 AARRRMQEELDAKAEEYKEKQKQEEEEKR 115 (190)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555555555555554444444443333
No 175
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.12 E-value=1.1e+02 Score=28.65 Aligned_cols=24 Identities=29% Similarity=0.409 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHh
Q 017706 115 KELLKELEAMGFPVARATRALHYS 138 (367)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~t 138 (367)
.++++.|+++||++..|.+|+..-
T Consensus 150 ~e~~~aL~~LGy~~~ea~~ai~~i 173 (195)
T PRK14604 150 RELSEILISLGYSAAEAAAAIAAL 173 (195)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 578999999999999999998664
No 176
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=33.91 E-value=16 Score=31.30 Aligned_cols=29 Identities=21% Similarity=0.331 Sum_probs=24.0
Q ss_pred hcccccCCCCCCCccccccccccccccccccchh
Q 017706 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTS 75 (367)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~ 75 (367)
...||.||.. |+..+..+++.+.-|..++
T Consensus 72 ~~~CpkCg~~-----ea~y~~~QtRsaDEp~T~F 100 (113)
T COG1594 72 KEKCPKCGNK-----EAYYWQLQTRSADEPETRF 100 (113)
T ss_pred cccCCCCCCc-----eeEEEeeehhccCCCceEE
Confidence 5689999974 6788999999998887765
No 177
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=33.40 E-value=2.8e+02 Score=23.82 Aligned_cols=29 Identities=31% Similarity=0.373 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhhHHHHH
Q 017706 175 KSSLTPEEIKLKAQELRERARKKKEEEEK 203 (367)
Q Consensus 175 k~~lT~EEk~~k~~el~~k~r~kr~eeek 203 (367)
+-.||.||.+.-+++|..+++..+.+-+.
T Consensus 36 kGeln~eEak~~vddl~~q~k~~~~e~e~ 64 (108)
T COG3937 36 KGELNAEEAKRFVDDLLRQAKEAQGELEE 64 (108)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHhhhHHH
Confidence 34799999999999999999866654433
No 178
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=33.01 E-value=23 Score=27.18 Aligned_cols=28 Identities=25% Similarity=0.558 Sum_probs=23.0
Q ss_pred ceeecCCCcccccchHHHHHHHhhhccCC
Q 017706 4 VSLKCGDCGALLRSVQEAQEHAELTSHSN 32 (367)
Q Consensus 4 ~~l~C~~C~~v~~g~~~aq~h~~~tgh~~ 32 (367)
.-|+|..||.++..+.+-..|.. -.|-.
T Consensus 16 ~~lrCPRC~~~FR~~K~Y~RHVN-KaH~~ 43 (65)
T COG4049 16 EFLRCPRCGMVFRRRKDYIRHVN-KAHGW 43 (65)
T ss_pred eeeeCCchhHHHHHhHHHHHHhh-HHhhh
Confidence 35899999999999999999988 44543
No 179
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=32.96 E-value=17 Score=37.74 Aligned_cols=27 Identities=33% Similarity=0.876 Sum_probs=0.0
Q ss_pred cCCCcccccchHHHHHHHhhhcc--------CCCCcchhhhhh-cccccCCCC
Q 017706 8 CGDCGALLRSVQEAQEHAELTSH--------SNFSESTEAVLN-LVCATCGKP 51 (367)
Q Consensus 8 C~~C~~v~~g~~~aq~h~~~tgh--------~~F~e~~e~v~~-~~C~~Cg~~ 51 (367)
|..||| +|- -+|-|. |+- |.||+||.+
T Consensus 42 Cm~Cg~--------------nG~TRlllT~IP~fREv---VimSF~CpHCG~k 77 (460)
T KOG2703|consen 42 CMNCGE--------------NGTTRLLLTSIPYFREV---VIMSFECPHCGHK 77 (460)
T ss_pred hhhccc--------------CCceeEEEeecchhhee---eeEEeecCccCCc
No 180
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=32.59 E-value=37 Score=31.45 Aligned_cols=11 Identities=36% Similarity=1.117 Sum_probs=9.1
Q ss_pred hhcccccCCCC
Q 017706 41 LNLVCATCGKP 51 (367)
Q Consensus 41 ~~~~C~~Cg~~ 51 (367)
.+|.||.||..
T Consensus 131 ~~F~Cp~Cg~~ 141 (176)
T COG1675 131 LGFTCPKCGED 141 (176)
T ss_pred hCCCCCCCCch
Confidence 34999999985
No 181
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=32.41 E-value=27 Score=23.84 Aligned_cols=13 Identities=31% Similarity=1.094 Sum_probs=9.3
Q ss_pred CceeecCCCcccc
Q 017706 3 GVSLKCGDCGALL 15 (367)
Q Consensus 3 ~~~l~C~~C~~v~ 15 (367)
+..++|..||.++
T Consensus 23 g~~v~C~~C~~~f 35 (36)
T PF13717_consen 23 GRKVRCSKCGHVF 35 (36)
T ss_pred CcEEECCCCCCEe
Confidence 5677888887764
No 182
>PF05890 Ebp2: Eukaryotic rRNA processing protein EBP2; InterPro: IPR008610 This family consists of several eukaryotic rRNA processing protein EBP2 sequences. Ebp2p is required for the maturation of 25S rRNA and 60S subunit assembly. Ebp2p may be one of the target proteins of Rrs1p for executing the signal to regulate ribosome biogenesis [].
Probab=32.40 E-value=3.4e+02 Score=26.72 Aligned_cols=53 Identities=25% Similarity=0.369 Sum_probs=30.0
Q ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Q 017706 188 QELRERARKKKEEEEKRMEREREKERIRIGKELLEAKRIEEENERKRILALRK 240 (367)
Q Consensus 188 ~el~~k~r~kr~eeek~~~~e~E~~Rr~~gKe~~~~k~~~ee~e~k~~~e~rr 240 (367)
+.++.++-.+....+..++..+-++-.+.||.+|..+...+..+.+..++..+
T Consensus 121 ~KVr~kLl~~~~~ie~~E~~rk~Re~KKfgKqvQ~ek~~eR~keKk~~le~Ik 173 (271)
T PF05890_consen 121 EKVRQKLLKEQKRIEASEEARKQRELKKFGKQVQVEKLQERAKEKKEMLEKIK 173 (271)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444443333334444555566777789999987766555555555544443
No 183
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=32.20 E-value=31 Score=24.69 Aligned_cols=17 Identities=41% Similarity=0.700 Sum_probs=12.7
Q ss_pred cccccCCCCCCCcccccccccccc
Q 017706 43 LVCATCGKPCRSKTETDLHRKRTG 66 (367)
Q Consensus 43 ~~C~~Cg~~~~~~~e~~~a~K~t~ 66 (367)
.+||.||.. .+.-++|.
T Consensus 20 irC~~CG~r-------IlyK~R~~ 36 (44)
T smart00659 20 VRCRECGYR-------ILYKKRTK 36 (44)
T ss_pred eECCCCCce-------EEEEeCCC
Confidence 699999986 66666554
No 184
>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=31.74 E-value=29 Score=25.96 Aligned_cols=34 Identities=24% Similarity=0.514 Sum_probs=19.7
Q ss_pred CCceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCC
Q 017706 2 AGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (367)
Q Consensus 2 ~~~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~ 50 (367)
+.+.|-|..|... .|=+- .+..+.+ .|+|+.||.
T Consensus 19 ~r~aLIC~~C~~h-------------NGla~-~~~~~~i-~y~C~~Cg~ 52 (54)
T PF10058_consen 19 NRYALICSKCFSH-------------NGLAP-KEEFEEI-QYRCPYCGA 52 (54)
T ss_pred CceeEECcccchh-------------hcccc-cccCCce-EEEcCCCCC
Confidence 3567888888632 12211 2322333 699999985
No 185
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=31.65 E-value=6.4e+02 Score=26.61 Aligned_cols=8 Identities=25% Similarity=0.547 Sum_probs=3.5
Q ss_pred HHHHHHHH
Q 017706 257 LEEDKAER 264 (367)
Q Consensus 257 Ie~Dk~eR 264 (367)
|++-|+.|
T Consensus 373 ~~~~~~~~ 380 (429)
T PRK00247 373 MARARARR 380 (429)
T ss_pred HHHHHHHH
Confidence 44444444
No 186
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=31.57 E-value=10 Score=29.11 Aligned_cols=13 Identities=31% Similarity=0.690 Sum_probs=9.5
Q ss_pred eecCCCcccccch
Q 017706 6 LKCGDCGALLRSV 18 (367)
Q Consensus 6 l~C~~C~~v~~g~ 18 (367)
..|..||+.+.+.
T Consensus 8 ~~CtSCg~~i~~~ 20 (59)
T PRK14890 8 PKCTSCGIEIAPR 20 (59)
T ss_pred ccccCCCCcccCC
Confidence 4688999887643
No 187
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=31.32 E-value=7.5e+02 Score=27.93 Aligned_cols=18 Identities=11% Similarity=0.316 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHhhhcc
Q 017706 320 KVKRAFQTLLTYIGNVAK 337 (367)
Q Consensus 320 ~~~~a~~tL~kyl~Ni~~ 337 (367)
.+.+|+..|.+||+..+.
T Consensus 702 ~~~eA~~~l~~~ld~a~~ 719 (771)
T TIGR01069 702 RSEEALDRLEKFLNDALL 719 (771)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 478888888888887553
No 188
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=31.23 E-value=31 Score=30.44 Aligned_cols=17 Identities=24% Similarity=0.640 Sum_probs=12.2
Q ss_pred ccCCCCcchhhhhhcccccCCCC
Q 017706 29 SHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 29 gh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
||.+|=.- -.||.||++
T Consensus 36 G~v~~PPr------~~Cp~C~~~ 52 (140)
T COG1545 36 GRVYFPPR------AYCPKCGSE 52 (140)
T ss_pred CeEEcCCc------ccCCCCCCC
Confidence 56666554 489999986
No 189
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=31.17 E-value=48 Score=29.71 Aligned_cols=14 Identities=29% Similarity=0.795 Sum_probs=11.5
Q ss_pred ceeecCCCcccccc
Q 017706 4 VSLKCGDCGALLRS 17 (367)
Q Consensus 4 ~~l~C~~C~~v~~g 17 (367)
+.++|..|+.....
T Consensus 104 ~~~~C~~C~~~~~~ 117 (178)
T PF02146_consen 104 FRLRCSKCGKEYDR 117 (178)
T ss_dssp EEEEETTTSBEEEG
T ss_pred ceeeecCCCccccc
Confidence 57899999998754
No 190
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=30.76 E-value=26 Score=27.80 Aligned_cols=27 Identities=22% Similarity=0.262 Sum_probs=20.8
Q ss_pred CHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 017706 127 PVARATRALHYSGNANVEAAVNWVVEHE 154 (367)
Q Consensus 127 ~~~~a~kAL~~tgn~~~E~A~~Wl~~h~ 154 (367)
|....+.||.+... +++.|++||++..
T Consensus 45 ~e~~i~eal~~~~f-DvekAl~~Ll~~~ 71 (79)
T PF08938_consen 45 PEEQIKEALWHYYF-DVEKALDYLLSKF 71 (79)
T ss_dssp -CCHHHHHHHHTTT--CCHHHHHHHHCC
T ss_pred CHHHHHHHHHHHcC-CHHHHHHHHHHhc
Confidence 67777888888776 9999999999854
No 191
>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=30.71 E-value=22 Score=28.64 Aligned_cols=27 Identities=22% Similarity=0.331 Sum_probs=20.3
Q ss_pred hcccccCCCCCCCccccccccccccccccccchhccc
Q 017706 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAA 78 (367)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L~v~~ 78 (367)
+-.|+.||++. . .+.|.-||+-.++|.
T Consensus 78 ~~~C~vC~k~l--------~--~~~f~~~p~~~v~H~ 104 (109)
T PF10367_consen 78 STKCSVCGKPL--------G--NSVFVVFPCGHVVHY 104 (109)
T ss_pred CCCccCcCCcC--------C--CceEEEeCCCeEEec
Confidence 35799999972 2 267999999877764
No 192
>PRK14474 F0F1 ATP synthase subunit B; Provisional
Probab=30.61 E-value=5e+02 Score=25.02 Aligned_cols=14 Identities=7% Similarity=0.062 Sum_probs=6.1
Q ss_pred HHHHHHHHHHHHHH
Q 017706 181 EEIKLKAQELRERA 194 (367)
Q Consensus 181 EEk~~k~~el~~k~ 194 (367)
++|+.++..-...+
T Consensus 35 ~eR~~~I~~~l~~A 48 (250)
T PRK14474 35 KKRQQRIANRWQDA 48 (250)
T ss_pred HHHHHHHHHHHHHH
Confidence 34444444444443
No 193
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=30.16 E-value=39 Score=28.99 Aligned_cols=45 Identities=16% Similarity=0.445 Sum_probs=27.8
Q ss_pred eeecCCCcccc--------------cchHHHHHHHhhhccCCCCcchhhhhhcccccCC
Q 017706 5 SLKCGDCGALL--------------RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCG 49 (367)
Q Consensus 5 ~l~C~~C~~v~--------------~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg 49 (367)
.++|..||+.. .+...+.++.++.--..|.=..=.+.-++|-+|-
T Consensus 20 ~V~C~nCgr~vPKDKAIkrf~irniVe~aa~rDl~~a~v~~~y~lPKly~k~~YCVSCA 78 (108)
T PTZ00172 20 PVRCSNCGRCVPKDKAIKRFVVRNIVDAASVRDIAEASVYYGYPLPKLYMKQQYCVSCA 78 (108)
T ss_pred cEEeCCccccccccceEEEEeccCCccHHHHHHHHHhhchhccccccceeeeEEeeehh
Confidence 58999999987 4555566777643332222222224457999995
No 194
>smart00355 ZnF_C2H2 zinc finger.
Probab=30.03 E-value=43 Score=19.22 Aligned_cols=20 Identities=30% Similarity=0.830 Sum_probs=15.3
Q ss_pred ecCCCcccccchHHHHHHHh
Q 017706 7 KCGDCGALLRSVQEAQEHAE 26 (367)
Q Consensus 7 ~C~~C~~v~~g~~~aq~h~~ 26 (367)
+|..|+..+.+...-+.|..
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 58888888877777777765
No 195
>KOG2891 consensus Surface glycoprotein [General function prediction only]
Probab=29.83 E-value=6e+02 Score=25.68 Aligned_cols=73 Identities=27% Similarity=0.300 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH--HHHHHHHhHHHHHHHHHHHHH
Q 017706 183 IKLKAQELRERARKKKEEEEKRMEREREKERIRIGKELLEAKRIEEENERKR--ILALRKAEKEEEKRAREKIRQ 255 (367)
Q Consensus 183 k~~k~~el~~k~r~kr~eeek~~~~e~E~~Rr~~gKe~~~~k~~~ee~e~k~--~~e~rrrEK~ee~~ar~rir~ 255 (367)
|+.++..-..+-=+..++++++.+.+.|...|..-|+..++.+.-....+.. -+-.+--||.++...|.+-+.
T Consensus 324 kkrqlerqekqeleqmaeeekkr~eeaeerqraeekeq~eaee~~ra~kr~egvkllkf~fekieareerrkqke 398 (445)
T KOG2891|consen 324 KKRQLERQEKQELEQMAEEEKKREEEAEERQRAEEKEQKEAEELERARKREEGVKLLKFEFEKIEAREERRKQKE 398 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhH
No 196
>PF04641 Rtf2: Rtf2 RING-finger
Probab=29.33 E-value=12 Score=36.07 Aligned_cols=49 Identities=14% Similarity=0.207 Sum_probs=32.0
Q ss_pred CceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhh-hcccccCCCCC
Q 017706 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVL-NLVCATCGKPC 52 (367)
Q Consensus 3 ~~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~-~~~C~~Cg~~~ 52 (367)
...+.|.+++..+.|..-.--+.. +||+.=...-..+. +-.||.||++|
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~-cG~V~s~~alke~k~~~~Cp~c~~~f 160 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRP-CGCVFSEKALKELKKSKKCPVCGKPF 160 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcC-CCCEeeHHHHHhhcccccccccCCcc
Confidence 456788888888866554444444 67754444434444 56799999984
No 197
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=29.21 E-value=9.9e+02 Score=28.06 Aligned_cols=80 Identities=28% Similarity=0.390 Sum_probs=45.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhH--HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH--HHHHHHHHHHhHHHHHHHHHH
Q 017706 177 SLTPEEIKLKAQELRERARKKKE--EEEKRMEREREKERIRIGKELLEAKRIEEENE--RKRILALRKAEKEEEKRAREK 252 (367)
Q Consensus 177 ~lT~EEk~~k~~el~~k~r~kr~--eeek~~~~e~E~~Rr~~gKe~~~~k~~~ee~e--~k~~~e~rrrEK~ee~~ar~r 252 (367)
.-|++|-++++.+|.+++..-|- .+++..-+|-++.+|.- ..+++.|-++-+++ ..|.+..-|.|+.+-..++++
T Consensus 223 skte~eLr~QvrdLtEkLetlR~kR~EDk~Kl~Elekmkiql-eqlqEfkSkim~qqa~Lqrel~raR~e~keaqe~ke~ 301 (1243)
T KOG0971|consen 223 SKTEEELRAQVRDLTEKLETLRLKRAEDKAKLKELEKMKIQL-EQLQEFKSKIMEQQADLQRELKRARKEAKEAQEAKER 301 (1243)
T ss_pred ccchHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45889999999999999754432 23333333334444432 23445554443332 345556666666666677766
Q ss_pred HHHhH
Q 017706 253 IRQKL 257 (367)
Q Consensus 253 ir~qI 257 (367)
-+..+
T Consensus 302 ~k~em 306 (1243)
T KOG0971|consen 302 YKEEM 306 (1243)
T ss_pred HHHHH
Confidence 65544
No 198
>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=28.82 E-value=62 Score=23.55 Aligned_cols=38 Identities=39% Similarity=0.667 Sum_probs=28.8
Q ss_pred eeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCC
Q 017706 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~ 50 (367)
...|..||. .....+=..|.. +-|.+ +. ..+.||.|..
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~-~~H~~--~~----~~v~CPiC~~ 39 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCE-DEHRS--ES----KNVVCPICSS 39 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHH-hHCcC--CC----CCccCCCchh
Confidence 357999999 777888889988 66664 11 2479999975
No 199
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.41 E-value=66 Score=30.26 Aligned_cols=24 Identities=29% Similarity=0.343 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHh
Q 017706 115 KELLKELEAMGFPVARATRALHYS 138 (367)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~t 138 (367)
+++++.|+++||++..|.+|+..-
T Consensus 145 ~ea~~AL~~LGy~~~ea~~al~~v 168 (196)
T PRK13901 145 KELEQSIVNMGFDRKLVNSAIKEI 168 (196)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 578999999999999999998643
No 200
>PF05262 Borrelia_P83: Borrelia P83/100 protein; InterPro: IPR007926 This family consists of several Borrelia P83/P100 antigen proteins.
Probab=27.53 E-value=7e+02 Score=26.80 Aligned_cols=8 Identities=13% Similarity=-0.433 Sum_probs=4.2
Q ss_pred ccchhccc
Q 017706 71 VDKTSEAA 78 (367)
Q Consensus 71 P~~L~v~~ 78 (367)
-.|.|+++
T Consensus 49 ~~y~ii~~ 56 (489)
T PF05262_consen 49 GRYYIIHA 56 (489)
T ss_pred CcEEEEEe
Confidence 45555544
No 201
>PHA00616 hypothetical protein
Probab=27.41 E-value=32 Score=24.87 Aligned_cols=21 Identities=33% Similarity=0.694 Sum_probs=17.7
Q ss_pred eecCCCcccccchHHHHHHHh
Q 017706 6 LKCGDCGALLRSVQEAQEHAE 26 (367)
Q Consensus 6 l~C~~C~~v~~g~~~aq~h~~ 26 (367)
-+|..||.++.--.+=..|..
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r 22 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLL 22 (44)
T ss_pred CccchhhHHHhhHHHHHHHHH
Confidence 379999999988888888875
No 202
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.07 E-value=34 Score=26.05 Aligned_cols=14 Identities=36% Similarity=0.990 Sum_probs=11.4
Q ss_pred CCceeecCCCcccc
Q 017706 2 AGVSLKCGDCGALL 15 (367)
Q Consensus 2 ~~~~l~C~~C~~v~ 15 (367)
+..+|+|..||.+.
T Consensus 31 aDIkikC~nC~h~v 44 (60)
T COG4481 31 ADIKIKCENCGHSV 44 (60)
T ss_pred CcEEEEecCCCcEE
Confidence 46789999999865
No 203
>KOG2357 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.95 E-value=1.8e+02 Score=30.63 Aligned_cols=9 Identities=22% Similarity=0.158 Sum_probs=5.9
Q ss_pred ccccccCCC
Q 017706 93 EEAIDVDMS 101 (367)
Q Consensus 93 ~~~ldl~~~ 101 (367)
.+-.||+.|
T Consensus 242 ke~~DLs~F 250 (440)
T KOG2357|consen 242 KEMRDLSRF 250 (440)
T ss_pred HHHHHHHHH
Confidence 456777766
No 204
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=26.87 E-value=40 Score=24.92 Aligned_cols=39 Identities=28% Similarity=0.560 Sum_probs=28.5
Q ss_pred CceeecCCCcccccchHHHHHHHhhhccCCC-CcchhhhhhcccccCCC
Q 017706 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNF-SESTEAVLNLVCATCGK 50 (367)
Q Consensus 3 ~~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F-~e~~e~v~~~~C~~Cg~ 50 (367)
.-.|.|-+||.-+.=..+-|..-.+-| | ++. -+|++|-+
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~eKg---f~n~p------~RC~~CR~ 41 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAEKG---FDNEP------KRCPSCRQ 41 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHhcC---CcCCC------ccCHHHHH
Confidence 346899999999987777777777544 5 333 48999843
No 205
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=26.73 E-value=5.2e+02 Score=28.09 Aligned_cols=46 Identities=17% Similarity=0.322 Sum_probs=26.0
Q ss_pred CHHHHHHHHhCCCCHHH----------HHHHHHHhCCCCHHHHHHHHHHhcCCCCC
Q 017706 114 DKELLKELEAMGFPVAR----------ATRALHYSGNANVEAAVNWVVEHENDPDI 159 (367)
Q Consensus 114 d~~~l~~L~~MGF~~~~----------a~kAL~~tgn~~~E~A~~Wl~~h~dd~d~ 159 (367)
-++.++.|.+-|.+-|- ---+|++.-..+.-..+-+++++.-||..
T Consensus 403 ~p~~ie~lken~lsgnf~~~pe~~~~ltsT~LH~aa~qg~~k~v~~~Leeg~Dp~~ 458 (591)
T KOG2505|consen 403 EPDSIEALKENLLSGNFDVTPEANDYLTSTFLHYAAAQGARKCVKYFLEEGCDPST 458 (591)
T ss_pred chhHHHHHHhcCCcccccccccccccccchHHHHHHhcchHHHHHHHHHhcCCchh
Confidence 36777777777665521 12345554433445555566666677764
No 206
>CHL00118 atpG ATP synthase CF0 B' subunit; Validated
Probab=26.67 E-value=4.5e+02 Score=23.19 Aligned_cols=17 Identities=18% Similarity=0.057 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHHHHh
Q 017706 181 EEIKLKAQELRERARKK 197 (367)
Q Consensus 181 EEk~~k~~el~~k~r~k 197 (367)
++|..++..-...+...
T Consensus 52 ~~R~~~I~~~l~~Ae~~ 68 (156)
T CHL00118 52 DERKEYIRKNLTKASEI 68 (156)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45555555554444333
No 207
>PF04361 DUF494: Protein of unknown function (DUF494); InterPro: IPR007456 Members of this family of uncharacterised proteins are often named Smg.
Probab=26.63 E-value=1.8e+02 Score=26.28 Aligned_cols=55 Identities=24% Similarity=0.329 Sum_probs=30.6
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
Q 017706 115 KELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHENDPDIDEMPMVPVSGGGGASKSSLTPEEIKL 185 (367)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~dd~d~dep~~~~~~~~~~~~k~~lT~EEk~~ 185 (367)
..+-..|.+.||...-.. .|++||..-..-.....+...+.. .+.+..|++|...
T Consensus 24 ~~L~~~L~~aGF~~~eI~------------~Al~WL~~L~~~~~~~~~~~~~~~----~s~Riyt~~E~~~ 78 (155)
T PF04361_consen 24 DDLTRELSAAGFEDEEIN------------KALDWLEGLAELQEEEPPAQFASP----RSMRIYTPEEQEK 78 (155)
T ss_pred HHHHHHHHHcCCCHHHHH------------HHHHHHHHHHhccccccccccCCC----CceEecCHHHHHH
Confidence 355688999999887654 466897643333211111111111 1245778877754
No 208
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=26.34 E-value=15 Score=33.57 Aligned_cols=37 Identities=19% Similarity=0.420 Sum_probs=23.5
Q ss_pred cCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 8 CGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 8 C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
|.+||.-. -..+...|-=-+|+++- +.-|.|++||-+
T Consensus 1 CP~Cg~~~-----~~~~~~~~~IP~F~evi--i~sf~C~~CGyr 37 (163)
T TIGR00340 1 CPVCGSRT-----LKAVTYDYDIPYFGKIM--LSTYICEKCGYR 37 (163)
T ss_pred CCCCCCcc-----eEeeeEeccCCCcceEE--EEEEECCCCCCc
Confidence 88898641 11112234556799872 446999999976
No 209
>PRK09173 F0F1 ATP synthase subunit B; Validated
Probab=26.10 E-value=4.5e+02 Score=23.06 Aligned_cols=14 Identities=7% Similarity=-0.045 Sum_probs=5.7
Q ss_pred HHHHHHHHHHHHHH
Q 017706 181 EEIKLKAQELRERA 194 (367)
Q Consensus 181 EEk~~k~~el~~k~ 194 (367)
+++...+..-...+
T Consensus 32 ~~R~~~I~~~l~~A 45 (159)
T PRK09173 32 DARADRIKNELAEA 45 (159)
T ss_pred HHHHHHHHHHHHHH
Confidence 34444444433333
No 210
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=25.89 E-value=51 Score=27.65 Aligned_cols=41 Identities=22% Similarity=0.469 Sum_probs=25.5
Q ss_pred eeecCCCcccc--------------cchHHHHHHHhhhccCCCCcchhhhhhcccccCC
Q 017706 5 SLKCGDCGALL--------------RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCG 49 (367)
Q Consensus 5 ~l~C~~C~~v~--------------~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg 49 (367)
.++|..||+.. .+...+.++.++ | +++--. .+.-++|.+|-
T Consensus 20 ~V~C~nCgr~vPKDKAIkrf~i~n~Ve~a~~rdl~~a-~-~~lpk~--~~k~~YCvSCA 74 (95)
T PRK09335 20 YVQCDNCGRRVPRDKAVCVTKMYSPVDPQLAKELEKK-G-AIIARY--PVTKCYCVNCA 74 (95)
T ss_pred cEEeCCCCCcCcCCceEEEEEecCCCCHHHHHHHHhC-c-eeeeee--eeeeEEechhh
Confidence 58999999987 455556666663 2 111111 14458999995
No 211
>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=25.86 E-value=58 Score=19.85 Aligned_cols=21 Identities=29% Similarity=0.790 Sum_probs=16.3
Q ss_pred eecCCCcccccchHHHHHHHh
Q 017706 6 LKCGDCGALLRSVQEAQEHAE 26 (367)
Q Consensus 6 l~C~~C~~v~~g~~~aq~h~~ 26 (367)
.+|..|+..+.....=..|..
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHC
T ss_pred CCCCccCCccCChhHHHHHhH
Confidence 478888888888877777764
No 212
>PLN00186 ribosomal protein S26; Provisional
Probab=25.85 E-value=58 Score=27.95 Aligned_cols=42 Identities=17% Similarity=0.424 Sum_probs=27.3
Q ss_pred eeecCCCcccc--------------cchHHHHHHHhhhccCCCCcch---hhhhhcccccCC
Q 017706 5 SLKCGDCGALL--------------RSVQEAQEHAELTSHSNFSEST---EAVLNLVCATCG 49 (367)
Q Consensus 5 ~l~C~~C~~v~--------------~g~~~aq~h~~~tgh~~F~e~~---e~v~~~~C~~Cg 49 (367)
.++|..||+.. .+...+.++.++.- |.... =.+.-++|-+|-
T Consensus 20 ~V~C~nCgr~vPKDKAIkrf~irniVe~aa~rDl~~a~v---y~~y~lPKly~K~~YCVSCA 78 (109)
T PLN00186 20 RIRCSNCGKCVPKDKAIKRFLVRNIVEQAALRDVQEACV---YDGYTLPKLYAKVQYCISCA 78 (109)
T ss_pred ceeeCCCcccccccceEEEEecccCccHHHHHHHHhhhc---ccccccchhhhceEEEEeeh
Confidence 58999999987 45566667776443 44431 223348899995
No 213
>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]
Probab=25.34 E-value=8.5e+02 Score=28.54 Aligned_cols=23 Identities=17% Similarity=0.196 Sum_probs=17.1
Q ss_pred HHHHHhCCCCHHHHHHHHHHhcCCC
Q 017706 133 RALHYSGNANVEAAVNWVVEHENDP 157 (367)
Q Consensus 133 kAL~~tgn~~~E~A~~Wl~~h~dd~ 157 (367)
+|++..|. ...|+.|+.--....
T Consensus 724 ra~y~~~~--~~eak~~ll~a~~~~ 746 (1018)
T KOG2002|consen 724 RAWYEAGK--LQEAKEALLKARHLA 746 (1018)
T ss_pred HHHHHhhh--HHHHHHHHHHHHHhC
Confidence 77777664 999999998655543
No 214
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=25.22 E-value=5e+02 Score=23.24 Aligned_cols=16 Identities=19% Similarity=0.123 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHHHHH
Q 017706 181 EEIKLKAQELRERARK 196 (367)
Q Consensus 181 EEk~~k~~el~~k~r~ 196 (367)
++|+..+..-...+..
T Consensus 49 ~~R~~~I~~~l~~A~~ 64 (174)
T PRK07352 49 EERREAILQALKEAEE 64 (174)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444444444444433
No 215
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=25.15 E-value=8.1e+02 Score=25.66 Aligned_cols=22 Identities=5% Similarity=-0.011 Sum_probs=11.3
Q ss_pred hhccCCChhhhhhhhccccccc
Q 017706 334 NVAKNPNEEKFRKIRLSNQTFQ 355 (367)
Q Consensus 334 Ni~~~P~eeK~rkIr~~N~~f~ 355 (367)
+++.||.-++-.|..+=+++|.
T Consensus 311 ~~L~~p~i~~~~K~~ll~~l~~ 332 (445)
T PRK13428 311 ILLSDYTVPADGRVALLRKVLG 332 (445)
T ss_pred HHHhCCCCCHHHHHHHHHHHHh
Confidence 3555555555555555444444
No 216
>COG0423 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=24.86 E-value=80 Score=34.13 Aligned_cols=49 Identities=24% Similarity=0.523 Sum_probs=27.8
Q ss_pred ceeecCCCcccccc-hHHHHHHHhhhccCCCCcc--hhhh--hhcccccCCCCCC
Q 017706 4 VSLKCGDCGALLRS-VQEAQEHAELTSHSNFSES--TEAV--LNLVCATCGKPCR 53 (367)
Q Consensus 4 ~~l~C~~C~~v~~g-~~~aq~h~~~tgh~~F~e~--~e~v--~~~~C~~Cg~~~~ 53 (367)
-...|.+||..++- .---..++. .+|.+++.. ++.+ -+.+||.||.+..
T Consensus 87 plv~c~~c~~~yRADHLiEe~l~~-~~~~~~~~~e~~~ii~~~~ir~p~~g~~l~ 140 (558)
T COG0423 87 PLVECKKCGERYRADHLIEEYLGK-DGHGNMSPEELTEIIREYDIRCPECGGELN 140 (558)
T ss_pred ceeeccccchhhhhhHHHHHHhhh-cccccCCHHHHHHHHHHcCCcCCCcCCccC
Confidence 45789999999842 111122222 235555554 2222 3579999998753
No 217
>PRK07353 F0F1 ATP synthase subunit B'; Validated
Probab=24.86 E-value=4.4e+02 Score=22.45 Aligned_cols=17 Identities=24% Similarity=0.229 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHHHHHHh
Q 017706 181 EEIKLKAQELRERARKK 197 (367)
Q Consensus 181 EEk~~k~~el~~k~r~k 197 (367)
+++..++..-...+...
T Consensus 35 ~~R~~~I~~~l~~Ae~~ 51 (140)
T PRK07353 35 EEREDYIRTNRAEAKER 51 (140)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45555555444444333
No 218
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 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. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=24.71 E-value=22 Score=30.70 Aligned_cols=46 Identities=15% Similarity=0.409 Sum_probs=23.8
Q ss_pred ceeecCCCcccc--------------cchHHHHHHHhhhccCCCCcchhhhhhcccccCC
Q 017706 4 VSLKCGDCGALL--------------RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCG 49 (367)
Q Consensus 4 ~~l~C~~C~~v~--------------~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg 49 (367)
-.++|..||+.. .+...+.+..+..-+..|.=..=.+.-++|.+|-
T Consensus 19 ~~V~C~nCgr~vPKDKAIkrf~i~niVeaaa~rdi~~a~v~~~y~lPKlyvK~~YCvSCA 78 (113)
T PF01283_consen 19 QPVRCDNCGRCVPKDKAIKRFVIRNIVEAAAVRDISEASVYDAYVLPKLYVKLYYCVSCA 78 (113)
T ss_dssp -EEE-TTTB-EEECCCSEEEEEEEESS-CCCHHHHHHCB-SSS--S-EEEEEEEE-CHHH
T ss_pred cCEeeCcccccCcCCceEEEEEccCCccHHHHHHHhhcceeeecccccceeEEEEeeeee
Confidence 368999999877 4445566777754443333212234568999993
No 219
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.58 E-value=42 Score=26.23 Aligned_cols=11 Identities=55% Similarity=1.407 Sum_probs=9.0
Q ss_pred hhcccccCCCC
Q 017706 41 LNLVCATCGKP 51 (367)
Q Consensus 41 ~~~~C~~Cg~~ 51 (367)
..-.||.||++
T Consensus 6 ~~v~CP~Cgkp 16 (65)
T COG3024 6 ITVPCPTCGKP 16 (65)
T ss_pred ccccCCCCCCc
Confidence 34589999997
No 220
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=24.08 E-value=5.2e+02 Score=23.11 Aligned_cols=14 Identities=21% Similarity=0.088 Sum_probs=5.7
Q ss_pred HHHHHHHHHHHHHH
Q 017706 181 EEIKLKAQELRERA 194 (367)
Q Consensus 181 EEk~~k~~el~~k~ 194 (367)
++|...+..-...+
T Consensus 46 ~~R~~~I~~~l~~A 59 (173)
T PRK13460 46 DERASGVQNDINKA 59 (173)
T ss_pred HHHHHHHHHHHHHH
Confidence 34444444333333
No 221
>PF03879 Cgr1: Cgr1 family; InterPro: IPR005579 Cgr1 is involved in nucleolar integrity and is required for processing pre-rRNA for the 60S ribosome subunit. In Saccharomyces cerevisiae, this protein is conserved and contributes to compartmentalisation of nucleolar constituents []. Cgr1 is a small hydrophilic protein and members of this family are coiled-coil proteins []. Its primary role appears to be in ribosome biogenesis [, ]. Expression of CGR1 is also associated with a cessation of yeast cell growth, which is a prerequisite for germination in this organism [].
Probab=24.06 E-value=4.6e+02 Score=22.47 Aligned_cols=12 Identities=25% Similarity=0.224 Sum_probs=6.2
Q ss_pred CCCCCHHHHHHH
Q 017706 175 KSSLTPEEIKLK 186 (367)
Q Consensus 175 k~~lT~EEk~~k 186 (367)
++.+|.=|++.+
T Consensus 27 ~~~~tSwekr~~ 38 (108)
T PF03879_consen 27 KKKRTSWEKRME 38 (108)
T ss_pred ccccCcHHHHHH
Confidence 345666555443
No 222
>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=24.05 E-value=39 Score=23.29 Aligned_cols=12 Identities=17% Similarity=0.706 Sum_probs=9.3
Q ss_pred hhhcccccCCCC
Q 017706 40 VLNLVCATCGKP 51 (367)
Q Consensus 40 v~~~~C~~Cg~~ 51 (367)
.++..||.|++.
T Consensus 3 ~i~v~CP~C~s~ 14 (36)
T PF03811_consen 3 KIDVHCPRCQST 14 (36)
T ss_pred cEeeeCCCCCCC
Confidence 356899999973
No 223
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.00 E-value=34 Score=33.31 Aligned_cols=16 Identities=31% Similarity=0.852 Sum_probs=12.6
Q ss_pred CCCceeecCCCccccc
Q 017706 1 MAGVSLKCGDCGALLR 16 (367)
Q Consensus 1 ~~~~~l~C~~C~~v~~ 16 (367)
|.-|+|+|+.||...+
T Consensus 36 m~Pf~~rC~tCgeyi~ 51 (253)
T KOG2989|consen 36 MTPFRLRCNTCGEYIY 51 (253)
T ss_pred cccceeecccccchhh
Confidence 4568999999987664
No 224
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=23.76 E-value=37 Score=30.07 Aligned_cols=13 Identities=38% Similarity=0.986 Sum_probs=11.3
Q ss_pred hhhhcccccCCCC
Q 017706 39 AVLNLVCATCGKP 51 (367)
Q Consensus 39 ~v~~~~C~~Cg~~ 51 (367)
.++++.||.||.|
T Consensus 25 kML~~hCp~Cg~P 37 (131)
T COG1645 25 KMLAKHCPKCGTP 37 (131)
T ss_pred HHHHhhCcccCCc
Confidence 4788999999986
No 225
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=23.54 E-value=55 Score=25.31 Aligned_cols=10 Identities=30% Similarity=0.813 Sum_probs=8.0
Q ss_pred eecCCCcccc
Q 017706 6 LKCGDCGALL 15 (367)
Q Consensus 6 l~C~~C~~v~ 15 (367)
-.|..||+++
T Consensus 10 ~~CtSCg~~i 19 (61)
T COG2888 10 PVCTSCGREI 19 (61)
T ss_pred ceeccCCCEe
Confidence 4688888887
No 226
>PF03801 Ndc80_HEC: HEC/Ndc80p family; InterPro: IPR005550 Members of this family are components of the mitotic spindle. It has been shown that Ndc80 from yeast is part of a complex called the Ndc80p complex []. This complex is thought to bind to the microtubules of the spindle.; PDB: 3IZ0_E 2VE7_B 2IGP_A.
Probab=23.43 E-value=89 Score=28.07 Aligned_cols=41 Identities=27% Similarity=0.591 Sum_probs=30.3
Q ss_pred ccCHHHHHHHHhCCCCH-HHHHHHHHHhCCC----CHHHHHHHHHH
Q 017706 112 EVDKELLKELEAMGFPV-ARATRALHYSGNA----NVEAAVNWVVE 152 (367)
Q Consensus 112 ~~d~~~l~~L~~MGF~~-~~a~kAL~~tgn~----~~E~A~~Wl~~ 152 (367)
-+.++++..|..+|||- ...+-+|..-|.. .+=.|+.||.+
T Consensus 92 k~eeev~~~lK~L~YP~~~isKS~L~a~gs~hsWP~lL~~L~WLv~ 137 (157)
T PF03801_consen 92 KFEEEVPFLLKALGYPFATISKSSLQAPGSPHSWPHLLGALHWLVE 137 (157)
T ss_dssp THHHHHHHHHHHTT-SS----HHHHHSTTSTTTHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHhCCCccccCHHHccCCCCcccHHHHHHHHHHHHH
Confidence 45678899999999999 9999999888864 36789999864
No 227
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=23.36 E-value=71 Score=32.80 Aligned_cols=19 Identities=16% Similarity=0.490 Sum_probs=16.6
Q ss_pred HHHHHHHHhCCCCHHHHHH
Q 017706 115 KELLKELEAMGFPVARATR 133 (367)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~k 133 (367)
.++++.+..|||+++.++-
T Consensus 322 ddvidKv~~MGf~rDqV~a 340 (358)
T PF07223_consen 322 DDVIDKVASMGFRRDQVRA 340 (358)
T ss_pred HHHHHHHHHcCCcHHHHHH
Confidence 4789999999999999863
No 228
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=23.22 E-value=57 Score=36.59 Aligned_cols=39 Identities=31% Similarity=0.663 Sum_probs=27.9
Q ss_pred eeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCCC
Q 017706 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~~ 52 (367)
..+|..||+.|.-----.+|.. .|+. | .-|-|+.|+|.|
T Consensus 281 KFKCtECgKAFKfKHHLKEHlR--IHSG--E-----KPfeCpnCkKRF 319 (1007)
T KOG3623|consen 281 KFKCTECGKAFKFKHHLKEHLR--IHSG--E-----KPFECPNCKKRF 319 (1007)
T ss_pred cccccccchhhhhHHHHHhhhe--eecC--C-----CCcCCccccccc
Confidence 4689999999976555555554 6652 2 238999999987
No 229
>PRK02292 V-type ATP synthase subunit E; Provisional
Probab=23.01 E-value=5.6e+02 Score=23.05 Aligned_cols=19 Identities=32% Similarity=0.553 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHhhH
Q 017706 181 EEIKLKAQELRERARKKKE 199 (367)
Q Consensus 181 EEk~~k~~el~~k~r~kr~ 199 (367)
++.++.+++++..++++.+
T Consensus 12 ~~a~~e~~~I~~ea~~~~~ 30 (188)
T PRK02292 12 DEARARASEIRAEADEEAE 30 (188)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4556667777776665544
No 230
>KOG0681 consensus Actin-related protein - Arp5p [Cytoskeleton]
Probab=22.90 E-value=1.1e+03 Score=26.19 Aligned_cols=42 Identities=21% Similarity=0.211 Sum_probs=28.0
Q ss_pred HHHHHHHHhCC-------CCHHHHHHHHHHhCCC---CHHHHHHHHHHhcCCCC
Q 017706 115 KELLKELEAMG-------FPVARATRALHYSGNA---NVEAAVNWVVEHENDPD 158 (367)
Q Consensus 115 ~~~l~~L~~MG-------F~~~~a~kAL~~tgn~---~~E~A~~Wl~~h~dd~d 158 (367)
-+.|..||.|- |+..++.++++-.--. =.+.-..|+. ++..|
T Consensus 206 ~dYL~~Lmq~Kyp~~~~~~t~sk~E~l~~eHcyis~DY~eei~~~l~--~d~~d 257 (645)
T KOG0681|consen 206 GDYLSRLMQLKYPFHLNAFTGSKAERLLHEHCYISPDYREEIIKILE--MDYYD 257 (645)
T ss_pred HHHHHHHHhccCccchhhcCHHHHHHHhhhhceeCcchHHHHHHHhh--hhhhh
Confidence 36799999994 7778898887654322 3455667776 44443
No 231
>PF09831 DUF2058: Uncharacterized protein conserved in bacteria (DUF2058); InterPro: IPR018636 This family, found in various prokaryotic proteins, has no known function.
Probab=22.63 E-value=6.1e+02 Score=23.53 Aligned_cols=41 Identities=27% Similarity=0.450 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHHHH
Q 017706 224 KRIEEENERKRILALRKAEKEEEKRAREKIRQKLEEDKAER 264 (367)
Q Consensus 224 k~~~ee~e~k~~~e~rrrEK~ee~~ar~rir~qIe~Dk~eR 264 (367)
+...+..++-+++.+.|.+..+.+..+..|++-|+.-+..+
T Consensus 48 ~a~~ek~erdr~Ln~qr~~~~~~K~~~AqikQlI~~~~i~~ 88 (177)
T PF09831_consen 48 RARAEKAERDRELNRQRQAEAERKEIQAQIKQLIEQNRIPR 88 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 34445556777788888888888888889999998777554
No 232
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=22.58 E-value=8e+02 Score=24.68 Aligned_cols=8 Identities=13% Similarity=0.181 Sum_probs=3.1
Q ss_pred HHHHHHHH
Q 017706 207 REREKERI 214 (367)
Q Consensus 207 ~e~E~~Rr 214 (367)
++|++-|.
T Consensus 262 ~rN~~LK~ 269 (294)
T KOG4571|consen 262 KRNEELKD 269 (294)
T ss_pred HHHHHHHH
Confidence 33444333
No 233
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=22.56 E-value=52 Score=25.54 Aligned_cols=9 Identities=67% Similarity=1.582 Sum_probs=8.0
Q ss_pred cccccCCCC
Q 017706 43 LVCATCGKP 51 (367)
Q Consensus 43 ~~C~~Cg~~ 51 (367)
..||.||++
T Consensus 7 v~CP~C~k~ 15 (62)
T PRK00418 7 VNCPTCGKP 15 (62)
T ss_pred ccCCCCCCc
Confidence 689999996
No 234
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=22.38 E-value=24 Score=35.52 Aligned_cols=45 Identities=27% Similarity=0.547 Sum_probs=29.3
Q ss_pred CceeecCCCcccccchHHHHHHHhhhccCCCCcchhhh---hhcccccCCCC
Q 017706 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAV---LNLVCATCGKP 51 (367)
Q Consensus 3 ~~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v---~~~~C~~Cg~~ 51 (367)
.+.|+|.-||++++.--.. .--||..-.|+.++. .+|.||.|..+
T Consensus 272 ~i~LkCplc~~Llrnp~kT----~cC~~~fc~eci~~al~dsDf~CpnC~rk 319 (427)
T COG5222 272 NISLKCPLCHCLLRNPMKT----PCCGHTFCDECIGTALLDSDFKCPNCSRK 319 (427)
T ss_pred CccccCcchhhhhhCcccC----ccccchHHHHHHhhhhhhccccCCCcccc
Confidence 4679999999998543221 113676666663321 36999999864
No 235
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=22.37 E-value=60 Score=29.73 Aligned_cols=46 Identities=20% Similarity=0.393 Sum_probs=30.8
Q ss_pred eecCCCcccccchHHHHHHHhhhccCCCCcc-hhhhh--hcccccCCCC
Q 017706 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSES-TEAVL--NLVCATCGKP 51 (367)
Q Consensus 6 l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~-~e~v~--~~~C~~Cg~~ 51 (367)
..|..||..+........-++.-+|..|.+. .+... -+.||.|..+
T Consensus 115 ~~C~~Cg~~f~~~k~i~~~~~~l~~~~~~~~~~~~~~~~~~~Cp~Cr~k 163 (181)
T PRK08222 115 QRCSRCERPFAPQKTVALAAELLAQQQNAPQNREMLRAQASVCPECKQR 163 (181)
T ss_pred CcCcccCCccCcHhHHHHHHHHhhhccCcHhhHHHHHHHhccCHHHHhh
Confidence 4699999999877776666665577777653 23222 2579999754
No 236
>PRK09174 F0F1 ATP synthase subunit B'; Validated
Probab=22.36 E-value=6.5e+02 Score=23.55 Aligned_cols=18 Identities=17% Similarity=0.128 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHHHhh
Q 017706 181 EEIKLKAQELRERARKKK 198 (367)
Q Consensus 181 EEk~~k~~el~~k~r~kr 198 (367)
++|..++..-...+...+
T Consensus 83 e~R~~~I~~~L~~Ae~~k 100 (204)
T PRK09174 83 ETRRDRIAQDLDQAARLK 100 (204)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 456666555555544443
No 237
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=22.29 E-value=58 Score=24.77 Aligned_cols=36 Identities=22% Similarity=0.460 Sum_probs=24.6
Q ss_pred ceeecCCCcccc---cchHHHHHHHhhhccCCCCcchhhhhhcccccCCC
Q 017706 4 VSLKCGDCGALL---RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (367)
Q Consensus 4 ~~l~C~~C~~v~---~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~ 50 (367)
++++|.-|+++. .+.-.|..+-.--.| -|-|+.|..
T Consensus 1 m~vkC~lCdk~~~Id~~~~~aKrLrnrPi~-----------tYmC~eC~~ 39 (56)
T PF09963_consen 1 MRVKCILCDKKEEIDEDTPEAKRLRNRPIH-----------TYMCDECKE 39 (56)
T ss_pred CeeEEEecCCEEEeccCCHHHHHhhcCCCc-----------ceeChhHHH
Confidence 578999999987 556667766653333 367777753
No 238
>PRK14472 F0F1 ATP synthase subunit B; Provisional
Probab=22.08 E-value=5.8e+02 Score=22.85 Aligned_cols=14 Identities=36% Similarity=0.245 Sum_probs=6.3
Q ss_pred HHHHHHHHHHHHHH
Q 017706 181 EEIKLKAQELRERA 194 (367)
Q Consensus 181 EEk~~k~~el~~k~ 194 (367)
++|...+..-...+
T Consensus 48 ~~R~~~I~~~l~~A 61 (175)
T PRK14472 48 EEREKGIQSSIDRA 61 (175)
T ss_pred HHHHHHHHHHHHHH
Confidence 44555444444443
No 239
>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=22.04 E-value=8.2 Score=26.61 Aligned_cols=14 Identities=50% Similarity=1.001 Sum_probs=11.0
Q ss_pred hhhhhcccccCCCC
Q 017706 38 EAVLNLVCATCGKP 51 (367)
Q Consensus 38 e~v~~~~C~~Cg~~ 51 (367)
+++.-++|+.||..
T Consensus 28 ~~vp~~~C~~CGE~ 41 (46)
T TIGR03831 28 ENVPALVCPQCGEE 41 (46)
T ss_pred eCCCccccccCCCE
Confidence 45677899999974
No 240
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=21.99 E-value=1.7e+02 Score=23.63 Aligned_cols=38 Identities=21% Similarity=0.305 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCC
Q 017706 115 KELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHEND 156 (367)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h~dd 156 (367)
..++..|..+|||...|.+.....|. .|++-|.+++=-
T Consensus 9 ~~~~~~L~~~gl~~~~a~kl~~~yg~----~ai~~l~~nPY~ 46 (94)
T PF14490_consen 9 RELMAFLQEYGLSPKLAMKLYKKYGD----DAIEILKENPYR 46 (94)
T ss_dssp HHHHHHHHHTT--HHHHHHHHHHH-T----THHHHHHH-STC
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHhH----HHHHHHHHChHH
Confidence 46789999999999999999988886 466667665433
No 241
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=21.79 E-value=1.7e+02 Score=29.78 Aligned_cols=40 Identities=28% Similarity=0.483 Sum_probs=35.1
Q ss_pred cCHHHHHHHH-hCCCCHHHHHHHHHHhCCCCHHHHHHHHHHh
Q 017706 113 VDKELLKELE-AMGFPVARATRALHYSGNANVEAAVNWVVEH 153 (367)
Q Consensus 113 ~d~~~l~~L~-~MGF~~~~a~kAL~~tgn~~~E~A~~Wl~~h 153 (367)
....+|.+|- .-|++..-|++||-..|| |+..|..||-.-
T Consensus 45 ~~~allk~LR~kTgas~~ncKkALee~~g-Dl~~A~~~L~k~ 85 (340)
T KOG1071|consen 45 SSKALLKKLREKTGASMVNCKKALEECGG-DLVLAEEWLHKK 85 (340)
T ss_pred ccHHHHHHHHHHcCCcHHHHHHHHHHhCC-cHHHHHHHHHHH
Confidence 4578888887 689999999999999997 999999999754
No 242
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=21.60 E-value=4.4 Score=31.66 Aligned_cols=45 Identities=18% Similarity=0.153 Sum_probs=32.9
Q ss_pred ccchHHHHHHHHhhhhhcCCChHHHHHHHHHHHHHHhhhccCCChhhhh
Q 017706 297 ATKVEQMRECLRSLKQNHKDDDAKVKRAFQTLLTYIGNVAKNPNEEKFR 345 (367)
Q Consensus 297 ~~~~~QlR~~l~sLk~~~~~~~a~~~~a~~tL~kyl~Ni~~~P~eeK~r 345 (367)
..+.++||+|+|+.....|..++.+. .|..||......+....|.
T Consensus 5 ~~~~I~vRlpdG~~l~~~F~~~~tl~----~l~~~v~~~~~~~~~~~f~ 49 (82)
T PF00789_consen 5 DVVRIQVRLPDGSRLQRRFPKSDTLQ----DLYDFVESQLFSPEESDFE 49 (82)
T ss_dssp SEEEEEEEETTSTEEEEEEETTSBHH----HHHHHHHHHHHCTTTSSEE
T ss_pred CEEEEEEECCCCCEEEEEECCcchHH----HHHHHHHHhcCCCCCccEE
Confidence 34678999999998888888876776 5566666666666655564
No 243
>PF07553 Lipoprotein_Ltp: Host cell surface-exposed lipoprotein; InterPro: IPR011434 This domain is found as 1-3 copies in a small family of proteins of unknown function.
Probab=21.55 E-value=1.2e+02 Score=22.18 Aligned_cols=22 Identities=27% Similarity=0.415 Sum_probs=17.7
Q ss_pred HHHHHHHHhC---CCCHHHHHHHHH
Q 017706 115 KELLKELEAM---GFPVARATRALH 136 (367)
Q Consensus 115 ~~~l~~L~~M---GF~~~~a~kAL~ 136 (367)
..+.+||.+- ||+.+.|..|+.
T Consensus 22 ~~l~~QL~se~ge~Ft~e~A~YAv~ 46 (48)
T PF07553_consen 22 QGLYDQLTSEYGEGFTEEEAQYAVD 46 (48)
T ss_pred HHHHHHHHhhcccCCCHHHHHHHHH
Confidence 4677888876 899999988874
No 244
>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=21.00 E-value=27 Score=21.85 Aligned_cols=9 Identities=44% Similarity=1.106 Sum_probs=7.8
Q ss_pred cccccCCCC
Q 017706 43 LVCATCGKP 51 (367)
Q Consensus 43 ~~C~~Cg~~ 51 (367)
|.|+.|++.
T Consensus 15 ~~C~~C~k~ 23 (26)
T PF13465_consen 15 YKCPYCGKS 23 (26)
T ss_dssp EEESSSSEE
T ss_pred CCCCCCcCe
Confidence 899999975
No 245
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=20.95 E-value=45 Score=31.97 Aligned_cols=32 Identities=19% Similarity=0.634 Sum_probs=22.5
Q ss_pred eeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCCC
Q 017706 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (367)
Q Consensus 5 ~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~~ 51 (367)
.|-|..|.|- .|-+.++|.. +++|+|+.|.-.
T Consensus 192 alIC~~C~hh-------------ngl~~~~ek~--~~efiC~~Cn~~ 223 (251)
T COG5415 192 ALICPQCHHH-------------NGLYRLAEKP--IIEFICPHCNHK 223 (251)
T ss_pred hhcccccccc-------------cccccccccc--chheecccchhh
Confidence 4678888653 4666777762 447999999754
No 246
>PRK08475 F0F1 ATP synthase subunit B; Validated
Probab=20.92 E-value=6.1e+02 Score=22.72 Aligned_cols=16 Identities=0% Similarity=0.187 Sum_probs=7.1
Q ss_pred HHHHHHHHHhHHHHHH
Q 017706 247 KRAREKIRQKLEEDKA 262 (367)
Q Consensus 247 ~~ar~rir~qIe~Dk~ 262 (367)
..+...+++||-.+--
T Consensus 132 ~~a~~elk~eii~~~~ 147 (167)
T PRK08475 132 RKMEREVVEEVLNELF 147 (167)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3344444555544433
No 247
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=20.59 E-value=78 Score=25.55 Aligned_cols=27 Identities=30% Similarity=0.572 Sum_probs=19.4
Q ss_pred hhhhhcccccCCCCCCCcccccccccccccc
Q 017706 38 EAVLNLVCATCGKPCRSKTETDLHRKRTGHT 68 (367)
Q Consensus 38 e~v~~~~C~~Cg~~~~~~~e~~~a~K~t~f~ 68 (367)
..+.|+.|..||+. -..+.|+|..+..
T Consensus 46 ~q~~El~C~~C~~~----k~ld~FSK~QR~~ 72 (84)
T PF12898_consen 46 GQVVELTCSPCGKT----KPLDEFSKNQRRK 72 (84)
T ss_pred CCcCcCEeccCCCC----cCHHHHhHHhhcC
Confidence 56788999999963 2246777777754
No 248
>KOG1265 consensus Phospholipase C [Lipid transport and metabolism]
Probab=20.46 E-value=5.9e+02 Score=29.70 Aligned_cols=9 Identities=22% Similarity=0.578 Sum_probs=5.7
Q ss_pred HHHHhHHHH
Q 017706 252 KIRQKLEED 260 (367)
Q Consensus 252 rir~qIe~D 260 (367)
-|++||+.+
T Consensus 1157 ~~leql~e~ 1165 (1189)
T KOG1265|consen 1157 EVLEQLAEE 1165 (1189)
T ss_pred HHHHHHHHh
Confidence 466677655
No 249
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.38 E-value=8.5e+02 Score=24.15 Aligned_cols=69 Identities=33% Similarity=0.346 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHH-----HHHHHHHhH-HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 017706 183 IKLKAQELRERARKKKEEEEKRMERER-----EKERIRIGK-ELLEAKRIEEENERKRILALRKAEKEEEKRARE 251 (367)
Q Consensus 183 k~~k~~el~~k~r~kr~eeek~~~~e~-----E~~Rr~~gK-e~~~~k~~~ee~e~k~~~e~rrrEK~ee~~ar~ 251 (367)
|.+|++..+++......++-.++++.+ |.+|.+.-- .-.++.++.++.+++.--++-+++-+|-.+-+.
T Consensus 107 K~aKleakqerr~qRe~E~~eREeRk~ke~~eE~erKkdEeR~~eEae~k~ee~~RkakEE~arkeheEylkmKa 181 (299)
T KOG3054|consen 107 KEAKLEAKQERRAQREAEEAEREERKRKEDYEEAERKKDEERLAEEAELKEEEKERKAKEEEARKEHEEYLKMKA 181 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHh
No 250
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.36 E-value=25 Score=28.50 Aligned_cols=16 Identities=31% Similarity=0.754 Sum_probs=11.6
Q ss_pred CCCceeecCCCccccc
Q 017706 1 MAGVSLKCGDCGALLR 16 (367)
Q Consensus 1 ~~~~~l~C~~C~~v~~ 16 (367)
|.-++-.|..||..+.
T Consensus 8 MPtY~Y~c~~cg~~~d 23 (82)
T COG2331 8 MPTYSYECTECGNRFD 23 (82)
T ss_pred ccceEEeecccchHHH
Confidence 3456788999997663
No 251
>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=20.29 E-value=42 Score=28.62 Aligned_cols=10 Identities=30% Similarity=0.913 Sum_probs=8.5
Q ss_pred cccccCCCCC
Q 017706 43 LVCATCGKPC 52 (367)
Q Consensus 43 ~~C~~Cg~~~ 52 (367)
..||+||++|
T Consensus 10 R~Cp~CG~kF 19 (108)
T PF09538_consen 10 RTCPSCGAKF 19 (108)
T ss_pred ccCCCCcchh
Confidence 5799999987
No 252
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=20.28 E-value=63 Score=31.44 Aligned_cols=34 Identities=21% Similarity=0.496 Sum_probs=21.6
Q ss_pred ceeecCCCcccccchHHHHHHHhhhccCCCCcchhhhhhcccccCCC
Q 017706 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (367)
Q Consensus 4 ~~l~C~~C~~v~~g~~~aq~h~~~tgh~~F~e~~e~v~~~~C~~Cg~ 50 (367)
++.+|..||+...+..-...+.. | .--.||.||.
T Consensus 121 ~~~~C~~C~~~~~~~~~~~~~~~--~-----------~~p~C~~Cg~ 154 (250)
T COG0846 121 KRVRCSKCGNQYYDEDVIKFIED--G-----------LIPRCPKCGG 154 (250)
T ss_pred eeeEeCCCcCccchhhhhhhccc--C-----------CCCcCccCCC
Confidence 46899999998876652111111 1 1148999997
No 253
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=20.23 E-value=38 Score=24.08 Aligned_cols=10 Identities=50% Similarity=1.338 Sum_probs=7.1
Q ss_pred eeecCCCccc
Q 017706 5 SLKCGDCGAL 14 (367)
Q Consensus 5 ~l~C~~C~~v 14 (367)
+++|..||.+
T Consensus 1 k~kC~~CG~~ 10 (40)
T PF15288_consen 1 KVKCKNCGAF 10 (40)
T ss_pred Cccccccccc
Confidence 4678888864
No 254
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=20.09 E-value=56 Score=32.21 Aligned_cols=11 Identities=36% Similarity=0.960 Sum_probs=8.4
Q ss_pred hhcccccCCCC
Q 017706 41 LNLVCATCGKP 51 (367)
Q Consensus 41 ~~~~C~~Cg~~ 51 (367)
.+..||+||+.
T Consensus 95 ~e~~Cp~C~St 105 (314)
T PF09567_consen 95 LEESCPNCGST 105 (314)
T ss_pred hhhcCCCCCcc
Confidence 45689999974
No 255
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=20.07 E-value=1.3e+03 Score=26.13 Aligned_cols=19 Identities=16% Similarity=0.328 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHhhhccC
Q 017706 320 KVKRAFQTLLTYIGNVAKN 338 (367)
Q Consensus 320 ~~~~a~~tL~kyl~Ni~~~ 338 (367)
.+.+|...|-.||+..+.+
T Consensus 713 ~~eeA~~~l~~fl~~a~~~ 731 (782)
T PRK00409 713 RYEEALERLDKYLDDALLA 731 (782)
T ss_pred CHHHHHHHHHHHHHHHHHc
Confidence 3678888888888776543
No 256
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=20.04 E-value=53 Score=28.96 Aligned_cols=45 Identities=22% Similarity=0.499 Sum_probs=26.3
Q ss_pred eeecCCCccccc----chHHHHHHHhhhccCCCCcc-hhhhhhcccccCCCC
Q 017706 5 SLKCGDCGALLR----SVQEAQEHAELTSHSNFSES-TEAVLNLVCATCGKP 51 (367)
Q Consensus 5 ~l~C~~C~~v~~----g~~~aq~h~~~tgh~~F~e~-~e~v~~~~C~~Cg~~ 51 (367)
-|.|..||.+.. +....+.... .+..|.=. ....+--.|+.|+..
T Consensus 93 HliC~~CG~v~e~~~~~i~~~~~~~~--~~~Gf~i~~~~l~~~G~C~~C~~~ 142 (145)
T COG0735 93 HLICLDCGKVIEFEDDEIEALQEEIA--KKLGFKLKDHTLEIYGICPDCQAK 142 (145)
T ss_pred EEEecCCCCEEEecchhHHHHHHHHH--HhcCCeeeeeEEEEEEECcchHhh
Confidence 478999999982 2334455554 44455433 122233459999864
No 257
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=20.04 E-value=6.4e+02 Score=22.61 Aligned_cols=17 Identities=6% Similarity=0.026 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHHh
Q 017706 181 EEIKLKAQELRERARKK 197 (367)
Q Consensus 181 EEk~~k~~el~~k~r~k 197 (367)
++|...+..-.+.+...
T Consensus 48 ~~R~~~I~~~l~~Ae~~ 64 (173)
T PRK13453 48 DKRERDINRDIDDAEQA 64 (173)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45555554444444433
Done!