Query 022703
Match_columns 293
No_of_seqs 284 out of 469
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 05:32:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022703.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022703hhsearch_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 2.3E-32 5E-37 275.2 6.5 156 4-169 439-626 (763)
2 COG5207 UBP14 Isopeptidase T [ 100.0 5.1E-29 1.1E-33 245.5 8.3 155 3-168 429-612 (749)
3 KOG2689 Predicted ubiquitin re 99.9 6.5E-26 1.4E-30 209.5 18.1 152 118-270 4-179 (290)
4 KOG2507 Ubiquitin regulatory p 99.3 6E-12 1.3E-16 123.0 6.3 105 175-281 190-297 (506)
5 PF00627 UBA: UBA/TS-N domain; 99.0 3.8E-10 8.2E-15 75.4 4.2 37 113-150 1-37 (37)
6 smart00165 UBA Ubiquitin assoc 98.8 5.5E-09 1.2E-13 69.2 4.9 37 114-151 1-37 (37)
7 cd00194 UBA Ubiquitin Associat 98.8 6.6E-09 1.4E-13 69.1 5.3 38 114-152 1-38 (38)
8 KOG0944 Ubiquitin-specific pro 98.6 5.2E-08 1.1E-12 100.1 5.1 49 112-161 633-681 (763)
9 KOG2699 Predicted ubiquitin re 98.5 7.6E-08 1.7E-12 94.5 4.4 237 21-274 5-253 (407)
10 cd02664 Peptidase_C19H A subfa 98.4 7.7E-08 1.7E-12 91.3 0.9 89 5-100 110-212 (327)
11 cd02660 Peptidase_C19D A subfa 98.3 2.7E-07 5.8E-12 86.4 1.0 65 28-100 181-252 (328)
12 cd02667 Peptidase_C19K A subfa 98.2 2.3E-07 4.9E-12 86.0 0.0 86 5-100 80-185 (279)
13 cd02668 Peptidase_C19L A subfa 98.2 2.8E-07 6E-12 87.1 0.3 89 4-100 128-234 (324)
14 cd02663 Peptidase_C19G A subfa 98.1 1.7E-06 3.7E-11 80.8 3.5 89 5-100 120-225 (300)
15 cd02658 Peptidase_C19B A subfa 98.1 7.3E-07 1.6E-11 83.1 0.2 51 29-89 184-237 (311)
16 cd02671 Peptidase_C19O A subfa 98.0 1.2E-06 2.6E-11 84.1 0.3 65 29-100 186-262 (332)
17 cd02657 Peptidase_C19A A subfa 98.0 1.8E-06 3.8E-11 80.2 1.4 85 4-100 128-233 (305)
18 cd02661 Peptidase_C19E A subfa 98.0 2.1E-06 4.5E-11 78.7 1.0 89 5-100 135-236 (304)
19 cd02659 peptidase_C19C A subfa 97.9 1.8E-06 3.9E-11 81.0 0.0 89 5-100 124-229 (334)
20 cd02674 Peptidase_C19R A subfa 97.9 3.9E-06 8.5E-11 74.3 0.8 88 4-99 50-160 (230)
21 cd02673 Peptidase_C19Q A subfa 97.8 6.8E-06 1.5E-10 75.9 1.2 70 5-85 81-161 (245)
22 KOG1865 Ubiquitin carboxyl-ter 97.6 4.3E-05 9.3E-10 77.6 3.5 87 5-100 239-340 (545)
23 COG5533 UBP5 Ubiquitin C-termi 97.5 3.1E-05 6.7E-10 74.4 1.5 79 4-89 234-326 (415)
24 cd02662 Peptidase_C19F A subfa 97.2 8.6E-05 1.9E-09 67.6 -0.1 75 5-96 63-158 (240)
25 TIGR00601 rad23 UV excision re 97.1 0.00059 1.3E-08 67.2 5.1 40 114-154 156-195 (378)
26 KOG4598 Putative ubiquitin-spe 97.1 0.0001 2.2E-09 76.9 -0.5 88 6-100 182-292 (1203)
27 COG5207 UBP14 Isopeptidase T [ 96.7 0.00073 1.6E-08 68.7 1.7 52 111-164 618-669 (749)
28 KOG1866 Ubiquitin carboxyl-ter 96.4 0.0003 6.4E-09 73.8 -3.3 56 38-100 262-324 (944)
29 KOG2561 Adaptor protein NUB1, 96.3 0.011 2.3E-07 59.6 6.8 48 110-158 425-472 (568)
30 cd02672 Peptidase_C19P A subfa 96.2 0.0016 3.4E-08 61.0 0.7 39 39-84 131-173 (268)
31 cd02257 Peptidase_C19 Peptidas 96.0 0.0032 7E-08 54.0 1.6 54 39-99 113-174 (255)
32 TIGR00601 rad23 UV excision re 95.8 0.014 2.9E-07 57.8 5.3 43 113-156 336-378 (378)
33 cd02669 Peptidase_C19M A subfa 95.6 0.0037 8E-08 62.3 0.6 54 40-100 309-368 (440)
34 COG5560 UBP12 Ubiquitin C-term 95.4 0.0037 8.1E-08 65.0 -0.2 68 26-100 672-752 (823)
35 KOG1868 Ubiquitin C-terminal h 95.3 0.0029 6.4E-08 66.3 -1.3 75 4-85 463-555 (653)
36 KOG0011 Nucleotide excision re 95.2 0.03 6.4E-07 54.3 4.9 40 114-154 298-337 (340)
37 KOG0011 Nucleotide excision re 94.6 0.041 8.9E-07 53.4 4.4 41 113-154 134-174 (340)
38 KOG2561 Adaptor protein NUB1, 94.1 0.17 3.8E-06 51.1 7.6 39 113-152 302-340 (568)
39 PF09288 UBA_3: Fungal ubiquit 93.8 0.063 1.4E-06 39.4 2.9 29 112-140 7-35 (55)
40 COG1773 Rubredoxin [Energy pro 93.7 0.013 2.9E-07 42.9 -0.8 42 5-50 3-44 (55)
41 PF00443 UCH: Ubiquitin carbox 93.6 0.016 3.5E-07 50.8 -0.6 47 42-100 142-196 (269)
42 PF14555 UBA_4: UBA-like domai 92.7 0.34 7.3E-06 33.1 5.0 40 117-157 3-43 (43)
43 smart00546 CUE Domain that may 92.6 0.26 5.7E-06 33.5 4.4 37 114-152 2-41 (43)
44 cd00350 rubredoxin_like Rubred 92.3 0.069 1.5E-06 34.8 1.2 25 6-51 2-26 (33)
45 KOG1863 Ubiquitin carboxyl-ter 92.2 0.068 1.5E-06 59.3 1.6 88 4-100 290-395 (1093)
46 PTZ00266 NIMA-related protein 91.9 2.5 5.3E-05 47.1 13.1 17 249-266 508-524 (1021)
47 cd02670 Peptidase_C19N A subfa 91.5 0.068 1.5E-06 49.7 0.6 41 60-100 88-133 (241)
48 PF08882 Acetone_carb_G: Aceto 90.8 0.11 2.3E-06 43.3 1.0 46 4-51 23-83 (112)
49 cd00730 rubredoxin Rubredoxin; 90.7 0.05 1.1E-06 39.0 -0.9 43 5-51 1-43 (50)
50 PF02845 CUE: CUE domain; Int 90.3 0.9 2E-05 30.7 5.2 38 115-153 2-41 (42)
51 KOG1864 Ubiquitin-specific pro 90.2 0.081 1.8E-06 55.1 -0.2 137 4-155 391-546 (587)
52 cd02665 Peptidase_C19I A subfa 90.0 0.095 2.1E-06 48.3 0.1 37 60-96 118-159 (228)
53 PHA02768 hypothetical protein; 89.6 0.37 7.9E-06 35.4 2.9 39 2-51 2-40 (55)
54 KOG0163 Myosin class VI heavy 89.5 5.4 0.00012 43.2 12.4 82 182-266 924-1012(1259)
55 PF00301 Rubredoxin: Rubredoxi 89.3 0.062 1.3E-06 38.1 -1.3 43 5-51 1-43 (47)
56 PF13423 UCH_1: Ubiquitin carb 89.0 0.1 2.2E-06 48.8 -0.5 53 41-100 179-236 (295)
57 KOG1029 Endocytic adaptor prot 88.8 7.4 0.00016 42.2 12.8 31 126-156 212-242 (1118)
58 KOG1870 Ubiquitin C-terminal h 88.1 0.097 2.1E-06 56.6 -1.4 57 37-100 711-773 (842)
59 KOG0418 Ubiquitin-protein liga 87.8 0.57 1.2E-05 42.4 3.5 39 113-152 161-199 (200)
60 PRK03824 hypA hydrogenase nick 87.7 0.24 5.1E-06 42.2 1.0 46 4-51 69-116 (135)
61 PF07499 RuvA_C: RuvA, C-termi 87.2 1.6 3.4E-05 30.4 4.8 32 114-145 3-37 (47)
62 PF12756 zf-C2H2_2: C2H2 type 85.8 0.18 3.9E-06 38.6 -0.7 65 7-72 1-80 (100)
63 COG5077 Ubiquitin carboxyl-ter 84.8 0.36 7.7E-06 51.8 0.7 51 42-100 358-415 (1089)
64 KOG1029 Endocytic adaptor prot 84.6 12 0.00026 40.8 11.6 19 114-132 214-232 (1118)
65 cd00729 rubredoxin_SM Rubredox 84.2 0.61 1.3E-05 30.7 1.4 26 5-51 2-27 (34)
66 smart00531 TFIIE Transcription 84.1 0.74 1.6E-05 39.4 2.3 37 2-51 96-132 (147)
67 KOG1144 Translation initiation 84.1 11 0.00023 41.1 11.1 13 187-199 216-228 (1064)
68 KOG0163 Myosin class VI heavy 83.8 16 0.00036 39.8 12.3 55 208-263 941-995 (1259)
69 PHA00732 hypothetical protein 83.7 1.3 2.7E-05 34.6 3.2 36 6-52 2-37 (79)
70 PF14353 CpXC: CpXC protein 82.6 0.75 1.6E-05 38.1 1.7 39 6-51 2-47 (128)
71 PRK12332 tsf elongation factor 82.4 2.5 5.5E-05 38.3 5.1 41 113-154 3-44 (198)
72 KOG4364 Chromatin assembly fac 81.3 70 0.0015 34.5 15.5 30 223-252 301-330 (811)
73 PF02148 zf-UBP: Zn-finger in 81.3 0.75 1.6E-05 33.8 1.1 44 5-50 11-57 (63)
74 PRK12380 hydrogenase nickel in 81.2 0.84 1.8E-05 37.7 1.4 27 4-51 69-95 (113)
75 PRK09377 tsf elongation factor 80.5 3 6.5E-05 40.1 5.1 41 113-154 4-45 (290)
76 TIGR00116 tsf translation elon 80.5 3 6.5E-05 40.0 5.1 41 113-154 3-44 (290)
77 PRK00398 rpoP DNA-directed RNA 79.9 1.2 2.7E-05 30.7 1.7 29 4-51 2-30 (46)
78 PF09723 Zn-ribbon_8: Zinc rib 79.0 1.6 3.5E-05 29.8 2.1 34 1-50 1-34 (42)
79 PRK03681 hypA hydrogenase nick 78.8 1.2 2.5E-05 36.9 1.5 10 4-13 69-78 (114)
80 KOG0010 Ubiquitin-like protein 78.7 2.9 6.2E-05 42.8 4.6 37 115-152 455-492 (493)
81 TIGR00100 hypA hydrogenase nic 78.5 1.1 2.3E-05 37.1 1.2 27 4-51 69-95 (115)
82 PF12756 zf-C2H2_2: C2H2 type 76.9 3 6.4E-05 31.7 3.3 32 5-36 50-81 (100)
83 smart00834 CxxC_CXXC_SSSS Puta 75.7 2.5 5.4E-05 27.8 2.2 35 1-51 1-35 (41)
84 CHL00098 tsf elongation factor 75.6 6.1 0.00013 36.0 5.4 38 116-154 3-41 (200)
85 TIGR02605 CxxC_CxxC_SSSS putat 75.5 2.4 5.2E-05 29.7 2.2 34 1-50 1-34 (52)
86 COG4416 Com Mu-like prophage p 75.4 0.85 1.8E-05 33.5 -0.2 30 4-50 3-32 (60)
87 TIGR00373 conserved hypothetic 75.3 2.6 5.7E-05 36.7 2.8 31 3-51 107-137 (158)
88 PF06676 DUF1178: Protein of u 74.6 3.4 7.4E-05 36.0 3.3 37 1-51 1-41 (148)
89 PRK06369 nac nascent polypepti 74.3 7.7 0.00017 32.6 5.2 41 111-152 73-114 (115)
90 PF00096 zf-C2H2: Zinc finger, 74.2 3.4 7.4E-05 23.8 2.3 21 7-27 2-22 (23)
91 PRK00564 hypA hydrogenase nick 74.0 1.6 3.5E-05 36.2 1.2 12 4-15 70-81 (117)
92 PF14599 zinc_ribbon_6: Zinc-r 73.3 1.5 3.3E-05 32.7 0.8 28 4-50 29-56 (61)
93 COG1996 RPC10 DNA-directed RNA 72.9 2.2 4.7E-05 30.7 1.5 30 3-51 4-33 (49)
94 KOG2412 Nuclear-export-signal 71.9 31 0.00067 36.1 9.9 15 64-78 20-34 (591)
95 PRK06266 transcription initiat 70.9 3.6 7.9E-05 36.6 2.7 31 3-51 115-145 (178)
96 TIGR00310 ZPR1_znf ZPR1 zinc f 70.3 0.8 1.7E-05 41.4 -1.6 56 6-84 1-57 (192)
97 PTZ00121 MAEBL; Provisional 70.1 74 0.0016 37.3 12.9 15 71-85 904-918 (2084)
98 PF11626 Rap1_C: TRF2-interact 69.3 7.7 0.00017 30.3 4.0 37 119-156 2-38 (87)
99 COG0375 HybF Zn finger protein 68.6 3 6.4E-05 35.0 1.6 12 40-51 84-95 (115)
100 smart00659 RPOLCX RNA polymera 67.8 3.7 8E-05 28.6 1.7 35 5-66 2-36 (44)
101 PHA00733 hypothetical protein 67.5 6.7 0.00015 33.0 3.5 37 5-52 73-109 (128)
102 PF07754 DUF1610: Domain of un 67.1 2.5 5.5E-05 26.0 0.7 11 40-50 14-24 (24)
103 PF07946 DUF1682: Protein of u 66.3 18 0.00038 34.9 6.6 8 71-78 110-117 (321)
104 PF01155 HypA: Hydrogenase exp 65.3 3.1 6.8E-05 34.2 1.1 27 4-51 69-95 (113)
105 KOG3993 Transcription factor ( 65.2 1.7 3.7E-05 43.9 -0.6 23 121-145 454-476 (500)
106 PF15236 CCDC66: Coiled-coil d 65.1 99 0.0022 27.3 12.0 6 177-182 40-45 (157)
107 PRK00762 hypA hydrogenase nick 64.9 3.9 8.6E-05 34.2 1.6 33 4-51 69-101 (124)
108 smart00709 Zpr1 Duplicated dom 64.6 1.5 3.3E-05 38.5 -1.0 37 7-51 2-38 (160)
109 smart00290 ZnF_UBP Ubiquitin C 64.4 3.9 8.5E-05 28.1 1.3 30 5-34 11-43 (50)
110 PF07227 DUF1423: Protein of u 64.0 55 0.0012 33.4 9.7 42 227-268 377-418 (446)
111 PF15236 CCDC66: Coiled-coil d 63.7 1.1E+02 0.0023 27.1 12.7 18 239-256 119-136 (157)
112 TIGR00264 alpha-NAC-related pr 62.9 17 0.00037 30.6 5.0 39 112-151 76-115 (116)
113 PF13894 zf-C2H2_4: C2H2-type 62.3 8.6 0.00019 21.5 2.3 21 7-27 2-22 (24)
114 PF10122 Mu-like_Com: Mu-like 61.6 4.2 9E-05 29.5 1.0 30 5-51 4-33 (51)
115 PTZ00121 MAEBL; Provisional 61.0 1.5E+02 0.0032 35.1 13.0 16 253-268 1254-1269(2084)
116 TIGR02098 MJ0042_CXXC MJ0042 f 60.4 6.7 0.00014 25.7 1.8 34 4-51 1-34 (38)
117 PF07946 DUF1682: Protein of u 60.2 41 0.00088 32.4 7.9 7 131-137 181-187 (321)
118 COG4049 Uncharacterized protei 59.6 4.9 0.00011 29.9 1.1 28 4-32 16-43 (65)
119 KOG2462 C2H2-type Zn-finger pr 59.2 4.9 0.00011 38.4 1.3 70 4-82 129-198 (279)
120 smart00355 ZnF_C2H2 zinc finge 59.1 8.3 0.00018 21.7 1.9 21 6-26 1-21 (26)
121 PF13912 zf-C2H2_6: C2H2-type 58.4 9 0.00019 22.9 2.0 21 6-26 2-22 (27)
122 PF05191 ADK_lid: Adenylate ki 58.4 7.6 0.00016 25.9 1.8 30 5-51 1-30 (36)
123 COG0264 Tsf Translation elonga 57.7 19 0.00041 34.8 5.0 40 113-153 4-44 (296)
124 PRK14890 putative Zn-ribbon RN 57.5 5.3 0.00012 29.8 1.0 13 6-18 8-20 (59)
125 PF12874 zf-met: Zinc-finger o 56.4 8.5 0.00018 22.5 1.6 22 6-27 1-22 (25)
126 COG1675 TFA1 Transcription ini 56.2 9.8 0.00021 34.1 2.6 31 3-51 111-141 (176)
127 COG2331 Uncharacterized protei 55.9 2.2 4.8E-05 33.4 -1.3 34 2-51 9-42 (82)
128 COG2888 Predicted Zn-ribbon RN 55.5 7.3 0.00016 29.2 1.4 10 6-15 10-19 (61)
129 PF11547 E3_UbLigase_EDD: E3 u 55.0 53 0.0011 23.7 5.6 45 111-156 6-52 (53)
130 PF09862 DUF2089: Protein of u 54.0 9.6 0.00021 31.9 2.1 12 40-51 10-21 (113)
131 PF12171 zf-C2H2_jaz: Zinc-fin 53.7 3.5 7.5E-05 25.1 -0.4 23 6-28 2-24 (27)
132 TIGR00340 zpr1_rel ZPR1-relate 53.6 3 6.5E-05 36.8 -1.0 37 8-51 1-37 (163)
133 PF06936 Selenoprotein_S: Sele 52.2 52 0.0011 29.8 6.7 29 222-250 87-115 (190)
134 PF01927 Mut7-C: Mut7-C RNAse 51.9 6.1 0.00013 33.7 0.6 43 5-51 91-133 (147)
135 PRK14606 ruvA Holliday junctio 51.1 30 0.00064 31.1 4.9 24 115-138 144-167 (188)
136 COG1656 Uncharacterized conser 50.8 8.9 0.00019 34.1 1.5 40 6-51 98-139 (165)
137 PF14690 zf-ISL3: zinc-finger 50.6 6.9 0.00015 26.5 0.6 40 43-82 3-43 (47)
138 COG4008 Predicted metal-bindin 49.1 50 0.0011 28.5 5.7 42 110-153 110-151 (153)
139 PRK00409 recombination and DNA 49.0 3.9E+02 0.0084 29.2 14.5 26 114-139 487-512 (782)
140 PF02146 SIR2: Sir2 family; I 48.8 16 0.00035 31.7 2.8 35 4-51 104-138 (178)
141 PRK14605 ruvA Holliday junctio 48.6 42 0.00091 30.2 5.5 38 114-151 148-188 (194)
142 KOG2462 C2H2-type Zn-finger pr 48.5 15 0.00032 35.3 2.6 16 3-18 185-200 (279)
143 KOG3654 Uncharacterized CH dom 47.9 1.3E+02 0.0029 31.5 9.4 38 221-258 414-451 (708)
144 PF09845 DUF2072: Zn-ribbon co 47.8 11 0.00025 32.2 1.6 26 7-51 3-28 (131)
145 PRK14601 ruvA Holliday junctio 47.7 45 0.00098 29.9 5.5 32 114-145 142-173 (183)
146 PF09855 DUF2082: Nucleic-acid 47.7 9.8 0.00021 28.7 1.1 38 43-85 1-38 (64)
147 KOG2891 Surface glycoprotein [ 47.4 1.7E+02 0.0037 28.6 9.6 22 67-88 106-127 (445)
148 PF11372 DUF3173: Domain of un 47.1 21 0.00046 26.6 2.8 20 119-138 7-26 (59)
149 TIGR00084 ruvA Holliday juncti 46.8 26 0.00057 31.4 3.9 25 114-138 147-171 (191)
150 TIGR01069 mutS2 MutS2 family p 46.3 4.1E+02 0.0088 29.0 13.4 26 114-139 482-507 (771)
151 PF06107 DUF951: Bacterial pro 46.2 11 0.00024 27.9 1.1 14 2-15 28-41 (57)
152 PF10058 DUF2296: Predicted in 46.2 13 0.00029 26.9 1.6 32 2-50 19-52 (54)
153 cd02669 Peptidase_C19M A subfa 45.6 8.9 0.00019 38.3 0.8 44 6-51 29-75 (440)
154 PF09986 DUF2225: Uncharacteri 45.0 4.1 8.9E-05 37.1 -1.6 48 4-51 4-57 (214)
155 PF10367 Vps39_2: Vacuolar sor 44.7 9.4 0.0002 29.7 0.6 26 43-78 79-104 (109)
156 KOG3080 Nucleolar protein-like 43.9 1.6E+02 0.0035 28.8 8.8 55 187-241 182-236 (328)
157 PF14205 Cys_rich_KTR: Cystein 43.4 13 0.00027 27.4 1.1 26 43-73 5-30 (55)
158 PRK09335 30S ribosomal protein 43.1 19 0.0004 29.4 2.1 43 4-50 19-75 (95)
159 KOG2907 RNA polymerase I trans 42.9 17 0.00036 30.6 1.8 37 6-51 75-111 (116)
160 KOG0435 Leucyl-tRNA synthetase 42.9 17 0.00036 39.2 2.3 64 5-79 436-506 (876)
161 KOG0978 E3 ubiquitin ligase in 42.9 12 0.00026 40.1 1.2 42 5-52 643-688 (698)
162 PRK05978 hypothetical protein; 42.6 16 0.00034 31.9 1.8 48 3-78 31-78 (148)
163 PRK00116 ruvA Holliday junctio 42.2 46 0.001 29.7 4.8 26 115-140 150-175 (192)
164 COG1198 PriA Primosomal protei 42.0 8.1 0.00018 41.6 -0.1 41 5-51 435-484 (730)
165 PF13717 zinc_ribbon_4: zinc-r 41.9 15 0.00034 24.2 1.2 13 3-15 23-35 (36)
166 COG1545 Predicted nucleic-acid 41.7 17 0.00036 31.1 1.8 17 29-51 36-52 (140)
167 PRK14600 ruvA Holliday junctio 41.2 66 0.0014 28.9 5.6 36 114-149 145-181 (186)
168 COG5189 SFP1 Putative transcri 41.2 15 0.00032 36.2 1.5 45 3-51 347-407 (423)
169 KOG0608 Warts/lats-like serine 41.2 17 0.00036 39.3 2.0 42 109-150 84-125 (1034)
170 COG1594 RPB9 DNA-directed RNA 41.0 8.5 0.00019 31.9 -0.1 29 42-75 72-100 (113)
171 PRK14602 ruvA Holliday junctio 40.7 68 0.0015 29.1 5.7 25 114-138 155-179 (203)
172 PF05605 zf-Di19: Drought indu 40.4 37 0.00079 24.0 3.1 38 5-50 2-39 (54)
173 PF10827 DUF2552: Protein of u 40.1 20 0.00043 27.9 1.7 17 141-157 59-75 (79)
174 COG1308 EGD2 Transcription fac 39.8 38 0.00082 28.8 3.5 38 112-150 82-120 (122)
175 PTZ00172 40S ribosomal protein 39.8 24 0.00051 29.4 2.3 46 5-50 20-79 (108)
176 KOG1144 Translation initiation 39.4 4.8E+02 0.01 29.2 12.2 15 184-198 216-230 (1064)
177 PRK08222 hydrogenase 4 subunit 39.0 22 0.00048 31.4 2.2 47 5-51 114-163 (181)
178 KOG2072 Translation initiation 38.9 5.4E+02 0.012 28.8 12.6 22 225-246 805-826 (988)
179 KOG3623 Homeobox transcription 38.5 16 0.00035 39.5 1.4 39 4-52 280-319 (1007)
180 PRK14603 ruvA Holliday junctio 38.0 75 0.0016 28.7 5.5 24 115-138 153-176 (197)
181 PRK08271 anaerobic ribonucleos 37.8 16 0.00034 38.8 1.1 9 43-51 581-589 (623)
182 PF08938 HBS1_N: HBS1 N-termin 37.7 19 0.00042 27.6 1.4 27 127-154 45-71 (79)
183 PF05890 Ebp2: Eukaryotic rRNA 37.5 2.5E+02 0.0055 26.7 9.1 55 187-241 120-174 (271)
184 COG3937 Uncharacterized conser 37.4 2.4E+02 0.0053 23.5 7.8 29 175-203 36-64 (108)
185 COG5134 Uncharacterized conser 37.3 17 0.00037 33.9 1.2 46 2-51 39-88 (272)
186 PRK14604 ruvA Holliday junctio 37.1 95 0.0021 28.0 5.9 24 115-138 150-173 (195)
187 cd01412 SIRT5_Af1_CobB SIRT5_A 36.8 22 0.00047 32.1 1.8 16 3-18 107-122 (224)
188 KOG1074 Transcriptional repres 36.7 21 0.00046 39.1 1.9 47 3-58 351-397 (958)
189 PHA00616 hypothetical protein 36.4 20 0.00044 25.1 1.2 28 6-33 2-30 (44)
190 PF04615 Utp14: Utp14 protein; 35.5 2.1E+02 0.0046 30.7 9.2 25 246-270 300-324 (735)
191 PF07553 Lipoprotein_Ltp: Host 35.4 50 0.0011 23.4 3.1 23 114-136 21-46 (48)
192 PF05672 MAP7: MAP7 (E-MAP-115 35.3 3.3E+02 0.0072 24.4 14.9 23 247-269 127-149 (171)
193 PLN00186 ribosomal protein S26 35.2 35 0.00076 28.4 2.6 46 5-50 20-79 (109)
194 PF05835 Synaphin: Synaphin pr 35.1 90 0.0019 27.0 5.2 11 247-257 58-68 (139)
195 TIGR02487 NrdD anaerobic ribon 35.0 18 0.00039 37.8 1.1 9 43-51 539-547 (579)
196 PRK07111 anaerobic ribonucleos 34.7 20 0.00044 38.6 1.5 8 43-50 694-701 (735)
197 KOG3576 Ovo and related transc 34.5 16 0.00034 34.1 0.5 11 41-51 172-182 (267)
198 KOG1867 Ubiquitin-specific pro 34.3 24 0.00052 36.3 1.8 53 40-99 352-410 (492)
199 KOG0971 Microtubule-associated 34.0 7.5E+02 0.016 28.2 14.0 80 177-257 223-306 (1243)
200 TIGR01206 lysW lysine biosynth 33.8 24 0.00052 25.7 1.3 30 5-51 2-31 (54)
201 PF01283 Ribosomal_S26e: Ribos 33.1 12 0.00026 31.4 -0.5 45 5-49 20-78 (113)
202 PF10083 DUF2321: Uncharacteri 33.0 7.6 0.00016 34.3 -1.7 39 6-52 40-78 (158)
203 PRK11639 zinc uptake transcrip 33.0 27 0.00059 30.5 1.7 44 5-51 100-149 (169)
204 PF05262 Borrelia_P83: Borreli 32.5 5.6E+02 0.012 26.6 11.3 14 123-136 95-109 (489)
205 COG0735 Fur Fe2+/Zn2+ uptake r 32.4 21 0.00045 30.5 0.9 45 5-51 93-142 (145)
206 COG4481 Uncharacterized protei 32.2 25 0.00053 26.1 1.1 14 2-15 31-44 (60)
207 TIGR00595 priA primosomal prot 32.1 13 0.00028 38.1 -0.5 41 5-51 213-262 (505)
208 COG0423 GRS1 Glycyl-tRNA synth 32.0 53 0.0012 34.4 3.8 48 4-52 87-139 (558)
209 KOG0804 Cytoplasmic Zn-finger 31.8 24 0.00052 36.1 1.3 29 6-34 241-272 (493)
210 PRK13901 ruvA Holliday junctio 31.8 55 0.0012 29.8 3.5 24 115-138 145-168 (196)
211 PF08050 Tet_res_leader: Tetra 31.4 17 0.00037 21.3 0.1 10 6-15 1-10 (20)
212 PHA00733 hypothetical protein 31.2 17 0.00036 30.6 0.1 54 4-61 39-92 (128)
213 KOG1071 Mitochondrial translat 31.0 95 0.0021 30.6 5.2 40 113-153 45-85 (340)
214 PRK00464 nrdR transcriptional 30.9 24 0.00052 30.9 1.0 9 43-51 1-9 (154)
215 KOG2072 Translation initiation 30.8 7.8E+02 0.017 27.6 12.2 26 230-255 829-854 (988)
216 PF09567 RE_MamI: MamI restric 30.6 22 0.00048 33.9 0.8 11 41-51 95-105 (314)
217 smart00451 ZnF_U1 U1-like zinc 30.6 46 0.00099 20.8 2.1 22 6-27 4-25 (35)
218 PF09963 DUF2197: Uncharacteri 30.3 29 0.00064 25.6 1.2 37 4-51 1-40 (56)
219 PLN03086 PRLI-interacting fact 30.3 2.8E+02 0.006 29.4 8.8 10 253-262 56-65 (567)
220 PRK08579 anaerobic ribonucleos 30.2 24 0.00051 37.4 1.0 9 43-51 583-591 (625)
221 PRK14704 anaerobic ribonucleos 30.1 27 0.00059 36.9 1.4 9 43-51 573-581 (618)
222 PRK00418 DNA gyrase inhibitor; 29.3 33 0.00072 25.8 1.4 10 42-51 6-15 (62)
223 COG3024 Uncharacterized protei 29.3 31 0.00067 26.2 1.2 12 40-51 5-16 (65)
224 PRK00247 putative inner membra 29.0 6.4E+02 0.014 25.8 11.3 6 176-181 277-282 (429)
225 cd01410 SIRT7 SIRT7: Eukaryoti 28.9 45 0.00097 30.1 2.5 14 3-16 93-106 (206)
226 PF08271 TF_Zn_Ribbon: TFIIB z 28.5 27 0.00059 23.6 0.8 9 43-51 1-9 (43)
227 PF03811 Zn_Tnp_IS1: InsA N-te 28.2 31 0.00067 23.0 1.0 12 40-51 3-14 (36)
228 PRK11546 zraP zinc resistance 28.2 4E+02 0.0087 23.2 8.2 63 176-238 42-116 (143)
229 KOG2505 Ankyrin repeat protein 28.0 5E+02 0.011 27.4 9.8 47 115-161 404-460 (591)
230 cd01407 SIR2-fam SIR2 family o 27.9 40 0.00087 30.3 2.0 14 3-16 107-120 (218)
231 COG0675 Transposase and inacti 27.7 27 0.00059 31.9 0.9 10 42-51 322-331 (364)
232 PF13597 NRDD: Anaerobic ribon 27.6 25 0.00054 36.5 0.7 10 42-51 504-513 (546)
233 PF09805 Nop25: Nucleolar prot 27.5 2.3E+02 0.005 24.1 6.5 16 210-225 31-46 (137)
234 PHA02776 E7 protein; Provision 27.5 15 0.00032 30.2 -0.8 42 6-51 59-100 (101)
235 COG0846 SIR2 NAD-dependent pro 27.5 36 0.00078 32.0 1.7 16 4-19 121-136 (250)
236 COG1779 C4-type Zn-finger prot 27.5 10 0.00023 34.6 -1.8 41 3-51 12-52 (201)
237 PF14490 HHH_4: Helix-hairpin- 27.0 1.3E+02 0.0027 23.6 4.5 36 115-154 9-44 (94)
238 PF07223 DUF1421: Protein of u 26.9 63 0.0014 32.1 3.3 22 114-135 321-342 (358)
239 PF13465 zf-H2C2_2: Zinc-finge 26.5 38 0.00082 20.5 1.1 8 43-50 15-22 (26)
240 PF13719 zinc_ribbon_5: zinc-r 26.5 40 0.00087 22.3 1.3 13 3-15 23-35 (37)
241 PF04641 Rtf2: Rtf2 RING-finge 26.3 12 0.00026 34.9 -1.7 49 3-52 111-160 (260)
242 PF03884 DUF329: Domain of unk 26.0 26 0.00056 25.9 0.3 9 43-51 3-11 (57)
243 PF03801 Ndc80_HEC: HEC/Ndc80p 26.0 82 0.0018 27.3 3.5 41 112-152 92-137 (157)
244 PRK08475 F0F1 ATP synthase sub 25.4 4.5E+02 0.0097 22.8 13.0 20 245-264 130-149 (167)
245 COG4830 RPS26B Ribosomal prote 25.3 40 0.00088 27.7 1.3 27 4-30 19-59 (108)
246 COG5222 Uncharacterized conser 25.2 43 0.00093 32.8 1.7 45 3-51 272-319 (427)
247 TIGR00375 conserved hypothetic 24.9 37 0.00081 33.8 1.3 9 42-51 259-267 (374)
248 KOG1871 Ubiquitin-specific pro 24.9 24 0.00052 35.5 -0.0 42 59-100 291-338 (420)
249 smart00504 Ubox Modified RING 24.4 15 0.00032 25.9 -1.2 41 6-51 2-44 (63)
250 KOG2412 Nuclear-export-signal 24.4 6.3E+02 0.014 26.8 9.9 8 151-158 115-122 (591)
251 PF04361 DUF494: Protein of un 24.3 2.1E+02 0.0046 24.9 5.7 21 115-135 24-44 (155)
252 COG1645 Uncharacterized Zn-fin 24.2 34 0.00073 29.4 0.7 12 40-51 26-37 (131)
253 PF12898 Stc1: Stc1 domain; I 24.1 57 0.0012 25.5 2.0 27 38-68 46-72 (84)
254 PF01921 tRNA-synt_1f: tRNA sy 23.9 24 0.00053 35.0 -0.2 34 4-51 173-208 (360)
255 COG3364 Zn-ribbon containing p 23.8 31 0.00067 28.6 0.4 13 5-17 2-14 (112)
256 PRK04023 DNA polymerase II lar 23.8 47 0.001 37.3 1.8 9 7-15 628-636 (1121)
257 TIGR00389 glyS_dimeric glycyl- 23.7 64 0.0014 33.8 2.8 48 3-51 82-133 (551)
258 KOG4571 Activating transcripti 23.7 6.9E+02 0.015 24.3 10.3 13 204-216 259-271 (294)
259 PF14803 Nudix_N_2: Nudix N-te 23.5 29 0.00063 22.9 0.2 13 38-50 18-30 (34)
260 TIGR00416 sms DNA repair prote 23.4 50 0.0011 33.4 1.9 26 3-51 5-30 (454)
261 PF04828 GFA: Glutathione-depe 23.2 29 0.00062 25.9 0.1 34 39-83 45-78 (92)
262 KOG2186 Cell growth-regulating 23.2 46 0.001 31.7 1.5 37 5-52 3-39 (276)
263 PLN03086 PRLI-interacting fact 23.0 6.7E+02 0.014 26.6 10.0 12 248-259 57-68 (567)
264 COG5319 Uncharacterized protei 23.0 75 0.0016 27.4 2.6 36 2-51 2-41 (142)
265 PF05262 Borrelia_P83: Borreli 22.9 8.7E+02 0.019 25.3 11.1 8 71-78 49-56 (489)
266 PF13451 zf-trcl: Probable zin 22.8 61 0.0013 23.3 1.7 39 3-50 2-41 (49)
267 PRK06260 threonine synthase; V 22.8 50 0.0011 32.5 1.8 26 5-51 3-28 (397)
268 COG3058 FdhE Uncharacterized p 22.7 18 0.00039 34.9 -1.3 9 41-49 224-232 (308)
269 PF09831 DUF2058: Uncharacteri 22.7 5.6E+02 0.012 23.0 8.5 41 224-264 48-88 (177)
270 PRK14138 NAD-dependent deacety 22.7 67 0.0014 29.7 2.5 14 3-16 117-130 (244)
271 PF01396 zf-C4_Topoisom: Topoi 22.7 44 0.00096 22.4 0.9 17 44-68 3-19 (39)
272 PF13909 zf-H2C2_5: C2H2-type 22.6 88 0.0019 18.0 2.2 21 6-27 1-21 (24)
273 PRK06231 F0F1 ATP synthase sub 22.3 5.8E+02 0.013 23.0 12.6 10 248-257 159-168 (205)
274 COG2260 Predicted Zn-ribbon RN 22.2 50 0.0011 24.6 1.2 9 43-51 18-26 (59)
275 KOG2989 Uncharacterized conser 22.2 39 0.00083 32.0 0.8 15 1-15 36-50 (253)
276 PRK14873 primosome assembly pr 22.1 29 0.00062 37.1 -0.1 10 42-51 422-431 (665)
277 CHL00174 accD acetyl-CoA carbo 22.0 61 0.0013 31.4 2.1 33 3-53 36-68 (296)
278 PF08209 Sgf11: Sgf11 (transcr 21.9 29 0.00063 22.9 -0.1 10 42-51 4-13 (33)
279 TIGR00515 accD acetyl-CoA carb 21.9 63 0.0014 31.0 2.2 33 3-53 24-56 (285)
280 PRK06568 F0F1 ATP synthase sub 21.6 5.5E+02 0.012 22.4 12.4 12 246-257 113-124 (154)
281 PHA00451 protein kinase 21.4 5.8E+02 0.013 25.1 8.4 44 150-194 201-244 (362)
282 PRK11823 DNA repair protein Ra 21.3 58 0.0013 32.8 1.9 26 3-51 5-30 (446)
283 COG3877 Uncharacterized protei 20.8 55 0.0012 27.4 1.3 12 40-51 18-29 (122)
284 COG3478 Predicted nucleic-acid 20.7 47 0.001 25.4 0.8 38 42-84 4-41 (68)
285 PRK05580 primosome assembly pr 20.5 26 0.00057 37.2 -0.8 31 118-149 570-600 (679)
286 PF09538 FYDLN_acid: Protein o 20.4 42 0.00091 27.7 0.5 11 43-53 10-20 (108)
287 COG4154 FucU Fucose dissimilat 20.3 1.3E+02 0.0028 26.1 3.5 43 111-154 7-61 (144)
288 PRK07218 replication factor A; 20.2 60 0.0013 32.9 1.7 12 4-15 296-307 (423)
289 PRK07591 threonine synthase; V 20.2 59 0.0013 32.4 1.7 26 4-51 17-42 (421)
No 1
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=2.3e-32 Score=275.20 Aligned_cols=156 Identities=29% Similarity=0.449 Sum_probs=133.5
Q ss_pred ceeecccCCccccCHHH---------------HHHHHHHhccCCCCcchhhhhccccCCCCCCCCCcccccccccccccc
Q 022703 4 VSLKCGDCGALLRSVQE---------------AQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHT 68 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~---------------aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~ 68 (293)
-+++|..|++|...... ++--...+.-++|... +.+|.|+.||.+ +.|+|+|+|+
T Consensus 439 ~Rv~C~~c~kVrYs~~~~~~i~lpv~~~~~v~~~v~~~~cleaff~pq---~~df~s~ac~~K-------~~a~kt~~~k 508 (763)
T KOG0944|consen 439 DRVSCLGCRKVRYSYESEYLIQLPVPMTNEVREKVPISACLEAFFEPQ---VDDFWSTACGEK-------KGATKTTRFK 508 (763)
T ss_pred hhhhhhccccccccchhheeeEeeccccccccccCCHHHHHHHhcCCc---chhhhhHhhcCc-------cccccccccc
Confidence 47899999999833222 1112333466788885 789999999998 8999999999
Q ss_pred ccccchhhccccccccc--Cccc---cCCccccccCC--CCC--CCCcc--------cccccCHHHHHHHHhCCCCHHHH
Q 022703 69 DFVDKTSEAAKPISLEV--PKAT---ADSEEAIDVDM--SGS--QPEEM--------VEPEVDKELLKELEAMGFPVARA 131 (293)
Q Consensus 69 tFP~~Lvv~~~Rf~l~~--p~K~---~~~~~~lDl~~--g~~--~~Ee~--------~~~~~~~~~l~~L~~MGF~~~~a 131 (293)
|||+|||||+.||.|.+ |+|+ |.+|+.|||+. |.| |+|+. ..+.+|+.++.+|++||||.++|
T Consensus 509 sfP~yLiiqv~rf~~~dw~pkKld~~iempe~ldls~~rs~g~~p~ee~lpde~~~~~~~~~d~s~i~qL~~MGFp~eac 588 (763)
T KOG0944|consen 509 SFPDYLIIQVGRFTLQDWVPKKLDVSIEMPEELDLSSYRSKGLQPGEEALPDEAPETSEFAADRSVISQLVEMGFPEEAC 588 (763)
T ss_pred cCCceEEEEeeEEEecCceeeeeccceecchhhchhhhhhcCCCCcccccCCcCcccCccchhHHHHHHHHHcCCCHHHH
Confidence 99999999999999987 9999 77899999998 444 77762 34558999999999999999999
Q ss_pred HHHHHHhCCCCHHHHHHHHHHhcCCCCCCCCCCCCCCC
Q 022703 132 TRALHYSGNANVEAAVNWVVEHENDPDIDEMPMVPVSG 169 (293)
Q Consensus 132 ~kAL~~tgn~~~E~A~~WL~~h~dD~didep~~~~~~~ 169 (293)
.|||++|||+++|+|||||++||+|||||+|+.+|+++
T Consensus 589 ~rAly~tgN~~aEaA~NWl~~HMdDpd~~~p~vvp~~~ 626 (763)
T KOG0944|consen 589 RRALYYTGNSGAEAASNWLMEHMDDPDIDDPFVVPGNS 626 (763)
T ss_pred HHHHhhhcCccHHHHHHHHHHhccCcccCCceecCCCC
Confidence 99999999999999999999999999999999998764
No 2
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=5.1e-29 Score=245.50 Aligned_cols=155 Identities=23% Similarity=0.370 Sum_probs=134.4
Q ss_pred cceeecccCCccc-------------cCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCCCCccccccccccccccc
Q 022703 3 GVSLKCGDCGALL-------------RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTD 69 (293)
Q Consensus 3 ~~~LkC~~Cg~v~-------------~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~t 69 (293)
.-+|.|+.|+.|. .++.++|+.-+. ..++|.+. .++|+|.+|+.+ .+|+++++|+|
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 ERRLSCSGCMDVSYSYESMLMICIFLEGNDEPQDIRKS-VEAFFLPD---TIEWSCENCKGK-------KKASRKPFIKS 497 (749)
T ss_pred cceecccccccccccccceEEEEeecccCcchhhHHHH-HHheECcc---ceeeehhhhcCc-------ccccccchhhc
Confidence 4589999999987 788899998888 99999998 699999999987 89999999999
Q ss_pred cccchhhccccccccc--Cccc-----cCCccccccCC--CC-CCCCc------ccccccCHHHHHHHHhCCCCHHHHHH
Q 022703 70 FVDKTSEAAKPISLEV--PKAT-----ADSEEAIDVDM--SG-SQPEE------MVEPEVDKELLKELEAMGFPVARATR 133 (293)
Q Consensus 70 FP~~Lvv~~~Rf~l~~--p~K~-----~~~~~~lDl~~--g~-~~~Ee------~~~~~~~~~~l~~L~~MGF~~~~a~k 133 (293)
||.||++|+.||.|.| ..|+ ++.++.++++. +. .|..| .....+|+.++.||++||||.++|.+
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 4455 33467788886 22 23333 23356799999999999999999999
Q ss_pred HHHHhCCCCHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 022703 134 ALHYSGNANVEAAVNWVVEHENDPDIDEMPMVPVS 168 (293)
Q Consensus 134 AL~~tgn~~~E~A~~WL~~h~dD~didep~~~~~~ 168 (293)
||..|||++.|.||||||+||||||+|+|+.+|++
T Consensus 578 AL~~tgNqDaEsAMNWLFqHMdDPdlndP~~~~~~ 612 (749)
T COG5207 578 ALGITGNQDAESAMNWLFQHMDDPDLNDPFVPPPN 612 (749)
T ss_pred HHhhccCcchHHHHHHHHhhccCcccCCCCCCCCC
Confidence 99999999999999999999999999999988875
No 3
>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=6.5e-26 Score=209.50 Aligned_cols=152 Identities=35% Similarity=0.563 Sum_probs=135.3
Q ss_pred HHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHH-HHhcCCCCCCCCCCCCCC--------------------CCCCCCCC
Q 022703 118 LKELEAMGFPVARATRALHYSGNANVEAAVNWV-VEHENDPDIDEMPMVPVS--------------------GGGGASKS 176 (293)
Q Consensus 118 l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL-~~h~dD~didep~~~~~~--------------------~~~~~~kk 176 (293)
+++|++|||+..++.+||..|||.+++.||+|| .+|.+||. |.|++.|.. +..+..++
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 88988884 777766531 01123689
Q ss_pred CCCHHHHHHHHHHHHHHHHH---hHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHH
Q 022703 177 SLTPEEIKLKAQELRERARK---KKEEEEKRMEREREKERIRIGKELLEAKRIEEENERKRILALRKAEKEEEKRAREKI 253 (293)
Q Consensus 177 ~lT~EEk~~k~~el~~k~r~---~r~eeek~e~~e~E~~Rrk~GKe~~~~k~~~ee~e~k~~~e~rrrEK~ee~~ar~ri 253 (293)
.||+||+.++...|++++.. ++++-+..+..++++.|+++|++|..+++.+++.++.+++++||++|.++..+|+||
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 99999999999999999854 455677888899999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcCC
Q 022703 254 RQKLEEDKAERRRRLGL 270 (293)
Q Consensus 254 r~qIe~Dk~eR~~r~~~ 270 (293)
+.||++||++|+++++.
T Consensus 163 ~~~Ie~DKaeRka~~e~ 179 (290)
T KOG2689|consen 163 LRQIERDKAERKAKYEN 179 (290)
T ss_pred HHHHHHhHHHHHHHhcc
Confidence 99999999999999884
No 4
>KOG2507 consensus Ubiquitin regulatory protein UBXD2, contains UAS and UBX domains [General function prediction only]
Probab=99.26 E-value=6e-12 Score=123.05 Aligned_cols=105 Identities=30% Similarity=0.395 Sum_probs=88.7
Q ss_pred CCCCCHHHHHHHHHHHHHHH---HHhHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHH
Q 022703 175 KSSLTPEEIKLKAQELRERA---RKKKEEEEKRMEREREKERIRIGKELLEAKRIEEENERKRILALRKAEKEEEKRARE 251 (293)
Q Consensus 175 kk~lT~EEk~~k~~el~~k~---r~~r~eeek~e~~e~E~~Rrk~GKe~~~~k~~~ee~e~k~~~e~rrrEK~ee~~ar~ 251 (293)
+.||..+ -.++.+|.+++ +.++.+++.+.++++|..||+.|||++..+....+...++++++|+|||.++..+|+
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 3444433 34555555554 555567788888999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCcCCCCC
Q 022703 252 KIRQKLEEDKAERRRRLGLPPEDPATTKSS 281 (293)
Q Consensus 252 rir~qIe~Dk~eR~~r~~~~~~~~~~~~~~ 281 (293)
||++||++||++|+.||+.+.+..++.+++
T Consensus 268 RI~aqiaadraera~rf~k~v~t~et~k~a 297 (506)
T KOG2507|consen 268 RILAQIAADRAERAIRFTKSVDTKETMKPA 297 (506)
T ss_pred HHHHHhhccHHHHHhhhcCccchhhhcchh
Confidence 999999999999999999988877776655
No 5
>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=99.01 E-value=3.8e-10 Score=75.37 Aligned_cols=37 Identities=41% Similarity=0.701 Sum_probs=34.1
Q ss_pred cCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHH
Q 022703 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWV 150 (293)
Q Consensus 113 ~~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL 150 (293)
+|++.|.+|++|||+.+.|.+||..++| |++.|++||
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 4688999999999999999999999998 999999998
No 6
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=98.84 E-value=5.5e-09 Score=69.20 Aligned_cols=37 Identities=35% Similarity=0.560 Sum_probs=34.4
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Q 022703 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVV 151 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~ 151 (293)
+++.+++|++|||+.+.|..||..++| +++.|++|||
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 7
>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=98.84 E-value=6.6e-09 Score=69.11 Aligned_cols=38 Identities=47% Similarity=0.754 Sum_probs=35.2
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Q 022703 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVE 152 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~ 152 (293)
+++.+++|++|||+.+.|..||..++| |++.|++|||+
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 8
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=98.57 E-value=5.2e-08 Score=100.12 Aligned_cols=49 Identities=41% Similarity=0.649 Sum_probs=44.6
Q ss_pred ccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCCCCCCC
Q 022703 112 EVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHENDPDIDE 161 (293)
Q Consensus 112 ~~~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~dD~dide 161 (293)
+++++.|.++++|||+.+.|++||..|+| |||.|+||||.|+|++-.|.
T Consensus 633 ~~~e~~v~si~smGf~~~qa~~aL~~~n~-nveravDWif~h~d~~~ed~ 681 (763)
T KOG0944|consen 633 EVDEESVASIVSMGFSRNQAIKALKATNN-NVERAVDWIFSHMDIPVEDA 681 (763)
T ss_pred CCChhHheeeeeecCcHHHHHHHHHhcCc-cHHHHHHHHHhccccccccc
Confidence 68999999999999999999999999977 99999999999999764443
No 9
>KOG2699 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.52 E-value=7.6e-08 Score=94.48 Aligned_cols=237 Identities=32% Similarity=0.390 Sum_probs=166.3
Q ss_pred HHHHHHHhccCCCCcchhhhhccccCCCCCCCCCccccccccccccccccccchhhcccccccccCccccCCc--ccccc
Q 022703 21 AQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEVPKATADSE--EAIDV 98 (293)
Q Consensus 21 aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~~p~K~~~~~--~~lDl 98 (293)
.+.|.+-+.|.+|...++.+.. .+++.....++.+.++.-+- ..-..+ |..+.+.+ ..+-+
T Consensus 5 k~~~~ef~~~~~~~ss~~~~~~-------------~e~~~~~~~~s~~~~~~~~~--~~~~~~--~~~~~~~~~~~~~~~ 67 (407)
T KOG2699|consen 5 KYNFQEFKCKVNLASSLNDVKH-------------QESVGEQAHTSSTDQSLPHL--PVTLDT--PWPLLNPAPKVNLLL 67 (407)
T ss_pred HHHHHHHhhcccccccccchhh-------------hHHHHHHhhccCCCCCCCCC--Cccccc--chhhhccCCCCcccc
Confidence 4567777778888766333322 24577777777777665433 222222 22221110 11111
Q ss_pred CC--CCC-CCCcccccccCHHHHHHHHhCCCCH-HHHHHHHHHhCCCCHHH-HHHHHHHhcCCCCCCCCCCCCCC---CC
Q 022703 99 DM--SGS-QPEEMVEPEVDKELLKELEAMGFPV-ARATRALHYSGNANVEA-AVNWVVEHENDPDIDEMPMVPVS---GG 170 (293)
Q Consensus 99 ~~--g~~-~~Ee~~~~~~~~~~l~~L~~MGF~~-~~a~kAL~~tgn~~~E~-A~~WL~~h~dD~didep~~~~~~---~~ 170 (293)
+. +.| ....+..+.+....+.-...|||+. .+...+++..|+...++ |.+|...|..+......+..+.+ ++
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 11 222 2222344555566677788899999 77778899999988888 99999988887654443333332 22
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHhHHHHHHHHHH--HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHH
Q 022703 171 GGASKSSLTPEEIKLKAQELRERARKKKEEEEKRMER--EREKERIRIGKELLEAKRIEEENERKRILALRKAEKEEEKR 248 (293)
Q Consensus 171 ~~~~kk~lT~EEk~~k~~el~~k~r~~r~eeek~e~~--e~E~~Rrk~GKe~~~~k~~~ee~e~k~~~e~rrrEK~ee~~ 248 (293)
....++.+|...-..+.++|.+..+.-+.++++...+ ++|++|.+.|+++.+.+..-.....+..+..+.-+++|+..
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 2335677888888888999999999999988888888 99999999999999888765566666667888889999999
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCC
Q 022703 249 AREKIRQKLEEDKAERRRRLGLPPED 274 (293)
Q Consensus 249 ar~rir~qIe~Dk~eR~~r~~~~~~~ 274 (293)
.++.++.+.+.++.+|++.+|.|+.+
T Consensus 228 ~~e~~l~k~~s~~ser~~~l~~P~~t 253 (407)
T KOG2699|consen 228 LVEKTLRKLQSLKSERKRLLGAPPVT 253 (407)
T ss_pred HHHHHHHHHHHHhhhhhhhhcCCccc
Confidence 99999999999999999999998883
No 10
>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=98.39 E-value=7.7e-08 Score=91.28 Aligned_cols=89 Identities=10% Similarity=0.133 Sum_probs=63.3
Q ss_pred eeecccCCccccCHHHHHHH------HHHhccCCCCcc-hhhhhccccCCCCCCCCCccccccccccccccccccchhhc
Q 022703 5 SLKCGDCGALLRSVQEAQEH------AELTSHSNFSES-TEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEA 77 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~h------a~~TgH~~F~e~-~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~ 77 (293)
.++|..|+.+.........+ .......+|..+ .+....|.|+.||++ ..+.|++.|.++|++|+||
T Consensus 110 ~i~C~~C~~~s~~~e~f~~l~L~i~sl~~~l~~~~~~E~l~g~n~~~C~~C~~~-------~~a~k~~~i~~lP~vLii~ 182 (327)
T cd02664 110 TIRCLNCNSTSARTERFRDLDLSFPSVQDLLNYFLSPEKLTGDNQYYCEKCASL-------QDAEKEMKVTGAPEYLILT 182 (327)
T ss_pred EEEcCCCCCEecccccceeeecCCCCHHHHHHHhcCeeEccCCCceeCCccCCc-------cceeEEEEcccCChhhEEE
Confidence 58999999776332221111 122244455433 233345999999987 6899999999999999999
Q ss_pred cccccccc----Cccc---cCCccccccCC
Q 022703 78 AKPISLEV----PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 78 ~~Rf~l~~----p~K~---~~~~~~lDl~~ 100 (293)
++||.++. ..|+ |.+|..|||+.
T Consensus 183 LkRF~~~~~~~~~~Ki~~~v~fp~~ldl~~ 212 (327)
T cd02664 183 LLRFSYDQKTHVREKIMDNVSINEVLSLPV 212 (327)
T ss_pred eeeeEEccccCcceecCceEecCCEEecCc
Confidence 99999874 5677 66788899875
No 11
>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=98.25 E-value=2.7e-07 Score=86.41 Aligned_cols=65 Identities=8% Similarity=0.070 Sum_probs=51.2
Q ss_pred hccCCCCcch-hhhhccccCCCCCCCCCccccccccccccccccccchhhccccccccc---Cccc---cCCccccccCC
Q 022703 28 TSHSNFSEST-EAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV---PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 28 TgH~~F~e~~-d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~~---p~K~---~~~~~~lDl~~ 100 (293)
.+..+|.++. +... |.|+.||.+ +.+.|++.|.++|++|+|+++||.++. +.|+ +.+|..|||+.
T Consensus 181 ~L~~~~~~e~~~~~~-~~C~~C~~~-------~~~~~~~~i~~lP~~Lii~lkRf~~~~~~~~~K~~~~v~fp~~Ldl~~ 252 (328)
T cd02660 181 CLDRFTRPEKLGDFA-YKCSGCGST-------QEATKQLSIKKLPPVLCFQLKRFEHSLNKTSRKIDTYVQFPLELNMTP 252 (328)
T ss_pred HHHHhcCccccCCCC-ccCCCCCCc-------cceEEEEEecCCCceeEEEEEeEEecCCCCCcCCCcEEeCCCEechhh
Confidence 3555565441 2222 799999997 689999999999999999999999885 6787 66788899875
No 12
>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=98.23 E-value=2.3e-07 Score=86.03 Aligned_cols=86 Identities=14% Similarity=0.169 Sum_probs=61.5
Q ss_pred eeecccCCccccCHHHHHH-------------HHHHhccCCCCcc-hhhhhccccCCCCCCCCCcccccccccccccccc
Q 022703 5 SLKCGDCGALLRSVQEAQE-------------HAELTSHSNFSES-TEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDF 70 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~-------------ha~~TgH~~F~e~-~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tF 70 (293)
.++|..|+.+......... -.+.....+|..+ .+....|.|+.|++ |+|++.|.++
T Consensus 80 ~i~C~~C~~~s~~~E~f~~L~Lp~~~~~~~~~sL~~~L~~~~~~E~l~~~~~~~C~~C~~----------a~k~~~i~~~ 149 (279)
T cd02667 80 TIMCESCGTVSLVYEPFLDLSLPRSDEIKSECSIESCLKQFTEVEILEGNNKFACENCTK----------AKKQYLISKL 149 (279)
T ss_pred EEEcCCCCCEeCccccceEEecCCCcccCCCCCHHHHHHhhcCeeEecCCCcccCCccCc----------eeeEeEhhhC
Confidence 5789999988743222111 1222244556544 22223489999977 6889999999
Q ss_pred ccchhhccccccccc---Cccc---cCCccccccCC
Q 022703 71 VDKTSEAAKPISLEV---PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 71 P~~Lvv~~~Rf~l~~---p~K~---~~~~~~lDl~~ 100 (293)
|++|+|+++||.++. +.|+ |.+|..|||+.
T Consensus 150 P~~Lii~LkRF~~~~~~~~~Ki~~~v~fP~~Ldl~~ 185 (279)
T cd02667 150 PPVLVIHLKRFQQPRSANLRKVSRHVSFPEILDLAP 185 (279)
T ss_pred CCeEEEEEeccccCcccCceecCceEeCCCccchhh
Confidence 999999999999994 6787 66888999986
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=98.22 E-value=2.8e-07 Score=87.09 Aligned_cols=89 Identities=13% Similarity=0.153 Sum_probs=62.2
Q ss_pred ceeecccCCccccCHHHH----------HHHHHHhccCCCCcc-hhhhhccccCCCCCCCCCcccccccccccccccccc
Q 022703 4 VSLKCGDCGALLRSVQEA----------QEHAELTSHSNFSES-TEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVD 72 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~a----------q~ha~~TgH~~F~e~-~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~ 72 (293)
..++|..||.+....... ... ......+|..+ .+....|.|+.|+++ +.+.|++.|.++|+
T Consensus 128 ~~~~C~~C~~~s~~~e~f~~l~l~i~~~~sl-~~~L~~~~~~e~l~g~~~~~C~~C~~~-------~~a~k~~~i~~lP~ 199 (324)
T cd02668 128 YVTQCSKCGRESSLPSKFYELELQLKGHKTL-EECIDEFLKEEQLTGDNQYFCESCNSK-------TDATRRIRLTTLPP 199 (324)
T ss_pred EEEEeCCCCCccccccccEEEEEEecccCCH-HHHHHHhhCceecCCCccccCCCCCce-------eeeEEEEEecCCCC
Confidence 358899999874221111 111 11133345433 122234899999987 78999999999999
Q ss_pred chhhccccccccc----Cccc---cCCccccccCC
Q 022703 73 KTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 73 ~Lvv~~~Rf~l~~----p~K~---~~~~~~lDl~~ 100 (293)
+|+|+++||.++. +.|+ +.+|..|||+.
T Consensus 200 iLii~LkRf~~d~~~~~~~Ki~~~v~fp~~Ldl~~ 234 (324)
T cd02668 200 TLNFQLLRFVFDRKTGAKKKLNASISFPEILDMGE 234 (324)
T ss_pred eEEEEEEcceeecccCcceeCCcEEECCCeEechh
Confidence 9999999999874 6777 66888999985
No 14
>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=98.12 E-value=1.7e-06 Score=80.85 Aligned_cols=89 Identities=8% Similarity=-0.007 Sum_probs=62.2
Q ss_pred eeecccCCccccCHHHHH---------HHHHHhccCCCCcc-hhhhhccccCCCCCCCCCccccccccccccccccccch
Q 022703 5 SLKCGDCGALLRSVQEAQ---------EHAELTSHSNFSES-TEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKT 74 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq---------~ha~~TgH~~F~e~-~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L 74 (293)
.++|..|+.+........ .....+...+|..+ .+....|+|+.|+++ ..|+|++.|..+|++|
T Consensus 120 ~~~C~~C~~~s~~~e~f~~Lsl~i~~~~sl~~~L~~~~~~E~l~~~~~~~C~~C~~~-------~~a~k~~~i~~lP~vL 192 (300)
T cd02663 120 ETRCLTCETVSSRDETFLDLSIDVEQNTSITSCLRQFSATETLCGRNKFYCDECCSL-------QEAEKRMKIKKLPKIL 192 (300)
T ss_pred eEEeCCCCCCccccceeEEeccCCCCcCCHHHHHHHhhcccccCCCCcEECCCCCCc-------eeEEEEEEeccCCcee
Confidence 579999998763222111 01122233445433 222345999999987 7899999999999999
Q ss_pred hhccccccccc----Cccc---cCCccccccCC
Q 022703 75 SEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 75 vv~~~Rf~l~~----p~K~---~~~~~~lDl~~ 100 (293)
+|+++||.++. ..|+ |.+|..||+..
T Consensus 193 ii~LkRF~~~~~~~~~~Ki~~~v~fp~~L~~~~ 225 (300)
T cd02663 193 ALHLKRFKYDEQLNRYIKLFYRVVFPLELRLFN 225 (300)
T ss_pred EEEEEeEEeecccCCceecCceEecCcEEeccc
Confidence 99999999884 5677 66788888874
No 15
>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=98.08 E-value=7.3e-07 Score=83.13 Aligned_cols=51 Identities=25% Similarity=0.361 Sum_probs=43.2
Q ss_pred ccCCCCcchhhhhccccCCCCCCCCCccccccccccccccccccchhhcccccccc-c--Cccc
Q 022703 29 SHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLE-V--PKAT 89 (293)
Q Consensus 29 gH~~F~e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~-~--p~K~ 89 (293)
...+|..+ .+++.|+.||++ ..|.|++.|.++|++|+||++||.+. + |+|+
T Consensus 184 L~~~~~~e---~i~~~C~~C~~~-------~~a~k~~~i~~lP~vLii~LkRF~~~~~~~~~Ki 237 (311)
T cd02658 184 LKAYFAPE---TIEDFCSTCKEK-------TTATKTTGFKTFPDYLVINMKRFQLLENWVPKKL 237 (311)
T ss_pred HHHHcCcc---cccccccCCCCc-------ccEEEEEEeecCCceEEEEeEEEEecCCCceEee
Confidence 55556654 567899999987 78999999999999999999999994 3 8887
No 16
>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=98.02 E-value=1.2e-06 Score=84.14 Aligned_cols=65 Identities=6% Similarity=-0.040 Sum_probs=47.1
Q ss_pred ccCCCCcc-hhhhhccccCCCCCCCCCccccccccccccccccccchhhccccccccc--------Cccc---cCCcccc
Q 022703 29 SHSNFSES-TEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--------PKAT---ADSEEAI 96 (293)
Q Consensus 29 gH~~F~e~-~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~~--------p~K~---~~~~~~l 96 (293)
...+|.++ .+....|.|+.|+++ +.|+|++.|.++|++|+|+++||.+.. ..|+ +..|..|
T Consensus 186 L~~f~~~E~l~g~n~y~C~~C~~~-------~~a~k~~~~~~~P~vL~i~LkRF~~~~~~~~~~~~~~Ki~~~v~fp~~L 258 (332)
T cd02671 186 ISQFASVERIVGEDKYFCENCHHY-------TEAERSLLFDKLPEVITIHLKCFAANGSEFDCYGGLSKVNTPLLTPLKL 258 (332)
T ss_pred HHHhCCcceecCCCCeeCCCCCCc-------eeEEEEEEEecCCCEEEEEeeeeccccccccccCCceecCccccCcccc
Confidence 34455444 111234999999987 789999999999999999999999652 4455 5556666
Q ss_pred ccCC
Q 022703 97 DVDM 100 (293)
Q Consensus 97 Dl~~ 100 (293)
|+..
T Consensus 259 ~~~~ 262 (332)
T cd02671 259 SLEE 262 (332)
T ss_pred cccc
Confidence 6653
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=98.02 E-value=1.8e-06 Score=80.24 Aligned_cols=85 Identities=9% Similarity=0.037 Sum_probs=59.6
Q ss_pred ceeecccCC-ccc-------------cCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCCCCccccccccccccccc
Q 022703 4 VSLKCGDCG-ALL-------------RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTD 69 (293)
Q Consensus 4 ~~LkC~~Cg-~v~-------------~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~t 69 (293)
.+++|..|+ .+- .+...... ...+....|.+. +...|+.||.. ..++|++.|.+
T Consensus 128 ~~~~C~~C~~~~~~~~e~f~~Lsl~i~~~~~~~~-l~~~L~~~~~~~----~~~~~~~~~~~-------~~~~k~~~i~~ 195 (305)
T cd02657 128 TKMKCTESPDEEEVSTESEYKLQCHISITTEVNY-LQDGLKKGLEEE----IEKHSPTLGRD-------AIYTKTSRISR 195 (305)
T ss_pred EEEEcCCCCCCCccccccceEEEeecCCCccccc-HHHHHHHhhhhh----hhhcCcccCCC-------ceEEEEEEecc
Confidence 468999999 333 11111111 223355566655 33589999886 67899999999
Q ss_pred cccchhhccccccccc----Cccc---cCCccccccCC
Q 022703 70 FVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 70 FP~~Lvv~~~Rf~l~~----p~K~---~~~~~~lDl~~ 100 (293)
+|++|+|+++||.+++ ..|+ |.+|..||++.
T Consensus 196 lP~vLii~LkRF~~~~~~~~~~Ki~~~v~fP~~Ldl~~ 233 (305)
T cd02657 196 LPKYLTVQFVRFFWKRDIQKKAKILRKVKFPFELDLYE 233 (305)
T ss_pred CCcEEEEEEECCccccccCceeecCcEEECCceEeccc
Confidence 9999999999999874 4455 66788899874
No 18
>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=97.98 E-value=2.1e-06 Score=78.74 Aligned_cols=89 Identities=13% Similarity=0.085 Sum_probs=62.1
Q ss_pred eeecccCCccccCHHHHH---------HHHHHhccCCCCcc-hhhhhccccCCCCCCCCCccccccccccccccccccch
Q 022703 5 SLKCGDCGALLRSVQEAQ---------EHAELTSHSNFSES-TEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKT 74 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq---------~ha~~TgH~~F~e~-~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L 74 (293)
.++|..||.+........ .....+...+|... .+....|.|+.||++ ..+.+++.|.++|++|
T Consensus 135 ~~~C~~C~~~s~~~e~~~~l~l~i~~~~~l~~~l~~~~~~e~~~~~~~~~C~~C~~~-------~~~~~~~~i~~~P~iL 207 (304)
T cd02661 135 QVKCLNCKHVSNTYDPFLDLSLDIKGADSLEDALEQFTKPEQLDGENKYKCERCKKK-------VKASKQLTIHRAPNVL 207 (304)
T ss_pred eEEeCCCCCCcCccccceeeeeecCCCCcHHHHHHHhcCceeeCCCCCeeCCCCCCc-------cceEEEEEEecCCcEE
Confidence 578999997764322110 12223344456543 233334899999997 6789999999999999
Q ss_pred hhcccccccccCccc---cCCccccccCC
Q 022703 75 SEAAKPISLEVPKAT---ADSEEAIDVDM 100 (293)
Q Consensus 75 vv~~~Rf~l~~p~K~---~~~~~~lDl~~ 100 (293)
+|+++||.++...|+ +.+|..|||+.
T Consensus 208 ~i~l~Rf~~~~~~Ki~~~v~f~~~L~l~~ 236 (304)
T cd02661 208 TIHLKRFSNFRGGKINKQISFPETLDLSP 236 (304)
T ss_pred EEEEeccccCCccccCCeEecCCeechhh
Confidence 999999999854555 55677888875
No 19
>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=97.95 E-value=1.8e-06 Score=81.04 Aligned_cols=89 Identities=12% Similarity=0.137 Sum_probs=61.8
Q ss_pred eeecccCCccccCHHHHH---------HHHHHhccCCCCcc-hhhhhccccCCCCCCCCCccccccccccccccccccch
Q 022703 5 SLKCGDCGALLRSVQEAQ---------EHAELTSHSNFSES-TEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKT 74 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq---------~ha~~TgH~~F~e~-~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~L 74 (293)
.++|..|+.+........ .....+...+|..+ .+....|.|++||++ +.+.|+..|.++|++|
T Consensus 124 ~~~C~~C~~~s~~~e~f~~l~l~i~~~~~l~~~l~~~~~~e~l~~~~~~~C~~C~~~-------~~~~k~~~i~~lP~vL 196 (334)
T cd02659 124 YIICKECPHESEREEYFLDLQVAVKGKKNLEESLDAYVQGETLEGDNKYFCEKCGKK-------VDAEKGVCFKKLPPVL 196 (334)
T ss_pred EEEecCCCceecccccceEEEEEcCCCCCHHHHHHHhcCeeEecCCccEecCcCCCc-------ccEEEEEEeecCCCEE
Confidence 578999987642221110 11222344555543 222334999999997 6889999999999999
Q ss_pred hhccccccccc----Cccc---cCCccccccCC
Q 022703 75 SEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 75 vv~~~Rf~l~~----p~K~---~~~~~~lDl~~ 100 (293)
+|+++||.++. .+|+ +.+|..|||+.
T Consensus 197 ii~l~Rf~~~~~~~~~~K~~~~v~fp~~Ldl~~ 229 (334)
T cd02659 197 TLQLKRFEFDFETMMRIKINDRFEFPLELDMEP 229 (334)
T ss_pred EEEeeeeEEccccCcceeCCceEeCCceecCcc
Confidence 99999999863 5676 66788899875
No 20
>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=97.87 E-value=3.9e-06 Score=74.30 Aligned_cols=88 Identities=14% Similarity=0.162 Sum_probs=60.6
Q ss_pred ceeecccCCccccCHHH----------------HHHHHHHhccCCCCcc-hhhhhccccCCCCCCCCCcccccccccccc
Q 022703 4 VSLKCGDCGALLRSVQE----------------AQEHAELTSHSNFSES-TEAVLNLVCATCGKPCRSKTETDLHRKRTG 66 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~----------------aq~ha~~TgH~~F~e~-~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~ 66 (293)
-+++|..||.+...... .....+ ....+|... .+....+.|+.||.. +.+.++..
T Consensus 50 ~~~~C~~C~~~~~~~e~~~~l~l~ip~~~~~~~~~sl~~-~L~~~~~~e~~~~~~~~~C~~C~~~-------~~~~~~~~ 121 (230)
T cd02674 50 SRLTCLTCGKTSTTFEPFTYLSLPIPSGSGDAPKVTLED-CLRLFTKEETLDGDNAWKCPKCKKK-------RKATKKLT 121 (230)
T ss_pred CcEEcCCCcCCcceecceeEEEEecccccCCCCCCCHHH-HHHHhcCccccCCCCceeCCCCCCc-------cceEEEEE
Confidence 35799999987632110 011112 245556543 233456999999987 78899999
Q ss_pred ccccccchhhccccccccc--Cccc---cCCc-cccccC
Q 022703 67 HTDFVDKTSEAAKPISLEV--PKAT---ADSE-EAIDVD 99 (293)
Q Consensus 67 f~tFP~~Lvv~~~Rf~l~~--p~K~---~~~~-~~lDl~ 99 (293)
|.++|++|+|+++||...+ ..|+ +.+| +.||++
T Consensus 122 i~~lP~iLii~l~R~~~~~~~~~K~~~~v~~~~~~l~l~ 160 (230)
T cd02674 122 ISRLPKVLIIHLKRFSFSRGSTRKLTTPVTFPLNDLDLT 160 (230)
T ss_pred EecCChhhEeEhhheecCCCCcccCCceEeccccccccc
Confidence 9999999999999999986 6666 4444 457765
No 21
>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=97.80 E-value=6.8e-06 Score=75.91 Aligned_cols=70 Identities=17% Similarity=0.107 Sum_probs=47.6
Q ss_pred eeecccCCccccCHHHHHHH-----------HHHhccCCCCcchhhhhccccCCCCCCCCCccccccccccccccccccc
Q 022703 5 SLKCGDCGALLRSVQEAQEH-----------AELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDK 73 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~h-----------a~~TgH~~F~e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~ 73 (293)
+++|..||.+-......-++ .+......|.+. .++|.|+.|+.. .+.|+++|.+||++
T Consensus 81 ~i~C~~C~~~s~~~e~~~~L~L~i~~~~~~~le~l~~~~~~~~---~~e~~C~~C~~~--------~a~k~~~i~~~P~v 149 (245)
T cd02673 81 SYVCIGCSFEENVSDVGNFLDVSMIDNKLDIDELLISNFKTWS---PIEKDCSSCKCE--------SAISSERIMTFPEC 149 (245)
T ss_pred EEEecCCCCeeeeccccceeccccccCCcchHHHHHHHhhccc---ccCccCCCCCCc--------cceeechhhhCChh
Confidence 58999999886222111110 111122233333 467999999874 67889999999999
Q ss_pred hhhccccccccc
Q 022703 74 TSEAAKPISLEV 85 (293)
Q Consensus 74 Lvv~~~Rf~l~~ 85 (293)
|+||++||.+..
T Consensus 150 L~i~lkRf~~~~ 161 (245)
T cd02673 150 LSINLKRYKLRI 161 (245)
T ss_pred hEEeeEeeeecc
Confidence 999999998764
No 22
>KOG1865 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=97.60 E-value=4.3e-05 Score=77.64 Aligned_cols=87 Identities=16% Similarity=0.218 Sum_probs=65.2
Q ss_pred eeecccCCccccC----------HHHHHHHHHHhccCCCC--cchhhhhccccCCCCCCCCCcccccccccccccccccc
Q 022703 5 SLKCGDCGALLRS----------VQEAQEHAELTSHSNFS--ESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVD 72 (293)
Q Consensus 5 ~LkC~~Cg~v~~~----------~~~aq~ha~~TgH~~F~--e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~ 72 (293)
.|+|..|..|..- -.+++.+.+. + ..|. |.+|-..-|+|..|.++ +.|.|+..+-.-|+
T Consensus 239 ~vkC~~C~~vS~tyE~~~dltvei~d~~sl~~A-L-~qFt~~E~L~gen~Y~C~~Ck~~-------v~A~K~lti~raPn 309 (545)
T KOG1865|consen 239 QIKCLHCKGVSDTYEPYLDLTLEIQDASSLQQA-L-EQFTKPEKLDGENAYHCGRCKQK-------VPASKQLTIHRAPN 309 (545)
T ss_pred ceecccCCCcccccccccceEEEeccchhHHHH-H-HHhhhHHhhCCccccccchhhhh-------CcccceeeeecCCc
Confidence 5899999999721 1133332222 0 0243 44444456999999997 89999999999999
Q ss_pred chhhcccccccccCccc---cCCccccccCC
Q 022703 73 KTSEAAKPISLEVPKAT---ADSEEAIDVDM 100 (293)
Q Consensus 73 ~Lvv~~~Rf~l~~p~K~---~~~~~~lDl~~ 100 (293)
+|.|+++||+.+.--|+ |.+|+.|||..
T Consensus 310 VLTi~LKRF~~~~~gKI~K~I~fPE~LDl~P 340 (545)
T KOG1865|consen 310 VLTLHLKRFSNGTGGKISKPVSFPETLDLQP 340 (545)
T ss_pred eEEEeeehhccCcccccccccCCcccccccc
Confidence 99999999999875555 88899999997
No 23
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=97.54 E-value=3.1e-05 Score=74.40 Aligned_cols=79 Identities=19% Similarity=0.233 Sum_probs=52.0
Q ss_pred ceeecccCCccccCHHHHHHHH---HHhccCC-------CCcc--hhhhhccccCCCCCCCCCccccccccccccccccc
Q 022703 4 VSLKCGDCGALLRSVQEAQEHA---ELTSHSN-------FSES--TEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFV 71 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha---~~TgH~~-------F~e~--~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP 71 (293)
-+|+|..||.....-+-...++ -++-|.+ |.+. .+-...|.||.||++ ..+.|+..+.-.|
T Consensus 234 srlqC~~C~~TStT~a~fs~l~vp~~~v~~~~l~eC~~~f~~~e~L~g~d~W~CpkC~~k-------~ss~K~~~I~~lP 306 (415)
T COG5533 234 SRLQCEACNYTSTTIAMFSTLLVPPYEVVQLGLQECIDRFYEEEKLEGKDAWRCPKCGRK-------ESSRKRMEILVLP 306 (415)
T ss_pred hhhhhhhcCCceeEEeccceeeeccchheeecHHHHHHHhhhHHhhcCcccccCchhccc-------ccchheEEEEecC
Confidence 4789999998762221111110 0111222 4322 333455999999998 6788999999999
Q ss_pred cchhhccccccccc--Cccc
Q 022703 72 DKTSEAAKPISLEV--PKAT 89 (293)
Q Consensus 72 ~~Lvv~~~Rf~l~~--p~K~ 89 (293)
++|+||++||++-. |.|+
T Consensus 307 ~~LII~i~RF~i~V~~~~ki 326 (415)
T COG5533 307 DVLIIHISRFHISVMGRKKI 326 (415)
T ss_pred ceEEEEeeeeeEEeeccccc
Confidence 99999999999543 6665
No 24
>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=97.18 E-value=8.6e-05 Score=67.58 Aligned_cols=75 Identities=13% Similarity=0.168 Sum_probs=49.9
Q ss_pred eeecccCCccccCHHH---------H------HHHHHHhccCCCCcchhhhhccccCCCCCCCCCccccccccccccccc
Q 022703 5 SLKCGDCGALLRSVQE---------A------QEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTD 69 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~---------a------q~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~t 69 (293)
.++|..||.+.....+ + ....+.....+|..+ .+..|.|+.| ++.|.+
T Consensus 63 ~i~C~~C~~~s~~~~e~f~~LsL~ip~~~~~~~~sl~~~L~~~~~~E--~l~~~~C~~C---------------~~~i~~ 125 (240)
T cd02662 63 RIVCLQCGESSKVRYESFTMLSLPVPNQSSGSGTTLEHCLDDFLSTE--IIDDYKCDRC---------------QTVIVR 125 (240)
T ss_pred EEEeCCCCCccCcceeeeeeeEecccccCCCCCCCHHHHHHHhcCcc--cccCcCCCCC---------------eEEeec
Confidence 5899999987432111 0 112233355566544 1335999999 345999
Q ss_pred cccchhhccccccccc---Cccc---cCCcccc
Q 022703 70 FVDKTSEAAKPISLEV---PKAT---ADSEEAI 96 (293)
Q Consensus 70 FP~~Lvv~~~Rf~l~~---p~K~---~~~~~~l 96 (293)
+|++|+|+++||.++. +.|+ +.+|..|
T Consensus 126 lP~vLii~LkRF~~~~~~~~~K~~~~v~fp~~l 158 (240)
T cd02662 126 LPQILCIHLSRSVFDGRGTSTKNSCKVSFPERL 158 (240)
T ss_pred CCcEEEEEEEEEEEcCCCceeeeccEEECCCcc
Confidence 9999999999999885 6777 5556555
No 25
>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=97.12 E-value=0.00059 Score=67.24 Aligned_cols=40 Identities=25% Similarity=0.379 Sum_probs=36.9
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 022703 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~ 154 (293)
-+..|..|++|||+++.+.+||++.-| |.++|++||+...
T Consensus 156 ~e~~I~~i~eMGf~R~qV~~ALRAafN-NPdRAVEYL~tGI 195 (378)
T TIGR00601 156 RETTIEEIMEMGYEREEVERALRAAFN-NPDRAVEYLLTGI 195 (378)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHhC-CHHHHHHHHHhCC
Confidence 467899999999999999999999988 8999999999874
No 26
>KOG4598 consensus Putative ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=97.10 E-value=0.0001 Score=76.92 Aligned_cols=88 Identities=15% Similarity=0.158 Sum_probs=64.0
Q ss_pred eecccCCcccc---------------CHHHHHHHHHHhccCCCC-cchhhhhccccCCCCCCCCCccccccccccccccc
Q 022703 6 LKCGDCGALLR---------------SVQEAQEHAELTSHSNFS-ESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTD 69 (293)
Q Consensus 6 LkC~~Cg~v~~---------------~~~~aq~ha~~TgH~~F~-e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~t 69 (293)
.+|..||.-.. |.--|-...++...++-. |..|-...|-|..|+++| -|.|..+|++
T Consensus 182 v~cl~c~~e~~~~d~fld~pl~v~pfg~~~ay~sieeal~afvqpe~ldg~nqy~ce~ck~k~-------dahkgl~~~~ 254 (1203)
T KOG4598|consen 182 VACLKCGRESVKTDYFLDLPLAVKPFGAIHAYKSVEEALTAFVQPELLDGSNQYMCENCKSKQ-------DAHKGLRITQ 254 (1203)
T ss_pred HHHHHcCccccccceeecccccccCCcchhhhhhHHHHHHHhcChhhcCCccHHHHhhhhhhh-------hhhcCceeec
Confidence 47889987652 222233333332333333 334666679999999984 6899999999
Q ss_pred cccchhhcccccccc-c---Cccc---cCCccccccCC
Q 022703 70 FVDKTSEAAKPISLE-V---PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 70 FP~~Lvv~~~Rf~l~-~---p~K~---~~~~~~lDl~~ 100 (293)
||=.|.||++||+|+ | -+|| +.+|+.|||+.
T Consensus 255 fpy~lt~~lkrfdfdy~tmhriklnd~~tfp~~l~ln~ 292 (1203)
T KOG4598|consen 255 FPYLLTIQLKRFDFDYNTMHRIKLNDKMTFPDVLDLND 292 (1203)
T ss_pred cceeeEEeeecccccchheeeeeecccccCcccccHHH
Confidence 999999999999999 3 7888 55899999964
No 27
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=96.70 E-value=0.00073 Score=68.70 Aligned_cols=52 Identities=19% Similarity=0.309 Sum_probs=44.1
Q ss_pred cccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCCCCCCCCCC
Q 022703 111 PEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHENDPDIDEMPM 164 (293)
Q Consensus 111 ~~~~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~dD~didep~~ 164 (293)
.+||+..+..|.+|||..+.|++||..+++ +++.+++|++.|.|. .+++|..
T Consensus 618 keVdE~~~~Slle~Gln~n~~Rkal~~~n~-d~~r~V~w~~N~~D~-tF~EP~v 669 (749)
T COG5207 618 KEVDESKARSLLENGLNPNLCRKALMDMNT-DSKRRVVWCINDDDG-TFPEPEV 669 (749)
T ss_pred ccccHHHHHHHHHcCCCHHHHHHHHHHccC-CchheEEEEEeCCCC-CCCCCCC
Confidence 368999999999999999999999988765 999999999996544 4666643
No 28
>KOG1866 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=96.38 E-value=0.0003 Score=73.83 Aligned_cols=56 Identities=14% Similarity=0.115 Sum_probs=48.3
Q ss_pred hhhhccccCCCCCCCCCccccccccccccccccccchhhcccccccc--c--Cccc---cCCccccccCC
Q 022703 38 EAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLE--V--PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 38 d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~--~--p~K~---~~~~~~lDl~~ 100 (293)
|-..-|.|..|.++ +.-+|+|.|+..|.+|+||++||.++ + .+|- +.+|-.||+..
T Consensus 262 EG~nAYhCeKCdeK-------~~TvkRt~ik~LPsvl~IqLkRF~yD~e~~~~iK~n~~frFP~~ldMeP 324 (944)
T KOG1866|consen 262 EGANAYHCEKCDEK-------VDTVKRTCIKKLPSVLAIQLKRFDYDWERECAIKFNDYFRFPRELDMEP 324 (944)
T ss_pred cCcchhhhhhhhhh-------hHhHHHHHHhhCChhheehhhhccchhhhccccccchhcccchhhcCCc
Confidence 44456999999998 78899999999999999999999998 2 7777 66788899875
No 29
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=96.25 E-value=0.011 Score=59.57 Aligned_cols=48 Identities=31% Similarity=0.385 Sum_probs=42.9
Q ss_pred ccccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCCCC
Q 022703 110 EPEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHENDPD 158 (293)
Q Consensus 110 ~~~~~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~dD~d 158 (293)
++.||...|++|+.|||+...|.-||..+|| +++.|+..|..+..++.
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 4458999999999999999999999999888 89999999988877764
No 30
>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=96.20 E-value=0.0016 Score=61.01 Aligned_cols=39 Identities=21% Similarity=0.137 Sum_probs=34.8
Q ss_pred hhhccccCCCCCCCCCcccccccccccccccccc----chhhcccccccc
Q 022703 39 AVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVD----KTSEAAKPISLE 84 (293)
Q Consensus 39 ~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~----~Lvv~~~Rf~l~ 84 (293)
.+..+.|+.|+++ ..++|+++|.+||+ +|+||++||..+
T Consensus 131 ~~~~~~C~~C~~~-------~~a~k~~~i~~lP~~L~~VL~i~lkrf~~~ 173 (268)
T cd02672 131 KVTKAWCDTCCKY-------QPLEQTTSIRHLPDILLLVLVINLSVTNGE 173 (268)
T ss_pred hcccccccccCcc-------cccEEEEEeecCCCcccceEEEEEeccChh
Confidence 3557899999987 78999999999999 999999999854
No 31
>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=95.99 E-value=0.0032 Score=54.05 Aligned_cols=54 Identities=15% Similarity=0.100 Sum_probs=43.4
Q ss_pred hhhccccCCCC--CCCCCccccccccccccccccccchhhccccccccc---Cccc---cCCccccccC
Q 022703 39 AVLNLVCATCG--KPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV---PKAT---ADSEEAIDVD 99 (293)
Q Consensus 39 ~i~~~~C~~Cg--~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~~---p~K~---~~~~~~lDl~ 99 (293)
.+..+.|..|+ +. ..+.++..|.++|++|+|++.||.... +.|+ +.+++.|++.
T Consensus 113 ~~~~~~~~~c~~~~~-------~~~~~~~~i~~lP~~L~i~l~R~~~~~~~~~~k~~~~v~~~~~l~~~ 174 (255)
T cd02257 113 ILEGDNCYKCEKKKK-------QEATKRLKIKKLPPVLIIHLKRFSFNEDGTKEKLNTKVSFPLELDLS 174 (255)
T ss_pred ccCCCCcccCCCCcc-------cceeEEEecccCCceeEEEeeceeeccccccccCCCeEeCCCcccCc
Confidence 35568899998 33 678899999999999999999999874 6666 5567777764
No 32
>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=95.83 E-value=0.014 Score=57.77 Aligned_cols=43 Identities=28% Similarity=0.383 Sum_probs=39.2
Q ss_pred cCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCC
Q 022703 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHEND 156 (293)
Q Consensus 113 ~~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~dD 156 (293)
-+.++|+.|.+|||+++.+.-|-++++ +|-|.|.||||+|..|
T Consensus 336 eE~~AIeRL~~LGF~r~~viqaY~ACd-KNEelAAn~Lf~~~~~ 378 (378)
T TIGR00601 336 EEKEAIERLCALGFDRGLVIQAYFACD-KNEELAANYLLSQNFD 378 (378)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhcC-CcHHHHHHHHHhhcCC
Confidence 377899999999999999999999886 5999999999999776
No 33
>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=95.64 E-value=0.0037 Score=62.26 Aligned_cols=54 Identities=11% Similarity=-0.104 Sum_probs=43.3
Q ss_pred hhccccCCCCCCCCCccccccccccccccccccchhhccccccccc--Cccc---cCCccc-cccCC
Q 022703 40 VLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSEEA-IDVDM 100 (293)
Q Consensus 40 i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~~--p~K~---~~~~~~-lDl~~ 100 (293)
...|.|+.|... ..++|+..+...|++|+||.+||...+ ..|. |.+|.. |||+.
T Consensus 309 L~ky~~~~c~~~-------~~a~k~~~I~~LP~vLiihLKRF~~~~~~~~K~~t~V~FP~~~LDm~~ 368 (440)
T cd02669 309 LKKYDGKTETEL-------KDSLKRYLISRLPKYLIFHIKRFSKNNFFKEKNPTIVNFPIKNLDLSD 368 (440)
T ss_pred HHhcCCccceec-------ccceEEEEEeeCCcEEEEEEecccCCCCccccCCCEEECCCCccchhh
Confidence 344999999875 567999999999999999999999875 3444 556764 78875
No 34
>COG5560 UBP12 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=95.43 E-value=0.0037 Score=65.00 Aligned_cols=68 Identities=16% Similarity=0.050 Sum_probs=52.6
Q ss_pred HHhccCC-----CC--cchhhhhccccCCCCCCCCCccccccccccccccccccchhhccccccccc--Cccc---cCC-
Q 022703 26 ELTSHSN-----FS--ESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADS- 92 (293)
Q Consensus 26 ~~TgH~~-----F~--e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~~--p~K~---~~~- 92 (293)
.+|+.-+ |+ |.......|+||.|+.. -.|+|+.-+-..|++|+||++||.-++ +.|. |+.
T Consensus 672 ~rtiTL~dCl~eFskpEqLgl~DswyCpgCkef-------rqasKqmelwrlP~iLiihLkRFss~rsfrdKiddlVeyP 744 (823)
T COG5560 672 ERTITLQDCLNEFSKPEQLGLSDSWYCPGCKEF-------RQASKQMELWRLPMILIIHLKRFSSVRSFRDKIDDLVEYP 744 (823)
T ss_pred cCCCcHHHHHHHhccHhhcCCcccccCCchHhh-------hhhhhhhhhhcCChheeeehhhhhhcccchhhhhhhhccc
Confidence 5555443 65 33455567999999876 789999999999999999999999887 8888 443
Q ss_pred ccccccCC
Q 022703 93 EEAIDVDM 100 (293)
Q Consensus 93 ~~~lDl~~ 100 (293)
-+.|||+.
T Consensus 745 iddldLs~ 752 (823)
T COG5560 745 IDDLDLSG 752 (823)
T ss_pred cccccccc
Confidence 34577774
No 35
>KOG1868 consensus Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=95.35 E-value=0.0029 Score=66.29 Aligned_cols=75 Identities=16% Similarity=0.159 Sum_probs=49.4
Q ss_pred ceeecccCCccccCHHHHHHHHHHh---ccC------------CCCcc-hhhhhccccCCCCCCCCCccccccc--cccc
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELT---SHS------------NFSES-TEAVLNLVCATCGKPCRSKTETDLH--RKRT 65 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~T---gH~------------~F~e~-~d~i~~~~C~~Cg~~~~~~~e~~~a--~K~t 65 (293)
..|+|..||..-.+-.-.....-.- |+. ++.++ .|.-..|.||.|+.+ ... +|+.
T Consensus 463 s~Lkc~~cg~~s~t~~~f~~lslpIp~~~~~~~~~~L~~C~~~ft~~ekle~~~~w~Cp~c~~~-------~~~~~lK~~ 535 (653)
T KOG1868|consen 463 SYLKCQACGYTSTTFETFTDLSLPIPKKGFAGGKVSLEDCLSLFTKEEKLEGDEAWLCPRCKHK-------ESSKTLKKL 535 (653)
T ss_pred hheehhhcCCcceeeecceeeEEecccccccccccchHhhhccccchhhcccccccCCccccCc-------cccccccee
Confidence 5799999999874443322222111 111 22222 233334999999987 222 5999
Q ss_pred cccccccchhhccccccccc
Q 022703 66 GHTDFVDKTSEAAKPISLEV 85 (293)
Q Consensus 66 ~f~tFP~~Lvv~~~Rf~l~~ 85 (293)
.|-.||++|+|+++||..+.
T Consensus 536 ~i~~lp~iLiihL~Rf~~~~ 555 (653)
T KOG1868|consen 536 TILRLPKILIIHLKRFSSDG 555 (653)
T ss_pred eeecCCHHHHHHHHHhccCc
Confidence 99999999999999999984
No 36
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=95.16 E-value=0.03 Score=54.33 Aligned_cols=40 Identities=38% Similarity=0.588 Sum_probs=37.0
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 022703 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~ 154 (293)
+.++++-|..|||++..+.-|.+++. .|-|.|.||||+|+
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 66889999999999999999998875 58999999999999
No 37
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=94.64 E-value=0.041 Score=53.36 Aligned_cols=41 Identities=24% Similarity=0.341 Sum_probs=37.2
Q ss_pred cCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 022703 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (293)
Q Consensus 113 ~~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~ 154 (293)
..+..|.+|++||+.+....+||++.=| |.++|++||+...
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 4678899999999999999999999888 8999999998753
No 38
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=94.10 E-value=0.17 Score=51.15 Aligned_cols=39 Identities=33% Similarity=0.544 Sum_probs=35.1
Q ss_pred cCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Q 022703 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVE 152 (293)
Q Consensus 113 ~~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~ 152 (293)
++.+-++.|++|||-+..|+.||+...+ +|+.|++||.+
T Consensus 302 i~d~~lsllv~mGfeesdaRlaLRsc~g-~Vd~AvqfI~e 340 (568)
T KOG2561|consen 302 INDETLSLLVGMGFEESDARLALRSCNG-DVDSAVQFIIE 340 (568)
T ss_pred ccchHHHHHHHcCCCchHHHHHHHhccc-cHHHHHHHHHH
Confidence 6778899999999999999999998866 89999999843
No 39
>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=93.81 E-value=0.063 Score=39.37 Aligned_cols=29 Identities=31% Similarity=0.565 Sum_probs=22.1
Q ss_pred ccCHHHHHHHHhCCCCHHHHHHHHHHhCC
Q 022703 112 EVDKELLKELEAMGFPVARATRALHYSGN 140 (293)
Q Consensus 112 ~~~~~~l~~L~~MGF~~~~a~kAL~~tgn 140 (293)
-+|.++|+++.+|||+.+.+..||+.-|=
T Consensus 7 Gi~~~lVd~F~~mGF~~dkVvevlrrlgi 35 (55)
T PF09288_consen 7 GIDKDLVDQFENMGFERDKVVEVLRRLGI 35 (55)
T ss_dssp --SHHHHHHHHHHT--HHHHHHHHHHS--
T ss_pred CCCHHHHHHHHHcCCcHHHHHHHHHHhCC
Confidence 36899999999999999999999998763
No 40
>COG1773 Rubredoxin [Energy production and conversion]
Probab=93.68 E-value=0.013 Score=42.89 Aligned_cols=42 Identities=19% Similarity=0.455 Sum_probs=34.8
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~ 50 (293)
+.+|..||+|.....+...+.-. +-+-|.+. -.++.||-||-
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~gi~-pgT~fedl---Pd~w~CP~Cg~ 44 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRCGIA-PGTPFEDL---PDDWVCPECGV 44 (55)
T ss_pred ceEecCCceEeccccCCccCCCC-CCCchhhC---CCccCCCCCCC
Confidence 67999999999888887777766 55568888 57799999984
No 41
>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=93.56 E-value=0.016 Score=50.77 Aligned_cols=47 Identities=13% Similarity=0.292 Sum_probs=35.5
Q ss_pred ccccCCCCCCCCCccccccccccccccccccchhhccccccccc----Cccc---cCCc-cccccCC
Q 022703 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSE-EAIDVDM 100 (293)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~~----p~K~---~~~~-~~lDl~~ 100 (293)
.+.|..|+.. ...|.++|++|+|+.+||.+.. ..|. +.+| +.|||+.
T Consensus 142 ~~~c~~c~~~------------~~~~~~~P~~L~i~l~R~~~~~~~~~~~K~~~~v~~~~~~l~l~~ 196 (269)
T PF00443_consen 142 SIKCSSCKNS------------QSSISSLPPILIIQLKRFEFDQETGRSKKINNPVEFPLEELDLSP 196 (269)
T ss_dssp EEEETTTTCE------------EEEEEEBBSEEEEEEE-EEEESTSSEEEE--CEEB--SSEEEGGG
T ss_pred cccccccccc------------ccccccccceeeeccccceeccccccccccccccccCchhhhhhh
Confidence 4789999883 7889999999999999996663 5666 6678 6899986
No 42
>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=92.66 E-value=0.34 Score=33.12 Aligned_cols=40 Identities=23% Similarity=0.223 Sum_probs=29.4
Q ss_pred HHHHHH-hCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCCC
Q 022703 117 LLKELE-AMGFPVARATRALHYSGNANVEAAVNWVVEHENDP 157 (293)
Q Consensus 117 ~l~~L~-~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~dD~ 157 (293)
.|.+++ -.|.+...|...|..+++ +++.|++-.|++.++|
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 344444 248899999999999887 9999999999987765
No 43
>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=92.62 E-value=0.26 Score=33.46 Aligned_cols=37 Identities=35% Similarity=0.532 Sum_probs=30.3
Q ss_pred CHHHHHHHHhCCCCH---HHHHHHHHHhCCCCHHHHHHHHHH
Q 022703 114 DKELLKELEAMGFPV---ARATRALHYSGNANVEAAVNWVVE 152 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~---~~a~kAL~~tgn~~~E~A~~WL~~ 152 (293)
+.+.+.+|.+| ||. ..+++.|...+| +++.|++-|++
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 777888887665 89999999875
No 44
>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=92.31 E-value=0.069 Score=34.76 Aligned_cols=25 Identities=32% Similarity=0.821 Sum_probs=20.2
Q ss_pred eecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
.+|.+||++..+.. ..+.||.||.+
T Consensus 2 ~~C~~CGy~y~~~~---------------------~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEE---------------------APWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCc---------------------CCCcCcCCCCc
Confidence 58999999876654 45799999985
No 45
>KOG1863 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=92.15 E-value=0.068 Score=59.32 Aligned_cols=88 Identities=14% Similarity=0.023 Sum_probs=63.0
Q ss_pred ceeecccCCccccCH----------HHHHHHHHHhccCCCCcc-hhhhhccccCCCCCCCCCcccccccccccccccccc
Q 022703 4 VSLKCGDCGALLRSV----------QEAQEHAELTSHSNFSES-TEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVD 72 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~----------~~aq~ha~~TgH~~F~e~-~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~ 72 (293)
..+.|..|+.-.... .+.-. ...+.|.+|+.+ .+.... .|..|... ..|.|...|.+||.
T Consensus 290 ~~i~c~~~~~~s~r~e~f~d~ql~~~g~~n-l~~sf~~y~~~E~l~gdn~-~~~~~~~~-------~~a~k~~~f~~lPp 360 (1093)
T KOG1863|consen 290 SVIKCIDVDFESSRSESFLDLQLNGKGVKN-LEDSLHLYFEAEILLGDNK-YDAECHGL-------QDAKKGVLFDSLPP 360 (1093)
T ss_pred eEEEEEeeeeeccccccccCccccccchhh-HHHHHHHhhhHHHhcCCcc-ccccccch-------hhhhcceeeccCCc
Confidence 467888877655111 11112 555689999844 333332 79999875 67888999999999
Q ss_pred chhhccccccccc----Cccc---cCCccccccCC
Q 022703 73 KTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 73 ~Lvv~~~Rf~l~~----p~K~---~~~~~~lDl~~ 100 (293)
+|.+++.||.++. ++|+ ..+|..||++.
T Consensus 361 vl~~qL~Rf~~~~~~~~~~Ki~d~~~fp~~i~~d~ 395 (1093)
T KOG1863|consen 361 VLFIQLMRFEYDFSTGQKIKINDKFEFPLIIDMDR 395 (1093)
T ss_pred hhhhhhhheeeeccCCceeehhhccCCccccccch
Confidence 9999999999984 8888 44677888876
No 46
>PTZ00266 NIMA-related protein kinase; Provisional
Probab=91.95 E-value=2.5 Score=47.05 Aligned_cols=17 Identities=41% Similarity=0.806 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 022703 249 AREKIRQKLEEDKAERRR 266 (293)
Q Consensus 249 ar~rir~qIe~Dk~eR~~ 266 (293)
.++|++ .++.++.+|++
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 344443 34555555554
No 47
>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=91.49 E-value=0.068 Score=49.66 Aligned_cols=41 Identities=7% Similarity=-0.137 Sum_probs=33.9
Q ss_pred cccccccccccccchhhccccccccc--Cccc---cCCccccccCC
Q 022703 60 LHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 60 ~a~K~t~f~tFP~~Lvv~~~Rf~l~~--p~K~---~~~~~~lDl~~ 100 (293)
.+.+...|..+|++|+||++||.+.. +.|+ |.+|..|||+.
T Consensus 88 ~~~~~e~i~~lP~vLiIhLKRF~~~~~~~~Kl~~~I~fP~~Ldl~~ 133 (241)
T cd02670 88 QYFNNSVFAKAPSCLIICLKRYGKTEGKAQKMFKKILIPDEIDIPD 133 (241)
T ss_pred HHhchhhhhhCCCeEEEEEEccccCCCcceeCCcEECCCCcCCchh
Confidence 34444459999999999999999975 7888 77888999986
No 48
>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=90.76 E-value=0.11 Score=43.25 Aligned_cols=46 Identities=24% Similarity=0.549 Sum_probs=28.8
Q ss_pred ceeecccCCccccCHHH------------HH-HHHHHhccCCCCcc--hhhhhccccCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQE------------AQ-EHAELTSHSNFSES--TEAVLNLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~------------aq-~ha~~TgH~~F~e~--~d~i~~~~C~~Cg~~ 51 (293)
..++| +||+.|-+-.+ .. .|.+- .-..|... -..+.+|.||.||..
T Consensus 23 k~vkc-~CGh~f~d~r~NwK~~alv~vRd~~E~~~~i-Yp~~~aPdp~w~~irEyyCP~Cgt~ 83 (112)
T PF08882_consen 23 KVVKC-DCGHEFCDARENWKLGALVYVRDPEEIHPEI-YPFTMAPDPEWQVIREYYCPGCGTQ 83 (112)
T ss_pred ceeec-cCCCeecChhcChhhCcEEEecChHHhhhhh-cccccCCCCCcEEEEEEECCCCcce
Confidence 36788 89999933222 22 23222 34446533 366899999999985
No 49
>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=90.65 E-value=0.05 Score=39.03 Aligned_cols=43 Identities=19% Similarity=0.480 Sum_probs=28.2
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
+.+|..||+|.....+-..+.-..| +.|... -.+|+||.||.+
T Consensus 1 ~y~C~~CgyiYd~~~Gd~~~~i~pG-t~f~~L---p~~w~CP~C~a~ 43 (50)
T cd00730 1 KYECRICGYIYDPAEGDPDEGIPPG-TPFEDL---PDDWVCPVCGAG 43 (50)
T ss_pred CcCCCCCCeEECCCCCCcccCcCCC-CCHhHC---CCCCCCCCCCCc
Confidence 3689999999976554333333322 335555 456999999875
No 50
>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=90.31 E-value=0.9 Score=30.72 Aligned_cols=38 Identities=24% Similarity=0.395 Sum_probs=30.3
Q ss_pred HHHHHHHHhC--CCCHHHHHHHHHHhCCCCHHHHHHHHHHh
Q 022703 115 KELLKELEAM--GFPVARATRALHYSGNANVEAAVNWVVEH 153 (293)
Q Consensus 115 ~~~l~~L~~M--GF~~~~a~kAL~~tgn~~~E~A~~WL~~h 153 (293)
++.+.+|.+| .++......+|..++| +++.|++-|++.
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 5678899998 3556888888977766 899999999874
No 51
>KOG1864 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=90.20 E-value=0.081 Score=55.13 Aligned_cols=137 Identities=11% Similarity=0.139 Sum_probs=85.6
Q ss_pred ceeecccCCccccCHHHHHHHHHHhc---c-------CCCC--cchhhhhccccCCCCCCCCCccccccccccccccccc
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTS---H-------SNFS--ESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFV 71 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~Tg---H-------~~F~--e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP 71 (293)
+..+|..|+++-.-.+..++.--.+. + .+|. |......-|.|..|... ..|.++.+++..|
T Consensus 391 ~et~Clsc~t~T~~de~f~D~~~~v~~de~~si~~~l~~~~~~e~l~g~nky~c~~c~s~-------qeae~~l~~k~lp 463 (587)
T KOG1864|consen 391 NETRCLSCETITSRDEGFLDLSVAVEIDENTSITNLLKSFSSTETLSGENKYSCENCCSL-------QEAERRLKIKKLP 463 (587)
T ss_pred eeeeeccccccccccccccccceeccccccccHHHHHHHhcchhhccCCCcccccccCch-------hhHHHhccccCCc
Confidence 56789999998844443332222211 0 1232 22233456999999886 6899999999999
Q ss_pred cchhhccccccccc----Cccc---cCCccccccCCCCCCCCcccccccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHH
Q 022703 72 DKTSEAAKPISLEV----PKAT---ADSEEAIDVDMSGSQPEEMVEPEVDKELLKELEAMGFPVARATRALHYSGNANVE 144 (293)
Q Consensus 72 ~~Lvv~~~Rf~l~~----p~K~---~~~~~~lDl~~g~~~~Ee~~~~~~~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E 144 (293)
.+|+|+.+||..+- =+|+ +++|-.|++-...+.+ ..+..-..+++.++.+|-++++..+--+.--+
T Consensus 464 ~~L~l~Lkrfk~~~~~~~~~kl~~~v~~plel~l~~~~~~~---~~~~~~Y~L~avVvH~G~~p~~GHYia~~r~~---- 536 (587)
T KOG1864|consen 464 YVLTLHLKRFKYSEQQNRYTKLLYRVVFPLELRLKDTLKDD---NNPDRKYDLVAVVVHLGSTPNRGHYVAYVKSL---- 536 (587)
T ss_pred ceeeeehhccccccccccccccccccccccceeeccccccc---cCccceeeEEEEEEeccCCCCCcceEEEEeeC----
Confidence 99999999999984 3455 5556666665311111 11123456778888999999988864322111
Q ss_pred HHHHHHHHhcC
Q 022703 145 AAVNWVVEHEN 155 (293)
Q Consensus 145 ~A~~WL~~h~d 155 (293)
+.+||+-..|
T Consensus 537 -~~nWl~fdD~ 546 (587)
T KOG1864|consen 537 -DFNWLLFDDD 546 (587)
T ss_pred -CCCceecccc
Confidence 2239876433
No 52
>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=89.96 E-value=0.095 Score=48.33 Aligned_cols=37 Identities=8% Similarity=0.048 Sum_probs=29.0
Q ss_pred cccccccccccccchhhccccccccc--Cccc---cCCcccc
Q 022703 60 LHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSEEAI 96 (293)
Q Consensus 60 ~a~K~t~f~tFP~~Lvv~~~Rf~l~~--p~K~---~~~~~~l 96 (293)
.+.|+..|..+|++|+|+++||.+.. ..|+ +.+|..|
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 6666 4455433
No 53
>PHA02768 hypothetical protein; Provisional
Probab=89.57 E-value=0.37 Score=35.39 Aligned_cols=39 Identities=23% Similarity=0.416 Sum_probs=32.2
Q ss_pred CcceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 2 AGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 2 ~~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
+-+-.+|..||+.+.....-+.|... |+ ..|+|..||+-
T Consensus 2 ~~~~y~C~~CGK~Fs~~~~L~~H~r~--H~---------k~~kc~~C~k~ 40 (55)
T PHA02768 2 ALLGYECPICGEIYIKRKSMITHLRK--HN---------TNLKLSNCKRI 40 (55)
T ss_pred cccccCcchhCCeeccHHHHHHHHHh--cC---------CcccCCcccce
Confidence 44456999999999999888999987 66 25799999985
No 54
>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]
Probab=89.53 E-value=5.4 Score=43.24 Aligned_cols=82 Identities=30% Similarity=0.369 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHc------HHHHHHHH-HHHH
Q 022703 182 EIKLKAQELRERARKKKEEEEKRMEREREKERIRIGKELLEAKRIEEENERKRILALRKAE------KEEEKRAR-EKIR 254 (293)
Q Consensus 182 Ek~~k~~el~~k~r~~r~eeek~e~~e~E~~Rrk~GKe~~~~k~~~ee~e~k~~~e~rrrE------K~ee~~ar-~rir 254 (293)
|+..+++|+.+.-|+.|+.+|++... .+--+..+.-+++|+++++.++++.-+.-++= +.+..... .+-+
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 ERLRKIQELAEAERKRREAEEKRRRE---EEEKKRAKAEMETKRKAEEEQRKAQEEEERRLALELQEQLAKEAEEEAKRQ 1000 (1259)
T ss_pred HHHHHHHHHHHHHHHhhhhhHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45556777776666666655443332 23333344455677777776666554443331 11111111 1334
Q ss_pred HHHHHHHHHHHH
Q 022703 255 QKLEEDKAERRR 266 (293)
Q Consensus 255 ~qIe~Dk~eR~~ 266 (293)
.|++++|+.+.-
T Consensus 1001 ~~~Eqer~D~~l 1012 (1259)
T KOG0163|consen 1001 NQLEQERRDHEL 1012 (1259)
T ss_pred hHHHHHHHHHHH
Confidence 557777777653
No 55
>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=89.34 E-value=0.062 Score=38.10 Aligned_cols=43 Identities=23% Similarity=0.532 Sum_probs=24.1
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
+.+|.+||+|-....+=-.+.-. --+-|.+. -.+|+||.||..
T Consensus 1 ky~C~~CgyvYd~~~Gd~~~~i~-pGt~F~~L---p~~w~CP~C~a~ 43 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPENGIP-PGTPFEDL---PDDWVCPVCGAP 43 (47)
T ss_dssp EEEETTTSBEEETTTBBGGGTB--TT--GGGS----TT-B-TTTSSB
T ss_pred CcCCCCCCEEEcCCcCCcccCcC-CCCCHHHC---CCCCcCcCCCCc
Confidence 46899999999654432222111 22447766 456999999864
No 56
>PF13423 UCH_1: Ubiquitin carboxyl-terminal hydrolase
Probab=89.01 E-value=0.1 Score=48.76 Aligned_cols=53 Identities=19% Similarity=0.156 Sum_probs=38.9
Q ss_pred hccccCCCCCCCCCccccccccccccccccccchhhccccccccc--Cccc---cCCccccccCC
Q 022703 41 LNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 41 ~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~~--p~K~---~~~~~~lDl~~ 100 (293)
....|+.|++. ....-+..|.+.|++|+|++.+...+. +.|. +.+|..++++.
T Consensus 179 ~~a~C~~C~~~-------~~~~~~r~i~~LPpVL~In~~~~~~~~~w~~~~~~~~~ip~~i~~~~ 236 (295)
T PF13423_consen 179 TRAWCEKCNKY-------QPTEQRRTIRSLPPVLSINLNRYSEEEFWPKKNWLKIWIPPSINLPH 236 (295)
T ss_pred ccccccccccc-------cceeeeeeccCCCcEEEEEccCCCcccccccccCCceecceeeeccc
Confidence 34789999986 456667778999999999999988883 5444 44455565554
No 57
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=88.84 E-value=7.4 Score=42.23 Aligned_cols=31 Identities=23% Similarity=0.275 Sum_probs=20.5
Q ss_pred CCHHHHHHHHHHhCCCCHHHHHHHHHHhcCC
Q 022703 126 FPVARATRALHYSGNANVEAAVNWVVEHEND 156 (293)
Q Consensus 126 F~~~~a~kAL~~tgn~~~E~A~~WL~~h~dD 156 (293)
.+-..|+-||-.+|=.....|-=|-++..|-
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 4556777788777655566677777665553
No 58
>KOG1870 consensus Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=88.14 E-value=0.097 Score=56.65 Aligned_cols=57 Identities=9% Similarity=0.059 Sum_probs=45.0
Q ss_pred hhhhhccccCCCCCCCCCccccccccccccccccccchhhccccccccc--Cccc---cC-CccccccCC
Q 022703 37 TEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---AD-SEEAIDVDM 100 (293)
Q Consensus 37 ~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~~--p~K~---~~-~~~~lDl~~ 100 (293)
.+.-..|.||.|.+. ..|+|..-.-..|++||||.+||.+.+ .-|+ ++ +...||++.
T Consensus 711 L~~~~~w~C~~Cke~-------~~A~Kk~~lwrlPeiLiihLKrF~~~r~~~~k~~~~v~fPi~~ld~s~ 773 (842)
T KOG1870|consen 711 LGKDDRWYCPQCKEL-------RQATKKLDLWRLPEILIIHLKRFQYSRESSSKVKTKVEFPLGSLDLSE 773 (842)
T ss_pred CCccccccChHHHHH-------HHHhhhhhhhhCCceEEEEeecceeechhhhhhCccccCCCcCCCcch
Confidence 344456999999986 889999999999999999999999997 4444 44 345577665
No 59
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.78 E-value=0.57 Score=42.37 Aligned_cols=39 Identities=28% Similarity=0.273 Sum_probs=33.1
Q ss_pred cCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Q 022703 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVE 152 (293)
Q Consensus 113 ~~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~ 152 (293)
.+...++.|.+|||+++.+..+|...+- +++.|.+.|++
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 4778899999999999999999977654 78888887765
No 60
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=87.68 E-value=0.24 Score=42.18 Aligned_cols=46 Identities=22% Similarity=0.412 Sum_probs=26.7
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCC--CcchhhhhccccCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNF--SESTEAVLNLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F--~e~~d~i~~~~C~~Cg~~ 51 (293)
....|.+||..+.... ++.+...+.++.| ...+.. ..+.||.||+.
T Consensus 69 ~~~~C~~CG~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKE-VKESLDEEIREAIHFIPEVVH-AFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEeccc-ccccccccccccccccccccc-cCcCCcCCCCC
Confidence 5689999998876553 2222223344443 333211 23679999985
No 61
>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=87.19 E-value=1.6 Score=30.43 Aligned_cols=32 Identities=25% Similarity=0.361 Sum_probs=23.7
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHh---CCCCHHH
Q 022703 114 DKELLKELEAMGFPVARATRALHYS---GNANVEA 145 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL~~t---gn~~~E~ 145 (293)
-++++..|++.||++..+.+|+... .+.+++.
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 3578999999999999999998765 3345553
No 62
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=85.76 E-value=0.18 Score=38.58 Aligned_cols=65 Identities=22% Similarity=0.392 Sum_probs=23.0
Q ss_pred ecccCCccccCHHHHHHHHHHhccCC-CCcc-------------hhhhhc-cccCCCCCCCCCccccccccccccccccc
Q 022703 7 KCGDCGALLRSVQEAQEHAELTSHSN-FSES-------------TEAVLN-LVCATCGKPCRSKTETDLHRKRTGHTDFV 71 (293)
Q Consensus 7 kC~~Cg~v~~~~~~aq~ha~~TgH~~-F~e~-------------~d~i~~-~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP 71 (293)
+|..|+..+.+......|... -|.. +... ...+.. +.|+.|++.+++...+..|..+.++..+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~-~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~ 79 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKK-KHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKHHKKRN 79 (100)
T ss_dssp -------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTTTTC-S
T ss_pred Ccccccccccccccccccccc-ccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCccCCCcc
Confidence 699999999999999999976 5543 2210 022333 89999999988888888888887777654
Q ss_pred c
Q 022703 72 D 72 (293)
Q Consensus 72 ~ 72 (293)
.
T Consensus 80 ~ 80 (100)
T PF12756_consen 80 S 80 (100)
T ss_dssp -
T ss_pred c
Confidence 3
No 63
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=84.78 E-value=0.36 Score=51.82 Aligned_cols=51 Identities=10% Similarity=-0.059 Sum_probs=41.1
Q ss_pred ccccCCCCCCCCCccccccccccccccccccchhhccccccccc----Cccc---cCCccccccCC
Q 022703 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~~----p~K~---~~~~~~lDl~~ 100 (293)
.|.|..-|- .-|.|.--|.|||++|-+|++||..+. -+|+ -.+|..+|+.+
T Consensus 358 ~Y~ae~~Gl--------qdAkKGViFeSlPpVlhlqLKRFeyDfe~d~mvKINDryEFP~eiDl~p 415 (1089)
T COG5077 358 RYNAEKHGL--------QDAKKGVIFESLPPVLHLQLKRFEYDFERDMMVKINDRYEFPLEIDLLP 415 (1089)
T ss_pred ccccccccc--------hhhccceeeccCchHHHHHHHHhccccccCceeeecccccCcchhcccc
Confidence 355555554 578999999999999999999999985 6676 44788999876
No 64
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=84.62 E-value=12 Score=40.79 Aligned_cols=19 Identities=16% Similarity=0.298 Sum_probs=13.2
Q ss_pred CHHHHHHHHhCCCCHHHHH
Q 022703 114 DKELLKELEAMGFPVARAT 132 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~ 132 (293)
.+.+-..|+--|.|.+.--
T Consensus 214 g~qaR~aL~qS~Lpq~~LA 232 (1118)
T KOG1029|consen 214 GQQARSALGQSGLPQNQLA 232 (1118)
T ss_pred cHHHHHHHHhcCCchhhHh
Confidence 4556677888888876543
No 65
>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=84.23 E-value=0.61 Score=30.68 Aligned_cols=26 Identities=27% Similarity=0.653 Sum_probs=19.8
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
..+|.+||.+..|.. .-..||.||.+
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 468999999987752 11399999986
No 66
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=84.15 E-value=0.74 Score=39.41 Aligned_cols=37 Identities=22% Similarity=0.541 Sum_probs=25.3
Q ss_pred CcceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 2 AGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 2 ~~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
+...+.|..||..+. ..+|..+.. +. ..|.||.||..
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 456789999998887 445544321 11 23899999985
No 67
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=84.10 E-value=11 Score=41.14 Aligned_cols=13 Identities=23% Similarity=0.465 Sum_probs=5.1
Q ss_pred HHHHHHHHHHhHH
Q 022703 187 AQELRERARKKKE 199 (293)
Q Consensus 187 ~~el~~k~r~~r~ 199 (293)
+..|++.+...++
T Consensus 216 v~~~qe~La~~qe 228 (1064)
T KOG1144|consen 216 VRAMQEALAKRQE 228 (1064)
T ss_pred HHHHHHHHHHHHH
Confidence 3344444433333
No 68
>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]
Probab=83.83 E-value=16 Score=39.75 Aligned_cols=55 Identities=35% Similarity=0.401 Sum_probs=34.5
Q ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHH
Q 022703 208 EREKERIRIGKELLEAKRIEEENERKRILALRKAEKEEEKRAREKIRQKLEEDKAE 263 (293)
Q Consensus 208 e~E~~Rrk~GKe~~~~k~~~ee~e~k~~~e~rrrEK~ee~~ar~rir~qIe~Dk~e 263 (293)
+.|..||+.--+-..++.+++ ..+|.+-++++++++++...---|-+|++....+
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 444455555445445555444 3355555667778888888878888888777665
No 69
>PHA00732 hypothetical protein
Probab=83.71 E-value=1.3 Score=34.58 Aligned_cols=36 Identities=28% Similarity=0.565 Sum_probs=29.7
Q ss_pred eecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCC
Q 022703 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~ 52 (293)
.+|..||..+.....-+.|... .|.. +.|+.||+.+
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~-~H~~----------~~C~~CgKsF 37 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARR-NHTL----------TKCPVCNKSY 37 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhc-ccCC----------CccCCCCCEe
Confidence 4799999999999999999875 4553 3799999974
No 70
>PF14353 CpXC: CpXC protein
Probab=82.61 E-value=0.75 Score=38.12 Aligned_cols=39 Identities=26% Similarity=0.628 Sum_probs=22.5
Q ss_pred eecccCCccccC-------HHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 6 LKCGDCGALLRS-------VQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 6 LkC~~Cg~v~~~-------~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
|.|..||+.+.- ...-.+.-++ -++++ ...++||+||..
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~----il~g~---l~~~~CP~Cg~~ 47 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEK----ILDGS---LFSFTCPSCGHK 47 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHH----HHcCC---cCEEECCCCCCc
Confidence 689999998811 1111111111 12333 567999999996
No 71
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=82.43 E-value=2.5 Score=38.34 Aligned_cols=41 Identities=27% Similarity=0.519 Sum_probs=35.2
Q ss_pred cCHHHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 022703 113 VDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (293)
Q Consensus 113 ~~~~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~ 154 (293)
++..++..|-+ -|.+.-.|.+||..++| |++.|++||-.+.
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 56678888875 58999999999999987 9999999998754
No 72
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=81.30 E-value=70 Score=34.48 Aligned_cols=30 Identities=10% Similarity=0.242 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHcHHHHHHHHHH
Q 022703 223 AKRIEEENERKRILALRKAEKEEEKRAREK 252 (293)
Q Consensus 223 ~k~~~ee~e~k~~~e~rrrEK~ee~~ar~r 252 (293)
.++..+.++.++..+++|+.++++..-+++
T Consensus 301 lekd~KKqqkekEkeEKrrKdE~Ek~kKqe 330 (811)
T KOG4364|consen 301 LEKDIKKQQKEKEKEEKRRKDEQEKLKKQE 330 (811)
T ss_pred HHHHHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence 333444444444455555544444444433
No 73
>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=81.26 E-value=0.75 Score=33.81 Aligned_cols=44 Identities=20% Similarity=0.277 Sum_probs=30.8
Q ss_pred eeecccCCccccC---HHHHHHHHHHhccCCCCcchhhhhccccCCCCC
Q 022703 5 SLKCGDCGALLRS---VQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (293)
Q Consensus 5 ~LkC~~Cg~v~~~---~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~ 50 (293)
..-|..||.++=+ +.-|..|++.|||..|-... .....|-.|+.
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 4569999999955 47799999999999987663 23357777764
No 74
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=81.23 E-value=0.84 Score=37.70 Aligned_cols=27 Identities=22% Similarity=0.495 Sum_probs=18.3
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
..++|+.||..+.-.. ..|.||.||+.
T Consensus 69 ~~~~C~~Cg~~~~~~~---------------------~~~~CP~Cgs~ 95 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ---------------------HDAQCPHCHGE 95 (113)
T ss_pred cEEEcccCCCEEecCC---------------------cCccCcCCCCC
Confidence 4678999995543211 33679999985
No 75
>PRK09377 tsf elongation factor Ts; Provisional
Probab=80.53 E-value=3 Score=40.06 Aligned_cols=41 Identities=24% Similarity=0.494 Sum_probs=35.7
Q ss_pred cCHHHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 022703 113 VDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (293)
Q Consensus 113 ~~~~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~ 154 (293)
++..++..|-+ -|.+.-.|.+||..++| |++.|++||-.+.
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 58999999999999987 9999999998764
No 76
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=80.47 E-value=3 Score=40.03 Aligned_cols=41 Identities=24% Similarity=0.353 Sum_probs=35.6
Q ss_pred cCHHHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 022703 113 VDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (293)
Q Consensus 113 ~~~~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~ 154 (293)
++..++..|-+ -|.+.-.|++||..++| |++.|++||-.+.
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 56778888875 58999999999999988 9999999998764
No 77
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.91 E-value=1.2 Score=30.70 Aligned_cols=29 Identities=28% Similarity=0.607 Sum_probs=20.0
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
..++|..||..+.- .+. ...++||.||.+
T Consensus 2 ~~y~C~~CG~~~~~----------------~~~---~~~~~Cp~CG~~ 30 (46)
T PRK00398 2 AEYKCARCGREVEL----------------DEY---GTGVRCPYCGYR 30 (46)
T ss_pred CEEECCCCCCEEEE----------------CCC---CCceECCCCCCe
Confidence 35789999987643 222 124799999986
No 78
>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=78.97 E-value=1.6 Score=29.76 Aligned_cols=34 Identities=26% Similarity=0.615 Sum_probs=22.7
Q ss_pred CCcceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCC
Q 022703 1 MAGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (293)
Q Consensus 1 ~~~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~ 50 (293)
|--+.++|..||..+.- ...+++. ....||.||.
T Consensus 1 MP~Yey~C~~Cg~~fe~------------~~~~~~~----~~~~CP~Cg~ 34 (42)
T PF09723_consen 1 MPIYEYRCEECGHEFEV------------LQSISED----DPVPCPECGS 34 (42)
T ss_pred CCCEEEEeCCCCCEEEE------------EEEcCCC----CCCcCCCCCC
Confidence 34567899999988742 2233331 3358999998
No 79
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=78.76 E-value=1.2 Score=36.93 Aligned_cols=10 Identities=20% Similarity=0.544 Sum_probs=8.0
Q ss_pred ceeecccCCc
Q 022703 4 VSLKCGDCGA 13 (293)
Q Consensus 4 ~~LkC~~Cg~ 13 (293)
-+.+|.+||.
T Consensus 69 ~~~~C~~Cg~ 78 (114)
T PRK03681 69 AECWCETCQQ 78 (114)
T ss_pred cEEEcccCCC
Confidence 3678999996
No 80
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=78.72 E-value=2.9 Score=42.84 Aligned_cols=37 Identities=30% Similarity=0.502 Sum_probs=31.5
Q ss_pred HHHHHHHHhCCC-CHHHHHHHHHHhCCCCHHHHHHHHHH
Q 022703 115 KELLKELEAMGF-PVARATRALHYSGNANVEAAVNWVVE 152 (293)
Q Consensus 115 ~~~l~~L~~MGF-~~~~a~kAL~~tgn~~~E~A~~WL~~ 152 (293)
+.-+.||.+||| ++.+...||.+||+ ++.+|++-|+.
T Consensus 455 q~QLeQL~~MGF~nre~nlqAL~atgG-di~aAverll~ 492 (493)
T KOG0010|consen 455 QTQLEQLNDMGFLDREANLQALRATGG-DINAAVERLLG 492 (493)
T ss_pred HHHHHHHHhcCCccHHHHHHHHHHhcC-cHHHHHHHHhc
Confidence 344899999997 56888999999998 99999998863
No 81
>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=78.54 E-value=1.1 Score=37.15 Aligned_cols=27 Identities=22% Similarity=0.437 Sum_probs=18.9
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
-+..|++||..+.-.. ..+.||.||+.
T Consensus 69 ~~~~C~~Cg~~~~~~~---------------------~~~~CP~Cgs~ 95 (115)
T TIGR00100 69 VECECEDCSEEVSPEI---------------------DLYRCPKCHGI 95 (115)
T ss_pred cEEEcccCCCEEecCC---------------------cCccCcCCcCC
Confidence 3678999996653321 13689999986
No 82
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=76.93 E-value=3 Score=31.69 Aligned_cols=32 Identities=28% Similarity=0.484 Sum_probs=26.5
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcc
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSES 36 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~ 36 (293)
.+.|..|+..+.+...-+.|....+|..+...
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 48999999999999999999999999998654
No 83
>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=75.73 E-value=2.5 Score=27.84 Aligned_cols=35 Identities=29% Similarity=0.651 Sum_probs=22.1
Q ss_pred CCcceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 1 MAGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 1 ~~~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
|--+.++|..||..+..... +++. ....||.||..
T Consensus 1 Mp~Y~y~C~~Cg~~fe~~~~------------~~~~----~~~~CP~Cg~~ 35 (41)
T smart00834 1 MPIYEYRCEDCGHTFEVLQK------------ISDD----PLATCPECGGD 35 (41)
T ss_pred CCCEEEEcCCCCCEEEEEEe------------cCCC----CCCCCCCCCCc
Confidence 34577899999998753221 1111 22489999984
No 84
>CHL00098 tsf elongation factor Ts
Probab=75.64 E-value=6.1 Score=36.01 Aligned_cols=38 Identities=26% Similarity=0.367 Sum_probs=31.8
Q ss_pred HHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 022703 116 ELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (293)
Q Consensus 116 ~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~ 154 (293)
.++..|-+ -|.+.-.|.+||..++| |++.|++||-.+.
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 45666654 58999999999999998 9999999998764
No 85
>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=75.50 E-value=2.4 Score=29.66 Aligned_cols=34 Identities=24% Similarity=0.594 Sum_probs=21.9
Q ss_pred CCcceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCC
Q 022703 1 MAGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (293)
Q Consensus 1 ~~~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~ 50 (293)
|--+.++|.+||..+... ..+++. ....||.||.
T Consensus 1 MP~Yey~C~~Cg~~fe~~------------~~~~~~----~~~~CP~Cg~ 34 (52)
T TIGR02605 1 MPIYEYRCTACGHRFEVL------------QKMSDD----PLATCPECGG 34 (52)
T ss_pred CCCEEEEeCCCCCEeEEE------------EecCCC----CCCCCCCCCC
Confidence 345678999999988632 112221 2247999998
No 86
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=75.41 E-value=0.85 Score=33.55 Aligned_cols=30 Identities=27% Similarity=0.666 Sum_probs=22.0
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~ 50 (293)
-.|+|..||+++. + +.|... ++-+||.|..
T Consensus 3 ~tiRC~~CnKlLa---------~----a~~~~y----le~KCPrCK~ 32 (60)
T COG4416 3 QTIRCAKCNKLLA---------E----AEGQAY----LEKKCPRCKE 32 (60)
T ss_pred eeeehHHHhHHHH---------h----ccccee----eeecCCccce
Confidence 3689999999873 2 234555 6779999985
No 87
>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=75.27 E-value=2.6 Score=36.68 Aligned_cols=31 Identities=29% Similarity=0.563 Sum_probs=22.4
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
+.-..|..|| ....+.+|.+ .+|.||.||..
T Consensus 107 ~~~Y~Cp~c~-~r~tf~eA~~-----------------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICPNMC-VRFTFNEAME-----------------LNFTCPRCGAM 137 (158)
T ss_pred CCeEECCCCC-cEeeHHHHHH-----------------cCCcCCCCCCE
Confidence 4457899998 4455666664 26999999985
No 88
>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=74.62 E-value=3.4 Score=36.05 Aligned_cols=37 Identities=24% Similarity=0.426 Sum_probs=25.6
Q ss_pred CCcceeecccCCccc----cCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 1 MAGVSLKCGDCGALL----RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 1 ~~~~~LkC~~Cg~v~----~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
|=.|.|+|. ||+.| .+..+......+ --..||.||+.
T Consensus 1 MI~y~L~C~-~gH~FEgWF~ss~~fd~Q~~~-------------glv~CP~Cgs~ 41 (148)
T PF06676_consen 1 MIVYDLRCE-NGHEFEGWFRSSAAFDRQQAR-------------GLVSCPVCGST 41 (148)
T ss_pred CeeEEEecC-CCCccceecCCHHHHHHHHHc-------------CCccCCCCCCC
Confidence 345899999 99988 445555554444 12689999995
No 89
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=74.30 E-value=7.7 Score=32.56 Aligned_cols=41 Identities=17% Similarity=0.229 Sum_probs=35.7
Q ss_pred cccCHHHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Q 022703 111 PEVDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVE 152 (293)
Q Consensus 111 ~~~~~~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~WL~~ 152 (293)
..++++.+..+++ -|.|...|.+||..++| ++-.|+-||.+
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 4688888888875 68999999999999987 89999999864
No 90
>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=74.16 E-value=3.4 Score=23.77 Aligned_cols=21 Identities=29% Similarity=0.517 Sum_probs=18.3
Q ss_pred ecccCCccccCHHHHHHHHHH
Q 022703 7 KCGDCGALLRSVQEAQEHAEL 27 (293)
Q Consensus 7 kC~~Cg~v~~~~~~aq~ha~~ 27 (293)
+|..||..+.....-+.|...
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHhH
Confidence 699999999999998888764
No 91
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=74.03 E-value=1.6 Score=36.18 Aligned_cols=12 Identities=42% Similarity=1.077 Sum_probs=9.0
Q ss_pred ceeecccCCccc
Q 022703 4 VSLKCGDCGALL 15 (293)
Q Consensus 4 ~~LkC~~Cg~v~ 15 (293)
....|+.||..+
T Consensus 70 ~~~~C~~Cg~~~ 81 (117)
T PRK00564 70 VELECKDCSHVF 81 (117)
T ss_pred CEEEhhhCCCcc
Confidence 467899998554
No 92
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=73.31 E-value=1.5 Score=32.70 Aligned_cols=28 Identities=39% Similarity=0.815 Sum_probs=13.6
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~ 50 (293)
-.|.||+|+.. +.+.|+ ++..+|++||+
T Consensus 29 v~IlCNDC~~~--------------s~v~fH-----~lg~KC~~C~S 56 (61)
T PF14599_consen 29 VWILCNDCNAK--------------SEVPFH-----FLGHKCSHCGS 56 (61)
T ss_dssp EEEEESSS--E--------------EEEE-------TT----TTTS-
T ss_pred EEEECCCCCCc--------------cceeee-----HhhhcCCCCCC
Confidence 35789999863 344554 46679999997
No 93
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=72.93 E-value=2.2 Score=30.65 Aligned_cols=30 Identities=27% Similarity=0.657 Sum_probs=21.3
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
-+..+|..||..+ +.........||.||..
T Consensus 4 ~~~Y~C~~Cg~~~-------------------~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREV-------------------ELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCee-------------------ehhhccCceeCCCCCcE
Confidence 4678999999887 11122345799999985
No 94
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=71.91 E-value=31 Score=36.11 Aligned_cols=15 Identities=27% Similarity=0.255 Sum_probs=10.2
Q ss_pred cccccccccchhhcc
Q 022703 64 RTGHTDFVDKTSEAA 78 (293)
Q Consensus 64 ~t~f~tFP~~Lvv~~ 78 (293)
...|-+|||...+++
T Consensus 20 ~epn~~fpdl~a~~a 34 (591)
T KOG2412|consen 20 PEPNWNFPDLVAEIA 34 (591)
T ss_pred CCCCCCchhHHHHhh
Confidence 455667888877654
No 95
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=70.91 E-value=3.6 Score=36.59 Aligned_cols=31 Identities=26% Similarity=0.638 Sum_probs=21.7
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
..-..|..||..+ ...+|.+ .+|.||.||..
T Consensus 115 ~~~Y~Cp~C~~ry-tf~eA~~-----------------~~F~Cp~Cg~~ 145 (178)
T PRK06266 115 NMFFFCPNCHIRF-TFDEAME-----------------YGFRCPQCGEM 145 (178)
T ss_pred CCEEECCCCCcEE-eHHHHhh-----------------cCCcCCCCCCC
Confidence 4457899999655 3445532 26999999986
No 96
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=70.28 E-value=0.8 Score=41.39 Aligned_cols=56 Identities=23% Similarity=0.455 Sum_probs=33.9
Q ss_pred eecccCCccccCHHHHHHHHHHhc-cCCCCcchhhhhccccCCCCCCCCCccccccccccccccccccchhhcccccccc
Q 022703 6 LKCGDCGALLRSVQEAQEHAELTS-HSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLE 84 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~~Tg-H~~F~e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~ 84 (293)
|.|..||.-+.-.- ..|- ==+|++.. +..|.|++||-+ ..-++..+ .++++||.|.
T Consensus 1 ~~Cp~C~~~~~~~~------~~~~~IP~F~evi--i~sf~C~~CGyr-------~~ev~~~g--------~~~p~r~~l~ 57 (192)
T TIGR00310 1 IDCPSCGGECETVM------KTVNDIPYFGEVL--ETSTICEHCGYR-------SNDVKTLG--------AKEPKRYILK 57 (192)
T ss_pred CcCCCCCCCCEEEE------EEEcCCCCcceEE--EEEEECCCCCCc-------cceeEECC--------CCCCEEEEEE
Confidence 57999987542211 1222 24699983 446999999986 44444444 2345577766
No 97
>PTZ00121 MAEBL; Provisional
Probab=70.11 E-value=74 Score=37.33 Aligned_cols=15 Identities=13% Similarity=0.158 Sum_probs=8.3
Q ss_pred ccchhhccccccccc
Q 022703 71 VDKTSEAAKPISLEV 85 (293)
Q Consensus 71 P~~Lvv~~~Rf~l~~ 85 (293)
|||=-..|.||-|.|
T Consensus 904 PDyEtKCPPR~PLkn 918 (2084)
T PTZ00121 904 PDYEEKCPPRFPLKS 918 (2084)
T ss_pred CcccccCCCCCCCCC
Confidence 555555555555554
No 98
>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=69.28 E-value=7.7 Score=30.32 Aligned_cols=37 Identities=24% Similarity=0.318 Sum_probs=30.8
Q ss_pred HHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCC
Q 022703 119 KELEAMGFPVARATRALHYSGNANVEAAVNWVVEHEND 156 (293)
Q Consensus 119 ~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~dD 156 (293)
..+.+.||+...+..||++|.+ ++..|..+++.+...
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 3477899999999999999976 999999999887543
No 99
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=68.55 E-value=3 Score=34.99 Aligned_cols=12 Identities=33% Similarity=0.827 Sum_probs=10.1
Q ss_pred hhccccCCCCCC
Q 022703 40 VLNLVCATCGKP 51 (293)
Q Consensus 40 i~~~~C~~Cg~~ 51 (293)
..+|.||.||+.
T Consensus 84 ~~~~~CP~C~s~ 95 (115)
T COG0375 84 ELDYRCPKCGSI 95 (115)
T ss_pred hheeECCCCCCC
Confidence 577889999986
No 100
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=67.75 E-value=3.7 Score=28.59 Aligned_cols=35 Identities=34% Similarity=0.529 Sum_probs=23.1
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCCCCcccccccccccc
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTG 66 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~ 66 (293)
.+.|.+||..+.-. . ....+||.||.. ..+-+++.
T Consensus 2 ~Y~C~~Cg~~~~~~-----------------~---~~~irC~~CG~r-------IlyK~R~~ 36 (44)
T smart00659 2 IYICGECGRENEIK-----------------S---KDVVRCRECGYR-------ILYKKRTK 36 (44)
T ss_pred EEECCCCCCEeecC-----------------C---CCceECCCCCce-------EEEEeCCC
Confidence 57899999865421 1 123599999986 56555543
No 101
>PHA00733 hypothetical protein
Probab=67.47 E-value=6.7 Score=33.03 Aligned_cols=37 Identities=30% Similarity=0.547 Sum_probs=23.5
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~ 52 (293)
...|..||+.+.....-..|.....| .|.|+.||+.+
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r~h~~-----------~~~C~~CgK~F 109 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIRYTEH-----------SKVCPVCGKEF 109 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHhcCCc-----------CccCCCCCCcc
Confidence 45677777777777766666653111 26777887753
No 102
>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=67.11 E-value=2.5 Score=26.02 Aligned_cols=11 Identities=27% Similarity=0.857 Sum_probs=8.9
Q ss_pred hhccccCCCCC
Q 022703 40 VLNLVCATCGK 50 (293)
Q Consensus 40 i~~~~C~~Cg~ 50 (293)
.+.|.||+||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 35699999995
No 103
>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=66.33 E-value=18 Score=34.89 Aligned_cols=8 Identities=13% Similarity=0.156 Sum_probs=4.2
Q ss_pred ccchhhcc
Q 022703 71 VDKTSEAA 78 (293)
Q Consensus 71 P~~Lvv~~ 78 (293)
+|++.|-+
T Consensus 110 ~D~v~i~i 117 (321)
T PF07946_consen 110 KDRVTIEI 117 (321)
T ss_pred CCeEEEEE
Confidence 55555544
No 104
>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=65.28 E-value=3.1 Score=34.16 Aligned_cols=27 Identities=30% Similarity=0.929 Sum_probs=16.7
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
.+.+|..||+.+.-.. ..+.||.||+.
T Consensus 69 ~~~~C~~Cg~~~~~~~---------------------~~~~CP~Cgs~ 95 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDE---------------------FDFSCPRCGSP 95 (113)
T ss_dssp -EEEETTTS-EEECHH---------------------CCHH-SSSSSS
T ss_pred CcEECCCCCCEEecCC---------------------CCCCCcCCcCC
Confidence 4678999998764321 12569999996
No 105
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=65.20 E-value=1.7 Score=43.87 Aligned_cols=23 Identities=13% Similarity=0.203 Sum_probs=15.7
Q ss_pred HHhCCCCHHHHHHHHHHhCCCCHHH
Q 022703 121 LEAMGFPVARATRALHYSGNANVEA 145 (293)
Q Consensus 121 L~~MGF~~~~a~kAL~~tgn~~~E~ 145 (293)
...-||+...|--+++.+-| +..
T Consensus 454 ~~~q~f~~ky~~atfyss~~--ltr 476 (500)
T KOG3993|consen 454 IAEQGFTCKYCPATFYSSPG--LTR 476 (500)
T ss_pred chhhccccccchHhhhcCcc--hHh
Confidence 34568998888877776654 444
No 106
>PF15236 CCDC66: Coiled-coil domain-containing protein 66
Probab=65.09 E-value=99 Score=27.31 Aligned_cols=6 Identities=33% Similarity=0.623 Sum_probs=2.7
Q ss_pred CCCHHH
Q 022703 177 SLTPEE 182 (293)
Q Consensus 177 ~lT~EE 182 (293)
+|+|..
T Consensus 40 llDpa~ 45 (157)
T PF15236_consen 40 LLDPAQ 45 (157)
T ss_pred cCCHHH
Confidence 444443
No 107
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=64.94 E-value=3.9 Score=34.24 Aligned_cols=33 Identities=24% Similarity=0.570 Sum_probs=19.1
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
.+..| .||..+..... ...|..| .+.||.||+.
T Consensus 69 ~~~~C-~Cg~~~~~~~~------~~~~~~~--------~~~CP~Cgs~ 101 (124)
T PRK00762 69 VEIEC-ECGYEGVVDED------EIDHYAA--------VIECPVCGNK 101 (124)
T ss_pred eeEEe-eCcCccccccc------chhcccc--------CCcCcCCCCC
Confidence 46789 99976543321 1012111 3679999975
No 108
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=64.59 E-value=1.5 Score=38.47 Aligned_cols=37 Identities=30% Similarity=0.599 Sum_probs=24.3
Q ss_pred ecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 7 KCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 7 kC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
.|..||+-+. .+...|-==||.+.. +..|.|++||-+
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 4999987542 222233334599993 346999999986
No 109
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=64.42 E-value=3.9 Score=28.12 Aligned_cols=30 Identities=30% Similarity=0.348 Sum_probs=23.5
Q ss_pred eeecccCCccccC---HHHHHHHHHHhccCCCC
Q 022703 5 SLKCGDCGALLRS---VQEAQEHAELTSHSNFS 34 (293)
Q Consensus 5 ~LkC~~Cg~v~~~---~~~aq~ha~~TgH~~F~ 34 (293)
...|..|+.++-+ ..-++.|...|||..+-
T Consensus 11 l~~CL~C~~~~c~~~~~~h~~~H~~~t~H~~~~ 43 (50)
T smart00290 11 LWLCLTCGQVGCGRYQLGHALEHFEETGHPLVV 43 (50)
T ss_pred eEEecCCCCcccCCCCCcHHHHHhhhhCCCEEE
Confidence 4578889988853 34599999999998764
No 110
>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=63.95 E-value=55 Score=33.44 Aligned_cols=42 Identities=33% Similarity=0.495 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 022703 227 EEENERKRILALRKAEKEEEKRAREKIRQKLEEDKAERRRRL 268 (293)
Q Consensus 227 ~ee~e~k~~~e~rrrEK~ee~~ar~rir~qIe~Dk~eR~~r~ 268 (293)
.+|-+.-+-+...|.+|.|+.=|-.-.+-.|..--++|+.+|
T Consensus 377 RrEAE~LqrI~~aK~~k~EEEYas~~~kl~l~eaee~r~~~~ 418 (446)
T PF07227_consen 377 RREAEGLQRIALAKSEKIEEEYASRYLKLRLNEAEEERKKKF 418 (446)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence 344444455556666777777666666666666666666554
No 111
>PF15236 CCDC66: Coiled-coil domain-containing protein 66
Probab=63.73 E-value=1.1e+02 Score=27.15 Aligned_cols=18 Identities=22% Similarity=0.231 Sum_probs=6.7
Q ss_pred HHHcHHHHHHHHHHHHHH
Q 022703 239 RKAEKEEEKRAREKIRQK 256 (293)
Q Consensus 239 rrrEK~ee~~ar~rir~q 256 (293)
++.+..-+.+.+....++
T Consensus 119 ~k~~~l~e~~q~Aqe~A~ 136 (157)
T PF15236_consen 119 RKTQELYEAMQRAQEEAQ 136 (157)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 333333333333333333
No 112
>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=62.87 E-value=17 Score=30.59 Aligned_cols=39 Identities=18% Similarity=0.239 Sum_probs=34.1
Q ss_pred ccCHHHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHH
Q 022703 112 EVDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVV 151 (293)
Q Consensus 112 ~~~~~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~WL~ 151 (293)
.++++.+..+++ -|.|...|.+||..++| ++-.|+-||.
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 588888888875 68999999999999987 8999998884
No 113
>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=62.31 E-value=8.6 Score=21.52 Aligned_cols=21 Identities=33% Similarity=0.645 Sum_probs=16.9
Q ss_pred ecccCCccccCHHHHHHHHHH
Q 022703 7 KCGDCGALLRSVQEAQEHAEL 27 (293)
Q Consensus 7 kC~~Cg~v~~~~~~aq~ha~~ 27 (293)
+|..||..+....+-..|...
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHHh
Confidence 799999999999999999765
No 114
>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=61.64 E-value=4.2 Score=29.48 Aligned_cols=30 Identities=27% Similarity=0.696 Sum_probs=19.9
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
.++|..|++.+-. . |.+. .++.+||.||.-
T Consensus 4 eiRC~~CnklLa~---------~-g~~~-------~leIKCpRC~ti 33 (51)
T PF10122_consen 4 EIRCGHCNKLLAK---------A-GEVI-------ELEIKCPRCKTI 33 (51)
T ss_pred ceeccchhHHHhh---------h-cCcc-------EEEEECCCCCcc
Confidence 4789999987632 1 2221 255799999983
No 115
>PTZ00121 MAEBL; Provisional
Probab=60.98 E-value=1.5e+02 Score=35.11 Aligned_cols=16 Identities=38% Similarity=0.268 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHHhc
Q 022703 253 IRQKLEEDKAERRRRL 268 (293)
Q Consensus 253 ir~qIe~Dk~eR~~r~ 268 (293)
+|..=+++.+++++|.
T Consensus 1254 ~Rk~Eear~a~~A~r~ 1269 (2084)
T PTZ00121 1254 IRKFEEARMAHFARRQ 1269 (2084)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 3433444444444444
No 116
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=60.42 E-value=6.7 Score=25.67 Aligned_cols=34 Identities=21% Similarity=0.572 Sum_probs=21.4
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
|.+.|..||..+.-..+.- ... -....||.||..
T Consensus 1 M~~~CP~C~~~~~v~~~~~-----------~~~---~~~v~C~~C~~~ 34 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQL-----------GAN---GGKVRCGKCGHV 34 (38)
T ss_pred CEEECCCCCCEEEeCHHHc-----------CCC---CCEEECCCCCCE
Confidence 4689999998875443321 001 124689999985
No 117
>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=60.17 E-value=41 Score=32.42 Aligned_cols=7 Identities=29% Similarity=0.306 Sum_probs=3.2
Q ss_pred HHHHHHH
Q 022703 131 ATRALHY 137 (293)
Q Consensus 131 a~kAL~~ 137 (293)
...||..
T Consensus 181 ~~~~l~~ 187 (321)
T PF07946_consen 181 LIKALNK 187 (321)
T ss_pred HHHHHHh
Confidence 4455543
No 118
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=59.57 E-value=4.9 Score=29.92 Aligned_cols=28 Identities=25% Similarity=0.532 Sum_probs=24.3
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSN 32 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~ 32 (293)
--|+|..||.+|+.+.+-..|... .|-+
T Consensus 16 ~~lrCPRC~~~FR~~K~Y~RHVNK-aH~~ 43 (65)
T COG4049 16 EFLRCPRCGMVFRRRKDYIRHVNK-AHGW 43 (65)
T ss_pred eeeeCCchhHHHHHhHHHHHHhhH-Hhhh
Confidence 458999999999999999999988 5654
No 119
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=59.22 E-value=4.9 Score=38.44 Aligned_cols=70 Identities=21% Similarity=0.379 Sum_probs=49.1
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCCCCccccccccccccccccccchhhcccccc
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPIS 82 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~ 82 (293)
-+.+|.+||+....... .+-|-.|.=..|+..-+.|+.||+...|.++...++.+.. .|=.-.|--++|.
T Consensus 129 ~r~~c~eCgk~ysT~sn------LsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~---l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSN------LSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT---LPCECGICGKAFS 198 (279)
T ss_pred Cceeccccccccccccc------cchhhcccccccccccccCCCCCceeeehHHHhhHhhccC---CCccccccccccc
Confidence 46799999999854433 2346677777777788999999998887777777665543 4545555555443
No 120
>smart00355 ZnF_C2H2 zinc finger.
Probab=59.14 E-value=8.3 Score=21.69 Aligned_cols=21 Identities=29% Similarity=0.790 Sum_probs=17.7
Q ss_pred eecccCCccccCHHHHHHHHH
Q 022703 6 LKCGDCGALLRSVQEAQEHAE 26 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~ 26 (293)
++|..|+..+.+...-+.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 468999999998888888876
No 121
>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=58.42 E-value=9 Score=22.86 Aligned_cols=21 Identities=29% Similarity=0.790 Sum_probs=18.4
Q ss_pred eecccCCccccCHHHHHHHHH
Q 022703 6 LKCGDCGALLRSVQEAQEHAE 26 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~ 26 (293)
++|..|+..+.....-..|..
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 689999999999999888874
No 122
>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=58.42 E-value=7.6 Score=25.91 Aligned_cols=30 Identities=30% Similarity=0.748 Sum_probs=21.2
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
+.-|..||.+. |..|..- ..+-+|+.||..
T Consensus 1 Rr~C~~Cg~~Y--------------h~~~~pP---~~~~~Cd~cg~~ 30 (36)
T PF05191_consen 1 RRICPKCGRIY--------------HIEFNPP---KVEGVCDNCGGE 30 (36)
T ss_dssp EEEETTTTEEE--------------ETTTB-----SSTTBCTTTTEB
T ss_pred CcCcCCCCCcc--------------ccccCCC---CCCCccCCCCCe
Confidence 45688888775 6778765 466799999974
No 123
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=57.73 E-value=19 Score=34.84 Aligned_cols=40 Identities=28% Similarity=0.541 Sum_probs=31.6
Q ss_pred cCHHHHHHHHh-CCCCHHHHHHHHHHhCCCCHHHHHHHHHHh
Q 022703 113 VDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEH 153 (293)
Q Consensus 113 ~~~~~l~~L~~-MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h 153 (293)
+...+|..|-+ -|=+.--|.+||..|++ |+|.|++||-..
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 45566666654 36777899999999976 999999999764
No 124
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=57.45 E-value=5.3 Score=29.77 Aligned_cols=13 Identities=31% Similarity=0.690 Sum_probs=9.3
Q ss_pred eecccCCccccCH
Q 022703 6 LKCGDCGALLRSV 18 (293)
Q Consensus 6 LkC~~Cg~v~~~~ 18 (293)
.+|..||+.+.+.
T Consensus 8 ~~CtSCg~~i~~~ 20 (59)
T PRK14890 8 PKCTSCGIEIAPR 20 (59)
T ss_pred ccccCCCCcccCC
Confidence 4688888887643
No 125
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=56.40 E-value=8.5 Score=22.53 Aligned_cols=22 Identities=18% Similarity=0.383 Sum_probs=18.9
Q ss_pred eecccCCccccCHHHHHHHHHH
Q 022703 6 LKCGDCGALLRSVQEAQEHAEL 27 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~~ 27 (293)
+.|..|+..+.+....+.|..-
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4699999999999999999753
No 126
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=56.18 E-value=9.8 Score=34.11 Aligned_cols=31 Identities=29% Similarity=0.510 Sum_probs=19.5
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
..-+.| .|+++..+.++|-. .+|+||.||..
T Consensus 111 ~~~y~C-~~~~~r~sfdeA~~-----------------~~F~Cp~Cg~~ 141 (176)
T COG1675 111 NNYYVC-PNCHVKYSFDEAME-----------------LGFTCPKCGED 141 (176)
T ss_pred CCceeC-CCCCCcccHHHHHH-----------------hCCCCCCCCch
Confidence 334566 55555555555543 33999999996
No 127
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.94 E-value=2.2 Score=33.44 Aligned_cols=34 Identities=29% Similarity=0.707 Sum_probs=21.4
Q ss_pred CcceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 2 AGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 2 ~~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
--++.+|..||..+.-.+ .|++. -+ -.|+.||-+
T Consensus 9 PtY~Y~c~~cg~~~dvvq------------~~~dd---pl-t~ce~c~a~ 42 (82)
T COG2331 9 PTYSYECTECGNRFDVVQ------------AMTDD---PL-TTCEECGAR 42 (82)
T ss_pred cceEEeecccchHHHHHH------------hcccC---cc-ccChhhChH
Confidence 346889999998763221 13333 23 489999854
No 128
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=55.52 E-value=7.3 Score=29.17 Aligned_cols=10 Identities=30% Similarity=0.813 Sum_probs=7.2
Q ss_pred eecccCCccc
Q 022703 6 LKCGDCGALL 15 (293)
Q Consensus 6 LkC~~Cg~v~ 15 (293)
-.|+.||+++
T Consensus 10 ~~CtSCg~~i 19 (61)
T COG2888 10 PVCTSCGREI 19 (61)
T ss_pred ceeccCCCEe
Confidence 3577787777
No 129
>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=55.00 E-value=53 Score=23.75 Aligned_cols=45 Identities=20% Similarity=0.345 Sum_probs=33.1
Q ss_pred cccCHHHHHHHH--hCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhcCC
Q 022703 111 PEVDKELLKELE--AMGFPVARATRALHYSGNANVEAAVNWVVEHEND 156 (293)
Q Consensus 111 ~~~~~~~l~~L~--~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~dD 156 (293)
+.+.++++.+.. =-|-|++...+-|..|+ -++..|+|-|++..|+
T Consensus 6 ~~vPedlI~q~q~VLqgksR~vIirELqrTn-LdVN~AvNNlLsRDde 52 (53)
T PF11547_consen 6 SQVPEDLINQAQVVLQGKSRNVIIRELQRTN-LDVNLAVNNLLSRDDE 52 (53)
T ss_dssp GGS-HHHHHHHHHHSTTS-HHHHHHHHHHTT-T-HHHHHHHHHHHH--
T ss_pred ccCCHHHHHHHHHHHcCCcHHHHHHHHHHhc-ccHHHHHHHHhccccC
Confidence 456677776654 47999999999999995 5999999999997664
No 130
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=53.96 E-value=9.6 Score=31.86 Aligned_cols=12 Identities=42% Similarity=0.991 Sum_probs=9.4
Q ss_pred hhccccCCCCCC
Q 022703 40 VLNLVCATCGKP 51 (293)
Q Consensus 40 i~~~~C~~Cg~~ 51 (293)
|..++|++||..
T Consensus 10 vt~l~C~~C~t~ 21 (113)
T PF09862_consen 10 VTRLKCPSCGTE 21 (113)
T ss_pred EEEEEcCCCCCE
Confidence 456899999875
No 131
>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=53.66 E-value=3.5 Score=25.11 Aligned_cols=23 Identities=17% Similarity=0.485 Sum_probs=19.0
Q ss_pred eecccCCccccCHHHHHHHHHHh
Q 022703 6 LKCGDCGALLRSVQEAQEHAELT 28 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~~T 28 (293)
+-|..|+..+.+....+.|..-.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCcccCCCCcCCHHHHHHHHccC
Confidence 46999999999999988886543
No 132
>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=53.59 E-value=3 Score=36.80 Aligned_cols=37 Identities=19% Similarity=0.420 Sum_probs=23.1
Q ss_pred cccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 8 CGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 8 C~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
|..||.-. ...+...|-==||++.. +..|.|++||-+
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 88888631 11112233445699983 446999999986
No 133
>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=52.23 E-value=52 Score=29.82 Aligned_cols=29 Identities=24% Similarity=0.351 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHcHHHHHHHH
Q 022703 222 EAKRIEEENERKRILALRKAEKEEEKRAR 250 (293)
Q Consensus 222 ~~k~~~ee~e~k~~~e~rrrEK~ee~~ar 250 (293)
.++++|++..-+++++.+.++++++...|
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 45566666666666555544444433333
No 134
>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=51.91 E-value=6.1 Score=33.73 Aligned_cols=43 Identities=23% Similarity=0.391 Sum_probs=23.9
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
--+|..||..+...... .-...-....|... ..=|.||.||+-
T Consensus 91 ~sRC~~CN~~L~~v~~~-~v~~~vp~~v~~~~---~~f~~C~~C~ki 133 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKE-EVKDRVPPYVYETY---DEFWRCPGCGKI 133 (147)
T ss_pred CCccCCCCcEeeechhh-ccccccCccccccC---CeEEECCCCCCE
Confidence 35899999988655332 11111123333322 113899999974
No 135
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=51.10 E-value=30 Score=31.10 Aligned_cols=24 Identities=29% Similarity=0.501 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHh
Q 022703 115 KELLKELEAMGFPVARATRALHYS 138 (293)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~t 138 (293)
.++++.|+.+||++..|.+|+...
T Consensus 144 ~e~~~AL~~LGy~~~ea~~av~~~ 167 (188)
T PRK14606 144 HESLEALVSLGYPEKQAREAVKHV 167 (188)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 678999999999999999999865
No 136
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=50.82 E-value=8.9 Score=34.08 Aligned_cols=40 Identities=25% Similarity=0.451 Sum_probs=22.1
Q ss_pred eecccCCccccC--HHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 6 LKCGDCGALLRS--VQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 6 LkC~~Cg~v~~~--~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
-+|..||..+.- -.++..-.-. -|+-+.+. =|.||.||+-
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~-~~~~~~~~-----f~~C~~Cgki 139 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPE-KVYRNYEE-----FYRCPKCGKI 139 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccch-hhhhcccc-----eeECCCCccc
Confidence 479999999833 2233222222 13322222 1789999984
No 137
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=50.64 E-value=6.9 Score=26.52 Aligned_cols=40 Identities=10% Similarity=0.076 Sum_probs=22.0
Q ss_pred cccCCCCCCCCCc-cccccccccccccccccchhhcccccc
Q 022703 43 LVCATCGKPCRSK-TETDLHRKRTGHTDFVDKTSEAAKPIS 82 (293)
Q Consensus 43 ~~C~~Cg~~~~~~-~e~~~a~K~t~f~tFP~~Lvv~~~Rf~ 82 (293)
..||.||....-- --...-.....|-.+|=+|.|..+||.
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 4799999862000 001122234445566777777777764
No 138
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=49.06 E-value=50 Score=28.46 Aligned_cols=42 Identities=19% Similarity=0.157 Sum_probs=36.7
Q ss_pred ccccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHh
Q 022703 110 EPEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEH 153 (293)
Q Consensus 110 ~~~~~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h 153 (293)
.+++..+.+..|.+.|.+++.|++||..+| ++-.||.-|.+.
T Consensus 110 ~s~~~~e~v~v~a~a~v~~eeAr~aleeag--Dl~~A~k~l~~~ 151 (153)
T COG4008 110 HSEPPVEEVEVLADAFVTPEEAREALEEAG--DLRTAMKILRMK 151 (153)
T ss_pred cCCCcHHHHHHHHHhcCCHHHHHHHHHHcC--CHHHHHHHHHHh
Confidence 456788889999999999999999999998 799999887653
No 139
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=49.03 E-value=3.9e+02 Score=29.16 Aligned_cols=26 Identities=15% Similarity=0.256 Sum_probs=20.9
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhC
Q 022703 114 DKELLKELEAMGFPVARATRALHYSG 139 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL~~tg 139 (293)
+..++....-+|||.....+|-...+
T Consensus 487 ~S~a~~iA~~~Glp~~ii~~A~~~~~ 512 (782)
T PRK00409 487 KSNAFEIAKRLGLPENIIEEAKKLIG 512 (782)
T ss_pred CcHHHHHHHHhCcCHHHHHHHHHHHh
Confidence 55678888889999999988866654
No 140
>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=48.85 E-value=16 Score=31.67 Aligned_cols=35 Identities=20% Similarity=0.482 Sum_probs=22.0
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
+.++|..|+....... ....... . ..-.|+.||..
T Consensus 104 ~~~~C~~C~~~~~~~~-~~~~~~~-~-----------~~~~C~~C~~~ 138 (178)
T PF02146_consen 104 FRLRCSKCGKEYDRED-IVDSIDE-E-----------EPPRCPKCGGL 138 (178)
T ss_dssp EEEEETTTSBEEEGHH-HHHHHHT-T-----------SSCBCTTTSCB
T ss_pred ceeeecCCCccccchh-hcccccc-c-----------ccccccccCcc
Confidence 5789999999886533 2222222 0 11299999984
No 141
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=48.62 E-value=42 Score=30.19 Aligned_cols=38 Identities=21% Similarity=0.495 Sum_probs=28.9
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhC---CCCHHHHHHHHH
Q 022703 114 DKELLKELEAMGFPVARATRALHYSG---NANVEAAVNWVV 151 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL~~tg---n~~~E~A~~WL~ 151 (293)
..+++..|++.||+...|.+|+...+ +.+++..+-|.+
T Consensus 148 ~~e~~~aL~~LGy~~~~a~~ai~~~~~~~~~~~~~~ir~aL 188 (194)
T PRK14605 148 NSDILATLTALGYSSSEAAKAISSLGDNGDLPLEERIKLAL 188 (194)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhccCCCCHHHHHHHHH
Confidence 46789999999999999999998764 335565555443
No 142
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=48.51 E-value=15 Score=35.26 Aligned_cols=16 Identities=25% Similarity=0.654 Sum_probs=11.4
Q ss_pred cceeecccCCccccCH
Q 022703 3 GVSLKCGDCGALLRSV 18 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~ 18 (293)
.+..+|++||+.|..-
T Consensus 185 ~l~c~C~iCGKaFSRP 200 (279)
T KOG2462|consen 185 TLPCECGICGKAFSRP 200 (279)
T ss_pred CCCcccccccccccch
Confidence 4567788888887544
No 143
>KOG3654 consensus Uncharacterized CH domain protein [Cytoskeleton]
Probab=47.88 E-value=1.3e+02 Score=31.52 Aligned_cols=38 Identities=42% Similarity=0.501 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHH
Q 022703 221 LEAKRIEEENERKRILALRKAEKEEEKRAREKIRQKLE 258 (293)
Q Consensus 221 ~~~k~~~ee~e~k~~~e~rrrEK~ee~~ar~rir~qIe 258 (293)
+++.-++...|..|.+++-|.-|+|+...|+-||+...
T Consensus 414 leae~e~kreearrkaeeer~~keee~arrefirqey~ 451 (708)
T KOG3654|consen 414 LEAEKEQKREEARRKAEEERAPKEEEVARREFIRQEYE 451 (708)
T ss_pred HHHHHHHHHHHHHHhhHhhhcchhhhhhHHHHHHHHHH
Confidence 34445555666777778888888999998888887653
No 144
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=47.77 E-value=11 Score=32.25 Aligned_cols=26 Identities=27% Similarity=0.836 Sum_probs=17.8
Q ss_pred ecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 7 KCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 7 kC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
+|+.||.+|.+.. ..++. =||.||..
T Consensus 3 ~Ct~Cg~~f~dgs------------------~eil~-GCP~CGg~ 28 (131)
T PF09845_consen 3 QCTKCGRVFEDGS------------------KEILS-GCPECGGN 28 (131)
T ss_pred ccCcCCCCcCCCc------------------HHHHc-cCcccCCc
Confidence 7999999885421 12443 79999753
No 145
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.71 E-value=45 Score=29.88 Aligned_cols=32 Identities=19% Similarity=0.307 Sum_probs=25.4
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHH
Q 022703 114 DKELLKELEAMGFPVARATRALHYSGNANVEA 145 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~ 145 (293)
..++++.|+.+||++..|.+|+..-.+.+++.
T Consensus 142 ~~ea~~AL~~LGy~~~ea~~a~~~~~~~~~ee 173 (183)
T PRK14601 142 KSEALAALLTLGFKQEKIIKVLASCQSTGTSE 173 (183)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcccCCHHH
Confidence 36889999999999999999997654334443
No 146
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=47.69 E-value=9.8 Score=28.65 Aligned_cols=38 Identities=18% Similarity=0.249 Sum_probs=21.3
Q ss_pred cccCCCCCCCCCccccccccccccccccccchhhccccccccc
Q 022703 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV 85 (293)
Q Consensus 43 ~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~~ 85 (293)
|+||.||..- .+ +..+..++ ..|-..+-|+-++|.+..
T Consensus 1 y~C~KCg~~~---~e-~~~v~~tg-g~~skiFdvq~~~f~~v~ 38 (64)
T PF09855_consen 1 YKCPKCGNEE---YE-SGEVRATG-GGLSKIFDVQNKKFTTVS 38 (64)
T ss_pred CCCCCCCCcc---ee-cceEEccC-CeeEEEEEecCcEEEEEE
Confidence 7899999751 11 11122222 234445677888887763
No 147
>KOG2891 consensus Surface glycoprotein [General function prediction only]
Probab=47.37 E-value=1.7e+02 Score=28.58 Aligned_cols=22 Identities=18% Similarity=0.295 Sum_probs=13.2
Q ss_pred ccccccchhhcccccccccCcc
Q 022703 67 HTDFVDKTSEAAKPISLEVPKA 88 (293)
Q Consensus 67 f~tFP~~Lvv~~~Rf~l~~p~K 88 (293)
+.-|.+.|-|-+.-+.++.|..
T Consensus 106 lsgfad~lkvka~eakidfpsr 127 (445)
T KOG2891|consen 106 LSGFADILKVKAAEAKIDFPSR 127 (445)
T ss_pred ecccchHHhhhHHhhcCCCCcc
Confidence 3445566777666666665543
No 148
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=47.08 E-value=21 Score=26.56 Aligned_cols=20 Identities=25% Similarity=0.449 Sum_probs=16.7
Q ss_pred HHHHhCCCCHHHHHHHHHHh
Q 022703 119 KELEAMGFPVARATRALHYS 138 (293)
Q Consensus 119 ~~L~~MGF~~~~a~kAL~~t 138 (293)
..|++|||++..|..-++..
T Consensus 7 ~dLi~lGf~~~tA~~IIrqA 26 (59)
T PF11372_consen 7 KDLIELGFSESTARDIIRQA 26 (59)
T ss_pred HHHHHcCCCHHHHHHHHHHH
Confidence 57999999999999877653
No 149
>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=46.82 E-value=26 Score=31.39 Aligned_cols=25 Identities=24% Similarity=0.405 Sum_probs=22.0
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHh
Q 022703 114 DKELLKELEAMGFPVARATRALHYS 138 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL~~t 138 (293)
..++++.|..+||++..+.+|+..-
T Consensus 147 ~~e~~~aL~~LGy~~~e~~~ai~~~ 171 (191)
T TIGR00084 147 RDELFEALVSLGYKPQEIQQALKKI 171 (191)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4678999999999999999998764
No 150
>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=46.25 E-value=4.1e+02 Score=28.99 Aligned_cols=26 Identities=15% Similarity=0.232 Sum_probs=20.5
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhC
Q 022703 114 DKELLKELEAMGFPVARATRALHYSG 139 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL~~tg 139 (293)
...++....-+|||.....+|-...+
T Consensus 482 ~S~a~~iA~~~Glp~~ii~~A~~~~~ 507 (771)
T TIGR01069 482 ESYAFEIAQRYGIPHFIIEQAKTFYG 507 (771)
T ss_pred CcHHHHHHHHhCcCHHHHHHHHHHHH
Confidence 34677888889999999988876654
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=46.25 E-value=11 Score=27.93 Aligned_cols=14 Identities=36% Similarity=0.895 Sum_probs=12.1
Q ss_pred CcceeecccCCccc
Q 022703 2 AGVSLKCGDCGALL 15 (293)
Q Consensus 2 ~~~~LkC~~Cg~v~ 15 (293)
+.|+|+|..||.+.
T Consensus 28 aDikikC~gCg~~i 41 (57)
T PF06107_consen 28 ADIKIKCLGCGRQI 41 (57)
T ss_pred CcEEEEECCCCCEE
Confidence 47899999999876
No 152
>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=46.24 E-value=13 Score=26.93 Aligned_cols=32 Identities=28% Similarity=0.681 Sum_probs=19.7
Q ss_pred CcceeecccCCccccCHHHHHHHHHHhccCCCC--cchhhhhccccCCCCC
Q 022703 2 AGVSLKCGDCGALLRSVQEAQEHAELTSHSNFS--ESTEAVLNLVCATCGK 50 (293)
Q Consensus 2 ~~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~--e~~d~i~~~~C~~Cg~ 50 (293)
+.+.|-|..|.. |+... +..+.+ .|+|+.||.
T Consensus 19 ~r~aLIC~~C~~----------------hNGla~~~~~~~i-~y~C~~Cg~ 52 (54)
T PF10058_consen 19 NRYALICSKCFS----------------HNGLAPKEEFEEI-QYRCPYCGA 52 (54)
T ss_pred CceeEECcccch----------------hhcccccccCCce-EEEcCCCCC
Confidence 356788888864 22222 232333 699999986
No 153
>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=45.58 E-value=8.9 Score=38.31 Aligned_cols=44 Identities=20% Similarity=0.329 Sum_probs=33.5
Q ss_pred eecccCCcccc---CHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 6 LKCGDCGALLR---SVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 6 LkC~~Cg~v~~---~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
.-|..||+++. ++.-|..|+..|+|..|-... .....|-.|+--
T Consensus 29 ~~CL~cg~~~~g~~~~~ha~~H~~~~~H~~~v~l~--t~~~yc~~~~~~ 75 (440)
T cd02669 29 YACLVCGKYFQGRGKGSHAYTHSLEDNHHVFLNLE--TLKFYCLPDNYE 75 (440)
T ss_pred EEEcccCCeecCCCCCcHHHHHhhccCCCEEEECC--CCCEEEeCCCCE
Confidence 47999996652 456799999999999986542 245799999874
No 154
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=45.03 E-value=4.1 Score=37.12 Aligned_cols=48 Identities=21% Similarity=0.469 Sum_probs=24.8
Q ss_pred ceeecccCCccccCHHHHHHHHHH-hccCCCCcchhhhh-----ccccCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAEL-TSHSNFSESTEAVL-----NLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~-TgH~~F~e~~d~i~-----~~~C~~Cg~~ 51 (293)
..+.|.+||..+....=-..+..- .-+++|......+. -.+||+||-.
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA 57 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYA 57 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCc
Confidence 468999999998332221111111 12344432211111 1589999974
No 155
>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=44.74 E-value=9.4 Score=29.72 Aligned_cols=26 Identities=23% Similarity=0.336 Sum_probs=19.9
Q ss_pred cccCCCCCCCCCccccccccccccccccccchhhcc
Q 022703 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAA 78 (293)
Q Consensus 43 ~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~ 78 (293)
-.|+.||++. -.+.|.-||+--++|.
T Consensus 79 ~~C~vC~k~l----------~~~~f~~~p~~~v~H~ 104 (109)
T PF10367_consen 79 TKCSVCGKPL----------GNSVFVVFPCGHVVHY 104 (109)
T ss_pred CCccCcCCcC----------CCceEEEeCCCeEEec
Confidence 4799999972 1367999999877764
No 156
>KOG3080 consensus Nucleolar protein-like/EBNA1-binding protein [RNA processing and modification]
Probab=43.90 E-value=1.6e+02 Score=28.78 Aligned_cols=55 Identities=29% Similarity=0.420 Sum_probs=37.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 022703 187 AQELRERARKKKEEEEKRMEREREKERIRIGKELLEAKRIEEENERKRILALRKA 241 (293)
Q Consensus 187 ~~el~~k~r~~r~eeek~e~~e~E~~Rrk~GKe~~~~k~~~ee~e~k~~~e~rrr 241 (293)
++.++.++-.+....++.++..+-++-++.||.+|.+.-.....|-+..++..++
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 4455555544455555566666667778999999988877777776666666554
No 157
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=43.39 E-value=13 Score=27.43 Aligned_cols=26 Identities=23% Similarity=0.378 Sum_probs=17.5
Q ss_pred cccCCCCCCCCCccccccccccccccccccc
Q 022703 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDK 73 (293)
Q Consensus 43 ~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~ 73 (293)
+.||.||.+- .......|.++.||=|
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 4799998762 2445667777777754
No 158
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=43.06 E-value=19 Score=29.35 Aligned_cols=43 Identities=21% Similarity=0.393 Sum_probs=29.0
Q ss_pred ceeecccCCccc--------------cCHHHHHHHHHHhccCCCCcchhhhhccccCCCCC
Q 022703 4 VSLKCGDCGALL--------------RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (293)
Q Consensus 4 ~~LkC~~Cg~v~--------------~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~ 50 (293)
-.++|..||+.. .+...+.+..+. |- ++--.. +.-|+|.+|--
T Consensus 19 ~~V~C~nCgr~vPKDKAIkrf~i~n~Ve~a~~rdl~~a-~~-~lpk~~--~k~~YCvSCAi 75 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCVTKMYSPVDPQLAKELEKK-GA-IIARYP--VTKCYCVNCAV 75 (95)
T ss_pred ccEEeCCCCCcCcCCceEEEEEecCCCCHHHHHHHHhC-ce-eeeeee--eeeEEechhhh
Confidence 368999999876 567777788777 32 222222 34489999954
No 159
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=42.92 E-value=17 Score=30.58 Aligned_cols=37 Identities=22% Similarity=0.451 Sum_probs=21.5
Q ss_pred eecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
-+|..||+ .++..|...+=-++=+ . .+=|+|++|+.+
T Consensus 75 ~kCpkCgh-----e~m~Y~T~QlRSADEG-Q---TVFYTC~kC~~k 111 (116)
T KOG2907|consen 75 HKCPKCGH-----EEMSYHTLQLRSADEG-Q---TVFYTCPKCKYK 111 (116)
T ss_pred ccCcccCC-----chhhhhhhhcccccCC-c---eEEEEcCcccee
Confidence 35777764 4555666654443322 2 245888888776
No 160
>KOG0435 consensus Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=42.92 E-value=17 Score=39.22 Aligned_cols=64 Identities=28% Similarity=0.580 Sum_probs=38.4
Q ss_pred eeecccCCccccCHHH-HHHHHHHhccCCCCcc------hhhhhccccCCCCCCCCCccccccccccccccccccchhhc
Q 022703 5 SLKCGDCGALLRSVQE-AQEHAELTSHSNFSES------TEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEA 77 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~-aq~ha~~TgH~~F~e~------~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~ 77 (293)
-+.|.+||.|=....+ +-.+-+. ++|.+. .++-++..||.||++. ---+....||-|.-.-.
T Consensus 436 ivhc~~cG~vpVpes~LPV~LP~l---~~~~~kG~Pls~~~e~vn~~cP~cg~pA--------kRETDTMDTFvDSsWYY 504 (876)
T KOG0435|consen 436 IVHCDDCGAVPVPESELPVTLPEL---NDFTPKGPPLSKADEWVNVDCPRCGEPA--------KRETDTMDTFVDSSWYY 504 (876)
T ss_pred eEEcCCCCcccCcHHHCCcccccc---cccCCCCCcccchhhheeccCccCCCcc--------cccccccchhhccceee
Confidence 4789999988754443 3322222 334322 3667788999999972 12234466777765554
Q ss_pred cc
Q 022703 78 AK 79 (293)
Q Consensus 78 ~~ 79 (293)
.|
T Consensus 505 lR 506 (876)
T KOG0435|consen 505 LR 506 (876)
T ss_pred Ee
Confidence 43
No 161
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=42.88 E-value=12 Score=40.11 Aligned_cols=42 Identities=21% Similarity=0.342 Sum_probs=28.2
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCC----cchhhhhccccCCCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFS----ESTEAVLNLVCATCGKPC 52 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~----e~~d~i~~~~C~~Cg~~~ 52 (293)
.|+|..|+.-..+ + -...+||.+=. ..++..- -+||.|+..|
T Consensus 643 ~LkCs~Cn~R~Kd---~--vI~kC~H~FC~~Cvq~r~etRq-RKCP~Cn~aF 688 (698)
T KOG0978|consen 643 LLKCSVCNTRWKD---A--VITKCGHVFCEECVQTRYETRQ-RKCPKCNAAF 688 (698)
T ss_pred ceeCCCccCchhh---H--HHHhcchHHHHHHHHHHHHHhc-CCCCCCCCCC
Confidence 5899999944332 2 35678998743 2234454 4999999974
No 162
>PRK05978 hypothetical protein; Provisional
Probab=42.61 E-value=16 Score=31.90 Aligned_cols=48 Identities=21% Similarity=0.315 Sum_probs=27.7
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCCCCccccccccccccccccccchhhcc
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAA 78 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~ 78 (293)
+++.+|-.||...- |.... .+.-.|+.||..+ .--..+ .+|-|++|.+
T Consensus 31 Gl~grCP~CG~G~L----------------F~g~L--kv~~~C~~CG~~~---------~~~~a~-DgpAy~~i~i 78 (148)
T PRK05978 31 GFRGRCPACGEGKL----------------FRAFL--KPVDHCAACGEDF---------THHRAD-DLPAYLVIVI 78 (148)
T ss_pred HHcCcCCCCCCCcc----------------ccccc--ccCCCccccCCcc---------ccCCcc-ccCcchhHHH
Confidence 67889999986431 12221 2335899999862 111111 4777777654
No 163
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=42.21 E-value=46 Score=29.67 Aligned_cols=26 Identities=23% Similarity=0.317 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCC
Q 022703 115 KELLKELEAMGFPVARATRALHYSGN 140 (293)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~tgn 140 (293)
.+++..|..+||+...|.+++...+.
T Consensus 150 ~ev~~aL~~LG~~~~~a~~~~~~~~~ 175 (192)
T PRK00116 150 EEAVSALVALGYKPKEASKAVAKILK 175 (192)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 68999999999999999999988764
No 164
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=42.01 E-value=8.1 Score=41.61 Aligned_cols=41 Identities=22% Similarity=0.488 Sum_probs=25.6
Q ss_pred eeecccCCcccc---------CHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 5 SLKCGDCGALLR---------SVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~---------~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
.+.|.+|||+.. -+... +.-.+=|-++.+. +-..||.||+.
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~~--~~L~CH~Cg~~~~----~p~~Cp~Cgs~ 484 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHKAT--GQLRCHYCGYQEP----IPQSCPECGSE 484 (730)
T ss_pred eeecccCCCcccCCCCCcceEEecCC--CeeEeCCCCCCCC----CCCCCCCCCCC
Confidence 578888888881 11111 3334445556655 55799999985
No 165
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=41.86 E-value=15 Score=24.25 Aligned_cols=13 Identities=31% Similarity=1.094 Sum_probs=9.5
Q ss_pred cceeecccCCccc
Q 022703 3 GVSLKCGDCGALL 15 (293)
Q Consensus 3 ~~~LkC~~Cg~v~ 15 (293)
+..++|..||.++
T Consensus 23 g~~v~C~~C~~~f 35 (36)
T PF13717_consen 23 GRKVRCSKCGHVF 35 (36)
T ss_pred CcEEECCCCCCEe
Confidence 5577888888765
No 166
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=41.71 E-value=17 Score=31.09 Aligned_cols=17 Identities=24% Similarity=0.640 Sum_probs=12.2
Q ss_pred ccCCCCcchhhhhccccCCCCCC
Q 022703 29 SHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 29 gH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
||.+|=.. -.||.||++
T Consensus 36 G~v~~PPr------~~Cp~C~~~ 52 (140)
T COG1545 36 GRVYFPPR------AYCPKCGSE 52 (140)
T ss_pred CeEEcCCc------ccCCCCCCC
Confidence 55667655 479999986
No 167
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=41.25 E-value=66 Score=28.85 Aligned_cols=36 Identities=17% Similarity=0.295 Sum_probs=26.9
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHhC-CCCHHHHHHH
Q 022703 114 DKELLKELEAMGFPVARATRALHYSG-NANVEAAVNW 149 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL~~tg-n~~~E~A~~W 149 (293)
..+++..|+.+||++..+.+||..-. +.+++..+-+
T Consensus 145 ~~e~~~aL~~LGy~~~ea~~al~~v~~~~~~eelir~ 181 (186)
T PRK14600 145 NDDALAALISLGYEKTKAFNAIQKIKPNLSTQDIIRK 181 (186)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhcCCCHHHHHHH
Confidence 36789999999999999999997643 2355544443
No 168
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=41.22 E-value=15 Score=36.21 Aligned_cols=45 Identities=27% Similarity=0.462 Sum_probs=36.4
Q ss_pred cceeeccc--CCccccCHHHHHHHHHHhccCC--------------CCcchhhhhccccCCCCCC
Q 022703 3 GVSLKCGD--CGALLRSVQEAQEHAELTSHSN--------------FSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 3 ~~~LkC~~--Cg~v~~~~~~aq~ha~~TgH~~--------------F~e~~d~i~~~~C~~Cg~~ 51 (293)
+.-.+|.+ |.+....+++-..|... ||.+ |+-. -.-|+|+.|+|.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lh-GH~~~~~~~~p~p~~~~~F~~~---~KPYrCevC~KR 407 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLH-GHQNQKLHENPSPEKMNIFSAK---DKPYRCEVCDKR 407 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhc-cccCcccCCCCCcccccccccc---CCceeccccchh
Confidence 46688988 99999999999999999 9954 5322 245999999986
No 169
>KOG0608 consensus Warts/lats-like serine threonine kinases [Cell cycle control, cell division, chromosome partitioning]
Probab=41.17 E-value=17 Score=39.31 Aligned_cols=42 Identities=21% Similarity=0.268 Sum_probs=38.8
Q ss_pred cccccCHHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHH
Q 022703 109 VEPEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWV 150 (293)
Q Consensus 109 ~~~~~~~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL 150 (293)
....+|..++.-|+..||.+.-+..||..+++.++++|++++
T Consensus 84 a~s~sn~qmlq~lv~ag~d~~~a~~al~~pns~sie~sie~~ 125 (1034)
T KOG0608|consen 84 AGSESNSQMLQGLVGAGNDRHMALGALATPNSRSIEASIETI 125 (1034)
T ss_pred cccccchhhhHhhhhccccchhhhhhhcCCCccccchhhhcc
Confidence 345788999999999999999999999999999999999997
No 170
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=41.01 E-value=8.5 Score=31.88 Aligned_cols=29 Identities=21% Similarity=0.331 Sum_probs=23.7
Q ss_pred ccccCCCCCCCCCccccccccccccccccccchh
Q 022703 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTS 75 (293)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lv 75 (293)
..+||.||.. |+.-+..+++.+.-|.+++
T Consensus 72 ~~~CpkCg~~-----ea~y~~~QtRsaDEp~T~F 100 (113)
T COG1594 72 KEKCPKCGNK-----EAYYWQLQTRSADEPETRF 100 (113)
T ss_pred cccCCCCCCc-----eeEEEeeehhccCCCceEE
Confidence 4689999985 6788899999998887764
No 171
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=40.75 E-value=68 Score=29.06 Aligned_cols=25 Identities=20% Similarity=0.267 Sum_probs=22.1
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHh
Q 022703 114 DKELLKELEAMGFPVARATRALHYS 138 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL~~t 138 (293)
..+++..|+.+||++..|.+|+..-
T Consensus 155 ~~ea~~AL~~LGy~~~ea~~av~~~ 179 (203)
T PRK14602 155 FRDALAGLANLGYGEEEARPVLKEV 179 (203)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3678999999999999999999765
No 172
>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=40.38 E-value=37 Score=23.96 Aligned_cols=38 Identities=39% Similarity=0.632 Sum_probs=29.1
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~ 50 (293)
++.|..||. .-+...-..|... -|.+ +. ..+.||.|..
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~-~H~~--~~----~~v~CPiC~~ 39 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCED-EHRS--ES----KNVVCPICSS 39 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHh-HCcC--CC----CCccCCCchh
Confidence 468999999 6777888899888 6654 22 3479999976
No 173
>PF10827 DUF2552: Protein of unknown function (DUF2552) ; InterPro: IPR020157 This entry contains proteins with no known function.
Probab=40.08 E-value=20 Score=27.89 Aligned_cols=17 Identities=24% Similarity=0.546 Sum_probs=14.7
Q ss_pred CCHHHHHHHHHHhcCCC
Q 022703 141 ANVEAAVNWVVEHENDP 157 (293)
Q Consensus 141 ~~~E~A~~WL~~h~dD~ 157 (293)
..++.||+||-+||++-
T Consensus 59 ~tld~Ai~Wi~e~M~~i 75 (79)
T PF10827_consen 59 PTLDLAIAWIGEHMPHI 75 (79)
T ss_pred ccHHHHHHHHHhcccch
Confidence 36999999999999873
No 174
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=39.79 E-value=38 Score=28.77 Aligned_cols=38 Identities=21% Similarity=0.326 Sum_probs=30.1
Q ss_pred ccCHHHHHHHH-hCCCCHHHHHHHHHHhCCCCHHHHHHHH
Q 022703 112 EVDKELLKELE-AMGFPVARATRALHYSGNANVEAAVNWV 150 (293)
Q Consensus 112 ~~~~~~l~~L~-~MGF~~~~a~kAL~~tgn~~~E~A~~WL 150 (293)
.++++-+...+ --|-|++.|.+||..+|+ ++-.|+--|
T Consensus 82 ~i~eeDIkLV~eQa~VsreeA~kAL~e~~G-DlaeAIm~L 120 (122)
T COG1308 82 DISEEDIKLVMEQAGVSREEAIKALEEAGG-DLAEAIMKL 120 (122)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHHHHcCC-cHHHHHHHh
Confidence 46777776665 469999999999999988 787777554
No 175
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=39.79 E-value=24 Score=29.39 Aligned_cols=46 Identities=15% Similarity=0.420 Sum_probs=30.3
Q ss_pred eeecccCCccc--------------cCHHHHHHHHHHhccCCCCcchhhhhccccCCCCC
Q 022703 5 SLKCGDCGALL--------------RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (293)
Q Consensus 5 ~LkC~~Cg~v~--------------~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~ 50 (293)
.++|..||+.. .+...+.++.+.+.-..|.=-.=-+.-++|-+|--
T Consensus 20 ~V~C~nCgr~vPKDKAIkrf~irniVe~aa~rDl~~a~v~~~y~lPKly~k~~YCVSCAI 79 (108)
T PTZ00172 20 PVRCSNCGRCVPKDKAIKRFVVRNIVDAASVRDIAEASVYYGYPLPKLYMKQQYCVSCAI 79 (108)
T ss_pred cEEeCCccccccccceEEEEeccCCccHHHHHHHHHhhchhccccccceeeeEEeeehhh
Confidence 58999999876 66777888888854434431101133369999953
No 176
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=39.43 E-value=4.8e+02 Score=29.17 Aligned_cols=15 Identities=13% Similarity=0.116 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHHHhH
Q 022703 184 KLKAQELRERARKKK 198 (293)
Q Consensus 184 ~~k~~el~~k~r~~r 198 (293)
..-+++.+++.++.+
T Consensus 216 v~~~qe~La~~qe~e 230 (1064)
T KOG1144|consen 216 VRAMQEALAKRQEEE 230 (1064)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344455555544443
No 177
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=38.97 E-value=22 Score=31.44 Aligned_cols=47 Identities=19% Similarity=0.370 Sum_probs=32.7
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcc-hhhhh--ccccCCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSES-TEAVL--NLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~-~d~i~--~~~C~~Cg~~ 51 (293)
...|..||..+........-++.-+|..|.+. .+... -+.||.|..+
T Consensus 114 ~~~C~~Cg~~f~~~k~i~~~~~~l~~~~~~~~~~~~~~~~~~~Cp~Cr~k 163 (181)
T PRK08222 114 LQRCSRCERPFAPQKTVALAAELLAQQQNAPQNREMLRAQASVCPECKQR 163 (181)
T ss_pred cCcCcccCCccCcHhHHHHHHHHhhhccCcHhhHHHHHHHhccCHHHHhh
Confidence 34699999999877777766666677777744 23332 2689999864
No 178
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=38.90 E-value=5.4e+02 Score=28.79 Aligned_cols=22 Identities=36% Similarity=0.367 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHHHHHcHHHH
Q 022703 225 RIEEENERKRILALRKAEKEEE 246 (293)
Q Consensus 225 ~~~ee~e~k~~~e~rrrEK~ee 246 (293)
++.++...++.-|++.+++.++
T Consensus 805 re~EEEr~Rr~EEe~~ae~~ee 826 (988)
T KOG2072|consen 805 REIEEERARREEEEANAERQEE 826 (988)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444444444
No 179
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=38.49 E-value=16 Score=39.53 Aligned_cols=39 Identities=26% Similarity=0.582 Sum_probs=26.3
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCC-CcchhhhhccccCCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNF-SESTEAVLNLVCATCGKPC 52 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F-~e~~d~i~~~~C~~Cg~~~ 52 (293)
...||..||+.|.- .-|.++ |.-. +|+ .-|-|+.|+|.|
T Consensus 280 RKFKCtECgKAFKf----KHHLKE--HlRIHSGE----KPfeCpnCkKRF 319 (1007)
T KOG3623|consen 280 RKFKCTECGKAFKF----KHHLKE--HLRIHSGE----KPFECPNCKKRF 319 (1007)
T ss_pred ccccccccchhhhh----HHHHHh--hheeecCC----CCcCCccccccc
Confidence 45799999998853 334444 3332 244 458999999876
No 180
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=38.03 E-value=75 Score=28.68 Aligned_cols=24 Identities=21% Similarity=0.272 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHh
Q 022703 115 KELLKELEAMGFPVARATRALHYS 138 (293)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~t 138 (293)
.+++..|+.+||++..+.+||...
T Consensus 153 ~ea~~AL~~LGy~~~ea~~al~~i 176 (197)
T PRK14603 153 EDAVLALLALGFREAQVRSVVAEL 176 (197)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 578999999999999999999764
No 181
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=37.76 E-value=16 Score=38.80 Aligned_cols=9 Identities=33% Similarity=0.918 Sum_probs=7.8
Q ss_pred cccCCCCCC
Q 022703 43 LVCATCGKP 51 (293)
Q Consensus 43 ~~C~~Cg~~ 51 (293)
+.||.||+.
T Consensus 581 ~~CP~CGs~ 589 (623)
T PRK08271 581 KRCPICGSE 589 (623)
T ss_pred cCCcCCCCc
Confidence 799999974
No 182
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=37.69 E-value=19 Score=27.64 Aligned_cols=27 Identities=22% Similarity=0.262 Sum_probs=21.2
Q ss_pred CHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 022703 127 PVARATRALHYSGNANVEAAVNWVVEHE 154 (293)
Q Consensus 127 ~~~~a~kAL~~tgn~~~E~A~~WL~~h~ 154 (293)
|......||.+... +|+.|++||++..
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 77888889988876 8999999998853
No 183
>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=37.46 E-value=2.5e+02 Score=26.72 Aligned_cols=55 Identities=24% Similarity=0.349 Sum_probs=34.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 022703 187 AQELRERARKKKEEEEKRMEREREKERIRIGKELLEAKRIEEENERKRILALRKA 241 (293)
Q Consensus 187 ~~el~~k~r~~r~eeek~e~~e~E~~Rrk~GKe~~~~k~~~ee~e~k~~~e~rrr 241 (293)
++.++.++-......+..+.+.+-++-.+-||.++..+-..+..+-+..++..++
T Consensus 120 M~KVr~kLl~~~~~ie~~E~~rk~Re~KKfgKqvQ~ek~~eR~keKk~~le~Ik~ 174 (271)
T PF05890_consen 120 MEKVRQKLLKEQKRIEASEEARKQRELKKFGKQVQVEKLQERAKEKKEMLEKIKK 174 (271)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555555566666677778899999977766666655555554433
No 184
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=37.45 E-value=2.4e+02 Score=23.49 Aligned_cols=29 Identities=31% Similarity=0.373 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhHHHHHH
Q 022703 175 KSSLTPEEIKLKAQELRERARKKKEEEEK 203 (293)
Q Consensus 175 kk~lT~EEk~~k~~el~~k~r~~r~eeek 203 (293)
+-.||.||.+.-+++|..+++..+.+-+.
T Consensus 36 kGeln~eEak~~vddl~~q~k~~~~e~e~ 64 (108)
T COG3937 36 KGELNAEEAKRFVDDLLRQAKEAQGELEE 64 (108)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHhhhHHH
Confidence 34799999999999999999877654333
No 185
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=37.35 E-value=17 Score=33.90 Aligned_cols=46 Identities=15% Similarity=0.465 Sum_probs=26.5
Q ss_pred CcceeecccCCccc---cCHHHHHHHHHHhccCCCC-cchhhhhccccCCCCCC
Q 022703 2 AGVSLKCGDCGALL---RSVQEAQEHAELTSHSNFS-ESTEAVLNLVCATCGKP 51 (293)
Q Consensus 2 ~~~~LkC~~Cg~v~---~~~~~aq~ha~~TgH~~F~-e~~d~i~~~~C~~Cg~~ 51 (293)
.-|+++|..||.-. ...++-...+.. .++.+ ++. .....|+.|+.+
T Consensus 39 TPF~~RCL~C~~YI~K~~rfNavkE~~~d--K~y~~~kiY--Rf~I~C~~C~n~ 88 (272)
T COG5134 39 TPFPVRCLNCENYIQKGTRFNAVKEEIGD--KSYYTTKIY--RFSIKCHLCSNP 88 (272)
T ss_pred cCcceeecchhhhhhcccchhHHHHHhcc--cccceeEEE--EEEEEccCCCCc
Confidence 46999999999876 333333343333 12222 221 223579999985
No 186
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.05 E-value=95 Score=28.03 Aligned_cols=24 Identities=29% Similarity=0.409 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHh
Q 022703 115 KELLKELEAMGFPVARATRALHYS 138 (293)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~t 138 (293)
.+++..|+.+||++..+.+|+..-
T Consensus 150 ~e~~~aL~~LGy~~~ea~~ai~~i 173 (195)
T PRK14604 150 RELSEILISLGYSAAEAAAAIAAL 173 (195)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 578999999999999999998754
No 187
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=36.80 E-value=22 Score=32.10 Aligned_cols=16 Identities=19% Similarity=0.517 Sum_probs=12.1
Q ss_pred cceeecccCCccccCH
Q 022703 3 GVSLKCGDCGALLRSV 18 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~ 18 (293)
-+.++|..|+......
T Consensus 107 ~~~~~C~~C~~~~~~~ 122 (224)
T cd01412 107 LFRVRCSSCGYVGENN 122 (224)
T ss_pred cCccccCCCCCCCCcc
Confidence 3568999999887554
No 188
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=36.71 E-value=21 Score=39.09 Aligned_cols=47 Identities=23% Similarity=0.383 Sum_probs=35.6
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCCCCcccc
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTET 58 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~~~~~e~ 58 (293)
.|+-+|--|++||...-.-|-|..- |+ ++ .-|+|..||..|.+-.-.
T Consensus 351 ~~khkCr~CakvfgS~SaLqiHlRS--HT---GE----RPfqCnvCG~~FSTkGNL 397 (958)
T KOG1074|consen 351 FFKHKCRFCAKVFGSDSALQIHLRS--HT---GE----RPFQCNVCGNRFSTKGNL 397 (958)
T ss_pred cccchhhhhHhhcCchhhhhhhhhc--cC---CC----CCeeecccccccccccce
Confidence 5788999999999998888888765 43 23 448999999987544333
No 189
>PHA00616 hypothetical protein
Probab=36.37 E-value=20 Score=25.13 Aligned_cols=28 Identities=25% Similarity=0.552 Sum_probs=21.6
Q ss_pred eecccCCccccCHHHHHHHHHH-hccCCC
Q 022703 6 LKCGDCGALLRSVQEAQEHAEL-TSHSNF 33 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~~-TgH~~F 33 (293)
.+|..||.++....+-..|... |||..|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~ 30 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKL 30 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcc
Confidence 5899999999999999888854 344334
No 190
>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=35.53 E-value=2.1e+02 Score=30.69 Aligned_cols=25 Identities=20% Similarity=0.392 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCC
Q 022703 246 EKRAREKIRQKLEEDKAERRRRLGL 270 (293)
Q Consensus 246 e~~ar~rir~qIe~Dk~eR~~r~~~ 270 (293)
+.-+|+-|-+|+...+.-|+.-.+.
T Consensus 300 d~~~R~al~eql~~~~eL~~Ki~~~ 324 (735)
T PF04615_consen 300 DEEARQALQEQLRRGEELTRKIEGE 324 (735)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3446777777877777777655554
No 191
>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=35.39 E-value=50 Score=23.45 Aligned_cols=23 Identities=26% Similarity=0.404 Sum_probs=18.8
Q ss_pred CHHHHHHHHhC---CCCHHHHHHHHH
Q 022703 114 DKELLKELEAM---GFPVARATRALH 136 (293)
Q Consensus 114 ~~~~l~~L~~M---GF~~~~a~kAL~ 136 (293)
...+.+||++- ||+.+.|..|+.
T Consensus 21 k~~l~~QL~se~ge~Ft~e~A~YAv~ 46 (48)
T PF07553_consen 21 KQGLYDQLTSEYGEGFTEEEAQYAVD 46 (48)
T ss_pred HHHHHHHHHhhcccCCCHHHHHHHHH
Confidence 45678999876 899999999874
No 192
>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=35.33 E-value=3.3e+02 Score=24.41 Aligned_cols=23 Identities=35% Similarity=0.725 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcC
Q 022703 247 KRAREKIRQKLEEDKAERRRRLG 269 (293)
Q Consensus 247 ~~ar~rir~qIe~Dk~eR~~r~~ 269 (293)
+..+++|.+|+++.+.+|..|+-
T Consensus 127 r~ErE~~~~q~eqERleRKKRiE 149 (171)
T PF05672_consen 127 RKERERIMQQEEQERLERKKRIE 149 (171)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678899999999999998754
No 193
>PLN00186 ribosomal protein S26; Provisional
Probab=35.23 E-value=35 Score=28.42 Aligned_cols=46 Identities=13% Similarity=0.355 Sum_probs=29.4
Q ss_pred eeecccCCccc--------------cCHHHHHHHHHHhccCCCCcchhhhhccccCCCCC
Q 022703 5 SLKCGDCGALL--------------RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (293)
Q Consensus 5 ~LkC~~Cg~v~--------------~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~ 50 (293)
.++|+.||+.. .+...+.++.+.+....|.=-.=-+.-++|-+|--
T Consensus 20 ~V~C~nCgr~vPKDKAIkrf~irniVe~aa~rDl~~a~vy~~y~lPKly~K~~YCVSCAI 79 (109)
T PLN00186 20 RIRCSNCGKCVPKDKAIKRFLVRNIVEQAALRDVQEACVYDGYTLPKLYAKVQYCISCAI 79 (109)
T ss_pred ceeeCCCcccccccceEEEEecccCccHHHHHHHHhhhcccccccchhhhceEEEEeehh
Confidence 58999999987 57778888888854322220000122378999953
No 194
>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=35.11 E-value=90 Score=27.02 Aligned_cols=11 Identities=45% Similarity=0.770 Sum_probs=7.4
Q ss_pred HHHHHHHHHHH
Q 022703 247 KRAREKIRQKL 257 (293)
Q Consensus 247 ~~ar~rir~qI 257 (293)
.+.|+.+|++|
T Consensus 58 eaERe~mRq~I 68 (139)
T PF05835_consen 58 EAEREKMRQHI 68 (139)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 34567777777
No 195
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=34.97 E-value=18 Score=37.78 Aligned_cols=9 Identities=33% Similarity=0.863 Sum_probs=7.7
Q ss_pred cccCCCCCC
Q 022703 43 LVCATCGKP 51 (293)
Q Consensus 43 ~~C~~Cg~~ 51 (293)
+.||.||+.
T Consensus 539 ~~CP~Cgs~ 547 (579)
T TIGR02487 539 DKCPKCGSH 547 (579)
T ss_pred CcCcCCCCc
Confidence 689999974
No 196
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=34.69 E-value=20 Score=38.59 Aligned_cols=8 Identities=38% Similarity=1.016 Sum_probs=7.2
Q ss_pred cccCCCCC
Q 022703 43 LVCATCGK 50 (293)
Q Consensus 43 ~~C~~Cg~ 50 (293)
+.||.||+
T Consensus 694 ~~CP~CG~ 701 (735)
T PRK07111 694 DKCPKCGS 701 (735)
T ss_pred ccCcCCCC
Confidence 79999996
No 197
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=34.53 E-value=16 Score=34.05 Aligned_cols=11 Identities=27% Similarity=0.628 Sum_probs=7.2
Q ss_pred hccccCCCCCC
Q 022703 41 LNLVCATCGKP 51 (293)
Q Consensus 41 ~~~~C~~Cg~~ 51 (293)
.-|+|..|++.
T Consensus 172 rpykc~~c~ka 182 (267)
T KOG3576|consen 172 RPYKCSLCEKA 182 (267)
T ss_pred cccchhhhhHH
Confidence 44777777764
No 198
>KOG1867 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=34.35 E-value=24 Score=36.34 Aligned_cols=53 Identities=8% Similarity=0.071 Sum_probs=40.6
Q ss_pred hhccccCCCCCCCCCccccccccccccccccccchhhccccccccc---Cccc---cCCccccccC
Q 022703 40 VLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV---PKAT---ADSEEAIDVD 99 (293)
Q Consensus 40 i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~~---p~K~---~~~~~~lDl~ 99 (293)
...++|..|+.. ..++|+..+...|-+|-++.+||.... -.|. +.+|..|++.
T Consensus 352 ~~~~~c~~c~~~-------~~~~kql~~~~lP~~l~~~lkRfe~~~~~~~~ki~~~v~fp~~l~m~ 410 (492)
T KOG1867|consen 352 DSKYKCSSCKSK-------QESTKQLTIRKLPAVLCLHLKRFEHSATGAREKIDSYVSFPVLLNMK 410 (492)
T ss_pred ccccccCCcccc-------cccccccccccCCceeeeeeccccccccccccccCcccccchhhcCC
Confidence 456899999987 789999999999999999999987653 2244 3345555554
No 199
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=34.05 E-value=7.5e+02 Score=28.15 Aligned_cols=80 Identities=28% Similarity=0.390 Sum_probs=47.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHhHH--HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH--HHHHHHHHHHcHHHHHHHHHH
Q 022703 177 SLTPEEIKLKAQELRERARKKKE--EEEKRMEREREKERIRIGKELLEAKRIEEENE--RKRILALRKAEKEEEKRAREK 252 (293)
Q Consensus 177 ~lT~EEk~~k~~el~~k~r~~r~--eeek~e~~e~E~~Rrk~GKe~~~~k~~~ee~e--~k~~~e~rrrEK~ee~~ar~r 252 (293)
.-|++|-++++.+|.++....|- .+.+..-++=++.+|.- ..+++.|-++-+++ ..|.+-..|.|+.+-..+.++
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 34889999999999999754443 23333333444444432 34555665554433 345555666677777777777
Q ss_pred HHHHH
Q 022703 253 IRQKL 257 (293)
Q Consensus 253 ir~qI 257 (293)
-+..+
T Consensus 302 ~k~em 306 (1243)
T KOG0971|consen 302 YKEEM 306 (1243)
T ss_pred HHHHH
Confidence 66554
No 200
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=33.76 E-value=24 Score=25.72 Aligned_cols=30 Identities=27% Similarity=0.723 Sum_probs=19.0
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
..+|..||..+ +.+.+..+. + ..||.||..
T Consensus 2 ~~~CP~CG~~i------------ev~~~~~Ge---i--V~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEI------------ELENPELGE---L--VICDECGAE 31 (54)
T ss_pred ccCCCCCCCEE------------ecCCCccCC---E--EeCCCCCCE
Confidence 35899999855 223333333 3 489999984
No 201
>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=33.08 E-value=12 Score=31.38 Aligned_cols=45 Identities=16% Similarity=0.429 Sum_probs=25.8
Q ss_pred eeecccCCccc--------------cCHHHHHHHHHHhccCCCCcchhhhhccccCCCC
Q 022703 5 SLKCGDCGALL--------------RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCG 49 (293)
Q Consensus 5 ~LkC~~Cg~v~--------------~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg 49 (293)
.++|..||+.. .+...+.+..+.+.+..|.=-.=-+.-|+|.+|-
T Consensus 20 ~V~C~nCgr~vPKDKAIkrf~i~niVeaaa~rdi~~a~v~~~y~lPKlyvK~~YCvSCA 78 (113)
T PF01283_consen 20 PVRCDNCGRCVPKDKAIKRFVIRNIVEAAAVRDISEASVYDAYVLPKLYVKLYYCVSCA 78 (113)
T ss_dssp EEE-TTTB-EEECCCSEEEEEEEESS-CCCHHHHHHCB-SSS--S-EEEEEEEE-CHHH
T ss_pred CEeeCcccccCcCCceEEEEEccCCccHHHHHHHhhcceeeecccccceeEEEEeeeee
Confidence 68999999877 5556788888886665554110114458999993
No 202
>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=33.05 E-value=7.6 Score=34.27 Aligned_cols=39 Identities=26% Similarity=0.522 Sum_probs=24.2
Q ss_pred eecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCC
Q 022703 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~ 52 (293)
..|..|+.-.+|. .|.. |-.+|+... ..-.+|..||+++
T Consensus 40 ~~Cp~C~~~IrG~----y~v~--gv~~~g~~~--~~PsYC~~CGkpy 78 (158)
T PF10083_consen 40 TSCPNCSTPIRGD----YHVE--GVFGLGGHY--EAPSYCHNCGKPY 78 (158)
T ss_pred HHCcCCCCCCCCc----eecC--CeeeeCCCC--CCChhHHhCCCCC
Confidence 3577888888776 2322 333453332 3557999999985
No 203
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=33.01 E-value=27 Score=30.47 Aligned_cols=44 Identities=20% Similarity=0.388 Sum_probs=25.4
Q ss_pred eeecccCCccccCH----HHHH-HHHHHhccCCCCcc-hhhhhccccCCCCCC
Q 022703 5 SLKCGDCGALLRSV----QEAQ-EHAELTSHSNFSES-TEAVLNLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~----~~aq-~ha~~TgH~~F~e~-~d~i~~~~C~~Cg~~ 51 (293)
-+.|..||.+..=. .+.. ..+.. .+|.-. ..-++.-.|+.|.++
T Consensus 100 H~iC~~CGki~~i~~~~l~~~~~~~~~~---~gf~i~~~~l~~~GiC~~C~~~ 149 (169)
T PRK11639 100 MFICDRCGAVKEECAEGVEDIMHTLAAK---MGFALRHNVIEAHGLCAACVEV 149 (169)
T ss_pred eEEeCCCCCEEEecccHHHHHHHHHHHH---cCCEEeccEEEEEEEChhhcCc
Confidence 48999999999432 1222 22333 366533 222344579999775
No 204
>PF05262 Borrelia_P83: Borrelia P83/100 protein; InterPro: IPR007926 This family consists of several Borrelia P83/P100 antigen proteins.
Probab=32.54 E-value=5.6e+02 Score=26.62 Aligned_cols=14 Identities=29% Similarity=0.292 Sum_probs=7.8
Q ss_pred hCCCCHHHHH-HHHH
Q 022703 123 AMGFPVARAT-RALH 136 (293)
Q Consensus 123 ~MGF~~~~a~-kAL~ 136 (293)
..||+..-|. -|.|
T Consensus 95 aygY~~~~a~~lA~f 109 (489)
T PF05262_consen 95 AYGYSDEDAETLATF 109 (489)
T ss_pred hcCCChhhHHHHHHH
Confidence 5778775443 4433
No 205
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=32.40 E-value=21 Score=30.49 Aligned_cols=45 Identities=22% Similarity=0.434 Sum_probs=25.5
Q ss_pred eeecccCCccccCHH----HHHHHHHHhccCCCCcc-hhhhhccccCCCCCC
Q 022703 5 SLKCGDCGALLRSVQ----EAQEHAELTSHSNFSES-TEAVLNLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~----~aq~ha~~TgH~~F~e~-~d~i~~~~C~~Cg~~ 51 (293)
-|.|..||.|..=.. ..+.... ...+|.=. ..-.+--.|+.|+..
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 478999999994333 3333333 35566522 111233459999864
No 206
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.17 E-value=25 Score=26.07 Aligned_cols=14 Identities=36% Similarity=0.990 Sum_probs=11.5
Q ss_pred CcceeecccCCccc
Q 022703 2 AGVSLKCGDCGALL 15 (293)
Q Consensus 2 ~~~~LkC~~Cg~v~ 15 (293)
+..+|+|..||.+.
T Consensus 31 aDIkikC~nC~h~v 44 (60)
T COG4481 31 ADIKIKCENCGHSV 44 (60)
T ss_pred CcEEEEecCCCcEE
Confidence 35789999999876
No 207
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.13 E-value=13 Score=38.05 Aligned_cols=41 Identities=24% Similarity=0.538 Sum_probs=22.7
Q ss_pred eeecccCCcccc---------CHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 5 SLKCGDCGALLR---------SVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~---------~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
.|.|..|||+.. -... .+.-.+-|-+|... ....||.||+.
T Consensus 213 ~~~C~~Cg~~~~C~~C~~~l~~h~~--~~~l~Ch~Cg~~~~----~~~~Cp~C~s~ 262 (505)
T TIGR00595 213 NLLCRSCGYILCCPNCDVSLTYHKK--EGKLRCHYCGYQEP----IPKTCPQCGSE 262 (505)
T ss_pred eeEhhhCcCccCCCCCCCceEEecC--CCeEEcCCCcCcCC----CCCCCCCCCCC
Confidence 467777777762 1110 11223344455555 44699999885
No 208
>COG0423 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=31.95 E-value=53 Score=34.37 Aligned_cols=48 Identities=21% Similarity=0.457 Sum_probs=27.8
Q ss_pred ceeecccCCccccC-HHHHHHHHHHhccCCCCcc-hhhh---hccccCCCCCCC
Q 022703 4 VSLKCGDCGALLRS-VQEAQEHAELTSHSNFSES-TEAV---LNLVCATCGKPC 52 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~-~~~aq~ha~~TgH~~F~e~-~d~i---~~~~C~~Cg~~~ 52 (293)
-...|.+||..++- +---...... +|-+++.. .+++ -+.+||.||.+.
T Consensus 87 plv~c~~c~~~yRADHLiEe~l~~~-~~~~~~~~e~~~ii~~~~ir~p~~g~~l 139 (558)
T COG0423 87 PLVECKKCGERYRADHLIEEYLGKD-GHGNMSPEELTEIIREYDIRCPECGGEL 139 (558)
T ss_pred ceeeccccchhhhhhHHHHHHhhhc-ccccCCHHHHHHHHHHcCCcCCCcCCcc
Confidence 35789999999952 2222222232 35555533 1222 237899999874
No 209
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=31.84 E-value=24 Score=36.10 Aligned_cols=29 Identities=28% Similarity=0.257 Sum_probs=22.7
Q ss_pred eecccCCccc---cCHHHHHHHHHHhccCCCC
Q 022703 6 LKCGDCGALL---RSVQEAQEHAELTSHSNFS 34 (293)
Q Consensus 6 LkC~~Cg~v~---~~~~~aq~ha~~TgH~~F~ 34 (293)
..|..||.|+ .-..-|+.|=++|||.|-=
T Consensus 241 wicliCg~vgcgrY~eghA~rHweet~H~yal 272 (493)
T KOG0804|consen 241 WICLICGNVGCGRYKEGHARRHWEETGHCYAL 272 (493)
T ss_pred EEEEEccceecccccchhHHHHHHhhcceEEE
Confidence 4577788887 4456699999999999853
No 210
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.76 E-value=55 Score=29.79 Aligned_cols=24 Identities=29% Similarity=0.343 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHh
Q 022703 115 KELLKELEAMGFPVARATRALHYS 138 (293)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~t 138 (293)
+++++.|+++||++..|.+|+..-
T Consensus 145 ~ea~~AL~~LGy~~~ea~~al~~v 168 (196)
T PRK13901 145 KELEQSIVNMGFDRKLVNSAIKEI 168 (196)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 578999999999999999998653
No 211
>PF08050 Tet_res_leader: Tetracycline resistance leader peptide; InterPro: IPR012618 The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can reverse its effects. Tetracycline resistance genes are often located on mobile elements, such as plasmids, transposons and/or conjugative transposons, which can sometimes be transferred between bacterial species. In certain cases, tetracycline can enhance the transfer of these elements, thereby promoting resistance amongst a bacterial colony. There are three types of tetracycline resistance: tetracycline efflux, ribosomal protection, and tetracycline modification [, ]: Tetracycline efflux proteins belong to the major facilitator superfamily. Efflux proteins are membrane-associated proteins that recognise and export tetracycline from the cell. They are found in both Gram-positive and Gram-negative bacteria []. There are at least 22 different tetracycline efflux proteins, grouped according to sequence similarity: Group 1 are Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G), Tet(H), Tet(J), Tet(Z) and Tet(30); Group 2 are Tet(K) and Tet(L); Group 3 are Otr(B) and Tcr(3); Group 4 is TetA(P); Group 5 is Tet(V). In addition, there are the efflux proteins Tet(31), Tet(33), Tet(V), Tet(Y), Tet(34), and Tet(35). Ribosomal protection proteins are cytoplasmic proteins that display homology with the elongation factors EF-Tu and EF-G. Protection proteins bind the ribosome, causing an alteration in ribosomal conformation that prevents tetracycline from binding. There are at least ten ribosomal protection proteins: Tet(M), Tet(O), Tet(S), Tet(W), Tet(32), Tet(36), Tet(Q), Tet(T), Otr(A), and TetB(P). Both Tet(M) and Tet(O) have ribosome-dependent GTPase activity, the hydrolysis of GTP providing the energy for the ribosomal conformational changes. Tetracycline modification proteins include the enzymes Tet(37) and Tet(X), both of which inactivate tetracycline. In addition, there are the tetracycline resistance proteins Tet(U) and Otr(C). The expression of several of these tet genes is controlled by a family of tetracycline transcriptional regulators known as TetR. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity []. The TetR proteins identified in over 115 genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the tetracycline resistance leader peptide, which can be found in Tet(L) efflux proteins. Tet(L) is a transmembrane protein that can function as a metal-tetracycline/H+ antiporter. Its sequence is preceded by a leader region region that contains a 20-amino-acid open reading frame and an appropriately spaced ribosome binding site []. Expression of the gene is induced by addition of tetracycline, which is thought to act by binding to ribosomes that translate the tet(L) leader peptide coding sequence. The presence of three inverted repeats, which can form two different conformations of mRNA, suggests that the tetracycline resistance (TcR) region is regulated by a translational attenuation mechanism. A Rho-independent transcriptional terminator structure is present immediately after the translational stop codon of the Tet protein [].; GO: 0046677 response to antibiotic
Probab=31.36 E-value=17 Score=21.34 Aligned_cols=10 Identities=20% Similarity=0.584 Sum_probs=7.2
Q ss_pred eecccCCccc
Q 022703 6 LKCGDCGALL 15 (293)
Q Consensus 6 LkC~~Cg~v~ 15 (293)
.+|+.|++|-
T Consensus 1 MkC~k~Nrvq 10 (20)
T PF08050_consen 1 MKCNKMNRVQ 10 (20)
T ss_pred CcccccceEE
Confidence 3788888763
No 212
>PHA00733 hypothetical protein
Probab=31.16 E-value=17 Score=30.63 Aligned_cols=54 Identities=22% Similarity=0.182 Sum_probs=31.8
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCCCCccccccc
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLH 61 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~~~~~e~~~a 61 (293)
.++.|..|+..+..-.....|....-|..=.. ...|.|+.||+.+++......+
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~----~kPy~C~~Cgk~Fss~s~L~~H 92 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTSKA----VSPYVCPLCLMPFSSSVSLKQH 92 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhcccCC----CCCccCCCCCCcCCCHHHHHHH
Confidence 46789999988876554444422222221111 3459999999987655444333
No 213
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=30.97 E-value=95 Score=30.58 Aligned_cols=40 Identities=28% Similarity=0.483 Sum_probs=34.9
Q ss_pred cCHHHHHHHH-hCCCCHHHHHHHHHHhCCCCHHHHHHHHHHh
Q 022703 113 VDKELLKELE-AMGFPVARATRALHYSGNANVEAAVNWVVEH 153 (293)
Q Consensus 113 ~~~~~l~~L~-~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h 153 (293)
....+|.+|- .-|+|...|++||-..|| |+..|..||-.-
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 4678888986 689999999999999997 999999999653
No 214
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=30.89 E-value=24 Score=30.91 Aligned_cols=9 Identities=44% Similarity=1.357 Sum_probs=8.0
Q ss_pred cccCCCCCC
Q 022703 43 LVCATCGKP 51 (293)
Q Consensus 43 ~~C~~Cg~~ 51 (293)
++||.||.+
T Consensus 1 m~cp~c~~~ 9 (154)
T PRK00464 1 MRCPFCGHP 9 (154)
T ss_pred CcCCCCCCC
Confidence 589999987
No 215
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=30.79 E-value=7.8e+02 Score=27.64 Aligned_cols=26 Identities=23% Similarity=0.359 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHcHHHHHHHHHHHHH
Q 022703 230 NERKRILALRKAEKEEEKRAREKIRQ 255 (293)
Q Consensus 230 ~e~k~~~e~rrrEK~ee~~ar~rir~ 255 (293)
...++..++|..+....+..++|-++
T Consensus 829 e~akr~~~eRe~e~~~ak~ekqr~re 854 (988)
T KOG2072|consen 829 ERAKRTEEEREIENRVAKKEKQRQRE 854 (988)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 33444444444454444444455554
No 216
>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=30.62 E-value=22 Score=33.92 Aligned_cols=11 Identities=36% Similarity=0.960 Sum_probs=8.5
Q ss_pred hccccCCCCCC
Q 022703 41 LNLVCATCGKP 51 (293)
Q Consensus 41 ~~~~C~~Cg~~ 51 (293)
.+..||+||+.
T Consensus 95 ~e~~Cp~C~St 105 (314)
T PF09567_consen 95 LEESCPNCGST 105 (314)
T ss_pred hhhcCCCCCcc
Confidence 45689999974
No 217
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=30.59 E-value=46 Score=20.76 Aligned_cols=22 Identities=14% Similarity=0.291 Sum_probs=16.8
Q ss_pred eecccCCccccCHHHHHHHHHH
Q 022703 6 LKCGDCGALLRSVQEAQEHAEL 27 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~~ 27 (293)
..|..|+..+.+......|..-
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred eEccccCCccCCHHHHHHHHCh
Confidence 4588888888877777777654
No 218
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=30.33 E-value=29 Score=25.59 Aligned_cols=37 Identities=22% Similarity=0.449 Sum_probs=27.8
Q ss_pred ceeecccCCccc---cCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 4 VSLKCGDCGALL---RSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~---~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
+..+|..|+++. .+.-.|..+-.+-+|+ |-|+.|...
T Consensus 1 m~vkC~lCdk~~~Id~~~~~aKrLrnrPi~t-----------YmC~eC~~R 40 (56)
T PF09963_consen 1 MRVKCILCDKKEEIDEDTPEAKRLRNRPIHT-----------YMCDECKER 40 (56)
T ss_pred CeeEEEecCCEEEeccCCHHHHHhhcCCCcc-----------eeChhHHHH
Confidence 468999999988 6777788887775554 667778653
No 219
>PLN03086 PRLI-interacting factor K; Provisional
Probab=30.26 E-value=2.8e+02 Score=29.38 Aligned_cols=10 Identities=20% Similarity=0.524 Sum_probs=4.5
Q ss_pred HHHHHHHHHH
Q 022703 253 IRQKLEEDKA 262 (293)
Q Consensus 253 ir~qIe~Dk~ 262 (293)
|.+|+.+|..
T Consensus 56 ~~~~~~~~~~ 65 (567)
T PLN03086 56 IEAQIKADQQ 65 (567)
T ss_pred HHHHHHHHHH
Confidence 3444544443
No 220
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.15 E-value=24 Score=37.44 Aligned_cols=9 Identities=33% Similarity=0.962 Sum_probs=7.7
Q ss_pred cccCCCCCC
Q 022703 43 LVCATCGKP 51 (293)
Q Consensus 43 ~~C~~Cg~~ 51 (293)
+.||.||+.
T Consensus 583 ~~CP~CGs~ 591 (625)
T PRK08579 583 TRCPRCGSE 591 (625)
T ss_pred CcCcCCCCc
Confidence 699999974
No 221
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.06 E-value=27 Score=36.95 Aligned_cols=9 Identities=33% Similarity=0.992 Sum_probs=7.9
Q ss_pred cccCCCCCC
Q 022703 43 LVCATCGKP 51 (293)
Q Consensus 43 ~~C~~Cg~~ 51 (293)
+.||.||..
T Consensus 573 ~~CP~CG~~ 581 (618)
T PRK14704 573 NECPSCGNE 581 (618)
T ss_pred ccCcCCCCC
Confidence 799999975
No 222
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=29.34 E-value=33 Score=25.80 Aligned_cols=10 Identities=60% Similarity=1.441 Sum_probs=8.5
Q ss_pred ccccCCCCCC
Q 022703 42 NLVCATCGKP 51 (293)
Q Consensus 42 ~~~C~~Cg~~ 51 (293)
..+||.||++
T Consensus 6 ~v~CP~C~k~ 15 (62)
T PRK00418 6 TVNCPTCGKP 15 (62)
T ss_pred cccCCCCCCc
Confidence 3689999997
No 223
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.32 E-value=31 Score=26.22 Aligned_cols=12 Identities=50% Similarity=1.234 Sum_probs=9.6
Q ss_pred hhccccCCCCCC
Q 022703 40 VLNLVCATCGKP 51 (293)
Q Consensus 40 i~~~~C~~Cg~~ 51 (293)
.+.-.||.||++
T Consensus 5 ~~~v~CP~Cgkp 16 (65)
T COG3024 5 RITVPCPTCGKP 16 (65)
T ss_pred cccccCCCCCCc
Confidence 344689999998
No 224
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=28.96 E-value=6.4e+02 Score=25.76 Aligned_cols=6 Identities=50% Similarity=0.440 Sum_probs=2.6
Q ss_pred CCCCHH
Q 022703 176 SSLTPE 181 (293)
Q Consensus 176 k~lT~E 181 (293)
-|+|++
T Consensus 277 ~P~~~~ 282 (429)
T PRK00247 277 YPLTDE 282 (429)
T ss_pred cCCCcc
Confidence 344443
No 225
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=28.92 E-value=45 Score=30.06 Aligned_cols=14 Identities=21% Similarity=0.354 Sum_probs=10.8
Q ss_pred cceeecccCCcccc
Q 022703 3 GVSLKCGDCGALLR 16 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~ 16 (293)
-+.++|..|+....
T Consensus 93 ~~~~~C~~C~~~~~ 106 (206)
T cd01410 93 MFIEVCKSCGPEYV 106 (206)
T ss_pred cCcccCCCCCCccc
Confidence 46789999997653
No 226
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=28.49 E-value=27 Score=23.60 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=7.7
Q ss_pred cccCCCCCC
Q 022703 43 LVCATCGKP 51 (293)
Q Consensus 43 ~~C~~Cg~~ 51 (293)
|+||.||..
T Consensus 1 m~Cp~Cg~~ 9 (43)
T PF08271_consen 1 MKCPNCGSK 9 (43)
T ss_dssp ESBTTTSSS
T ss_pred CCCcCCcCC
Confidence 689999985
No 227
>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=28.24 E-value=31 Score=23.04 Aligned_cols=12 Identities=17% Similarity=0.706 Sum_probs=9.4
Q ss_pred hhccccCCCCCC
Q 022703 40 VLNLVCATCGKP 51 (293)
Q Consensus 40 i~~~~C~~Cg~~ 51 (293)
.++..||.|++.
T Consensus 3 ~i~v~CP~C~s~ 14 (36)
T PF03811_consen 3 KIDVHCPRCQST 14 (36)
T ss_pred cEeeeCCCCCCC
Confidence 356799999984
No 228
>PRK11546 zraP zinc resistance protein; Provisional
Probab=28.22 E-value=4e+02 Score=23.17 Aligned_cols=63 Identities=21% Similarity=0.238 Sum_probs=34.6
Q ss_pred CCCCHHHHH----------HHHHHHHHHHHHhHHHHHHHHHHHH--HHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022703 176 SSLTPEEIK----------LKAQELRERARKKKEEEEKRMERER--EKERIRIGKELLEAKRIEEENERKRILAL 238 (293)
Q Consensus 176 k~lT~EEk~----------~k~~el~~k~r~~r~eeek~e~~e~--E~~Rrk~GKe~~~~k~~~ee~e~k~~~e~ 238 (293)
.+||+|.-. .+...||.++..++.+-.......+ +..=+..-+||..++.++.++..+..++-
T Consensus 42 ~~LT~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~ELnALl~~~~pD~~kI~aL~kEI~~Lr~kL~e~r~~~~~~~ 116 (143)
T PRK11546 42 APLTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNALLTANPPDSSKINAVAKEMENLRQSLDELRVKRDIAM 116 (143)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 479987543 2355666666666654333322211 22334566777777777776655444443
No 229
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=27.98 E-value=5e+02 Score=27.41 Aligned_cols=47 Identities=17% Similarity=0.319 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCCHHH----------HHHHHHHhCCCCHHHHHHHHHHhcCCCCCCC
Q 022703 115 KELLKELEAMGFPVAR----------ATRALHYSGNANVEAAVNWVVEHENDPDIDE 161 (293)
Q Consensus 115 ~~~l~~L~~MGF~~~~----------a~kAL~~tgn~~~E~A~~WL~~h~dD~dide 161 (293)
++.|+.|.+-|.+-|- ---+|++.-..+.-..+-+++++.-||.+-+
T Consensus 404 p~~ie~lken~lsgnf~~~pe~~~~ltsT~LH~aa~qg~~k~v~~~Leeg~Dp~~kd 460 (591)
T KOG2505|consen 404 PDSIEALKENLLSGNFDVTPEANDYLTSTFLHYAAAQGARKCVKYFLEEGCDPSTKD 460 (591)
T ss_pred hhHHHHHHhcCCcccccccccccccccchHHHHHHhcchHHHHHHHHHhcCCchhcc
Confidence 6667777776655421 1123443322234444555566667776433
No 230
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=27.89 E-value=40 Score=30.31 Aligned_cols=14 Identities=21% Similarity=0.593 Sum_probs=11.2
Q ss_pred cceeecccCCcccc
Q 022703 3 GVSLKCGDCGALLR 16 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~ 16 (293)
-+.++|..|+....
T Consensus 107 ~~~~~C~~C~~~~~ 120 (218)
T cd01407 107 LFRVRCTKCGKEYP 120 (218)
T ss_pred cCcceeCCCcCCCc
Confidence 46789999998764
No 231
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.65 E-value=27 Score=31.95 Aligned_cols=10 Identities=30% Similarity=0.730 Sum_probs=8.0
Q ss_pred ccccCCCCCC
Q 022703 42 NLVCATCGKP 51 (293)
Q Consensus 42 ~~~C~~Cg~~ 51 (293)
.|.||.||..
T Consensus 322 ~~~C~~cg~~ 331 (364)
T COG0675 322 LFKCPRCGFV 331 (364)
T ss_pred eEECCCCCCe
Confidence 3899999973
No 232
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=27.62 E-value=25 Score=36.53 Aligned_cols=10 Identities=30% Similarity=0.810 Sum_probs=5.0
Q ss_pred ccccCCCCCC
Q 022703 42 NLVCATCGKP 51 (293)
Q Consensus 42 ~~~C~~Cg~~ 51 (293)
.+.||.||++
T Consensus 504 ~~~CP~CGs~ 513 (546)
T PF13597_consen 504 GDKCPKCGSE 513 (546)
T ss_dssp EEE-CCC---
T ss_pred CCCCCCCCCc
Confidence 4789999996
No 233
>PF09805 Nop25: Nucleolar protein 12 (25kDa); InterPro: IPR019186 Nop12 is a novel nucleolar protein required for pre-large subunit rRNA processing and in yeast normal rates of cell growth at low temperatures [].
Probab=27.53 E-value=2.3e+02 Score=24.08 Aligned_cols=16 Identities=31% Similarity=0.397 Sum_probs=7.1
Q ss_pred HHHHHHhhHHHHHHHH
Q 022703 210 EKERIRIGKELLEAKR 225 (293)
Q Consensus 210 E~~Rrk~GKe~~~~k~ 225 (293)
...||+.+++.++-+.
T Consensus 31 K~~Rrk~Aqe~~~~k~ 46 (137)
T PF09805_consen 31 KKQRRKKAQEQAEEKE 46 (137)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3445555444443333
No 234
>PHA02776 E7 protein; Provisional
Probab=27.49 E-value=15 Score=30.22 Aligned_cols=42 Identities=31% Similarity=0.486 Sum_probs=24.1
Q ss_pred eecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
-.|+.|+..++=.=.+....-++.+.-|-+. +.+.||.|-.+
T Consensus 59 t~C~~C~~~lRL~V~st~~~IR~lqqLLl~~----L~ivCp~Ca~~ 100 (101)
T PHA02776 59 TCCCGCDNNVRLVVECTEPDIQELHNLLLGS----LNIVCPICAPK 100 (101)
T ss_pred eECCCCCCeEEEEEEcChhhHHHHHHHhcCC----eEEECCCCCCC
Confidence 3588899877332222222333333334444 77999999764
No 235
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=27.47 E-value=36 Score=32.00 Aligned_cols=16 Identities=19% Similarity=0.603 Sum_probs=13.0
Q ss_pred ceeecccCCccccCHH
Q 022703 4 VSLKCGDCGALLRSVQ 19 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~ 19 (293)
++.+|..||+......
T Consensus 121 ~~~~C~~C~~~~~~~~ 136 (250)
T COG0846 121 KRVRCSKCGNQYYDED 136 (250)
T ss_pred eeeEeCCCcCccchhh
Confidence 4678999999887665
No 236
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=27.46 E-value=10 Score=34.63 Aligned_cols=41 Identities=29% Similarity=0.577 Sum_probs=27.6
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
.+.+-|..||..+. -|...+--=+|++.. +..+.|..||-.
T Consensus 12 ~~~~~CPvCg~~l~------~~~~~~~IPyFG~V~--i~t~~C~~CgYR 52 (201)
T COG1779 12 ETRIDCPVCGGTLK------AHMYLYDIPYFGEVL--ISTGVCERCGYR 52 (201)
T ss_pred eeeecCCcccceee------EEEeeecCCccceEE--EEEEEccccCCc
Confidence 46789999998442 233333344699884 334899999975
No 237
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=27.05 E-value=1.3e+02 Score=23.59 Aligned_cols=36 Identities=22% Similarity=0.337 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHHHHHhc
Q 022703 115 KELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (293)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~WL~~h~ 154 (293)
..++..|..+|||...|.+.....|. .|++-|.+|+
T Consensus 9 ~~~~~~L~~~gl~~~~a~kl~~~yg~----~ai~~l~~nP 44 (94)
T PF14490_consen 9 RELMAFLQEYGLSPKLAMKLYKKYGD----DAIEILKENP 44 (94)
T ss_dssp HHHHHHHHHTT--HHHHHHHHHHH-T----THHHHHHH-S
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHhH----HHHHHHHHCh
Confidence 46789999999999999999988875 4667776643
No 238
>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=26.88 E-value=63 Score=32.12 Aligned_cols=22 Identities=14% Similarity=0.418 Sum_probs=18.0
Q ss_pred CHHHHHHHHhCCCCHHHHHHHH
Q 022703 114 DKELLKELEAMGFPVARATRAL 135 (293)
Q Consensus 114 ~~~~l~~L~~MGF~~~~a~kAL 135 (293)
=.++|+.+..|||+++.++--+
T Consensus 321 ~ddvidKv~~MGf~rDqV~a~v 342 (358)
T PF07223_consen 321 YDDVIDKVASMGFRRDQVRATV 342 (358)
T ss_pred HHHHHHHHHHcCCcHHHHHHHH
Confidence 3478999999999999987443
No 239
>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=26.47 E-value=38 Score=20.48 Aligned_cols=8 Identities=50% Similarity=1.227 Sum_probs=3.8
Q ss_pred cccCCCCC
Q 022703 43 LVCATCGK 50 (293)
Q Consensus 43 ~~C~~Cg~ 50 (293)
|.|+.|++
T Consensus 15 ~~C~~C~k 22 (26)
T PF13465_consen 15 YKCPYCGK 22 (26)
T ss_dssp EEESSSSE
T ss_pred CCCCCCcC
Confidence 44555543
No 240
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=26.45 E-value=40 Score=22.27 Aligned_cols=13 Identities=31% Similarity=1.043 Sum_probs=9.1
Q ss_pred cceeecccCCccc
Q 022703 3 GVSLKCGDCGALL 15 (293)
Q Consensus 3 ~~~LkC~~Cg~v~ 15 (293)
+-.++|..|+.++
T Consensus 23 ~~~vrC~~C~~~f 35 (37)
T PF13719_consen 23 GRKVRCPKCGHVF 35 (37)
T ss_pred CcEEECCCCCcEe
Confidence 4567777777765
No 241
>PF04641 Rtf2: Rtf2 RING-finger
Probab=26.34 E-value=12 Score=34.92 Aligned_cols=49 Identities=14% Similarity=0.202 Sum_probs=33.0
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhh-ccccCCCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVL-NLVCATCGKPC 52 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~-~~~C~~Cg~~~ 52 (293)
...+.|.+++..+.|..-+..+ .-|||++=......+. +..||.||++|
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l-~~cG~V~s~~alke~k~~~~Cp~c~~~f 160 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYL-RPCGCVFSEKALKELKKSKKCPVCGKPF 160 (260)
T ss_pred CceeECCCCCcccCCceeEEEE-cCCCCEeeHHHHHhhcccccccccCCcc
Confidence 4567888888888665555444 3458765444445555 67899999983
No 242
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=26.04 E-value=26 Score=25.87 Aligned_cols=9 Identities=56% Similarity=1.486 Sum_probs=4.9
Q ss_pred cccCCCCCC
Q 022703 43 LVCATCGKP 51 (293)
Q Consensus 43 ~~C~~Cg~~ 51 (293)
.+||.||++
T Consensus 3 v~CP~C~k~ 11 (57)
T PF03884_consen 3 VKCPICGKP 11 (57)
T ss_dssp EE-TTT--E
T ss_pred ccCCCCCCe
Confidence 489999996
No 243
>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=26.04 E-value=82 Score=27.35 Aligned_cols=41 Identities=27% Similarity=0.591 Sum_probs=30.3
Q ss_pred ccCHHHHHHHHhCCCCH-HHHHHHHHHhCCC----CHHHHHHHHHH
Q 022703 112 EVDKELLKELEAMGFPV-ARATRALHYSGNA----NVEAAVNWVVE 152 (293)
Q Consensus 112 ~~~~~~l~~L~~MGF~~-~~a~kAL~~tgn~----~~E~A~~WL~~ 152 (293)
.+.++++..|..+|||. ...+-+|..-|.. .+=+|+.||.+
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 9999999888764 37789999854
No 244
>PRK08475 F0F1 ATP synthase subunit B; Validated
Probab=25.41 E-value=4.5e+02 Score=22.79 Aligned_cols=20 Identities=10% Similarity=0.235 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 022703 245 EEKRAREKIRQKLEEDKAER 264 (293)
Q Consensus 245 ee~~ar~rir~qIe~Dk~eR 264 (293)
|...+...+++||-.+--+.
T Consensus 130 Ek~~a~~elk~eii~~~~~~ 149 (167)
T PRK08475 130 EVRKMEREVVEEVLNELFES 149 (167)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 34455566666665554444
No 245
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=25.34 E-value=40 Score=27.75 Aligned_cols=27 Identities=19% Similarity=0.455 Sum_probs=20.1
Q ss_pred ceeecccCCccc--------------cCHHHHHHHHHHhcc
Q 022703 4 VSLKCGDCGALL--------------RSVQEAQEHAELTSH 30 (293)
Q Consensus 4 ~~LkC~~Cg~v~--------------~~~~~aq~ha~~TgH 30 (293)
-.|+|..||.+. .....+.++.+.++-
T Consensus 19 ~~v~CdnCg~~vPkdKAikr~~i~s~Ve~a~~rdL~~asIy 59 (108)
T COG4830 19 KYVRCDNCGKAVPKDKAIKRTAIRSPVEAAAARDLSEASIY 59 (108)
T ss_pred cceeeccccccCCccceeeEeeccCcccHHHHHHHhhceee
Confidence 468999999987 566777777755443
No 246
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=25.22 E-value=43 Score=32.83 Aligned_cols=45 Identities=27% Similarity=0.559 Sum_probs=27.2
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhh-h--hccccCCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEA-V--LNLVCATCGKP 51 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~-i--~~~~C~~Cg~~ 51 (293)
+.+|+|.-||+.++.--.. .-+||.+-.|-.++ . .+|+||.|..+
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 5689999999998643211 22355433333221 1 24999999775
No 247
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=24.93 E-value=37 Score=33.79 Aligned_cols=9 Identities=33% Similarity=0.840 Sum_probs=7.8
Q ss_pred ccccCCCCCC
Q 022703 42 NLVCATCGKP 51 (293)
Q Consensus 42 ~~~C~~Cg~~ 51 (293)
.++|| ||++
T Consensus 259 ~~~Cp-CG~~ 267 (374)
T TIGR00375 259 CANCP-CGGR 267 (374)
T ss_pred CCCCC-CCCc
Confidence 58999 9996
No 248
>KOG1871 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=24.87 E-value=24 Score=35.49 Aligned_cols=42 Identities=7% Similarity=-0.065 Sum_probs=33.1
Q ss_pred ccccccccccccccchhhccccccccc---Cccc---cCCccccccCC
Q 022703 59 DLHRKRTGHTDFVDKTSEAAKPISLEV---PKAT---ADSEEAIDVDM 100 (293)
Q Consensus 59 ~~a~K~t~f~tFP~~Lvv~~~Rf~l~~---p~K~---~~~~~~lDl~~ 100 (293)
+.+.+++.+..||.+|++|.+||.+.+ --|+ ++.+-.+.++.
T Consensus 291 V~~s~q~~leklp~vlilhlkrF~ye~tgg~~k~~K~i~~~~~l~i~~ 338 (420)
T KOG1871|consen 291 VEASSQTTLEKLPPVLILHLKRFVYEKTGGARKLGKKIEYPWTLKISK 338 (420)
T ss_pred echhhhhhHhhcchhhhhhhhHHHHHhccchhhhchhhhccceeeech
Confidence 789999999999999999999999994 4444 44455565554
No 249
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=24.38 E-value=15 Score=25.95 Aligned_cols=41 Identities=12% Similarity=0.112 Sum_probs=24.9
Q ss_pred eecccCCccccCHHHHHHHHHHhccCCCCcchhhhh--ccccCCCCCC
Q 022703 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVL--NLVCATCGKP 51 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~--~~~C~~Cg~~ 51 (293)
+.|..|+.++... ....+||.+=.+.....+ ..+||.||.+
T Consensus 2 ~~Cpi~~~~~~~P-----v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~ 44 (63)
T smart00504 2 FLCPISLEVMKDP-----VILPSGQTYERRAIEKWLLSHGTDPVTGQP 44 (63)
T ss_pred cCCcCCCCcCCCC-----EECCCCCEEeHHHHHHHHHHCCCCCCCcCC
Confidence 5688888888663 234568766322211111 3589999987
No 250
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=24.37 E-value=6.3e+02 Score=26.82 Aligned_cols=8 Identities=50% Similarity=0.974 Sum_probs=3.5
Q ss_pred HHhcCCCC
Q 022703 151 VEHENDPD 158 (293)
Q Consensus 151 ~~h~dD~d 158 (293)
+.|.++.|
T Consensus 115 ~~~e~~~~ 122 (591)
T KOG2412|consen 115 FDHENEQD 122 (591)
T ss_pred hhcchhhh
Confidence 33544443
No 251
>PF04361 DUF494: Protein of unknown function (DUF494); InterPro: IPR007456 Members of this family of uncharacterised proteins are often named Smg.
Probab=24.26 E-value=2.1e+02 Score=24.93 Aligned_cols=21 Identities=38% Similarity=0.596 Sum_probs=15.6
Q ss_pred HHHHHHHHhCCCCHHHHHHHH
Q 022703 115 KELLKELEAMGFPVARATRAL 135 (293)
Q Consensus 115 ~~~l~~L~~MGF~~~~a~kAL 135 (293)
..+...|.+.||...-..+||
T Consensus 24 ~~L~~~L~~aGF~~~eI~~Al 44 (155)
T PF04361_consen 24 DDLTRELSAAGFEDEEINKAL 44 (155)
T ss_pred HHHHHHHHHcCCCHHHHHHHH
Confidence 355688999999987665554
No 252
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=24.20 E-value=34 Score=29.41 Aligned_cols=12 Identities=42% Similarity=1.079 Sum_probs=10.9
Q ss_pred hhccccCCCCCC
Q 022703 40 VLNLVCATCGKP 51 (293)
Q Consensus 40 i~~~~C~~Cg~~ 51 (293)
.+++.||.||.|
T Consensus 26 ML~~hCp~Cg~P 37 (131)
T COG1645 26 MLAKHCPKCGTP 37 (131)
T ss_pred HHHhhCcccCCc
Confidence 788999999997
No 253
>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=24.12 E-value=57 Score=25.48 Aligned_cols=27 Identities=30% Similarity=0.572 Sum_probs=18.7
Q ss_pred hhhhccccCCCCCCCCCcccccccccccccc
Q 022703 38 EAVLNLVCATCGKPCRSKTETDLHRKRTGHT 68 (293)
Q Consensus 38 d~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~ 68 (293)
..+.++.|..||+. ...+.++|+++..
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 45788999999964 2246677777644
No 254
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=23.89 E-value=24 Score=34.98 Aligned_cols=34 Identities=18% Similarity=0.570 Sum_probs=18.1
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCC--cchhhhhccccCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFS--ESTEAVLNLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~--e~~d~i~~~~C~~Cg~~ 51 (293)
|.--|..||.|..- --..|. .. .+.|.|+.||..
T Consensus 173 f~piC~~cGri~tt-----------~v~~~d~~~~---~v~Y~c~~cG~~ 208 (360)
T PF01921_consen 173 FLPICEKCGRIDTT-----------EVTEYDPEGG---TVTYRCEECGHE 208 (360)
T ss_dssp EEEEETTTEE--EE-----------EEEEE--SSS---EEEEE--TTS--
T ss_pred eeeeccccCCcccc-----------eeeEeecCCC---EEEEEecCCCCE
Confidence 66789999997632 112232 33 578999999986
No 255
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=23.79 E-value=31 Score=28.61 Aligned_cols=13 Identities=23% Similarity=0.825 Sum_probs=10.1
Q ss_pred eeecccCCccccC
Q 022703 5 SLKCGDCGALLRS 17 (293)
Q Consensus 5 ~LkC~~Cg~v~~~ 17 (293)
--+|+.||.++..
T Consensus 2 pH~CtrCG~vf~~ 14 (112)
T COG3364 2 PHQCTRCGEVFDD 14 (112)
T ss_pred Cceeccccccccc
Confidence 3589999998854
No 256
>PRK04023 DNA polymerase II large subunit; Validated
Probab=23.75 E-value=47 Score=37.34 Aligned_cols=9 Identities=44% Similarity=1.006 Sum_probs=6.1
Q ss_pred ecccCCccc
Q 022703 7 KCGDCGALL 15 (293)
Q Consensus 7 kC~~Cg~v~ 15 (293)
.|+.||+..
T Consensus 628 fCpsCG~~t 636 (1121)
T PRK04023 628 KCPSCGKET 636 (1121)
T ss_pred cCCCCCCcC
Confidence 577777763
No 257
>TIGR00389 glyS_dimeric glycyl-tRNA synthetase, dimeric type. This model describes a glycyl-tRNA synthetase distinct from the two alpha and two beta chains of the tetrameric E. coli glycyl-tRNA synthetase. This enzyme is a homodimeric class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes His, Ser, Pro, and this set of glycyl-tRNA synthetases.
Probab=23.71 E-value=64 Score=33.82 Aligned_cols=48 Identities=23% Similarity=0.432 Sum_probs=27.4
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCC--cchhhhh--ccccCCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFS--ESTEAVL--NLVCATCGKP 51 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~--e~~d~i~--~~~C~~Cg~~ 51 (293)
.+.++|..||..++--.--.++... +-.+++ +..+.+. +.+||.||..
T Consensus 82 D~mv~~~~~~~~~RaD~l~e~~~~~-~~~~~~~~~~~~~i~~~~i~~p~~g~~ 133 (551)
T TIGR00389 82 DWMVDCKSCKERFRADHLIEEKLGK-RLWGFSGPELNEVMEKYDINCPNCGGE 133 (551)
T ss_pred CceeecCCCCCEecchHHHHHHhhh-hcccCCHHHHHHHHHHcCCCCCCCCCC
Confidence 5678999999999644433333322 112333 2222232 2689999974
No 258
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=23.68 E-value=6.9e+02 Score=24.34 Aligned_cols=13 Identities=15% Similarity=0.268 Sum_probs=5.9
Q ss_pred HHHHHHHHHHHHh
Q 022703 204 RMEREREKERIRI 216 (293)
Q Consensus 204 ~e~~e~E~~Rrk~ 216 (293)
..+++|+.-|.+.
T Consensus 259 ~Le~rN~~LK~qa 271 (294)
T KOG4571|consen 259 GLEKRNEELKDQA 271 (294)
T ss_pred HHHHHHHHHHHHH
Confidence 3444555444443
No 259
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=23.54 E-value=29 Score=22.92 Aligned_cols=13 Identities=38% Similarity=0.833 Sum_probs=9.6
Q ss_pred hhhhccccCCCCC
Q 022703 38 EAVLNLVCATCGK 50 (293)
Q Consensus 38 d~i~~~~C~~Cg~ 50 (293)
|+..++.|++||.
T Consensus 18 d~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 18 DDRERLVCPACGF 30 (34)
T ss_dssp -SS-EEEETTTTE
T ss_pred CCccceECCCCCC
Confidence 5678899999986
No 260
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=23.36 E-value=50 Score=33.44 Aligned_cols=26 Identities=23% Similarity=0.411 Sum_probs=18.7
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
...+.|..||+... ..-++||.|+.-
T Consensus 5 ~~~y~C~~Cg~~~~-----------------------~~~g~Cp~C~~w 30 (454)
T TIGR00416 5 KSKFVCQHCGADSP-----------------------KWQGKCPACHAW 30 (454)
T ss_pred CCeEECCcCCCCCc-----------------------cccEECcCCCCc
Confidence 35689999986432 234899999875
No 261
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=23.23 E-value=29 Score=25.90 Aligned_cols=34 Identities=24% Similarity=0.344 Sum_probs=22.3
Q ss_pred hhhccccCCCCCCCCCccccccccccccccccccchhhccccccc
Q 022703 39 AVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISL 83 (293)
Q Consensus 39 ~i~~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l 83 (293)
.+..+.|+.||.+ ..+. ...+|+++.|++.-|+-
T Consensus 45 ~~~r~FC~~CGs~-------l~~~----~~~~~~~~~V~~g~ld~ 78 (92)
T PF04828_consen 45 GVERYFCPTCGSP-------LFSE----DERDPDLVGVNAGTLDD 78 (92)
T ss_dssp SCEEEEETTT--E-------EEEE----ESSTTTEEEEEGGGBTT
T ss_pred cCcCcccCCCCCe-------eecc----cCCCCCEEEEEeEeeCC
Confidence 4667999999996 2222 56789999988864443
No 262
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=23.16 E-value=46 Score=31.74 Aligned_cols=37 Identities=24% Similarity=0.588 Sum_probs=27.3
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~ 52 (293)
-+.|++||-.+.-.+-.+ |..++-.++ |+|--||+.|
T Consensus 3 ~FtCnvCgEsvKKp~vek-H~srCrn~~----------fSCIDC~k~F 39 (276)
T KOG2186|consen 3 FFTCNVCGESVKKPQVEK-HMSRCRNAY----------FSCIDCGKTF 39 (276)
T ss_pred EEehhhhhhhccccchHH-HHHhccCCe----------eEEeeccccc
Confidence 368999999887766666 888843333 6788899864
No 263
>PLN03086 PRLI-interacting factor K; Provisional
Probab=22.99 E-value=6.7e+02 Score=26.62 Aligned_cols=12 Identities=33% Similarity=0.446 Sum_probs=5.0
Q ss_pred HHHHHHHHHHHH
Q 022703 248 RAREKIRQKLEE 259 (293)
Q Consensus 248 ~ar~rir~qIe~ 259 (293)
.|..+..++.++
T Consensus 57 ~~~~~~~~~~~~ 68 (567)
T PLN03086 57 EAQIKADQQMQE 68 (567)
T ss_pred HHHHHHHHHHHH
Confidence 333344444443
No 264
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.97 E-value=75 Score=27.40 Aligned_cols=36 Identities=25% Similarity=0.522 Sum_probs=21.1
Q ss_pred CcceeecccC----CccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 2 AGVSLKCGDC----GALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 2 ~~~~LkC~~C----g~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
-.|.|.|..= || |.+..+.+...++ -+ ..||.||+.
T Consensus 2 i~y~L~Cd~~HeFEGW-F~ssaDfd~Q~~r------------gL-v~CPvCgs~ 41 (142)
T COG5319 2 IRYALRCDKGHEFEGW-FGSSADFDRQRER------------GL-VTCPVCGST 41 (142)
T ss_pred ceeeeeccCCCccccc-ccCchhHHHHHHc------------Cc-eeCCCCCcH
Confidence 3577888762 22 2344444444444 12 699999984
No 265
>PF05262 Borrelia_P83: Borrelia P83/100 protein; InterPro: IPR007926 This family consists of several Borrelia P83/P100 antigen proteins.
Probab=22.93 E-value=8.7e+02 Score=25.26 Aligned_cols=8 Identities=13% Similarity=-0.433 Sum_probs=3.4
Q ss_pred ccchhhcc
Q 022703 71 VDKTSEAA 78 (293)
Q Consensus 71 P~~Lvv~~ 78 (293)
-.|-||++
T Consensus 49 ~~y~ii~~ 56 (489)
T PF05262_consen 49 GRYYIIHA 56 (489)
T ss_pred CcEEEEEe
Confidence 34444443
No 266
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=22.85 E-value=61 Score=23.25 Aligned_cols=39 Identities=28% Similarity=0.560 Sum_probs=25.6
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCC-CcchhhhhccccCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNF-SESTEAVLNLVCATCGK 50 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F-~e~~d~i~~~~C~~Cg~ 50 (293)
...|.|-+||.-+.=...-|..=.. -+| ++- -.|+.|-.
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~e---Kgf~n~p------~RC~~CR~ 41 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAE---KGFDNEP------KRCPSCRQ 41 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHh---cCCcCCC------ccCHHHHH
Confidence 4579999999998655555554444 236 222 48999954
No 267
>PRK06260 threonine synthase; Validated
Probab=22.79 E-value=50 Score=32.47 Aligned_cols=26 Identities=31% Similarity=0.687 Sum_probs=17.9
Q ss_pred eeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 5 ~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
.|+|..||+.... . ...|.||.||.+
T Consensus 3 ~~~C~~cg~~~~~------------------~---~~~~~Cp~cg~~ 28 (397)
T PRK06260 3 WLKCIECGKEYDP------------------D---EIIYTCPECGGL 28 (397)
T ss_pred EEEECCCCCCCCC------------------C---CccccCCCCCCe
Confidence 5899999865421 1 134799999875
No 268
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=22.75 E-value=18 Score=34.88 Aligned_cols=9 Identities=22% Similarity=0.962 Sum_probs=4.4
Q ss_pred hccccCCCC
Q 022703 41 LNLVCATCG 49 (293)
Q Consensus 41 ~~~~C~~Cg 49 (293)
++-+|++||
T Consensus 224 VR~KC~nC~ 232 (308)
T COG3058 224 VRVKCSNCE 232 (308)
T ss_pred HHHHhcccc
Confidence 344555554
No 269
>PF09831 DUF2058: Uncharacterized protein conserved in bacteria (DUF2058); InterPro: IPR018636 This family, found in various prokaryotic proteins, has no known function.
Probab=22.74 E-value=5.6e+02 Score=23.00 Aligned_cols=41 Identities=27% Similarity=0.450 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHH
Q 022703 224 KRIEEENERKRILALRKAEKEEEKRAREKIRQKLEEDKAER 264 (293)
Q Consensus 224 k~~~ee~e~k~~~e~rrrEK~ee~~ar~rir~qIe~Dk~eR 264 (293)
+...+..++-+++-+.|.+..+.+.....|++-|+.-+..+
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 34445566777777777788888888889999998877655
No 270
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=22.71 E-value=67 Score=29.72 Aligned_cols=14 Identities=21% Similarity=0.385 Sum_probs=11.2
Q ss_pred cceeecccCCcccc
Q 022703 3 GVSLKCGDCGALLR 16 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~ 16 (293)
-+.++|..|+....
T Consensus 117 ~~~~~C~~C~~~~~ 130 (244)
T PRK14138 117 VEEYYCVRCGKRYT 130 (244)
T ss_pred cCeeEECCCCCccc
Confidence 46789999998764
No 271
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=22.67 E-value=44 Score=22.41 Aligned_cols=17 Identities=35% Similarity=0.770 Sum_probs=11.4
Q ss_pred ccCCCCCCCCCcccccccccccccc
Q 022703 44 VCATCGKPCRSKTETDLHRKRTGHT 68 (293)
Q Consensus 44 ~C~~Cg~~~~~~~e~~~a~K~t~f~ 68 (293)
.||.||.. ...|++.+.
T Consensus 3 ~CP~Cg~~--------lv~r~~k~g 19 (39)
T PF01396_consen 3 KCPKCGGP--------LVLRRGKKG 19 (39)
T ss_pred CCCCCCce--------eEEEECCCC
Confidence 79999964 455555554
No 272
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=22.64 E-value=88 Score=18.02 Aligned_cols=21 Identities=19% Similarity=0.374 Sum_probs=14.9
Q ss_pred eecccCCccccCHHHHHHHHHH
Q 022703 6 LKCGDCGALLRSVQEAQEHAEL 27 (293)
Q Consensus 6 LkC~~Cg~v~~~~~~aq~ha~~ 27 (293)
.+|..|+.... ...-..|...
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 47999998887 7778888765
No 273
>PRK06231 F0F1 ATP synthase subunit B; Validated
Probab=22.27 E-value=5.8e+02 Score=22.97 Aligned_cols=10 Identities=10% Similarity=0.398 Sum_probs=4.3
Q ss_pred HHHHHHHHHH
Q 022703 248 RAREKIRQKL 257 (293)
Q Consensus 248 ~ar~rir~qI 257 (293)
.++..++.+|
T Consensus 159 ~a~~~Lk~ei 168 (205)
T PRK06231 159 ELKEQLQKES 168 (205)
T ss_pred HHHHHHHHHH
Confidence 3444444444
No 274
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=22.23 E-value=50 Score=24.64 Aligned_cols=9 Identities=33% Similarity=0.874 Sum_probs=6.8
Q ss_pred cccCCCCCC
Q 022703 43 LVCATCGKP 51 (293)
Q Consensus 43 ~~C~~Cg~~ 51 (293)
-+||.||..
T Consensus 18 e~Cp~CG~~ 26 (59)
T COG2260 18 EKCPVCGGD 26 (59)
T ss_pred ccCCCCCCc
Confidence 378899884
No 275
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.22 E-value=39 Score=31.97 Aligned_cols=15 Identities=33% Similarity=0.948 Sum_probs=12.0
Q ss_pred CCcceeecccCCccc
Q 022703 1 MAGVSLKCGDCGALL 15 (293)
Q Consensus 1 ~~~~~LkC~~Cg~v~ 15 (293)
|.-|+|+|+.||...
T Consensus 36 m~Pf~~rC~tCgeyi 50 (253)
T KOG2989|consen 36 MTPFRLRCNTCGEYI 50 (253)
T ss_pred cccceeecccccchh
Confidence 356899999999766
No 276
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.05 E-value=29 Score=37.05 Aligned_cols=10 Identities=30% Similarity=0.953 Sum_probs=8.6
Q ss_pred ccccCCCCCC
Q 022703 42 NLVCATCGKP 51 (293)
Q Consensus 42 ~~~C~~Cg~~ 51 (293)
.+.||.||+.
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 5799999985
No 277
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=21.98 E-value=61 Score=31.40 Aligned_cols=33 Identities=18% Similarity=0.381 Sum_probs=21.5
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCR 53 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~~ 53 (293)
++-.+|..|+.++.... .+. .-+.||.||-.++
T Consensus 36 ~lw~kc~~C~~~~~~~~-----l~~-------------~~~vcp~c~~h~r 68 (296)
T CHL00174 36 HLWVQCENCYGLNYKKF-----LKS-------------KMNICEQCGYHLK 68 (296)
T ss_pred CCeeECCCccchhhHHH-----HHH-------------cCCCCCCCCCCcC
Confidence 45679999998764322 111 1279999997653
No 278
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=21.89 E-value=29 Score=22.86 Aligned_cols=10 Identities=40% Similarity=1.305 Sum_probs=7.5
Q ss_pred ccccCCCCCC
Q 022703 42 NLVCATCGKP 51 (293)
Q Consensus 42 ~~~C~~Cg~~ 51 (293)
.+.||.|+.+
T Consensus 4 ~~~C~nC~R~ 13 (33)
T PF08209_consen 4 YVECPNCGRP 13 (33)
T ss_dssp EEE-TTTSSE
T ss_pred eEECCCCcCC
Confidence 4799999986
No 279
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=21.88 E-value=63 Score=30.97 Aligned_cols=33 Identities=39% Similarity=0.740 Sum_probs=21.4
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCR 53 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~~~ 53 (293)
++-.+|..|+.++.... .+... +.||.||..++
T Consensus 24 ~~~~~c~~c~~~~~~~~-----------------l~~~~-~vc~~c~~h~r 56 (285)
T TIGR00515 24 GVWTKCPKCGQVLYTKE-----------------LERNL-EVCPKCDHHMR 56 (285)
T ss_pred CCeeECCCCcchhhHHH-----------------HHhhC-CCCCCCCCcCc
Confidence 45679999998764322 11112 79999998753
No 280
>PRK06568 F0F1 ATP synthase subunit B; Validated
Probab=21.57 E-value=5.5e+02 Score=22.40 Aligned_cols=12 Identities=8% Similarity=0.393 Sum_probs=5.7
Q ss_pred HHHHHHHHHHHH
Q 022703 246 EKRAREKIRQKL 257 (293)
Q Consensus 246 e~~ar~rir~qI 257 (293)
...|..-||.++
T Consensus 113 k~~Al~elr~ev 124 (154)
T PRK06568 113 KSTASKELQDEF 124 (154)
T ss_pred HHHHHHHHHHHH
Confidence 334444555554
No 281
>PHA00451 protein kinase
Probab=21.42 E-value=5.8e+02 Score=25.08 Aligned_cols=44 Identities=11% Similarity=0.228 Sum_probs=27.7
Q ss_pred HHHhcCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q 022703 150 VVEHENDPDIDEMPMVPVSGGGGASKSSLTPEEIKLKAQELRERA 194 (293)
Q Consensus 150 L~~h~dD~didep~~~~~~~~~~~~kk~lT~EEk~~k~~el~~k~ 194 (293)
.|+.++-|-|-+|.+....-.-+.+ =||.|+|-.+.++.+..+.
T Consensus 201 Mf~~~g~p~ITDPVSFS~dr~re~G-F~ldPd~LiaEvEaia~~~ 244 (362)
T PHA00451 201 MFDQDGVPYITDPVSFSHDREREPG-FPLDPDELIAEVEAIANQR 244 (362)
T ss_pred eeCCCCCeEecCCccccCccccCCC-CCCCHHHHHHHHHHHHHHH
Confidence 4666666667777655433222322 5899999988877776554
No 282
>PRK11823 DNA repair protein RadA; Provisional
Probab=21.29 E-value=58 Score=32.83 Aligned_cols=26 Identities=27% Similarity=0.498 Sum_probs=18.5
Q ss_pred cceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 3 ~~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
...+.|..||.... ..-++||+||.-
T Consensus 5 ~~~y~C~~Cg~~~~-----------------------~~~g~Cp~C~~w 30 (446)
T PRK11823 5 KTAYVCQECGAESP-----------------------KWLGRCPECGAW 30 (446)
T ss_pred CCeEECCcCCCCCc-----------------------ccCeeCcCCCCc
Confidence 45688999986431 233799999874
No 283
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.85 E-value=55 Score=27.40 Aligned_cols=12 Identities=33% Similarity=0.814 Sum_probs=8.1
Q ss_pred hhccccCCCCCC
Q 022703 40 VLNLVCATCGKP 51 (293)
Q Consensus 40 i~~~~C~~Cg~~ 51 (293)
|-+++|+.|+..
T Consensus 18 VTeL~c~~~etT 29 (122)
T COG3877 18 VTELKCSNCETT 29 (122)
T ss_pred eEEEecCCCCce
Confidence 455777777765
No 284
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.66 E-value=47 Score=25.35 Aligned_cols=38 Identities=13% Similarity=0.295 Sum_probs=19.4
Q ss_pred ccccCCCCCCCCCccccccccccccccccccchhhcccccccc
Q 022703 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLE 84 (293)
Q Consensus 42 ~~~C~~Cg~~~~~~~e~~~a~K~t~f~tFP~~Lvv~~~Rf~l~ 84 (293)
.++||.||..-- -|-..+.-.++ +...+-||.++|...
T Consensus 4 ~~kCpKCgn~~~--~ekei~~tg~~---lskifdvq~n~f~~i 41 (68)
T COG3478 4 AFKCPKCGNTNY--EEKEIAATGGG---LSKIFDVQNNKFIVI 41 (68)
T ss_pred cccCCCcCCcch--hhceeeccCCC---cceeEEecccEEEEE
Confidence 367999997411 11112222222 335566777777655
No 285
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.50 E-value=26 Score=37.18 Aligned_cols=31 Identities=29% Similarity=0.362 Sum_probs=17.3
Q ss_pred HHHHHhCCCCHHHHHHHHHHhCCCCHHHHHHH
Q 022703 118 LKELEAMGFPVARATRALHYSGNANVEAAVNW 149 (293)
Q Consensus 118 l~~L~~MGF~~~~a~kAL~~tgn~~~E~A~~W 149 (293)
+..-..+|||+-...-.|...|. +.+.|.++
T Consensus 570 l~~R~~~~~PPf~~l~~i~~~~~-~~~~~~~~ 600 (679)
T PRK05580 570 LEERRAAGYPPFGRLALLRASAK-DEEKAEKF 600 (679)
T ss_pred HHHHHhcCCCCHHHhhEeEEecC-CHHHHHHH
Confidence 44445677777665555544443 55555544
No 286
>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=20.43 E-value=42 Score=27.71 Aligned_cols=11 Identities=27% Similarity=0.775 Sum_probs=8.9
Q ss_pred cccCCCCCCCC
Q 022703 43 LVCATCGKPCR 53 (293)
Q Consensus 43 ~~C~~Cg~~~~ 53 (293)
..||+||++|-
T Consensus 10 R~Cp~CG~kFY 20 (108)
T PF09538_consen 10 RTCPSCGAKFY 20 (108)
T ss_pred ccCCCCcchhc
Confidence 48999999863
No 287
>COG4154 FucU Fucose dissimilation pathway protein FucU [Carbohydrate transport and metabolism]
Probab=20.29 E-value=1.3e+02 Score=26.13 Aligned_cols=43 Identities=23% Similarity=0.356 Sum_probs=30.9
Q ss_pred cccCHHHHHHHHhCCCCH------------HHHHHHHHHhCCCCHHHHHHHHHHhc
Q 022703 111 PEVDKELLKELEAMGFPV------------ARATRALHYSGNANVEAAVNWVVEHE 154 (293)
Q Consensus 111 ~~~~~~~l~~L~~MGF~~------------~~a~kAL~~tgn~~~E~A~~WL~~h~ 154 (293)
|-.++++|.+|.+||... ..+.+-|+.-| -++-.+++-|++-.
T Consensus 7 p~LspdlL~tLr~MGHGDeivl~DanfPa~s~a~~lir~Dg-~s~~~~l~AIlsll 61 (144)
T COG4154 7 PLLSPDLLKTLREMGHGDEIVLSDANFPAHSVARRVIRADG-VSAADLLDAILSLL 61 (144)
T ss_pred cccCHHHHHHHHHhCCCCeEEEecCCCChhHhhhheEecCC-cchHHHHHHHHhcc
Confidence 567999999999999643 45556565554 47777777776643
No 288
>PRK07218 replication factor A; Provisional
Probab=20.23 E-value=60 Score=32.89 Aligned_cols=12 Identities=25% Similarity=0.960 Sum_probs=6.3
Q ss_pred ceeecccCCccc
Q 022703 4 VSLKCGDCGALL 15 (293)
Q Consensus 4 ~~LkC~~Cg~v~ 15 (293)
|--+|..|+.++
T Consensus 296 li~rCP~C~r~v 307 (423)
T PRK07218 296 LIERCPECGRVI 307 (423)
T ss_pred ceecCcCccccc
Confidence 344555555554
No 289
>PRK07591 threonine synthase; Validated
Probab=20.21 E-value=59 Score=32.42 Aligned_cols=26 Identities=42% Similarity=0.846 Sum_probs=17.9
Q ss_pred ceeecccCCccccCHHHHHHHHHHhccCCCCcchhhhhccccCCCCCC
Q 022703 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (293)
Q Consensus 4 ~~LkC~~Cg~v~~~~~~aq~ha~~TgH~~F~e~~d~i~~~~C~~Cg~~ 51 (293)
+.|+|..||.... -. .. |.||.||..
T Consensus 17 ~~l~C~~Cg~~~~------------------~~---~~-~~C~~cg~~ 42 (421)
T PRK07591 17 VALKCRECGAEYP------------------LG---PI-HVCEECFGP 42 (421)
T ss_pred eEEEeCCCCCcCC------------------CC---CC-ccCCCCCCe
Confidence 3599999986432 11 23 899999875
Done!