Query 027011
Match_columns 229
No_of_seqs 294 out of 741
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 03:42:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027011.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027011hhsearch_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 2.8E-33 6.2E-38 273.6 7.5 192 2-200 437-669 (763)
2 COG5207 UBP14 Isopeptidase T [ 100.0 3.3E-29 7.1E-34 240.4 9.3 189 1-200 427-655 (749)
3 PF00627 UBA: UBA/TS-N domain; 99.2 3.5E-11 7.6E-16 78.0 4.2 37 113-150 1-37 (37)
4 KOG2689 Predicted ubiquitin re 99.1 1.2E-10 2.7E-15 105.5 7.3 81 118-199 4-105 (290)
5 smart00165 UBA Ubiquitin assoc 99.0 5E-10 1.1E-14 71.9 5.1 37 114-151 1-37 (37)
6 cd00194 UBA Ubiquitin Associat 99.0 6.9E-10 1.5E-14 71.5 5.4 38 114-152 1-38 (38)
7 KOG0944 Ubiquitin-specific pro 98.7 2.1E-08 4.5E-13 100.0 5.4 51 112-163 633-683 (763)
8 cd02664 Peptidase_C19H A subfa 98.0 3.6E-06 7.8E-11 76.6 3.0 52 42-100 154-212 (327)
9 cd02660 Peptidase_C19D A subfa 97.9 1.9E-06 4.2E-11 77.1 0.3 51 43-100 196-252 (328)
10 TIGR00601 rad23 UV excision re 97.9 1.6E-05 3.5E-10 75.4 5.5 43 113-156 155-197 (378)
11 cd02667 Peptidase_C19K A subfa 97.8 4.7E-06 1E-10 74.1 -0.3 48 43-100 132-185 (279)
12 cd02663 Peptidase_C19G A subfa 97.7 2.6E-05 5.7E-10 69.9 3.8 52 42-100 167-225 (300)
13 cd02657 Peptidase_C19A A subfa 97.7 1.1E-05 2.3E-10 71.7 1.2 51 43-100 176-233 (305)
14 cd02661 Peptidase_C19E A subfa 97.7 2.2E-05 4.7E-10 68.8 2.3 51 43-100 183-236 (304)
15 cd02658 Peptidase_C19B A subfa 97.7 1.1E-05 2.4E-10 72.0 0.2 43 40-89 192-237 (311)
16 cd02674 Peptidase_C19R A subfa 97.6 4.1E-05 8.9E-10 64.8 2.7 52 41-99 103-160 (230)
17 cd02671 Peptidase_C19O A subfa 97.6 5.4E-05 1.2E-09 69.9 3.6 52 42-100 200-262 (332)
18 cd02659 peptidase_C19C A subfa 97.6 3.9E-05 8.5E-10 68.9 2.3 52 42-100 171-229 (334)
19 cd02668 Peptidase_C19L A subfa 97.5 2.8E-05 6E-10 70.4 0.8 52 42-100 176-234 (324)
20 cd02673 Peptidase_C19Q A subfa 97.4 4.2E-05 9.2E-10 68.0 0.4 38 40-85 124-161 (245)
21 KOG0011 Nucleotide excision re 97.0 0.0013 2.9E-08 61.6 6.3 43 113-156 134-176 (340)
22 COG5207 UBP14 Isopeptidase T [ 97.0 0.00032 6.9E-09 69.3 2.1 50 111-162 618-667 (749)
23 KOG1865 Ubiquitin carboxyl-ter 96.6 0.0016 3.5E-08 64.4 3.3 60 41-107 285-348 (545)
24 TIGR00601 rad23 UV excision re 96.5 0.0041 8.9E-08 59.2 5.3 42 114-156 337-378 (378)
25 KOG2561 Adaptor protein NUB1, 96.5 0.0066 1.4E-07 59.3 6.7 48 110-158 425-472 (568)
26 KOG0011 Nucleotide excision re 96.3 0.0061 1.3E-07 57.2 4.9 40 114-154 298-337 (340)
27 PHA02768 hypothetical protein; 96.2 0.0047 1E-07 44.1 2.9 40 1-51 1-40 (55)
28 cd02672 Peptidase_C19P A subfa 95.9 0.0025 5.5E-08 57.4 0.5 40 38-84 130-173 (268)
29 cd02257 Peptidase_C19 Peptidas 95.6 0.0062 1.3E-07 49.8 1.6 55 38-99 112-174 (255)
30 PF09288 UBA_3: Fungal ubiquit 95.3 0.018 3.9E-07 41.1 3.0 30 112-141 7-36 (55)
31 COG5533 UBP5 Ubiquitin C-termi 95.0 0.0077 1.7E-07 56.8 0.4 41 42-89 284-326 (415)
32 cd02662 Peptidase_C19F A subfa 94.7 0.0095 2.1E-07 52.0 0.3 44 38-96 109-158 (240)
33 cd02669 Peptidase_C19M A subfa 94.6 0.013 2.8E-07 56.1 1.0 56 38-100 307-368 (440)
34 PHA00732 hypothetical protein 94.5 0.034 7.3E-07 42.0 2.8 36 6-52 2-37 (79)
35 smart00546 CUE Domain that may 94.4 0.1 2.2E-06 34.4 4.7 38 114-153 2-42 (43)
36 KOG0418 Ubiquitin-protein liga 93.7 0.078 1.7E-06 46.5 3.8 39 113-152 161-199 (200)
37 PF14555 UBA_4: UBA-like domai 93.6 0.23 5.1E-06 32.8 5.2 41 116-157 2-43 (43)
38 PF02845 CUE: CUE domain; Int 93.4 0.26 5.5E-06 32.4 5.1 38 115-153 2-41 (42)
39 KOG2561 Adaptor protein NUB1, 93.3 0.11 2.4E-06 51.1 4.5 43 113-156 374-416 (568)
40 PF00096 zf-C2H2: Zinc finger, 93.0 0.077 1.7E-06 30.0 1.9 22 6-27 1-22 (23)
41 KOG1866 Ubiquitin carboxyl-ter 92.9 0.024 5.1E-07 58.4 -0.7 64 30-100 245-324 (944)
42 PF00443 UCH: Ubiquitin carbox 91.7 0.036 7.8E-07 46.3 -0.9 47 42-100 142-196 (269)
43 KOG4598 Putative ubiquitin-spe 91.2 0.052 1.1E-06 56.0 -0.6 52 42-100 234-292 (1203)
44 COG5560 UBP12 Ubiquitin C-term 90.7 0.071 1.5E-06 54.3 -0.0 53 41-100 694-752 (823)
45 PF13894 zf-C2H2_4: C2H2-type 90.2 0.31 6.8E-06 26.9 2.4 22 6-27 1-22 (24)
46 KOG0010 Ubiquitin-like protein 89.9 0.5 1.1E-05 46.7 5.0 38 114-152 454-492 (493)
47 PF07499 RuvA_C: RuvA, C-termi 89.7 0.88 1.9E-05 30.7 4.7 32 115-146 4-38 (47)
48 cd00350 rubredoxin_like Rubred 89.7 0.19 4.1E-06 31.8 1.3 26 5-51 1-26 (33)
49 PRK12332 tsf elongation factor 89.6 0.75 1.6E-05 40.3 5.4 41 113-154 3-44 (198)
50 KOG2699 Predicted ubiquitin re 89.5 0.12 2.7E-06 49.8 0.5 123 20-159 4-133 (407)
51 PRK09377 tsf elongation factor 89.2 0.76 1.6E-05 42.6 5.4 42 112-154 3-45 (290)
52 TIGR00116 tsf translation elon 89.1 0.78 1.7E-05 42.5 5.4 41 113-154 3-44 (290)
53 KOG2462 C2H2-type Zn-finger pr 88.3 0.33 7.1E-06 44.8 2.4 40 3-51 213-252 (279)
54 PRK06369 nac nascent polypepti 88.3 1.4 3E-05 35.9 5.7 41 111-152 73-114 (115)
55 KOG1868 Ubiquitin C-terminal h 87.4 0.26 5.7E-06 50.2 1.2 36 43-85 518-555 (653)
56 PF12756 zf-C2H2_2: C2H2 type 87.2 0.13 2.9E-06 37.7 -0.7 64 7-71 1-79 (100)
57 cd02670 Peptidase_C19N A subfa 87.2 0.22 4.8E-06 44.6 0.6 40 61-100 89-133 (241)
58 COG5189 SFP1 Putative transcri 87.1 0.3 6.5E-06 46.3 1.4 48 3-51 347-407 (423)
59 cd02665 Peptidase_C19I A subfa 87.0 0.22 4.8E-06 44.2 0.5 31 59-89 117-149 (228)
60 PF12756 zf-C2H2_2: C2H2 type 86.8 0.74 1.6E-05 33.6 3.1 32 5-36 50-81 (100)
61 COG1773 Rubredoxin [Energy pro 86.6 0.13 2.8E-06 36.8 -1.1 43 4-50 2-44 (55)
62 CHL00098 tsf elongation factor 86.5 1.4 3.1E-05 38.7 5.2 38 116-154 3-41 (200)
63 PHA00733 hypothetical protein 86.3 0.9 2E-05 37.0 3.6 38 4-52 72-109 (128)
64 PRK00398 rpoP DNA-directed RNA 86.1 0.36 7.9E-06 32.3 1.0 29 4-51 2-30 (46)
65 PF13912 zf-C2H2_6: C2H2-type 84.2 0.79 1.7E-05 26.8 1.8 21 6-26 2-22 (27)
66 TIGR00264 alpha-NAC-related pr 83.5 2.9 6.4E-05 34.1 5.3 39 112-151 76-115 (116)
67 cd00729 rubredoxin_SM Rubredox 83.5 0.68 1.5E-05 29.6 1.3 26 5-51 2-27 (34)
68 smart00355 ZnF_C2H2 zinc finge 83.0 0.89 1.9E-05 25.1 1.6 21 6-26 1-21 (26)
69 KOG2462 C2H2-type Zn-finger pr 82.7 0.47 1E-05 43.8 0.5 55 4-64 129-183 (279)
70 cd00730 rubredoxin Rubredoxin; 82.6 0.23 5.1E-06 34.6 -1.2 43 5-51 1-43 (50)
71 COG1996 RPC10 DNA-directed RNA 82.3 0.72 1.6E-05 32.3 1.2 31 2-51 3-33 (49)
72 PRK03824 hypA hydrogenase nick 81.6 0.57 1.2E-05 38.5 0.6 48 3-51 68-116 (135)
73 KOG3623 Homeobox transcription 81.5 0.64 1.4E-05 48.3 1.0 40 4-52 280-319 (1007)
74 smart00531 TFIIE Transcription 81.3 1 2.2E-05 37.1 2.0 36 3-51 97-132 (147)
75 PHA00616 hypothetical protein 80.7 0.87 1.9E-05 31.1 1.1 26 5-31 1-26 (44)
76 PRK12380 hydrogenase nickel in 80.4 0.83 1.8E-05 36.4 1.1 28 3-51 68-95 (113)
77 smart00834 CxxC_CXXC_SSSS Puta 78.6 0.36 7.8E-06 30.9 -1.2 35 1-51 1-35 (41)
78 COG1308 EGD2 Transcription fac 78.6 6.1 0.00013 32.5 5.6 40 110-150 80-120 (122)
79 TIGR00100 hypA hydrogenase nic 78.5 0.96 2.1E-05 36.1 0.9 29 2-51 67-95 (115)
80 smart00659 RPOLCX RNA polymera 78.5 1.1 2.5E-05 30.3 1.2 35 5-66 2-36 (44)
81 PF00301 Rubredoxin: Rubredoxi 77.9 0.29 6.3E-06 33.7 -1.9 43 5-51 1-43 (47)
82 PF09723 Zn-ribbon_8: Zinc rib 77.2 1.3 2.8E-05 29.4 1.1 34 2-51 2-35 (42)
83 PRK06266 transcription initiat 77.2 1.3 2.8E-05 38.0 1.5 31 3-51 115-145 (178)
84 TIGR00373 conserved hypothetic 77.0 1.3 2.8E-05 37.2 1.4 31 3-51 107-137 (158)
85 PF12171 zf-C2H2_jaz: Zinc-fin 76.9 1.1 2.3E-05 26.6 0.6 21 6-26 2-22 (27)
86 PRK00564 hypA hydrogenase nick 76.7 1.3 2.9E-05 35.5 1.3 15 2-16 68-82 (117)
87 KOG1870 Ubiquitin C-terminal h 75.9 0.54 1.2E-05 49.1 -1.5 53 41-100 715-773 (842)
88 PF08882 Acetone_carb_G: Aceto 75.3 1.7 3.8E-05 35.2 1.6 46 4-51 23-83 (112)
89 PF12874 zf-met: Zinc-finger o 75.2 1.3 2.8E-05 25.3 0.7 21 6-26 1-21 (25)
90 PF11626 Rap1_C: TRF2-interact 74.9 5 0.00011 30.3 4.0 36 119-155 2-37 (87)
91 TIGR02605 CxxC_CxxC_SSSS putat 74.5 1.8 3.8E-05 29.3 1.3 34 2-51 2-35 (52)
92 PRK08222 hydrogenase 4 subunit 72.8 2.6 5.5E-05 36.1 2.1 47 5-51 114-163 (181)
93 PF05605 zf-Di19: Drought indu 71.5 5.1 0.00011 27.5 3.1 38 5-50 2-39 (54)
94 COG0264 Tsf Translation elonga 70.8 9.2 0.0002 35.8 5.4 40 113-153 4-44 (296)
95 PRK03681 hypA hydrogenase nick 70.6 2.4 5.3E-05 33.8 1.4 11 3-13 68-78 (114)
96 PF13423 UCH_1: Ubiquitin carb 70.3 2.1 4.7E-05 38.3 1.2 56 38-100 176-236 (295)
97 PF13465 zf-H2C2_2: Zinc-finge 68.9 2.8 6E-05 24.9 1.1 15 2-16 11-25 (26)
98 COG4049 Uncharacterized protei 68.3 2.3 5E-05 30.9 0.7 27 5-32 17-43 (65)
99 PF01155 HypA: Hydrogenase exp 66.9 1.8 3.9E-05 34.3 -0.0 28 3-51 68-95 (113)
100 smart00451 ZnF_U1 U1-like zinc 65.5 5.8 0.00013 24.2 2.1 23 5-27 3-25 (35)
101 COG0423 GRS1 Glycyl-tRNA synth 65.3 7.4 0.00016 39.2 3.8 79 6-84 89-189 (558)
102 PF14353 CpXC: CpXC protein 64.7 3.6 7.7E-05 32.8 1.3 12 40-51 36-47 (128)
103 PF06676 DUF1178: Protein of u 64.2 7.5 0.00016 32.8 3.2 37 1-51 1-41 (148)
104 KOG3576 Ovo and related transc 64.1 1.8 4E-05 39.0 -0.5 38 5-51 145-182 (267)
105 KOG3993 Transcription factor ( 64.0 2.3 4.9E-05 41.8 0.0 23 121-145 454-476 (500)
106 PF11372 DUF3173: Domain of un 63.6 8.1 0.00017 28.0 2.8 19 119-137 7-25 (59)
107 PRK14890 putative Zn-ribbon RN 63.5 3.1 6.7E-05 30.2 0.6 11 41-51 47-57 (59)
108 PF10122 Mu-like_Com: Mu-like 62.9 3.9 8.5E-05 28.9 1.0 31 4-51 3-33 (51)
109 PF14599 zinc_ribbon_6: Zinc-r 62.8 2.6 5.6E-05 30.6 0.1 27 5-50 30-56 (61)
110 PF07754 DUF1610: Domain of un 62.5 3.3 7.2E-05 24.9 0.5 10 41-50 15-24 (24)
111 PRK14601 ruvA Holliday junctio 62.2 15 0.00032 31.9 4.7 31 115-145 143-173 (183)
112 PRK00762 hypA hydrogenase nick 62.1 4.8 0.0001 32.6 1.6 35 2-51 67-101 (124)
113 KOG1863 Ubiquitin carboxyl-ter 61.8 3 6.5E-05 44.9 0.4 69 25-100 320-395 (1093)
114 PHA00733 hypothetical protein 61.5 4 8.6E-05 33.2 1.0 51 4-58 39-89 (128)
115 TIGR02098 MJ0042_CXXC MJ0042 f 61.5 2.2 4.7E-05 27.2 -0.4 34 4-51 1-34 (38)
116 PF13451 zf-trcl: Probable zin 60.4 5.2 0.00011 27.9 1.3 40 3-50 2-41 (49)
117 TIGR00084 ruvA Holliday juncti 60.0 13 0.00028 32.2 4.0 25 114-138 147-171 (191)
118 COG4008 Predicted metal-bindin 58.8 31 0.00067 29.0 5.8 41 110-152 110-150 (153)
119 PF02148 zf-UBP: Zn-finger in 58.7 4.8 0.0001 28.5 0.9 44 4-49 10-56 (63)
120 PRK14606 ruvA Holliday junctio 56.5 29 0.00063 30.1 5.6 24 115-138 144-167 (188)
121 COG4416 Com Mu-like prophage p 56.2 2.9 6.3E-05 30.1 -0.5 30 4-50 3-32 (60)
122 COG2888 Predicted Zn-ribbon RN 55.6 5.6 0.00012 29.0 0.9 10 42-51 50-59 (61)
123 PRK14605 ruvA Holliday junctio 55.5 30 0.00064 30.0 5.5 38 114-151 148-188 (194)
124 KOG1074 Transcriptional repres 55.1 6.7 0.00015 41.5 1.6 55 3-66 351-405 (958)
125 KOG3623 Homeobox transcription 54.5 5.1 0.00011 42.0 0.6 41 3-52 920-960 (1007)
126 PRK14602 ruvA Holliday junctio 54.4 33 0.00071 30.0 5.6 25 114-138 155-179 (203)
127 PRK14600 ruvA Holliday junctio 53.9 34 0.00073 29.7 5.5 36 114-149 145-181 (186)
128 KOG0477 DNA replication licens 53.5 5.9 0.00013 41.1 0.9 34 5-52 292-325 (854)
129 KOG1864 Ubiquitin-specific pro 52.8 6.5 0.00014 39.8 1.1 53 41-100 440-499 (587)
130 smart00290 ZnF_UBP Ubiquitin C 52.4 10 0.00022 25.1 1.7 31 5-35 11-44 (50)
131 COG5077 Ubiquitin carboxyl-ter 51.7 4.8 0.0001 42.4 -0.0 67 29-100 336-415 (1089)
132 PF07223 DUF1421: Protein of u 50.3 16 0.00035 35.0 3.3 23 114-136 321-343 (358)
133 PRK14603 ruvA Holliday junctio 49.1 40 0.00087 29.4 5.3 24 115-138 153-176 (197)
134 COG0375 HybF Zn finger protein 48.4 11 0.00024 30.7 1.6 12 40-51 84-95 (115)
135 PF14690 zf-ISL3: zinc-finger 48.4 7.4 0.00016 25.4 0.5 41 42-82 2-43 (47)
136 PLN03086 PRLI-interacting fact 47.4 16 0.00034 37.1 2.8 33 5-50 453-485 (567)
137 PRK13901 ruvA Holliday junctio 47.1 24 0.00051 31.1 3.5 24 115-138 145-168 (196)
138 PRK14604 ruvA Holliday junctio 46.1 49 0.0011 28.8 5.4 24 115-138 150-173 (195)
139 smart00661 RPOL9 RNA polymeras 46.0 3.7 8E-05 27.4 -1.3 10 42-51 20-29 (52)
140 PF14803 Nudix_N_2: Nudix N-te 46.0 1.9 4.1E-05 27.8 -2.6 11 40-50 20-30 (34)
141 KOG1071 Mitochondrial translat 45.6 47 0.001 31.7 5.4 40 113-153 45-85 (340)
142 PF08938 HBS1_N: HBS1 N-termin 44.9 11 0.00023 28.1 0.9 27 127-154 45-71 (79)
143 cd04787 HTH_HMRTR_unk Helix-Tu 44.8 1E+02 0.0022 24.7 6.7 21 117-137 49-69 (133)
144 PF10827 DUF2552: Protein of u 44.6 16 0.00035 27.7 1.8 16 141-156 59-74 (79)
145 PF12737 Mating_C: C-terminal 44.0 19 0.00041 35.2 2.7 30 174-203 388-417 (419)
146 KOG4702 Uncharacterized conser 43.4 21 0.00045 27.0 2.3 49 143-201 17-65 (77)
147 PF01927 Mut7-C: Mut7-C RNAse 43.0 8.6 0.00019 31.6 0.2 42 6-51 92-133 (147)
148 PF02146 SIR2: Sir2 family; I 42.7 17 0.00038 30.3 2.0 35 4-51 104-138 (178)
149 KOG3576 Ovo and related transc 41.9 11 0.00024 34.1 0.7 49 2-51 170-221 (267)
150 PF14205 Cys_rich_KTR: Cystein 41.8 13 0.00029 26.6 1.0 25 43-72 5-29 (55)
151 PF05191 ADK_lid: Adenylate ki 41.1 17 0.00037 23.5 1.3 30 5-51 1-30 (36)
152 COG2331 Uncharacterized protei 40.3 4.2 9.2E-05 31.1 -1.8 33 3-51 10-42 (82)
153 PRK00116 ruvA Holliday junctio 40.0 51 0.0011 28.3 4.5 27 114-140 149-175 (192)
154 KOG0608 Warts/lats-like serine 39.0 18 0.0004 37.9 1.8 42 110-151 85-126 (1034)
155 COG5319 Uncharacterized protei 39.0 28 0.0006 29.2 2.6 38 1-51 1-41 (142)
156 KOG1296 Uncharacterized conser 38.8 3.5 7.5E-05 35.2 -2.8 39 4-51 29-73 (161)
157 PRK14138 NAD-dependent deacety 38.2 22 0.00047 31.7 2.0 14 4-17 118-131 (244)
158 KOG1074 Transcriptional repres 38.1 16 0.00034 38.8 1.2 39 5-52 879-917 (958)
159 TIGR02698 CopY_TcrY copper tra 37.9 36 0.00078 27.5 3.1 29 177-209 101-130 (130)
160 PRK11639 zinc uptake transcrip 37.5 17 0.00036 30.6 1.1 43 6-51 101-149 (169)
161 PF11547 E3_UbLigase_EDD: E3 u 37.4 43 0.00093 23.7 2.9 43 112-155 7-51 (53)
162 PF09855 DUF2082: Nucleic-acid 37.3 18 0.00038 26.5 1.1 38 43-85 1-38 (64)
163 COG3024 Uncharacterized protei 37.1 19 0.00042 26.6 1.2 11 41-51 6-16 (65)
164 PF06906 DUF1272: Protein of u 37.0 6.5 0.00014 28.4 -1.2 45 4-50 4-49 (57)
165 cd01407 SIR2-fam SIR2 family o 34.8 25 0.00055 30.4 1.8 15 4-18 108-122 (218)
166 PF07553 Lipoprotein_Ltp: Host 33.9 57 0.0012 22.5 3.1 23 114-136 21-46 (48)
167 COG1675 TFA1 Transcription ini 33.5 24 0.00052 30.6 1.5 15 37-51 127-141 (176)
168 COG0632 RuvA Holliday junction 33.5 51 0.0011 29.1 3.5 22 117-138 159-180 (201)
169 PF07544 Med9: RNA polymerase 33.4 45 0.00098 25.1 2.8 26 177-202 51-76 (83)
170 PF14748 P5CR_dimer: Pyrroline 33.4 96 0.0021 24.1 4.7 39 115-157 25-63 (107)
171 PF08587 UBA_2: Ubiquitin asso 33.1 22 0.00047 24.6 0.9 26 113-138 1-27 (46)
172 PF09237 GAGA: GAGA factor; I 32.8 33 0.00071 24.5 1.8 24 4-27 23-46 (54)
173 COG1198 PriA Primosomal protei 32.4 12 0.00027 38.9 -0.6 43 5-51 435-484 (730)
174 PF01396 zf-C4_Topoisom: Topoi 32.2 23 0.0005 23.1 0.9 17 44-68 3-19 (39)
175 PF03811 Zn_Tnp_IS1: InsA N-te 32.2 22 0.00048 23.1 0.8 11 41-51 4-14 (36)
176 cd01412 SIRT5_Af1_CobB SIRT5_A 32.0 27 0.00059 30.2 1.6 15 4-18 108-122 (224)
177 PRK12387 formate hydrogenlyase 31.7 35 0.00076 28.8 2.2 45 6-51 115-161 (180)
178 PF05907 DUF866: Eukaryotic pr 31.6 4.6 9.9E-05 34.2 -3.2 39 4-51 29-73 (161)
179 PF10607 CLTH: CTLH/CRA C-term 31.3 60 0.0013 25.6 3.4 24 128-154 5-28 (145)
180 PF10367 Vps39_2: Vacuolar sor 31.3 19 0.00042 26.8 0.5 26 43-78 79-104 (109)
181 PRK00418 DNA gyrase inhibitor; 31.2 29 0.00063 25.4 1.3 10 42-51 6-15 (62)
182 PF12773 DZR: Double zinc ribb 30.9 23 0.0005 23.5 0.7 12 40-51 27-38 (50)
183 PF14490 HHH_4: Helix-hairpin- 30.9 1E+02 0.0022 23.3 4.4 36 115-154 9-44 (94)
184 PF02347 GDC-P: Glycine cleava 30.8 45 0.00098 32.7 3.0 40 177-216 46-85 (429)
185 KOG0435 Leucyl-tRNA synthetase 30.6 34 0.00074 35.9 2.2 64 6-78 437-505 (876)
186 COG0846 SIR2 NAD-dependent pro 30.5 30 0.00064 31.5 1.6 34 4-50 121-154 (250)
187 PRK10204 hypothetical protein; 30.2 54 0.0012 23.4 2.5 19 175-193 34-52 (55)
188 PHA02776 E7 protein; Provision 30.0 8.3 0.00018 30.7 -1.8 41 7-51 60-100 (101)
189 KOG0099 G protein subunit Galp 29.9 48 0.001 31.5 2.8 24 175-198 65-88 (379)
190 PF13913 zf-C2HC_2: zinc-finge 29.5 48 0.001 19.5 1.9 20 6-26 3-22 (25)
191 COG5222 Uncharacterized conser 29.0 14 0.00031 35.1 -0.7 45 3-51 272-319 (427)
192 PF13717 zinc_ribbon_4: zinc-r 28.6 32 0.00069 22.1 1.1 13 3-15 23-35 (36)
193 PF04502 DUF572: Family of unk 28.5 18 0.0004 33.7 -0.1 14 1-14 36-49 (324)
194 TIGR00389 glyS_dimeric glycyl- 28.2 65 0.0014 32.6 3.7 47 4-51 83-133 (551)
195 COG1656 Uncharacterized conser 28.1 28 0.0006 30.1 0.9 38 7-51 99-139 (165)
196 COG0735 Fur Fe2+/Zn2+ uptake r 28.1 30 0.00065 28.5 1.1 45 5-51 93-142 (145)
197 cd01410 SIRT7 SIRT7: Eukaryoti 28.0 43 0.00093 29.1 2.1 14 4-17 94-107 (206)
198 COG1631 RPL42A Ribosomal prote 27.9 18 0.00038 28.6 -0.3 14 38-51 64-77 (94)
199 PF03884 DUF329: Domain of unk 27.6 22 0.00048 25.5 0.2 9 43-51 3-11 (57)
200 PF08271 TF_Zn_Ribbon: TFIIB z 26.2 31 0.00068 22.5 0.7 9 43-51 1-9 (43)
201 PF03249 TSA: Type specific an 26.1 1.2E+02 0.0025 30.0 4.8 36 178-222 265-300 (503)
202 PF10832 DUF2559: Protein of u 26.1 65 0.0014 23.0 2.3 20 175-194 33-52 (54)
203 PF06348 DUF1059: Protein of u 25.8 44 0.00094 23.5 1.4 26 5-31 3-38 (57)
204 PF15178 TOM_sub5: Mitochondri 25.8 62 0.0013 22.7 2.1 15 175-189 8-22 (51)
205 PRK07634 pyrroline-5-carboxyla 25.4 84 0.0018 26.9 3.5 34 115-152 186-219 (245)
206 PF13909 zf-H2C2_5: C2H2-type 25.4 80 0.0017 17.6 2.3 21 6-27 1-21 (24)
207 PF06397 Desulfoferrod_N: Desu 25.4 30 0.00066 22.7 0.5 11 4-14 5-15 (36)
208 KOG3450 Huntingtin interacting 25.3 1E+02 0.0023 25.1 3.7 42 110-152 76-118 (119)
209 PRK00464 nrdR transcriptional 25.1 35 0.00077 28.9 1.0 9 43-51 1-9 (154)
210 PRK14351 ligA NAD-dependent DN 24.3 1.3E+02 0.0029 31.2 5.1 27 173-199 22-48 (689)
211 KOG2239 Transcription factor c 24.0 1.4E+02 0.003 26.7 4.6 35 113-148 170-205 (209)
212 PF08209 Sgf11: Sgf11 (transcr 24.0 25 0.00055 22.5 -0.0 10 42-51 4-13 (33)
213 PRK05333 NAD-dependent deacety 24.0 76 0.0016 28.8 3.0 15 3-17 126-140 (285)
214 PF07227 DUF1423: Protein of u 24.0 23 0.0005 35.0 -0.4 46 6-51 147-192 (446)
215 PF12898 Stc1: Stc1 domain; I 23.9 55 0.0012 24.7 1.8 27 38-68 46-72 (84)
216 KOG3991 Uncharacterized conser 23.7 1.1E+02 0.0023 28.2 3.8 39 183-221 52-92 (256)
217 COG3404 Methenyl tetrahydrofol 23.6 88 0.0019 28.0 3.2 36 175-210 93-128 (208)
218 PF11239 DUF3040: Protein of u 23.3 89 0.0019 23.2 2.8 20 177-197 2-21 (82)
219 TIGR01384 TFS_arch transcripti 23.1 30 0.00065 26.5 0.2 23 8-51 3-25 (104)
220 TIGR01926 peroxid_rel uncharac 23.0 1.4E+02 0.0031 24.3 4.2 29 111-139 130-158 (177)
221 smart00778 Prim_Zn_Ribbon Zinc 22.9 45 0.00099 21.8 1.0 9 43-51 4-12 (37)
222 COG1645 Uncharacterized Zn-fin 22.8 41 0.00089 28.0 1.0 14 38-51 24-37 (131)
223 PRK05367 glycine dehydrogenase 22.8 2.1E+02 0.0045 30.9 6.4 50 177-226 57-106 (954)
224 PF09862 DUF2089: Protein of u 22.6 48 0.001 26.9 1.3 12 40-51 10-21 (113)
225 PF04606 Ogr_Delta: Ogr/Delta- 22.6 39 0.00085 22.7 0.7 8 44-51 1-8 (47)
226 PF04558 tRNA_synt_1c_R1: Glut 22.5 43 0.00092 28.5 1.0 49 142-195 86-134 (164)
227 PF09538 FYDLN_acid: Protein o 22.5 36 0.00078 27.2 0.6 10 43-52 10-19 (108)
228 KOG2482 Predicted C2H2-type Zn 22.3 55 0.0012 31.7 1.8 32 4-35 194-225 (423)
229 PF09416 UPF1_Zn_bind: RNA hel 21.9 45 0.00096 28.4 1.0 47 5-51 14-69 (152)
230 PF10078 DUF2316: Uncharacteri 21.9 1.2E+02 0.0025 23.7 3.2 22 177-198 2-23 (89)
231 PF12907 zf-met2: Zinc-binding 21.7 57 0.0012 21.8 1.3 27 5-32 1-30 (40)
232 PRK08769 DNA polymerase III su 21.6 1.9E+02 0.0042 26.9 5.3 38 114-152 174-211 (319)
233 PF08838 DUF1811: Protein of u 21.5 87 0.0019 25.1 2.5 23 177-199 6-28 (102)
234 PF10440 WIYLD: Ubiquitin-bind 21.4 1.5E+02 0.0032 21.9 3.5 21 116-136 13-33 (65)
235 TIGR00515 accD acetyl-CoA carb 21.3 45 0.00098 30.8 1.0 31 5-53 26-56 (285)
236 PF02892 zf-BED: BED zinc fing 21.2 1.1E+02 0.0023 19.6 2.6 25 3-27 14-42 (45)
237 PRK06260 threonine synthase; V 21.2 55 0.0012 30.9 1.6 26 5-51 3-28 (397)
238 PF03801 Ndc80_HEC: HEC/Ndc80p 21.1 1.5E+02 0.0032 24.9 4.0 41 112-152 92-137 (157)
239 PTZ00408 NAD-dependent deacety 21.1 53 0.0012 29.4 1.4 13 4-16 116-128 (242)
240 PF04959 ARS2: Arsenite-resist 21.0 70 0.0015 28.5 2.1 30 3-33 75-104 (214)
241 PRK09678 DNA-binding transcrip 20.8 52 0.0011 24.6 1.1 19 43-69 2-20 (72)
242 PF14282 FlxA: FlxA-like prote 20.7 1.2E+02 0.0025 23.9 3.1 21 176-196 42-62 (106)
243 PF07688 KaiA: KaiA domain; I 20.6 1.8E+02 0.0039 27.2 4.7 46 175-220 179-226 (283)
244 KOG2186 Cell growth-regulating 20.4 58 0.0013 30.2 1.5 36 6-52 4-39 (276)
No 1
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=99.98 E-value=2.8e-33 Score=273.60 Aligned_cols=192 Identities=25% Similarity=0.361 Sum_probs=152.3
Q ss_pred CcceeeccccccccCCHHH---HHHHHH----HhCCCCCCchhh-----hhhhccCCCCCCCCCCccccccccccccccc
Q 027011 2 AGVSLKCGDCGALLRSVQE---AQEHAE----LTSHSNFSESTE-----AVLNLVCATCGKPCRSKTETDLHRKRTGHTD 69 (229)
Q Consensus 2 ~~~slkC~~Cg~~L~~~~~---aq~Ha~----~T~H~nFse~~E-----~vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~T 69 (229)
+.-|++|.-|++|=-+... .|--.. .--..+|+++-| .+.+|.|++||.| ++|+|+++|+|
T Consensus 437 ve~Rv~C~~c~kVrYs~~~~~~i~lpv~~~~~v~~~v~~~~cleaff~pq~~df~s~ac~~K-------~~a~kt~~~ks 509 (763)
T KOG0944|consen 437 VEDRVSCLGCRKVRYSYESEYLIQLPVPMTNEVREKVPISACLEAFFEPQVDDFWSTACGEK-------KGATKTTRFKS 509 (763)
T ss_pred hhhhhhhhccccccccchhheeeEeeccccccccccCCHHHHHHHhcCCcchhhhhHhhcCc-------ccccccccccc
Confidence 4568999999999111110 000000 102234444422 4678999999998 89999999999
Q ss_pred ccchhhhccccccccc--Cccc---cCCcccccCCC----CCCCCCcccCC--------CCCHHHHHHHHhCCCCHHHHH
Q 027011 70 FVDKTSEAAKPISLEV--PKAT---ADSEEAIDVDM----SGSQPEEMVEP--------EVDKELLKELEAMGFPVARAT 132 (229)
Q Consensus 70 FPd~Lvv~~~r~~l~~--P~Kl---v~~~e~lDls~----g~~~gEe~l~~--------~vd~~~l~qL~eMGF~~~~a~ 132 (229)
||+||+||+.||.+.+ |+|+ +++||.|||+. |.|||||.+++ ..|+..+.||++||||.++|+
T Consensus 510 fP~yLiiqv~rf~~~dw~pkKld~~iempe~ldls~~rs~g~~p~ee~lpde~~~~~~~~~d~s~i~qL~~MGFp~eac~ 589 (763)
T KOG0944|consen 510 FPDYLIIQVGRFTLQDWVPKKLDVSIEMPEELDLSSYRSKGLQPGEEALPDEAPETSEFAADRSVISQLVEMGFPEEACR 589 (763)
T ss_pred CCceEEEEeeEEEecCceeeeeccceecchhhchhhhhhcCCCCcccccCCcCcccCccchhHHHHHHHHHcCCCHHHHH
Confidence 9999999999999987 9999 47899999998 76899998843 379999999999999999999
Q ss_pred HHHHHcCCCCHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCC------------CCCCCCHHHHHHHHHHHHHHHHHhhcc
Q 027011 133 RALHYSGNANVEAAVNWVVEHENDPDIDEMPMVPVSGGGGA------------SKSSLTPEEIKLKAQELRYGIFYAVYF 200 (229)
Q Consensus 133 kAL~~Tgn~~~E~A~~WL~~h~dD~did~pl~~p~~s~s~~------------~~~~LTeEEkkaK~~ELr~ki~~~~~~ 200 (229)
|||++|||++.|+|+|||++||+|||+++|+.+|+.+.... -...+++-.+.+-|...-..+.|++++
T Consensus 590 rAly~tgN~~aEaA~NWl~~HMdDpd~~~p~vvp~~~~~a~~~~~~e~~v~si~smGf~~~qa~~aL~~~n~nveravDW 669 (763)
T KOG0944|consen 590 RALYYTGNSGAEAASNWLMEHMDDPDIDDPFVVPGNSPKADAREVDEESVASIVSMGFSRNQAIKALKATNNNVERAVDW 669 (763)
T ss_pred HHHhhhcCccHHHHHHHHHHhccCcccCCceecCCCCCccccCCCChhHheeeeeecCcHHHHHHHHHhcCccHHHHHHH
Confidence 99999999999999999999999999999999887532211 023467888888888888899999863
No 2
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=3.3e-29 Score=240.37 Aligned_cols=189 Identities=21% Similarity=0.324 Sum_probs=154.8
Q ss_pred CCcceeeccccccc-------------cCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCCCCccccccccccccc
Q 027011 1 MAGVSLKCGDCGAL-------------LRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGH 67 (229)
Q Consensus 1 ~~~~slkC~~Cg~~-------------L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~~~~~E~~~a~K~t~f 67 (229)
++..+|+|..|+++ |.+++++|..-++ -...|.+. .++++|.+|+.+ .+|+|+++|
T Consensus 427 e~e~rlsC~~C~~v~ySye~~~~i~i~le~n~E~~di~~~-v~a~f~pd---tiE~~CenCk~K-------~~a~~k~~~ 495 (749)
T COG5207 427 EVERRLSCSGCMDVSYSYESMLMICIFLEGNDEPQDIRKS-VEAFFLPD---TIEWSCENCKGK-------KKASRKPFI 495 (749)
T ss_pred hhcceecccccccccccccceEEEEeecccCcchhhHHHH-HHheECcc---ceeeehhhhcCc-------ccccccchh
Confidence 35679999999999 8899999998887 77888876 568999999887 899999999
Q ss_pred ccccchhhhccccccccc--Cccc---c--CCcccccCCC--CC-CCCCcccC------CCCCHHHHHHHHhCCCCHHHH
Q 027011 68 TDFVDKTSEAAKPISLEV--PKAT---A--DSEEAIDVDM--SG-SQPEEMVE------PEVDKELLKELEAMGFPVARA 131 (229)
Q Consensus 68 ~TFPd~Lvv~~~r~~l~~--P~Kl---v--~~~e~lDls~--g~-~~gEe~l~------~~vd~~~l~qL~eMGF~~~~a 131 (229)
+|||+||++|+.||.|.| ..|+ + ..++.++++. +. .|..|.+. ...|+.++.||++||||.++|
T Consensus 496 kslPk~LIlq~~R~~lqny~v~kls~pi~~~~D~m~~~~s~msk~~PqtEn~LPdedE~~t~Nqs~I~qL~~mGfp~~~~ 575 (749)
T COG5207 496 KSLPKYLILQVGRYSLQNYKVEKLSDPIEMRSDDMIKLGSFMSKFDPQTENLLPDEDEAFTDNQSLIRQLVDMGFPEEDA 575 (749)
T ss_pred hccCceeEEecceeeccceeehhccCceEEccccccchhhHhhccCCcccccCCccccccCchHHHHHHHHHcCCCHHHH
Confidence 999999999999999999 6666 2 3456788887 32 34444332 236899999999999999999
Q ss_pred HHHHHHcCCCCHHHHHHHHHhCCCCCCCCCCCCCCCCCC----CC-CC------CCCCCHHHHHHHHHHHHHHHHHhhcc
Q 027011 132 TRALHYSGNANVEAAVNWVVEHENDPDIDEMPMVPVSGG----GG-AS------KSSLTPEEIKLKAQELRYGIFYAVYF 200 (229)
Q Consensus 132 ~kAL~~Tgn~~~E~A~~WL~~h~dD~did~pl~~p~~s~----s~-~~------~~~LTeEEkkaK~~ELr~ki~~~~~~ 200 (229)
.|||..|||.+.|.||||||+||||||+++|+.+|+... +. +. ...||+.-.+.-+.+.+..+.|+|.+
T Consensus 576 ~rAL~~tgNqDaEsAMNWLFqHMdDPdlndP~~~~~~vPKkDkeVdE~~~~Slle~Gln~n~~Rkal~~~n~d~~r~V~w 655 (749)
T COG5207 576 ARALGITGNQDAESAMNWLFQHMDDPDLNDPFVPPPNVPKKDKEVDESKARSLLENGLNPNLCRKALMDMNTDSKRRVVW 655 (749)
T ss_pred HHHHhhccCcchHHHHHHHHhhccCcccCCCCCCCCCCCcccccccHHHHHHHHHcCCCHHHHHHHHHHccCCchheEEE
Confidence 999999999999999999999999999999998766411 10 10 23577778888888888888888765
No 3
>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=99.16 E-value=3.5e-11 Score=77.97 Aligned_cols=37 Identities=41% Similarity=0.701 Sum_probs=34.2
Q ss_pred CCHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHH
Q 027011 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWV 150 (229)
Q Consensus 113 vd~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL 150 (229)
+|++.|++|++|||++++|++||+.++| |++.|++||
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 4788999999999999999999999998 999999998
No 4
>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.12 E-value=1.2e-10 Score=105.48 Aligned_cols=81 Identities=30% Similarity=0.476 Sum_probs=67.3
Q ss_pred HHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHH-HhCCCCCCCCCCCCCCCC--------------------CCCCCCCC
Q 027011 118 LKELEAMGFPVARATRALHYSGNANVEAAVNWV-VEHENDPDIDEMPMVPVS--------------------GGGGASKS 176 (229)
Q Consensus 118 l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL-~~h~dD~did~pl~~p~~--------------------s~s~~~~~ 176 (229)
+++|++||||..++.+||.-+||.++|.||+|| .+|.+||. +.|...|.. +++.+.++
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 78888876 555433221 33446799
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhc
Q 027011 177 SLTPEEIKLKAQELRYGIFYAVY 199 (229)
Q Consensus 177 ~LTeEEkkaK~~ELr~ki~~~~~ 199 (229)
.||+||++++.+.|+++|.++..
T Consensus 83 ~ls~eE~~~~~~~i~ekik~k~~ 105 (290)
T KOG2689|consen 83 LLSEEEKKAQTKRILEKIKQKQI 105 (290)
T ss_pred ccChHHHHHHHHHHHHHhcchhH
Confidence 99999999999999999987653
No 5
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=99.02 E-value=5e-10 Score=71.85 Aligned_cols=37 Identities=35% Similarity=0.560 Sum_probs=34.6
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Q 027011 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVV 151 (229)
Q Consensus 114 d~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~ 151 (229)
+++.+++|++|||++++|++||+.++| +++.|++|||
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 367899999999999999999999998 8999999996
No 6
>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=99.01 E-value=6.9e-10 Score=71.50 Aligned_cols=38 Identities=47% Similarity=0.754 Sum_probs=35.4
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHh
Q 027011 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVE 152 (229)
Q Consensus 114 d~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~ 152 (229)
+++.+++|++|||++++|++||..++| |++.|++||++
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 367899999999999999999999998 99999999984
No 7
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=98.68 E-value=2.1e-08 Score=100.03 Aligned_cols=51 Identities=39% Similarity=0.616 Sum_probs=45.7
Q ss_pred CCCHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCCCCCCCCCC
Q 027011 112 EVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHENDPDIDEMP 163 (229)
Q Consensus 112 ~vd~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~dD~did~pl 163 (229)
+++++.|..+++|||++++|++||++++| |+|+|++|||+|+|++-+|.++
T Consensus 633 ~~~e~~v~si~smGf~~~qa~~aL~~~n~-nveravDWif~h~d~~~ed~~~ 683 (763)
T KOG0944|consen 633 EVDEESVASIVSMGFSRNQAIKALKATNN-NVERAVDWIFSHMDIPVEDAAE 683 (763)
T ss_pred CCChhHheeeeeecCcHHHHHHHHHhcCc-cHHHHHHHHHhcccccccccCc
Confidence 58999999999999999999999999987 9999999999999966555544
No 8
>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=98.00 E-value=3.6e-06 Score=76.65 Aligned_cols=52 Identities=12% Similarity=0.131 Sum_probs=44.9
Q ss_pred hccCCCCCCCCCCcccccccccccccccccchhhhccccccccc----Cccc---cCCcccccCCC
Q 027011 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (229)
Q Consensus 42 ~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~----P~Kl---v~~~e~lDls~ 100 (229)
.+.|+.|+++ ..+.|++.|.++|++|+|+.+||.++. ..|+ |..|..|||+.
T Consensus 154 ~~~C~~C~~~-------~~a~k~~~i~~lP~vLii~LkRF~~~~~~~~~~Ki~~~v~fp~~ldl~~ 212 (327)
T cd02664 154 QYYCEKCASL-------QDAEKEMKVTGAPEYLILTLLRFSYDQKTHVREKIMDNVSINEVLSLPV 212 (327)
T ss_pred ceeCCccCCc-------cceeEEEEcccCChhhEEEeeeeEEccccCcceecCceEecCCEEecCc
Confidence 4899999987 689999999999999999999999874 5677 45677888875
No 9
>cd02660 Peptidase_C19D A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.95 E-value=1.9e-06 Score=77.11 Aligned_cols=51 Identities=10% Similarity=0.156 Sum_probs=44.6
Q ss_pred ccCCCCCCCCCCcccccccccccccccccchhhhccccccccc---Cccc---cCCcccccCCC
Q 027011 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV---PKAT---ADSEEAIDVDM 100 (229)
Q Consensus 43 l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~---P~Kl---v~~~e~lDls~ 100 (229)
+.|+.|+++ +.+.|+..|.++|++|+|+.+||..+. +.|+ |..|+.|||+.
T Consensus 196 ~~C~~C~~~-------~~~~~~~~i~~lP~~Lii~lkRf~~~~~~~~~K~~~~v~fp~~Ldl~~ 252 (328)
T cd02660 196 YKCSGCGST-------QEATKQLSIKKLPPVLCFQLKRFEHSLNKTSRKIDTYVQFPLELNMTP 252 (328)
T ss_pred ccCCCCCCc-------cceEEEEEecCCCceeEEEEEeEEecCCCCCcCCCcEEeCCCEechhh
Confidence 689999997 689999999999999999999999985 6787 45677888875
No 10
>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=97.90 E-value=1.6e-05 Score=75.36 Aligned_cols=43 Identities=23% Similarity=0.352 Sum_probs=39.2
Q ss_pred CCHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCCC
Q 027011 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHEND 156 (229)
Q Consensus 113 vd~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~dD 156 (229)
..+..|++|++|||+|+++++||++.-| |.++|++||+....+
T Consensus 155 ~~e~~I~~i~eMGf~R~qV~~ALRAafN-NPdRAVEYL~tGIP~ 197 (378)
T TIGR00601 155 ERETTIEEIMEMGYEREEVERALRAAFN-NPDRAVEYLLTGIPE 197 (378)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHhC-CHHHHHHHHHhCCCc
Confidence 3578999999999999999999999988 999999999988653
No 11
>cd02667 Peptidase_C19K A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.78 E-value=4.7e-06 Score=74.06 Aligned_cols=48 Identities=15% Similarity=0.173 Sum_probs=42.3
Q ss_pred ccCCCCCCCCCCcccccccccccccccccchhhhccccccccc---Cccc---cCCcccccCCC
Q 027011 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV---PKAT---ADSEEAIDVDM 100 (229)
Q Consensus 43 l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~---P~Kl---v~~~e~lDls~ 100 (229)
+.|+.|++ |+|++.|.++|++|+|+.+||..+. +.|+ |..|+.|||+.
T Consensus 132 ~~C~~C~~----------a~k~~~i~~~P~~Lii~LkRF~~~~~~~~~Ki~~~v~fP~~Ldl~~ 185 (279)
T cd02667 132 FACENCTK----------AKKQYLISKLPPVLVIHLKRFQQPRSANLRKVSRHVSFPEILDLAP 185 (279)
T ss_pred ccCCccCc----------eeeEeEhhhCCCeEEEEEeccccCcccCceecCceEeCCCccchhh
Confidence 89999977 6899999999999999999999995 6887 46688899986
No 12
>cd02663 Peptidase_C19G A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.73 E-value=2.6e-05 Score=69.87 Aligned_cols=52 Identities=10% Similarity=0.015 Sum_probs=44.1
Q ss_pred hccCCCCCCCCCCcccccccccccccccccchhhhccccccccc----Cccc---cCCcccccCCC
Q 027011 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (229)
Q Consensus 42 ~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~----P~Kl---v~~~e~lDls~ 100 (229)
.+.|+.|+++ ..++|+..|..+|++|+|+.+||.... ..|+ |..|..||+..
T Consensus 167 ~~~C~~C~~~-------~~a~k~~~i~~lP~vLii~LkRF~~~~~~~~~~Ki~~~v~fp~~L~~~~ 225 (300)
T cd02663 167 KFYCDECCSL-------QEAEKRMKIKKLPKILALHLKRFKYDEQLNRYIKLFYRVVFPLELRLFN 225 (300)
T ss_pred cEECCCCCCc-------eeEEEEEEeccCCceeEEEEEeEEeecccCCceecCceEecCcEEeccc
Confidence 4899999987 689999999999999999999999884 5676 45677788764
No 13
>cd02657 Peptidase_C19A A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.72 E-value=1.1e-05 Score=71.73 Aligned_cols=51 Identities=8% Similarity=-0.044 Sum_probs=42.1
Q ss_pred ccCCCCCCCCCCcccccccccccccccccchhhhccccccccc----Cccc---cCCcccccCCC
Q 027011 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (229)
Q Consensus 43 l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~----P~Kl---v~~~e~lDls~ 100 (229)
..|+.|+.. ..++|+..|.++|++|+|+.+||.+.. ..|+ |..|..||++.
T Consensus 176 ~~~~~~~~~-------~~~~k~~~i~~lP~vLii~LkRF~~~~~~~~~~Ki~~~v~fP~~Ldl~~ 233 (305)
T cd02657 176 KHSPTLGRD-------AIYTKTSRISRLPKYLTVQFVRFFWKRDIQKKAKILRKVKFPFELDLYE 233 (305)
T ss_pred hcCcccCCC-------ceEEEEEEeccCCcEEEEEEECCccccccCceeecCcEEECCceEeccc
Confidence 579999886 678999999999999999999999875 4455 45677888874
No 14
>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=97.67 E-value=2.2e-05 Score=68.77 Aligned_cols=51 Identities=16% Similarity=0.060 Sum_probs=43.4
Q ss_pred ccCCCCCCCCCCcccccccccccccccccchhhhcccccccccCccc---cCCcccccCCC
Q 027011 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEVPKAT---ADSEEAIDVDM 100 (229)
Q Consensus 43 l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~P~Kl---v~~~e~lDls~ 100 (229)
+.|+.||++ ..+.|+..+.++|++|+|+.+||......|+ +..|+.|||+.
T Consensus 183 ~~C~~C~~~-------~~~~~~~~i~~~P~iL~i~l~Rf~~~~~~Ki~~~v~f~~~L~l~~ 236 (304)
T cd02661 183 YKCERCKKK-------VKASKQLTIHRAPNVLTIHLKRFSNFRGGKINKQISFPETLDLSP 236 (304)
T ss_pred eeCCCCCCc-------cceEEEEEEecCCcEEEEEEeccccCCccccCCeEecCCeechhh
Confidence 799999997 6789999999999999999999999865565 45567788875
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=97.65 E-value=1.1e-05 Score=72.00 Aligned_cols=43 Identities=28% Similarity=0.382 Sum_probs=38.3
Q ss_pred hhhccCCCCCCCCCCcccccccccccccccccchhhhcccccccc-c--Cccc
Q 027011 40 VLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLE-V--PKAT 89 (229)
Q Consensus 40 vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~-~--P~Kl 89 (229)
.++..|+.||++ ..+.|+..+.++|++|+|+.+||... + |+|+
T Consensus 192 ~i~~~C~~C~~~-------~~a~k~~~i~~lP~vLii~LkRF~~~~~~~~~Ki 237 (311)
T cd02658 192 TIEDFCSTCKEK-------TTATKTTGFKTFPDYLVINMKRFQLLENWVPKKL 237 (311)
T ss_pred cccccccCCCCc-------ccEEEEEEeecCCceEEEEeEEEEecCCCceEee
Confidence 456789999987 78999999999999999999999994 3 8887
No 16
>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=97.58 E-value=4.1e-05 Score=64.81 Aligned_cols=52 Identities=13% Similarity=0.150 Sum_probs=42.3
Q ss_pred hhccCCCCCCCCCCcccccccccccccccccchhhhccccccccc--Cccc---cCCc-ccccCC
Q 027011 41 LNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSE-EAIDVD 99 (229)
Q Consensus 41 l~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~--P~Kl---v~~~-e~lDls 99 (229)
..+.|+.||++ ..+.++..|.++|++|+|+.+||...+ ..|+ |..| +.+|++
T Consensus 103 ~~~~C~~C~~~-------~~~~~~~~i~~lP~iLii~l~R~~~~~~~~~K~~~~v~~~~~~l~l~ 160 (230)
T cd02674 103 NAWKCPKCKKK-------RKATKKLTISRLPKVLIIHLKRFSFSRGSTRKLTTPVTFPLNDLDLT 160 (230)
T ss_pred CceeCCCCCCc-------cceEEEEEEecCChhhEeEhhheecCCCCcccCCceEeccccccccc
Confidence 45899999987 778999999999999999999999986 6666 3333 456665
No 17
>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=97.58 E-value=5.4e-05 Score=69.92 Aligned_cols=52 Identities=6% Similarity=0.043 Sum_probs=41.4
Q ss_pred hccCCCCCCCCCCcccccccccccccccccchhhhccccccccc--------Cccc---cCCcccccCCC
Q 027011 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--------PKAT---ADSEEAIDVDM 100 (229)
Q Consensus 42 ~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~--------P~Kl---v~~~e~lDls~ 100 (229)
.+.|+.|+++ +.|+|+..|.++|++|+|+.+||.... ..|+ |..|..||+..
T Consensus 200 ~y~C~~C~~~-------~~a~k~~~~~~~P~vL~i~LkRF~~~~~~~~~~~~~~Ki~~~v~fp~~L~~~~ 262 (332)
T cd02671 200 KYFCENCHHY-------TEAERSLLFDKLPEVITIHLKCFAANGSEFDCYGGLSKVNTPLLTPLKLSLEE 262 (332)
T ss_pred CeeCCCCCCc-------eeEEEEEEEecCCCEEEEEeeeeccccccccccCCceecCccccCcccccccc
Confidence 4999999987 789999999999999999999999652 4455 34455566653
No 18
>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=97.56 E-value=3.9e-05 Score=68.89 Aligned_cols=52 Identities=13% Similarity=0.184 Sum_probs=44.4
Q ss_pred hccCCCCCCCCCCcccccccccccccccccchhhhccccccccc----Cccc---cCCcccccCCC
Q 027011 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (229)
Q Consensus 42 ~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~----P~Kl---v~~~e~lDls~ 100 (229)
.+.|+.|+++ ..+.|+..|.++|++|+|+.+||..+. .+|+ |..|..||++.
T Consensus 171 ~~~C~~C~~~-------~~~~k~~~i~~lP~vLii~l~Rf~~~~~~~~~~K~~~~v~fp~~Ldl~~ 229 (334)
T cd02659 171 KYFCEKCGKK-------VDAEKGVCFKKLPPVLTLQLKRFEFDFETMMRIKINDRFEFPLELDMEP 229 (334)
T ss_pred cEecCcCCCc-------ccEEEEEEeecCCCEEEEEeeeeEEccccCcceeCCceEeCCceecCcc
Confidence 3899999997 689999999999999999999999863 5666 45678888885
No 19
>cd02668 Peptidase_C19L A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.51 E-value=2.8e-05 Score=70.42 Aligned_cols=52 Identities=13% Similarity=0.178 Sum_probs=45.3
Q ss_pred hccCCCCCCCCCCcccccccccccccccccchhhhccccccccc----Cccc---cCCcccccCCC
Q 027011 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (229)
Q Consensus 42 ~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~----P~Kl---v~~~e~lDls~ 100 (229)
.+.|+.|+++ ..+.|+..|.++|++|+|+.+||.++. +.|+ |..|+.|||+.
T Consensus 176 ~~~C~~C~~~-------~~a~k~~~i~~lP~iLii~LkRf~~d~~~~~~~Ki~~~v~fp~~Ldl~~ 234 (324)
T cd02668 176 QYFCESCNSK-------TDATRRIRLTTLPPTLNFQLLRFVFDRKTGAKKKLNASISFPEILDMGE 234 (324)
T ss_pred cccCCCCCce-------eeeEEEEEecCCCCeEEEEEEcceeecccCcceeCCcEEECCCeEechh
Confidence 3899999987 789999999999999999999999874 6777 46678899885
No 20
>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=97.40 E-value=4.2e-05 Score=67.97 Aligned_cols=38 Identities=16% Similarity=0.176 Sum_probs=33.0
Q ss_pred hhhccCCCCCCCCCCcccccccccccccccccchhhhccccccccc
Q 027011 40 VLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV 85 (229)
Q Consensus 40 vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~ 85 (229)
..++.|+.|+++ .+.|+.+|.++|++|+|+.+||.+..
T Consensus 124 ~~e~~C~~C~~~--------~a~k~~~i~~~P~vL~i~lkRf~~~~ 161 (245)
T cd02673 124 PIEKDCSSCKCE--------SAISSERIMTFPECLSINLKRYKLRI 161 (245)
T ss_pred ccCccCCCCCCc--------cceeechhhhCChhhEEeeEeeeecc
Confidence 457899999874 67899999999999999999997654
No 21
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=97.04 E-value=0.0013 Score=61.59 Aligned_cols=43 Identities=23% Similarity=0.339 Sum_probs=39.1
Q ss_pred CCHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCCC
Q 027011 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHEND 156 (229)
Q Consensus 113 vd~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~dD 156 (229)
..+..+.+|++||++++..++||++.-| |.++|++||.....+
T Consensus 134 ~~e~~V~~Im~MGy~re~V~~AlRAafN-NPeRAVEYLl~GIP~ 176 (340)
T KOG0011|consen 134 EYEQTVQQIMEMGYDREEVERALRAAFN-NPERAVEYLLNGIPE 176 (340)
T ss_pred hhHHHHHHHHHhCccHHHHHHHHHHhhC-ChhhhHHHHhcCCcc
Confidence 4678899999999999999999999988 999999999987654
No 22
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=97.02 E-value=0.00032 Score=69.33 Aligned_cols=50 Identities=20% Similarity=0.302 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCCCCCCCCC
Q 027011 111 PEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHENDPDIDEM 162 (229)
Q Consensus 111 ~~vd~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~dD~did~p 162 (229)
.+||+..+..|++|||.++.|+|||..+++ +++++++|++.|.| ..+.+|
T Consensus 618 keVdE~~~~Slle~Gln~n~~Rkal~~~n~-d~~r~V~w~~N~~D-~tF~EP 667 (749)
T COG5207 618 KEVDESKARSLLENGLNPNLCRKALMDMNT-DSKRRVVWCINDDD-GTFPEP 667 (749)
T ss_pred ccccHHHHHHHHHcCCCHHHHHHHHHHccC-CchheEEEEEeCCC-CCCCCC
Confidence 368999999999999999999999999866 99999999999643 334444
No 23
>KOG1865 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=96.60 E-value=0.0016 Score=64.42 Aligned_cols=60 Identities=13% Similarity=0.064 Sum_probs=51.4
Q ss_pred hhccCCCCCCCCCCcccccccccccccccccchhhhcccccccccCccc---cCCcccccCCC-CCCCCCc
Q 027011 41 LNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEVPKAT---ADSEEAIDVDM-SGSQPEE 107 (229)
Q Consensus 41 l~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~P~Kl---v~~~e~lDls~-g~~~gEe 107 (229)
--|+|..|.++ +.|.|+..+..-|.+|.|+.|||+...--|+ |..|+.|||.+ -.+++|.
T Consensus 285 n~Y~C~~Ck~~-------v~A~K~lti~raPnVLTi~LKRF~~~~~gKI~K~I~fPE~LDl~PyMS~~~e~ 348 (545)
T KOG1865|consen 285 NAYHCGRCKQK-------VPASKQLTIHRAPNVLTLHLKRFSNGTGGKISKPVSFPETLDLQPYMSQPNEG 348 (545)
T ss_pred cccccchhhhh-------CcccceeeeecCCceEEEeeehhccCcccccccccCCcccccccccccCCCCC
Confidence 34999999987 8999999999999999999999999876676 66799999998 3355554
No 24
>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=96.50 E-value=0.0041 Score=59.24 Aligned_cols=42 Identities=29% Similarity=0.408 Sum_probs=38.5
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCCC
Q 027011 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHEND 156 (229)
Q Consensus 114 d~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~dD 156 (229)
+.++|+.|.+|||++..+..|-++.+ +|.|.|.||||+|..|
T Consensus 337 E~~AIeRL~~LGF~r~~viqaY~ACd-KNEelAAn~Lf~~~~~ 378 (378)
T TIGR00601 337 EKEAIERLCALGFDRGLVIQAYFACD-KNEELAANYLLSQNFD 378 (378)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcC-CcHHHHHHHHHhhcCC
Confidence 67899999999999999999999975 6999999999998665
No 25
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=96.49 E-value=0.0066 Score=59.34 Aligned_cols=48 Identities=31% Similarity=0.385 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCCCCC
Q 027011 110 EPEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHENDPD 158 (229)
Q Consensus 110 ~~~vd~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~dD~d 158 (229)
++++|...|.+|+.|||++..|+-||..+|| +++.|...|..+...+.
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 5668999999999999999999999999888 99999999987766554
No 26
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=96.26 E-value=0.0061 Score=57.21 Aligned_cols=40 Identities=38% Similarity=0.605 Sum_probs=37.2
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCC
Q 027011 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (229)
Q Consensus 114 d~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~ 154 (229)
+.++++.|.+|||++..+..|.++. ++|.|.|.||||+|+
T Consensus 298 e~eAIeRL~alGF~ralViqayfAC-dKNEelAAN~Ll~~~ 337 (340)
T KOG0011|consen 298 EKEAIERLEALGFPRALVIQAYFAC-DKNEELAANYLLSHS 337 (340)
T ss_pred HHHHHHHHHHhCCcHHHHHHHHHhc-CccHHHHHHHHHhhc
Confidence 5688999999999999999999987 579999999999998
No 27
>PHA02768 hypothetical protein; Provisional
Probab=96.18 E-value=0.0047 Score=44.09 Aligned_cols=40 Identities=25% Similarity=0.441 Sum_probs=35.0
Q ss_pred CCcceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 1 MAGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 1 ~~~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
|+-..++|..||+.|......+.|-.. |. .+++|..|++.
T Consensus 1 ~~~~~y~C~~CGK~Fs~~~~L~~H~r~--H~---------k~~kc~~C~k~ 40 (55)
T PHA02768 1 MALLGYECPICGEIYIKRKSMITHLRK--HN---------TNLKLSNCKRI 40 (55)
T ss_pred CcccccCcchhCCeeccHHHHHHHHHh--cC---------CcccCCcccce
Confidence 455678999999999999999999988 76 37899999985
No 28
>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=95.89 E-value=0.0025 Score=57.38 Aligned_cols=40 Identities=23% Similarity=0.164 Sum_probs=35.4
Q ss_pred hhhhhccCCCCCCCCCCcccccccccccccccccc----hhhhcccccccc
Q 027011 38 EAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVD----KTSEAAKPISLE 84 (229)
Q Consensus 38 E~vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd----~Lvv~~~r~~l~ 84 (229)
|.+..+.|++|+++ ..+.|++++.++|+ +|+||.+||..+
T Consensus 130 E~~~~~~C~~C~~~-------~~a~k~~~i~~lP~~L~~VL~i~lkrf~~~ 173 (268)
T cd02672 130 EKVTKAWCDTCCKY-------QPLEQTTSIRHLPDILLLVLVINLSVTNGE 173 (268)
T ss_pred hhcccccccccCcc-------cccEEEEEeecCCCcccceEEEEEeccChh
Confidence 44557899999987 78999999999999 999999999854
No 29
>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=95.58 E-value=0.0062 Score=49.78 Aligned_cols=55 Identities=16% Similarity=0.120 Sum_probs=43.4
Q ss_pred hhhhhccCCCCC--CCCCCcccccccccccccccccchhhhccccccccc---Cccc---cCCcccccCC
Q 027011 38 EAVLNLVCATCG--KPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV---PKAT---ADSEEAIDVD 99 (229)
Q Consensus 38 E~vl~l~C~~Cg--~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~---P~Kl---v~~~e~lDls 99 (229)
+.+....|..|+ +. ..+.++..+.++|++|+|+.+|+..+. +.|+ |..++.+++.
T Consensus 112 e~~~~~~~~~c~~~~~-------~~~~~~~~i~~lP~~L~i~l~R~~~~~~~~~~k~~~~v~~~~~l~~~ 174 (255)
T cd02257 112 EILEGDNCYKCEKKKK-------QEATKRLKIKKLPPVLIIHLKRFSFNEDGTKEKLNTKVSFPLELDLS 174 (255)
T ss_pred hccCCCCcccCCCCcc-------cceeEEEecccCCceeEEEeeceeeccccccccCCCeEeCCCcccCc
Confidence 456667899998 33 678899999999999999999999875 6676 3556666664
No 30
>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=95.29 E-value=0.018 Score=41.14 Aligned_cols=30 Identities=30% Similarity=0.542 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHhCCCCHHHHHHHHHHcCCC
Q 027011 112 EVDKELLKELEAMGFPVARATRALHYSGNA 141 (229)
Q Consensus 112 ~vd~~~l~qL~eMGF~~~~a~kAL~~Tgn~ 141 (229)
-+|.++|+++.+|||++.+...||++-|=+
T Consensus 7 Gi~~~lVd~F~~mGF~~dkVvevlrrlgik 36 (55)
T PF09288_consen 7 GIDKDLVDQFENMGFERDKVVEVLRRLGIK 36 (55)
T ss_dssp --SHHHHHHHHHHT--HHHHHHHHHHS--S
T ss_pred CCCHHHHHHHHHcCCcHHHHHHHHHHhCCC
Confidence 479999999999999999999999997643
No 31
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=94.97 E-value=0.0077 Score=56.77 Aligned_cols=41 Identities=22% Similarity=0.309 Sum_probs=35.7
Q ss_pred hccCCCCCCCCCCcccccccccccccccccchhhhccccccccc--Cccc
Q 027011 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT 89 (229)
Q Consensus 42 ~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~--P~Kl 89 (229)
...||.||++ ..+.|+..+.-.|++|+|+.+||++-. |+|+
T Consensus 284 ~W~CpkC~~k-------~ss~K~~~I~~lP~~LII~i~RF~i~V~~~~ki 326 (415)
T COG5533 284 AWRCPKCGRK-------ESSRKRMEILVLPDVLIIHISRFHISVMGRKKI 326 (415)
T ss_pred cccCchhccc-------ccchheEEEEecCceEEEEeeeeeEEeeccccc
Confidence 3789999998 678999999999999999999999654 6664
No 32
>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=94.70 E-value=0.0095 Score=52.01 Aligned_cols=44 Identities=11% Similarity=0.136 Sum_probs=34.0
Q ss_pred hhhhhccCCCCCCCCCCcccccccccccccccccchhhhccccccccc---Cccc---cCCcccc
Q 027011 38 EAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV---PKAT---ADSEEAI 96 (229)
Q Consensus 38 E~vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~---P~Kl---v~~~e~l 96 (229)
|.+..+.|+.| ++.|.++|++|+|+.+||.++. +.|+ |..|+.|
T Consensus 109 E~l~~~~C~~C---------------~~~i~~lP~vLii~LkRF~~~~~~~~~K~~~~v~fp~~l 158 (240)
T cd02662 109 EIIDDYKCDRC---------------QTVIVRLPQILCIHLSRSVFDGRGTSTKNSCKVSFPERL 158 (240)
T ss_pred ccccCcCCCCC---------------eEEeecCCcEEEEEEEEEEEcCCCceeeeccEEECCCcc
Confidence 34446899999 3679999999999999999886 7777 3445544
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=94.63 E-value=0.013 Score=56.11 Aligned_cols=56 Identities=11% Similarity=-0.097 Sum_probs=43.0
Q ss_pred hhhhhccCCCCCCCCCCcccccccccccccccccchhhhccccccccc--Cccc---cCCccc-ccCCC
Q 027011 38 EAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSEEA-IDVDM 100 (229)
Q Consensus 38 E~vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~--P~Kl---v~~~e~-lDls~ 100 (229)
|-...|.|+.|... ..++|+..+...|++|+|+.+||...+ ..|. |..|.. ||+++
T Consensus 307 e~L~ky~~~~c~~~-------~~a~k~~~I~~LP~vLiihLKRF~~~~~~~~K~~t~V~FP~~~LDm~~ 368 (440)
T cd02669 307 QLLKKYDGKTETEL-------KDSLKRYLISRLPKYLIFHIKRFSKNNFFKEKNPTIVNFPIKNLDLSD 368 (440)
T ss_pred HHHHhcCCccceec-------ccceEEEEEeeCCcEEEEEEecccCCCCccccCCCEEECCCCccchhh
Confidence 33445899999875 567999999999999999999999875 3444 344553 67775
No 34
>PHA00732 hypothetical protein
Probab=94.48 E-value=0.034 Score=42.02 Aligned_cols=36 Identities=28% Similarity=0.565 Sum_probs=30.4
Q ss_pred eeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCC
Q 027011 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~ 52 (229)
++|+.||+.+......+.|... .|.. +.|+.||+.+
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 6899999999999999999875 4653 3799999974
No 35
>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=94.42 E-value=0.1 Score=34.40 Aligned_cols=38 Identities=34% Similarity=0.506 Sum_probs=31.5
Q ss_pred CHHHHHHHHhCCCCH---HHHHHHHHHcCCCCHHHHHHHHHhC
Q 027011 114 DKELLKELEAMGFPV---ARATRALHYSGNANVEAAVNWVVEH 153 (229)
Q Consensus 114 d~~~l~qL~eMGF~~---~~a~kAL~~Tgn~~~E~A~~WL~~h 153 (229)
.++.+++|.+| ||. ..+++.|...+| +++.|++-|++.
T Consensus 2 ~~~~v~~L~~m-FP~l~~~~I~~~L~~~~g-~ve~~i~~LL~~ 42 (43)
T smart00546 2 NDEALHDLKDM-FPNLDEEVIKAVLEANNG-NVEATINNLLEG 42 (43)
T ss_pred hHHHHHHHHHH-CCCCCHHHHHHHHHHcCC-CHHHHHHHHHcC
Confidence 46789999999 765 788899998766 899999988763
No 36
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.68 E-value=0.078 Score=46.55 Aligned_cols=39 Identities=28% Similarity=0.273 Sum_probs=34.6
Q ss_pred CCHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHh
Q 027011 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVE 152 (229)
Q Consensus 113 vd~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~ 152 (229)
.+...++.|.+|||+++.+..+|...+. +++.|.+.+++
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 4678899999999999999999998876 88889888765
No 37
>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=93.56 E-value=0.23 Score=32.85 Aligned_cols=41 Identities=24% Similarity=0.246 Sum_probs=29.9
Q ss_pred HHHHHHH-hCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCCCC
Q 027011 116 ELLKELE-AMGFPVARATRALHYSGNANVEAAVNWVVEHENDP 157 (229)
Q Consensus 116 ~~l~qL~-eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~dD~ 157 (229)
+.|.+.+ =.|.++..|+.-|..+++ +++.|++-.+++.++|
T Consensus 2 e~i~~F~~iTg~~~~~A~~~L~~~~w-dle~Av~~y~~~~~~~ 43 (43)
T PF14555_consen 2 EKIAQFMSITGADEDVAIQYLEANNW-DLEAAVNAYFDDGEAP 43 (43)
T ss_dssp HHHHHHHHHH-SSHHHHHHHHHHTTT--HHHHHHHHHHSS-S-
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHcCC-CHHHHHHHHHhCCCCC
Confidence 3444544 248899999999999988 9999999999887664
No 38
>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=93.40 E-value=0.26 Score=32.40 Aligned_cols=38 Identities=24% Similarity=0.395 Sum_probs=31.0
Q ss_pred HHHHHHHHhC--CCCHHHHHHHHHHcCCCCHHHHHHHHHhC
Q 027011 115 KELLKELEAM--GFPVARATRALHYSGNANVEAAVNWVVEH 153 (229)
Q Consensus 115 ~~~l~qL~eM--GF~~~~a~kAL~~Tgn~~~E~A~~WL~~h 153 (229)
++.+++|.+| .++++..+.+|..++| ++|.|++-|++.
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 5778999998 3567888999988776 899999999863
No 39
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=93.31 E-value=0.11 Score=51.08 Aligned_cols=43 Identities=23% Similarity=0.441 Sum_probs=38.8
Q ss_pred CCHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCCC
Q 027011 113 VDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHEND 156 (229)
Q Consensus 113 vd~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~dD 156 (229)
||+..+..|++|||.+..|..||+.+.| ++..|++-|-.|.|.
T Consensus 374 vn~rs~~rL~~mGyer~la~eaL~r~~N-di~~aldllq~esde 416 (568)
T KOG2561|consen 374 VNPRSLERLVSMGYERELAAEALRRNEN-DIQKALDLLQDESDE 416 (568)
T ss_pred cCHHHHHHHHhcchHhHHHHHHHHhccC-cHHHHHHhcCCcchh
Confidence 7999999999999999999999999987 999999888777664
No 40
>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=93.05 E-value=0.077 Score=30.03 Aligned_cols=22 Identities=27% Similarity=0.493 Sum_probs=20.2
Q ss_pred eeccccccccCCHHHHHHHHHH
Q 027011 6 LKCGDCGALLRSVQEAQEHAEL 27 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~~ 27 (229)
++|.+||+.++.....+.|...
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 6899999999999999999875
No 41
>KOG1866 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=92.90 E-value=0.024 Score=58.41 Aligned_cols=64 Identities=19% Similarity=0.185 Sum_probs=50.4
Q ss_pred CCCCCchhh---------hhhhccCCCCCCCCCCcccccccccccccccccchhhhccccccccc----Cccc---cCCc
Q 027011 30 HSNFSESTE---------AVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSE 93 (229)
Q Consensus 30 H~nFse~~E---------~vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~----P~Kl---v~~~ 93 (229)
|.|..||-| -.--|.|..|.++ +.-+||+.|+..|.+|+||.+||.++- -.|- ...|
T Consensus 245 ~~nLeesLeqfv~gevlEG~nAYhCeKCdeK-------~~TvkRt~ik~LPsvl~IqLkRF~yD~e~~~~iK~n~~frFP 317 (944)
T KOG1866|consen 245 HQNLEESLEQFVKGEVLEGANAYHCEKCDEK-------VDTVKRTCIKKLPSVLAIQLKRFDYDWERECAIKFNDYFRFP 317 (944)
T ss_pred cchHHHHHHHHHHHHHhcCcchhhhhhhhhh-------hHhHHHHHHhhCChhheehhhhccchhhhccccccchhcccc
Confidence 777777632 2234899999998 788999999999999999999999983 5665 2456
Q ss_pred ccccCCC
Q 027011 94 EAIDVDM 100 (229)
Q Consensus 94 e~lDls~ 100 (229)
-.||+++
T Consensus 318 ~~ldMeP 324 (944)
T KOG1866|consen 318 RELDMEP 324 (944)
T ss_pred hhhcCCc
Confidence 6778776
No 42
>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=91.72 E-value=0.036 Score=46.28 Aligned_cols=47 Identities=13% Similarity=0.292 Sum_probs=34.8
Q ss_pred hccCCCCCCCCCCcccccccccccccccccchhhhccccccccc----Cccc---cCCc-ccccCCC
Q 027011 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSE-EAIDVDM 100 (229)
Q Consensus 42 ~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~----P~Kl---v~~~-e~lDls~ 100 (229)
.++|..|+.. +..|.++|++|+|+.+|+.+.. ..|. +..| +.|||+.
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 5789999873 6889999999999999996653 5666 4567 6899886
No 43
>KOG4598 consensus Putative ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=91.16 E-value=0.052 Score=55.96 Aligned_cols=52 Identities=13% Similarity=0.163 Sum_probs=44.9
Q ss_pred hccCCCCCCCCCCcccccccccccccccccchhhhccccccccc----Cccc---cCCcccccCCC
Q 027011 42 NLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (229)
Q Consensus 42 ~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~----P~Kl---v~~~e~lDls~ 100 (229)
.|-|..|+++| -|.|--+|++||=.|.++.|||.++- -.|| +-.|+.|||+.
T Consensus 234 qy~ce~ck~k~-------dahkgl~~~~fpy~lt~~lkrfdfdy~tmhriklnd~~tfp~~l~ln~ 292 (1203)
T KOG4598|consen 234 QYMCENCKSKQ-------DAHKGLRITQFPYLLTIQLKRFDFDYNTMHRIKLNDKMTFPDVLDLND 292 (1203)
T ss_pred HHHHhhhhhhh-------hhhcCceeeccceeeEEeeecccccchheeeeeecccccCcccccHHH
Confidence 38899999984 78899999999999999999999993 6777 35688999875
No 44
>COG5560 UBP12 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=90.75 E-value=0.071 Score=54.31 Aligned_cols=53 Identities=11% Similarity=0.021 Sum_probs=44.8
Q ss_pred hhccCCCCCCCCCCcccccccccccccccccchhhhccccccccc--Cccc---cC-CcccccCCC
Q 027011 41 LNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---AD-SEEAIDVDM 100 (229)
Q Consensus 41 l~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~--P~Kl---v~-~~e~lDls~ 100 (229)
...-||+|+.. -.|+|+.-+-..|++|+|+.+||.-++ +.|. |+ +-+.|||+.
T Consensus 694 DswyCpgCkef-------rqasKqmelwrlP~iLiihLkRFss~rsfrdKiddlVeyPiddldLs~ 752 (823)
T COG5560 694 DSWYCPGCKEF-------RQASKQMELWRLPMILIIHLKRFSSVRSFRDKIDDLVEYPIDDLDLSG 752 (823)
T ss_pred ccccCCchHhh-------hhhhhhhhhhcCChheeeehhhhhhcccchhhhhhhhccccccccccc
Confidence 35789999875 789999999999999999999999887 9998 42 345688885
No 45
>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=90.23 E-value=0.31 Score=26.88 Aligned_cols=22 Identities=32% Similarity=0.646 Sum_probs=18.1
Q ss_pred eeccccccccCCHHHHHHHHHH
Q 027011 6 LKCGDCGALLRSVQEAQEHAEL 27 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~~ 27 (229)
++|+.|++.+++..+.+.|...
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 5899999999999999999875
No 46
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=89.90 E-value=0.5 Score=46.68 Aligned_cols=38 Identities=29% Similarity=0.464 Sum_probs=33.3
Q ss_pred CHHHHHHHHhCCC-CHHHHHHHHHHcCCCCHHHHHHHHHh
Q 027011 114 DKELLKELEAMGF-PVARATRALHYSGNANVEAAVNWVVE 152 (229)
Q Consensus 114 d~~~l~qL~eMGF-~~~~a~kAL~~Tgn~~~E~A~~WL~~ 152 (229)
-+.-++||-+||| ++++..+||.+||+ ++.+|++-|+.
T Consensus 454 ~q~QLeQL~~MGF~nre~nlqAL~atgG-di~aAverll~ 492 (493)
T KOG0010|consen 454 YQTQLEQLNDMGFLDREANLQALRATGG-DINAAVERLLG 492 (493)
T ss_pred HHHHHHHHHhcCCccHHHHHHHHHHhcC-cHHHHHHHHhc
Confidence 4667999999997 57889999999998 99999998763
No 47
>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=89.70 E-value=0.88 Score=30.74 Aligned_cols=32 Identities=25% Similarity=0.390 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHc---CCCCHHHH
Q 027011 115 KELLKELEAMGFPVARATRALHYS---GNANVEAA 146 (229)
Q Consensus 115 ~~~l~qL~eMGF~~~~a~kAL~~T---gn~~~E~A 146 (229)
+++++.|+..||++..+.+|+... .+.+++..
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~~~~~~~~~e~~ 38 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKLLEKPGMDVEEL 38 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHHHHSTTS-HHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhhcCCCCCHHHH
Confidence 578999999999999999998876 33455543
No 48
>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=89.70 E-value=0.19 Score=31.77 Aligned_cols=26 Identities=31% Similarity=0.791 Sum_probs=20.6
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
+++|.+||.+..+.. .+.+||.||.+
T Consensus 1 ~~~C~~CGy~y~~~~---------------------~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIYDGEE---------------------APWVCPVCGAP 26 (33)
T ss_pred CEECCCCCCEECCCc---------------------CCCcCcCCCCc
Confidence 478999999876654 46799999975
No 49
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=89.56 E-value=0.75 Score=40.34 Aligned_cols=41 Identities=27% Similarity=0.519 Sum_probs=35.8
Q ss_pred CCHHHHHHHHh-CCCCHHHHHHHHHHcCCCCHHHHHHHHHhCC
Q 027011 113 VDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (229)
Q Consensus 113 vd~~~l~qL~e-MGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~ 154 (229)
++..++.+|-+ -|.+--.|++||..++| |++.|++||....
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 56778888875 58999999999999988 9999999998764
No 50
>KOG2699 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=89.52 E-value=0.12 Score=49.81 Aligned_cols=123 Identities=24% Similarity=0.260 Sum_probs=78.1
Q ss_pred HHHHHHHHhCCCCCCchhhhhhhccCCCCCCCCCCcccccccccccccccccchhhhcccccccccCcccc--CCccccc
Q 027011 20 EAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEVPKATA--DSEEAID 97 (229)
Q Consensus 20 ~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~P~Klv--~~~e~lD 97 (229)
-.+.|.+-+.|+||+.+...++.. |+++..+.++.+.++.-+. .+. +..|.++. .....+-
T Consensus 4 ~k~~~~ef~~~~~~~ss~~~~~~~-------------e~~~~~~~~s~~~~~~~~~--~~~--~~~~~~~~~~~~~~~~~ 66 (407)
T KOG2699|consen 4 VKYNFQEFKCKVNLASSLNDVKHQ-------------ESVGEQAHTSSTDQSLPHL--PVT--LDTPWPLLNPAPKVNLL 66 (407)
T ss_pred HHHHHHHHhhcccccccccchhhh-------------HHHHHHhhccCCCCCCCCC--Ccc--cccchhhhccCCCCccc
Confidence 356788888999999986655542 5677888888777665433 222 22233331 0001111
Q ss_pred CCC---CCCCCCcccCCCCCHHHHHHHHhCCCCH-HHHHHHHHHcCCCCHHH-HHHHHHhCCCCCCC
Q 027011 98 VDM---SGSQPEEMVEPEVDKELLKELEAMGFPV-ARATRALHYSGNANVEA-AVNWVVEHENDPDI 159 (229)
Q Consensus 98 ls~---g~~~gEe~l~~~vd~~~l~qL~eMGF~~-~~a~kAL~~Tgn~~~E~-A~~WL~~h~dD~di 159 (229)
++. ..|.......+.+....+.....|||+. .+...+++..|+...++ |.+|.-.|..+...
T Consensus 67 ~~k~~s~gqa~~~~~~~~~~~~i~~~~~~~g~~e~~~t~~~~~~~g~a~~~a~~~~~~~p~~~~~~~ 133 (407)
T KOG2699|consen 67 LSKSSSSGQAAKTNRRNIVFNTILARFDIMGRPEAARTSPALHPSGNQSLEAPAVNFKIPFTSEIQR 133 (407)
T ss_pred cccccccchhhhcccCCcccchhhccccccCCccccccccCcccchhhhhcCCCCcccccccccchh
Confidence 221 1133333444556667778888999999 77778899999977777 89999888776543
No 51
>PRK09377 tsf elongation factor Ts; Provisional
Probab=89.21 E-value=0.76 Score=42.59 Aligned_cols=42 Identities=24% Similarity=0.482 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHh-CCCCHHHHHHHHHHcCCCCHHHHHHHHHhCC
Q 027011 112 EVDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (229)
Q Consensus 112 ~vd~~~l~qL~e-MGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~ 154 (229)
.++..++.+|-+ -|.+--.|++||..++| |++.|++||....
T Consensus 3 ~is~~~IK~LR~~Tgagm~dCKkAL~e~~g-D~ekAi~~Lrk~G 45 (290)
T PRK09377 3 AITAALVKELRERTGAGMMDCKKALTEADG-DIEKAIEWLRKKG 45 (290)
T ss_pred ccCHHHHHHHHHHHCCCHHHHHHHHHHcCC-CHHHHHHHHHHhc
Confidence 367788888875 59999999999999988 9999999998764
No 52
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=89.10 E-value=0.78 Score=42.49 Aligned_cols=41 Identities=24% Similarity=0.353 Sum_probs=36.3
Q ss_pred CCHHHHHHHHh-CCCCHHHHHHHHHHcCCCCHHHHHHHHHhCC
Q 027011 113 VDKELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (229)
Q Consensus 113 vd~~~l~qL~e-MGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~ 154 (229)
++..++.+|-+ -|.+--.|++||..++| |++.|++||..+.
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 67788888875 59999999999999998 9999999998764
No 53
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=88.35 E-value=0.33 Score=44.82 Aligned_cols=40 Identities=28% Similarity=0.635 Sum_probs=20.6
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
.+.|.|..|||-|.|--....|... |++ ++.|.|+.|||.
T Consensus 213 EKPF~C~hC~kAFADRSNLRAHmQT--HS~-------~K~~qC~~C~Ks 252 (279)
T KOG2462|consen 213 EKPFSCPHCGKAFADRSNLRAHMQT--HSD-------VKKHQCPRCGKS 252 (279)
T ss_pred CCCccCCcccchhcchHHHHHHHHh--hcC-------CccccCcchhhH
Confidence 3445555555555555555555544 333 244666666663
No 54
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=88.28 E-value=1.4 Score=35.86 Aligned_cols=41 Identities=17% Similarity=0.227 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHH-hCCCCHHHHHHHHHHcCCCCHHHHHHHHHh
Q 027011 111 PEVDKELLKELE-AMGFPVARATRALHYSGNANVEAAVNWVVE 152 (229)
Q Consensus 111 ~~vd~~~l~qL~-eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~ 152 (229)
..++++.++.++ .-|-+++.|++||..++| |+-.|+-+|.+
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 568999999887 468999999999999988 99999998865
No 55
>KOG1868 consensus Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=87.37 E-value=0.26 Score=50.23 Aligned_cols=36 Identities=14% Similarity=0.137 Sum_probs=31.3
Q ss_pred ccCCCCCCCCCCccccccc--ccccccccccchhhhccccccccc
Q 027011 43 LVCATCGKPCRSKTETDLH--RKRTGHTDFVDKTSEAAKPISLEV 85 (229)
Q Consensus 43 l~C~~Cg~~~~~~~E~~~a--~K~t~f~TFPd~Lvv~~~r~~l~~ 85 (229)
..||.|+++ ... .|+.-|-.||++|+|+++||....
T Consensus 518 w~Cp~c~~~-------~~~~~lK~~~i~~lp~iLiihL~Rf~~~~ 555 (653)
T KOG1868|consen 518 WLCPRCKHK-------ESSKTLKKLTILRLPKILIIHLKRFSSDG 555 (653)
T ss_pred cCCccccCc-------ccccccceeeeecCCHHHHHHHHHhccCc
Confidence 799999987 222 499999999999999999999994
No 56
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=87.23 E-value=0.13 Score=37.67 Aligned_cols=64 Identities=22% Similarity=0.423 Sum_probs=22.3
Q ss_pred eccccccccCCHHHHHHHHHHhCCC-CCCch-------------hhhhhh-ccCCCCCCCCCCccccccccccccccccc
Q 027011 7 KCGDCGALLRSVQEAQEHAELTSHS-NFSES-------------TEAVLN-LVCATCGKPCRSKTETDLHRKRTGHTDFV 71 (229)
Q Consensus 7 kC~~Cg~~L~~~~~aq~Ha~~T~H~-nFse~-------------~E~vl~-l~C~~Cg~~~~~~~E~~~a~K~t~f~TFP 71 (229)
+|..|+..+.+......|... -|. ++... ...+.. +.|+.|++.+++......|.++.++..+.
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 699999999999999999876 665 33321 123444 89999999888888877788777776543
No 57
>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=87.20 E-value=0.22 Score=44.59 Aligned_cols=40 Identities=8% Similarity=-0.127 Sum_probs=32.8
Q ss_pred cccccccccccchhhhccccccccc--Cccc---cCCcccccCCC
Q 027011 61 HRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSEEAIDVDM 100 (229)
Q Consensus 61 a~K~t~f~TFPd~Lvv~~~r~~l~~--P~Kl---v~~~e~lDls~ 100 (229)
+.+...|..+|++|+|+.|||.... +.|+ |..|..|||+.
T Consensus 89 ~~~~e~i~~lP~vLiIhLKRF~~~~~~~~Kl~~~I~fP~~Ldl~~ 133 (241)
T cd02670 89 YFNNSVFAKAPSCLIICLKRYGKTEGKAQKMFKKILIPDEIDIPD 133 (241)
T ss_pred HhchhhhhhCCCeEEEEEEccccCCCcceeCCcEECCCCcCCchh
Confidence 3444449999999999999999986 7888 56788899986
No 58
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=87.13 E-value=0.3 Score=46.34 Aligned_cols=48 Identities=23% Similarity=0.372 Sum_probs=38.3
Q ss_pred cceeeccc--cccccCCHHHHHHHHHHhCCCCC------Cch-----hhhhhhccCCCCCCC
Q 027011 3 GVSLKCGD--CGALLRSVQEAQEHAELTSHSNF------SES-----TEAVLNLVCATCGKP 51 (229)
Q Consensus 3 ~~slkC~~--Cg~~L~~~~~aq~Ha~~T~H~nF------se~-----~E~vl~l~C~~Cg~~ 51 (229)
++.|||.+ |.|..+++++..+|.-. ||.|= ++. ...-++|+|+.|+|.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lh-GH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KR 407 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLH-GHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKR 407 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhc-cccCcccCCCCCccccccccccCCceeccccchh
Confidence 47899998 99999999999999988 99432 111 123589999999986
No 59
>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=87.02 E-value=0.22 Score=44.24 Aligned_cols=31 Identities=6% Similarity=-0.007 Sum_probs=26.4
Q ss_pred cccccccccccccchhhhccccccccc--Cccc
Q 027011 59 DLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT 89 (229)
Q Consensus 59 ~~a~K~t~f~TFPd~Lvv~~~r~~l~~--P~Kl 89 (229)
..+.|+..|..+|++|+|+.+||.... ..|+
T Consensus 117 ~~~~~~~~i~~lP~vL~i~LkRF~~~~~~~~Ki 149 (228)
T cd02665 117 VKSGQERWFTELPPVLTFELSRFEFNQGRPEKI 149 (228)
T ss_pred hhhhhhhhhhhCChhhEEEeEeeEEcCCccEEC
Confidence 346788899999999999999999975 6666
No 60
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=86.83 E-value=0.74 Score=33.64 Aligned_cols=32 Identities=28% Similarity=0.484 Sum_probs=26.7
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCch
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSES 36 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~ 36 (229)
.+.|..|++.+++....+.|....+|......
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 58999999999999999999999999998653
No 61
>COG1773 Rubredoxin [Energy production and conversion]
Probab=86.57 E-value=0.13 Score=36.82 Aligned_cols=43 Identities=19% Similarity=0.431 Sum_probs=34.3
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCC
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~ 50 (229)
.+++|..||.+......-..+... +-+-|++. -.+.+||-||-
T Consensus 2 ~~~~C~~CG~vYd~e~Gdp~~gi~-pgT~fedl---Pd~w~CP~Cg~ 44 (55)
T COG1773 2 KRWRCSVCGYVYDPEKGDPRCGIA-PGTPFEDL---PDDWVCPECGV 44 (55)
T ss_pred CceEecCCceEeccccCCccCCCC-CCCchhhC---CCccCCCCCCC
Confidence 379999999999998888887777 44558776 34689999984
No 62
>CHL00098 tsf elongation factor Ts
Probab=86.51 E-value=1.4 Score=38.72 Aligned_cols=38 Identities=26% Similarity=0.367 Sum_probs=32.4
Q ss_pred HHHHHHHh-CCCCHHHHHHHHHHcCCCCHHHHHHHHHhCC
Q 027011 116 ELLKELEA-MGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (229)
Q Consensus 116 ~~l~qL~e-MGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~ 154 (229)
.++.+|-+ -|-+--.|++||..++| |++.|++||..+.
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 45667764 58999999999999998 9999999998764
No 63
>PHA00733 hypothetical protein
Probab=86.34 E-value=0.9 Score=36.99 Aligned_cols=38 Identities=26% Similarity=0.455 Sum_probs=27.2
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCC
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~ 52 (229)
..++|..||+.++.......|-.... .+++|+.|++.+
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~h~-----------~~~~C~~CgK~F 109 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRYTE-----------HSKVCPVCGKEF 109 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhcCC-----------cCccCCCCCCcc
Confidence 45788888888888888887766411 137888888863
No 64
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=86.10 E-value=0.36 Score=32.32 Aligned_cols=29 Identities=28% Similarity=0.568 Sum_probs=20.4
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
..|+|..||..+.-. +. ....+||.||.+
T Consensus 2 ~~y~C~~CG~~~~~~----------------~~---~~~~~Cp~CG~~ 30 (46)
T PRK00398 2 AEYKCARCGREVELD----------------EY---GTGVRCPYCGYR 30 (46)
T ss_pred CEEECCCCCCEEEEC----------------CC---CCceECCCCCCe
Confidence 358999999876542 11 115799999986
No 65
>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=84.22 E-value=0.79 Score=26.76 Aligned_cols=21 Identities=29% Similarity=0.790 Sum_probs=19.3
Q ss_pred eeccccccccCCHHHHHHHHH
Q 027011 6 LKCGDCGALLRSVQEAQEHAE 26 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~ 26 (229)
++|+.|++.|.+...-..|-.
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 789999999999999999973
No 66
>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=83.51 E-value=2.9 Score=34.08 Aligned_cols=39 Identities=18% Similarity=0.240 Sum_probs=34.5
Q ss_pred CCCHHHHHHHH-hCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Q 027011 112 EVDKELLKELE-AMGFPVARATRALHYSGNANVEAAVNWVV 151 (229)
Q Consensus 112 ~vd~~~l~qL~-eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~ 151 (229)
+++++.++.++ .-|-+++.|++||..++| |+-.|+-+|.
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 58999999887 468999999999999988 9999998875
No 67
>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=83.46 E-value=0.68 Score=29.62 Aligned_cols=26 Identities=27% Similarity=0.653 Sum_probs=20.3
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
.++|.+||.+..+.. .+-+||.||.+
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 478999999877642 24599999986
No 68
>smart00355 ZnF_C2H2 zinc finger.
Probab=83.00 E-value=0.89 Score=25.08 Aligned_cols=21 Identities=29% Similarity=0.790 Sum_probs=19.0
Q ss_pred eeccccccccCCHHHHHHHHH
Q 027011 6 LKCGDCGALLRSVQEAQEHAE 26 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~ 26 (229)
++|..|++.+++....+.|-.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 579999999999999999976
No 69
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=82.75 E-value=0.47 Score=43.80 Aligned_cols=55 Identities=22% Similarity=0.436 Sum_probs=39.7
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCCCCcccccccccc
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKR 64 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~~~~~E~~~a~K~ 64 (229)
-+++|.+|||.+.+....-. |..|.-+-++.+-+.|+.|||...|..+...++.+
T Consensus 129 ~r~~c~eCgk~ysT~snLsr------HkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirT 183 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSR------HKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRT 183 (279)
T ss_pred Cceeccccccccccccccch------hhcccccccccccccCCCCCceeeehHHHhhHhhc
Confidence 47899999999887765433 55555555557789999999987666666555544
No 70
>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=82.62 E-value=0.23 Score=34.60 Aligned_cols=43 Identities=19% Similarity=0.480 Sum_probs=27.6
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
+++|..||.+.....+-..+....| +.|.+- -.+++||.||.+
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 5799999999776554433433322 234442 335899999875
No 71
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=82.25 E-value=0.72 Score=32.27 Aligned_cols=31 Identities=29% Similarity=0.662 Sum_probs=22.6
Q ss_pred CcceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 2 AGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 2 ~~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
+-..|+|..||+.+ +..+.-....||.||..
T Consensus 3 ~~~~Y~C~~Cg~~~-------------------~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 3 AMMEYKCARCGREV-------------------ELDQETRGIRCPYCGSR 33 (49)
T ss_pred ceEEEEhhhcCCee-------------------ehhhccCceeCCCCCcE
Confidence 34689999999988 22223456799999975
No 72
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=81.56 E-value=0.57 Score=38.50 Aligned_cols=48 Identities=23% Similarity=0.390 Sum_probs=26.2
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhh-hhccCCCCCCC
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAV-LNLVCATCGKP 51 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~v-l~l~C~~Cg~~ 51 (229)
...++|.+||..+.-.++.+.. .-+-+.-+.=..|.+ ..+.||.||+.
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESL-DEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ceEEECCCCCCEEecccccccc-cccccccccccccccccCcCCcCCCCC
Confidence 4678999999887655322221 111222222222222 23679999985
No 73
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=81.54 E-value=0.64 Score=48.28 Aligned_cols=40 Identities=28% Similarity=0.612 Sum_probs=31.9
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCC
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~ 52 (229)
.++||.+|||-|+=---...|... |+ + .++|-||.|+|.+
T Consensus 280 RKFKCtECgKAFKfKHHLKEHlRI--HS---G----EKPfeCpnCkKRF 319 (1007)
T KOG3623|consen 280 RKFKCTECGKAFKFKHHLKEHLRI--HS---G----EKPFECPNCKKRF 319 (1007)
T ss_pred ccccccccchhhhhHHHHHhhhee--ec---C----CCCcCCccccccc
Confidence 478999999999887777777654 54 3 3899999999865
No 74
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=81.27 E-value=1 Score=37.14 Aligned_cols=36 Identities=22% Similarity=0.542 Sum_probs=24.4
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
...|.|..||..+.-. +|..+. + .. -.|+||.||..
T Consensus 97 ~~~Y~Cp~C~~~y~~~-ea~~~~----d--~~------~~f~Cp~Cg~~ 132 (147)
T smart00531 97 NAYYKCPNCQSKYTFL-EANQLL----D--MD------GTFTCPRCGEE 132 (147)
T ss_pred CcEEECcCCCCEeeHH-HHHHhc----C--CC------CcEECCCCCCE
Confidence 4579999999998844 433321 1 11 23999999985
No 75
>PHA00616 hypothetical protein
Probab=80.72 E-value=0.87 Score=31.15 Aligned_cols=26 Identities=31% Similarity=0.581 Sum_probs=22.0
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHS 31 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~ 31 (229)
.++|..||+.|+...+...|..+ .|.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~-~hg 26 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS-VHK 26 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH-hcC
Confidence 37999999999999999999855 443
No 76
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=80.43 E-value=0.83 Score=36.43 Aligned_cols=28 Identities=21% Similarity=0.458 Sum_probs=19.6
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
..+++|.+||..+.-.. ..+.||.||+.
T Consensus 68 p~~~~C~~Cg~~~~~~~---------------------~~~~CP~Cgs~ 95 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQ---------------------HDAQCPHCHGE 95 (113)
T ss_pred CcEEEcccCCCEEecCC---------------------cCccCcCCCCC
Confidence 46789999996543321 23579999985
No 77
>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=78.60 E-value=0.36 Score=30.87 Aligned_cols=35 Identities=29% Similarity=0.601 Sum_probs=22.3
Q ss_pred CCcceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 1 MAGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 1 ~~~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
|--..|+|.+||+.+.-.... ++ -....||.||..
T Consensus 1 Mp~Y~y~C~~Cg~~fe~~~~~------------~~----~~~~~CP~Cg~~ 35 (41)
T smart00834 1 MPIYEYRCEDCGHTFEVLQKI------------SD----DPLATCPECGGD 35 (41)
T ss_pred CCCEEEEcCCCCCEEEEEEec------------CC----CCCCCCCCCCCc
Confidence 344679999999976532211 11 123689999984
No 78
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=78.59 E-value=6.1 Score=32.52 Aligned_cols=40 Identities=23% Similarity=0.343 Sum_probs=32.7
Q ss_pred CCCCCHHHHHHHH-hCCCCHHHHHHHHHHcCCCCHHHHHHHH
Q 027011 110 EPEVDKELLKELE-AMGFPVARATRALHYSGNANVEAAVNWV 150 (229)
Q Consensus 110 ~~~vd~~~l~qL~-eMGF~~~~a~kAL~~Tgn~~~E~A~~WL 150 (229)
...++++.+...+ .-|-|++.|++||..+|+ ++-.|+--|
T Consensus 80 ~~~i~eeDIkLV~eQa~VsreeA~kAL~e~~G-DlaeAIm~L 120 (122)
T COG1308 80 ESDISEEDIKLVMEQAGVSREEAIKALEEAGG-DLAEAIMKL 120 (122)
T ss_pred cCCCCHHHHHHHHHHhCCCHHHHHHHHHHcCC-cHHHHHHHh
Confidence 3458888888766 579999999999999988 888887554
No 79
>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=78.47 E-value=0.96 Score=36.12 Aligned_cols=29 Identities=21% Similarity=0.465 Sum_probs=20.3
Q ss_pred CcceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 2 AGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 2 ~~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
...+.+|.+||..+.-..- .+.||.||+.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~---------------------~~~CP~Cgs~ 95 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEID---------------------LYRCPKCHGI 95 (115)
T ss_pred eCcEEEcccCCCEEecCCc---------------------CccCcCCcCC
Confidence 3457899999976543211 3689999986
No 80
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=78.46 E-value=1.1 Score=30.26 Aligned_cols=35 Identities=34% Similarity=0.529 Sum_probs=24.4
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCCCCcccccccccccc
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTG 66 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~~~~~E~~~a~K~t~ 66 (229)
.|+|.+||.-+.-. . ....+||.||.. ....||+.
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 58999999865421 1 234799999986 66666654
No 81
>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=77.88 E-value=0.29 Score=33.74 Aligned_cols=43 Identities=23% Similarity=0.532 Sum_probs=23.5
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
+++|..||.+.....+-..+... --+-|++- -.+++||.|+..
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 58999999996554432222222 23346654 335899999864
No 82
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=77.24 E-value=1.3 Score=29.38 Aligned_cols=34 Identities=24% Similarity=0.577 Sum_probs=22.3
Q ss_pred CcceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 2 AGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 2 ~~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
--..|+|.+||..|.-. ..+++ -....||.||..
T Consensus 2 P~Yey~C~~Cg~~fe~~------------~~~~~----~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 2 PIYEYRCEECGHEFEVL------------QSISE----DDPVPCPECGST 35 (42)
T ss_pred CCEEEEeCCCCCEEEEE------------EEcCC----CCCCcCCCCCCC
Confidence 34578999999876421 22333 235699999983
No 83
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=77.20 E-value=1.3 Score=38.03 Aligned_cols=31 Identities=16% Similarity=0.485 Sum_probs=23.6
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
..-|.|..||..+.-.++.. .+|+||.||..
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~------------------~~F~Cp~Cg~~ 145 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME------------------YGFRCPQCGEM 145 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh------------------cCCcCCCCCCC
Confidence 35689999998887665431 26999999986
No 84
>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=77.05 E-value=1.3 Score=37.21 Aligned_cols=31 Identities=19% Similarity=0.457 Sum_probs=23.3
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
..-|.|..||..+.-.++.+ .+|+||.||.+
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~------------------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME------------------LNFTCPRCGAM 137 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH------------------cCCcCCCCCCE
Confidence 34588999998876555543 26999999985
No 85
>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=76.94 E-value=1.1 Score=26.62 Aligned_cols=21 Identities=19% Similarity=0.563 Sum_probs=17.7
Q ss_pred eeccccccccCCHHHHHHHHH
Q 027011 6 LKCGDCGALLRSVQEAQEHAE 26 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~ 26 (229)
+-|..|++.|.+....+.|-.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 579999999999998887754
No 86
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.67 E-value=1.3 Score=35.49 Aligned_cols=15 Identities=33% Similarity=0.897 Sum_probs=11.1
Q ss_pred CcceeeccccccccC
Q 027011 2 AGVSLKCGDCGALLR 16 (229)
Q Consensus 2 ~~~slkC~~Cg~~L~ 16 (229)
+..+++|.+||..+.
T Consensus 68 vp~~~~C~~Cg~~~~ 82 (117)
T PRK00564 68 EKVELECKDCSHVFK 82 (117)
T ss_pred cCCEEEhhhCCCccc
Confidence 356789999996653
No 87
>KOG1870 consensus Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=75.86 E-value=0.54 Score=49.08 Aligned_cols=53 Identities=9% Similarity=0.051 Sum_probs=43.2
Q ss_pred hhccCCCCCCCCCCcccccccccccccccccchhhhccccccccc--Cccc---c-CCcccccCCC
Q 027011 41 LNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---A-DSEEAIDVDM 100 (229)
Q Consensus 41 l~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~--P~Kl---v-~~~e~lDls~ 100 (229)
....||.|.+. ..|+|+.-.-..|++|||+.|||...+ ..|+ | .+...||+++
T Consensus 715 ~~w~C~~Cke~-------~~A~Kk~~lwrlPeiLiihLKrF~~~r~~~~k~~~~v~fPi~~ld~s~ 773 (842)
T KOG1870|consen 715 DRWYCPQCKEL-------RQATKKLDLWRLPEILIIHLKRFQYSRESSSKVKTKVEFPLGSLDLSE 773 (842)
T ss_pred ccccChHHHHH-------HHHhhhhhhhhCCceEEEEeecceeechhhhhhCccccCCCcCCCcch
Confidence 34789999886 889999999999999999999999998 5554 3 3556677775
No 88
>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=75.30 E-value=1.7 Score=35.20 Aligned_cols=46 Identities=24% Similarity=0.572 Sum_probs=30.8
Q ss_pred ceeeccccccccCCHHH-------------HHHHHHHhCCCCCCchh--hhhhhccCCCCCCC
Q 027011 4 VSLKCGDCGALLRSVQE-------------AQEHAELTSHSNFSEST--EAVLNLVCATCGKP 51 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~-------------aq~Ha~~T~H~nFse~~--E~vl~l~C~~Cg~~ 51 (229)
+.+|| +||..|-+-.+ .+.|.+. .-..|+... ..+.+|-||.||..
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 35778 79999655443 3444444 444566554 47889999999985
No 89
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=75.24 E-value=1.3 Score=25.33 Aligned_cols=21 Identities=19% Similarity=0.434 Sum_probs=19.1
Q ss_pred eeccccccccCCHHHHHHHHH
Q 027011 6 LKCGDCGALLRSVQEAQEHAE 26 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~ 26 (229)
+.|..|++.+.+....+.|..
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 579999999999999999975
No 90
>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=74.92 E-value=5 Score=30.31 Aligned_cols=36 Identities=25% Similarity=0.329 Sum_probs=30.5
Q ss_pred HHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCC
Q 027011 119 KELEAMGFPVARATRALHYSGNANVEAAVNWVVEHEN 155 (229)
Q Consensus 119 ~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~d 155 (229)
+.+.+.||+...+..||++|.+ ++..|..+++.+-.
T Consensus 2 ~~~~~~g~~~~~v~~aL~~tSg-d~~~a~~~vl~~l~ 37 (87)
T PF11626_consen 2 KHYEELGYSREFVTHALYATSG-DPELARRFVLNFLQ 37 (87)
T ss_dssp HHHHHHTB-HHHHHHHHHHTTT-BHHHHHHHHHHCHC
T ss_pred chHHHhCCCHHHHHHHHHHhCC-CHHHHHHHHHHHHH
Confidence 4578899999999999999976 99999999988743
No 91
>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=74.52 E-value=1.8 Score=29.29 Aligned_cols=34 Identities=24% Similarity=0.538 Sum_probs=21.6
Q ss_pred CcceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 2 AGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 2 ~~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
--..|+|.+||..|.... .+++ .....||.||..
T Consensus 2 P~Yey~C~~Cg~~fe~~~------------~~~~----~~~~~CP~Cg~~ 35 (52)
T TIGR02605 2 PIYEYRCTACGHRFEVLQ------------KMSD----DPLATCPECGGE 35 (52)
T ss_pred CCEEEEeCCCCCEeEEEE------------ecCC----CCCCCCCCCCCC
Confidence 346799999999775321 1122 123579999973
No 92
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=72.80 E-value=2.6 Score=36.07 Aligned_cols=47 Identities=19% Similarity=0.370 Sum_probs=36.6
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCch-hhhhh--hccCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSES-TEAVL--NLVCATCGKP 51 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~-~E~vl--~l~C~~Cg~~ 51 (229)
-.+|..||+.|......++-++.-+|+.|++. .|... -..||.|..+
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 45799999999999999988888888888754 23332 2589999864
No 93
>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=71.54 E-value=5.1 Score=27.47 Aligned_cols=38 Identities=39% Similarity=0.632 Sum_probs=30.7
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~ 50 (229)
+|.|..||+ .-+..+...|... -|.+ +. .+++||-|.+
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 588999999 6778899999998 7875 22 3589999976
No 94
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=70.77 E-value=9.2 Score=35.81 Aligned_cols=40 Identities=28% Similarity=0.534 Sum_probs=32.8
Q ss_pred CCHHHHHHHHhC-CCCHHHHHHHHHHcCCCCHHHHHHHHHhC
Q 027011 113 VDKELLKELEAM-GFPVARATRALHYSGNANVEAAVNWVVEH 153 (229)
Q Consensus 113 vd~~~l~qL~eM-GF~~~~a~kAL~~Tgn~~~E~A~~WL~~h 153 (229)
+...+|..|-++ |=.--.|+|||..+++ |+|.|++||...
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 556677777643 6777899999999977 999999999875
No 95
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=70.58 E-value=2.4 Score=33.80 Aligned_cols=11 Identities=18% Similarity=0.471 Sum_probs=9.1
Q ss_pred cceeecccccc
Q 027011 3 GVSLKCGDCGA 13 (229)
Q Consensus 3 ~~slkC~~Cg~ 13 (229)
..+++|.+||.
T Consensus 68 p~~~~C~~Cg~ 78 (114)
T PRK03681 68 EAECWCETCQQ 78 (114)
T ss_pred CcEEEcccCCC
Confidence 45789999996
No 96
>PF13423 UCH_1: Ubiquitin carboxyl-terminal hydrolase
Probab=70.30 E-value=2.1 Score=38.26 Aligned_cols=56 Identities=20% Similarity=0.159 Sum_probs=39.6
Q ss_pred hhhhhccCCCCCCCCCCcccccccccccccccccchhhhccccccccc--Cccc---cCCcccccCCC
Q 027011 38 EAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV--PKAT---ADSEEAIDVDM 100 (229)
Q Consensus 38 E~vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~--P~Kl---v~~~e~lDls~ 100 (229)
+......|+.|++. .....+..+++.|++|+|++++..-+. +.|. +.+|..++++.
T Consensus 176 e~~~~a~C~~C~~~-------~~~~~~r~i~~LPpVL~In~~~~~~~~~w~~~~~~~~~ip~~i~~~~ 236 (295)
T PF13423_consen 176 EQQTRAWCEKCNKY-------QPTEQRRTIRSLPPVLSINLNRYSEEEFWPKKNWLKIWIPPSINLPH 236 (295)
T ss_pred cccccccccccccc-------cceeeeeeccCCCcEEEEEccCCCcccccccccCCceecceeeeccc
Confidence 34455789999986 456666778999999999999988884 4444 23344455553
No 97
>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=68.85 E-value=2.8 Score=24.86 Aligned_cols=15 Identities=27% Similarity=0.580 Sum_probs=9.4
Q ss_pred CcceeeccccccccC
Q 027011 2 AGVSLKCGDCGALLR 16 (229)
Q Consensus 2 ~~~slkC~~Cg~~L~ 16 (229)
..+.++|..|++.|.
T Consensus 11 ~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 11 GEKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSSEEESSSSEEES
T ss_pred CCCCCCCCCCcCeeC
Confidence 345677777776654
No 98
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=68.26 E-value=2.3 Score=30.93 Aligned_cols=27 Identities=26% Similarity=0.575 Sum_probs=23.8
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSN 32 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~n 32 (229)
-|+|.-||++|+.+.+-..|..+ .|-.
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNK-aH~~ 43 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNK-AHGW 43 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhH-Hhhh
Confidence 48999999999999999999988 6654
No 99
>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=66.94 E-value=1.8 Score=34.34 Aligned_cols=28 Identities=29% Similarity=0.807 Sum_probs=16.8
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
..+.+|.+||+.+.-+.. .+.||.||+.
T Consensus 68 p~~~~C~~Cg~~~~~~~~---------------------~~~CP~Cgs~ 95 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEF---------------------DFSCPRCGSP 95 (113)
T ss_dssp --EEEETTTS-EEECHHC---------------------CHH-SSSSSS
T ss_pred CCcEECCCCCCEEecCCC---------------------CCCCcCCcCC
Confidence 457899999987643321 1459999986
No 100
>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=65.50 E-value=5.8 Score=24.18 Aligned_cols=23 Identities=13% Similarity=0.284 Sum_probs=19.4
Q ss_pred eeeccccccccCCHHHHHHHHHH
Q 027011 5 SLKCGDCGALLRSVQEAQEHAEL 27 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~ 27 (229)
.+.|..|++.|.+......|-.-
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 47799999999988888888654
No 101
>COG0423 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=65.28 E-value=7.4 Score=39.20 Aligned_cols=79 Identities=23% Similarity=0.365 Sum_probs=48.6
Q ss_pred eeccccccccCCHHHHHHHHHHhCCCCCCch--hhh--hhhccCCCCCCCCCCccccccccc------------------
Q 027011 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSES--TEA--VLNLVCATCGKPCRSKTETDLHRK------------------ 63 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~--~E~--vl~l~C~~Cg~~~~~~~E~~~a~K------------------ 63 (229)
..|..||..+|-.--...-....+|.|++.. ++. .-+.+||.||.+.....+..+.-|
T Consensus 89 v~c~~c~~~yRADHLiEe~l~~~~~~~~~~~e~~~ii~~~~ir~p~~g~~l~~v~~FNLMF~T~IGp~~~~~~YLRPETA 168 (558)
T COG0423 89 VECKKCGERYRADHLIEEYLGKDGHGNMSPEELTEIIREYDIRCPECGGELNEVREFNLMFKTTIGPVEDSLGYLRPETA 168 (558)
T ss_pred eeccccchhhhhhHHHHHHhhhcccccCCHHHHHHHHHHcCCcCCCcCCccCCcceeeeEEEeeecCCCCcceeeccccc
Confidence 6899999999966665555555467776665 222 245899999987544333322222
Q ss_pred ccccccccchhhhcccccccc
Q 027011 64 RTGHTDFVDKTSEAAKPISLE 84 (229)
Q Consensus 64 ~t~f~TFPd~Lvv~~~r~~l~ 84 (229)
+--|-.|++.+--+-+|.-+.
T Consensus 169 QGiFvnFk~l~~~~r~klPFg 189 (558)
T COG0423 169 QGIFVNFKNLLEFARNKLPFG 189 (558)
T ss_pred chhhhhhHHHHHHhccCCCeE
Confidence 234666666666555555554
No 102
>PF14353 CpXC: CpXC protein
Probab=64.71 E-value=3.6 Score=32.77 Aligned_cols=12 Identities=25% Similarity=1.057 Sum_probs=9.9
Q ss_pred hhhccCCCCCCC
Q 027011 40 VLNLVCATCGKP 51 (229)
Q Consensus 40 vl~l~C~~Cg~~ 51 (229)
.-.++||+||..
T Consensus 36 l~~~~CP~Cg~~ 47 (128)
T PF14353_consen 36 LFSFTCPSCGHK 47 (128)
T ss_pred cCEEECCCCCCc
Confidence 446899999996
No 103
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=64.24 E-value=7.5 Score=32.85 Aligned_cols=37 Identities=24% Similarity=0.426 Sum_probs=25.9
Q ss_pred CCcceeeccccccc----cCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 1 MAGVSLKCGDCGAL----LRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 1 ~~~~slkC~~Cg~~----L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
|-.+.|+|. ||.. |++..+=....++ .-+.||.||+.
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 445789999 8877 5555555555555 33799999985
No 104
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=64.08 E-value=1.8 Score=38.99 Aligned_cols=38 Identities=24% Similarity=0.495 Sum_probs=24.2
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
++-|.-|||.|.+.-+...|... |+. |-+|+|..|+|.
T Consensus 145 r~lct~cgkgfndtfdlkrh~rt--htg-------vrpykc~~c~ka 182 (267)
T KOG3576|consen 145 RHLCTFCGKGFNDTFDLKRHTRT--HTG-------VRPYKCSLCEKA 182 (267)
T ss_pred HHHHhhccCcccchhhhhhhhcc--ccC-------ccccchhhhhHH
Confidence 34466666666666666666554 332 567888888874
No 105
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=64.00 E-value=2.3 Score=41.79 Aligned_cols=23 Identities=13% Similarity=0.203 Sum_probs=16.0
Q ss_pred HHhCCCCHHHHHHHHHHcCCCCHHH
Q 027011 121 LEAMGFPVARATRALHYSGNANVEA 145 (229)
Q Consensus 121 L~eMGF~~~~a~kAL~~Tgn~~~E~ 145 (229)
..+-||+..-|--+++.+.| +.+
T Consensus 454 ~~~q~f~~ky~~atfyss~~--ltr 476 (500)
T KOG3993|consen 454 IAEQGFTCKYCPATFYSSPG--LTR 476 (500)
T ss_pred chhhccccccchHhhhcCcc--hHh
Confidence 34568888888888776644 555
No 106
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=63.64 E-value=8.1 Score=28.01 Aligned_cols=19 Identities=26% Similarity=0.454 Sum_probs=16.6
Q ss_pred HHHHhCCCCHHHHHHHHHH
Q 027011 119 KELEAMGFPVARATRALHY 137 (229)
Q Consensus 119 ~qL~eMGF~~~~a~kAL~~ 137 (229)
+.|++|||++.+|++-++.
T Consensus 7 ~dLi~lGf~~~tA~~IIrq 25 (59)
T PF11372_consen 7 KDLIELGFSESTARDIIRQ 25 (59)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 4689999999999988875
No 107
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=63.55 E-value=3.1 Score=30.23 Aligned_cols=11 Identities=27% Similarity=0.676 Sum_probs=7.5
Q ss_pred hhccCCCCCCC
Q 027011 41 LNLVCATCGKP 51 (229)
Q Consensus 41 l~l~C~~Cg~~ 51 (229)
..|+||.||-.
T Consensus 47 ~~Y~CP~CGF~ 57 (59)
T PRK14890 47 NPYTCPKCGFE 57 (59)
T ss_pred CceECCCCCCc
Confidence 45778888753
No 108
>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=62.94 E-value=3.9 Score=28.88 Aligned_cols=31 Identities=26% Similarity=0.697 Sum_probs=21.4
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
.-++|..|+++|-.. | .|. .++.+||.||.-
T Consensus 3 ~eiRC~~CnklLa~~----------g--~~~-----~leIKCpRC~ti 33 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKA----------G--EVI-----ELEIKCPRCKTI 33 (51)
T ss_pred cceeccchhHHHhhh----------c--Ccc-----EEEEECCCCCcc
Confidence 458999999987432 2 122 256799999984
No 109
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=62.84 E-value=2.6 Score=30.60 Aligned_cols=27 Identities=37% Similarity=0.803 Sum_probs=12.5
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~ 50 (229)
.+.||||++. +...|. ++-++|++||+
T Consensus 30 ~IlCNDC~~~--------------s~v~fH-----~lg~KC~~C~S 56 (61)
T PF14599_consen 30 WILCNDCNAK--------------SEVPFH-----FLGHKCSHCGS 56 (61)
T ss_dssp EEEESSS--E--------------EEEE-------TT----TTTS-
T ss_pred EEECCCCCCc--------------cceeee-----HhhhcCCCCCC
Confidence 5789999863 233333 56789999987
No 110
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=62.50 E-value=3.3 Score=24.91 Aligned_cols=10 Identities=30% Similarity=0.939 Sum_probs=8.2
Q ss_pred hhccCCCCCC
Q 027011 41 LNLVCATCGK 50 (229)
Q Consensus 41 l~l~C~~Cg~ 50 (229)
..|.||.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4699999985
No 111
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.23 E-value=15 Score=31.85 Aligned_cols=31 Identities=19% Similarity=0.311 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHcCCCCHHH
Q 027011 115 KELLKELEAMGFPVARATRALHYSGNANVEA 145 (229)
Q Consensus 115 ~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~ 145 (229)
+++++.|+.+||++..|.+|+..-.+.+++.
T Consensus 143 ~ea~~AL~~LGy~~~ea~~a~~~~~~~~~ee 173 (183)
T PRK14601 143 SEALAALLTLGFKQEKIIKVLASCQSTGTSE 173 (183)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhcccCCHHH
Confidence 6789999999999999999998764444444
No 112
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.10 E-value=4.8 Score=32.59 Aligned_cols=35 Identities=23% Similarity=0.540 Sum_probs=20.5
Q ss_pred CcceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 2 AGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 2 ~~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
+..+.+| +||..+.-....- .|.. ..+.||.||+.
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~------~~~~--------~~~~CP~Cgs~ 101 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEI------DHYA--------AVIECPVCGNK 101 (124)
T ss_pred cCeeEEe-eCcCcccccccch------hccc--------cCCcCcCCCCC
Confidence 4567899 9997754432100 1111 13679999975
No 113
>KOG1863 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=61.81 E-value=3 Score=44.94 Aligned_cols=69 Identities=14% Similarity=-0.019 Sum_probs=50.4
Q ss_pred HHHhCCCCCCchhhhhhhccCCCCCCCCCCcccccccccccccccccchhhhccccccccc----Cccc-c--CCccccc
Q 027011 25 AELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT-A--DSEEAID 97 (229)
Q Consensus 25 a~~T~H~nFse~~E~vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~----P~Kl-v--~~~e~lD 97 (229)
...+-|..|+..+-.-.+-.|..|... ..|.|-..|.++|.+|.++..||.++. +.|+ . ..|..||
T Consensus 320 l~~sf~~y~~~E~l~gdn~~~~~~~~~-------~~a~k~~~f~~lPpvl~~qL~Rf~~~~~~~~~~Ki~d~~~fp~~i~ 392 (1093)
T KOG1863|consen 320 LEDSLHLYFEAEILLGDNKYDAECHGL-------QDAKKGVLFDSLPPVLFIQLMRFEYDFSTGQKIKINDKFEFPLIID 392 (1093)
T ss_pred HHHHHHHhhhHHHhcCCccccccccch-------hhhhcceeeccCCchhhhhhhheeeeccCCceeehhhccCCccccc
Confidence 444567777744322333368889775 678888999999999999999999984 7777 2 4566777
Q ss_pred CCC
Q 027011 98 VDM 100 (229)
Q Consensus 98 ls~ 100 (229)
++.
T Consensus 393 ~d~ 395 (1093)
T KOG1863|consen 393 MDR 395 (1093)
T ss_pred cch
Confidence 765
No 114
>PHA00733 hypothetical protein
Probab=61.46 E-value=4 Score=33.24 Aligned_cols=51 Identities=24% Similarity=0.176 Sum_probs=33.0
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCCCCcccc
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTET 58 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~~~~~E~ 58 (229)
.++.|.+|++.+.+-.....|....-|..=. ...+++|+.||+.+++....
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~----~~kPy~C~~Cgk~Fss~s~L 89 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTSK----AVSPYVCPLCLMPFSSSVSL 89 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhcccC----CCCCccCCCCCCcCCCHHHH
Confidence 5789999999988766665553322222111 13579999999987554443
No 115
>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=61.46 E-value=2.2 Score=27.15 Aligned_cols=34 Identities=21% Similarity=0.535 Sum_probs=21.1
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
+.++|..||..++=..+.- ... -...+||.||..
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 3578999998866543321 000 114689999985
No 116
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=60.36 E-value=5.2 Score=27.94 Aligned_cols=40 Identities=25% Similarity=0.504 Sum_probs=28.1
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCC
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~ 50 (229)
...|.|-+||+-+.=...-|.+=.. .+| .+ .+-+|+.|-+
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~e---Kgf-~n----~p~RC~~CR~ 41 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAE---KGF-DN----EPKRCPSCRQ 41 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHh---cCC-cC----CCccCHHHHH
Confidence 4679999999998777766655444 346 11 3579999954
No 117
>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=59.98 E-value=13 Score=32.17 Aligned_cols=25 Identities=24% Similarity=0.405 Sum_probs=22.2
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHc
Q 027011 114 DKELLKELEAMGFPVARATRALHYS 138 (229)
Q Consensus 114 d~~~l~qL~eMGF~~~~a~kAL~~T 138 (229)
.+++++.|..+||++..|.+|+..-
T Consensus 147 ~~e~~~aL~~LGy~~~e~~~ai~~~ 171 (191)
T TIGR00084 147 RDELFEALVSLGYKPQEIQQALKKI 171 (191)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3678999999999999999999875
No 118
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=58.77 E-value=31 Score=29.02 Aligned_cols=41 Identities=20% Similarity=0.156 Sum_probs=36.2
Q ss_pred CCCCCHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHh
Q 027011 110 EPEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVE 152 (229)
Q Consensus 110 ~~~vd~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~ 152 (229)
..+++.+.+..|.+-|.+++.|++||..+| ++-.||.-|..
T Consensus 110 ~s~~~~e~v~v~a~a~v~~eeAr~aleeag--Dl~~A~k~l~~ 150 (153)
T COG4008 110 HSEPPVEEVEVLADAFVTPEEAREALEEAG--DLRTAMKILRM 150 (153)
T ss_pred cCCCcHHHHHHHHHhcCCHHHHHHHHHHcC--CHHHHHHHHHH
Confidence 466788999999999999999999999987 79999987754
No 119
>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=58.69 E-value=4.8 Score=28.49 Aligned_cols=44 Identities=20% Similarity=0.258 Sum_probs=28.4
Q ss_pred ceeeccccccccCCH---HHHHHHHHHhCCCCCCchhhhhhhccCCCCC
Q 027011 4 VSLKCGDCGALLRSV---QEAQEHAELTSHSNFSESTEAVLNLVCATCG 49 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~---~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg 49 (229)
..+-|..||.++=+. .-+..|++++||.-|-.... ...-|=.|+
T Consensus 10 ~lw~CL~Cg~~~C~~~~~~Ha~~H~~~~~H~l~v~~~~--~~i~C~~C~ 56 (63)
T PF02148_consen 10 NLWLCLTCGYVGCGRYSNGHALKHYKETGHPLAVSLST--GSIWCYACD 56 (63)
T ss_dssp SEEEETTTS-EEETTTSTSHHHHHHHHHT--EEEETTT--TCEEETTTT
T ss_pred ceEEeCCCCcccccCCcCcHHHHhhcccCCeEEEECCC--CeEEEcCCC
Confidence 456799999996664 66999999999998766422 123555554
No 120
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=56.49 E-value=29 Score=30.05 Aligned_cols=24 Identities=29% Similarity=0.501 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHc
Q 027011 115 KELLKELEAMGFPVARATRALHYS 138 (229)
Q Consensus 115 ~~~l~qL~eMGF~~~~a~kAL~~T 138 (229)
.++++.|+.+||++..|.+|+...
T Consensus 144 ~e~~~AL~~LGy~~~ea~~av~~~ 167 (188)
T PRK14606 144 HESLEALVSLGYPEKQAREAVKHV 167 (188)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 578999999999999999999876
No 121
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=56.24 E-value=2.9 Score=30.12 Aligned_cols=30 Identities=23% Similarity=0.612 Sum_probs=20.9
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCC
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~ 50 (229)
..|+|..|||+|.. . .|+. -++-+||.|..
T Consensus 3 ~tiRC~~CnKlLa~---------a----~~~~----yle~KCPrCK~ 32 (60)
T COG4416 3 QTIRCAKCNKLLAE---------A----EGQA----YLEKKCPRCKE 32 (60)
T ss_pred eeeehHHHhHHHHh---------c----ccce----eeeecCCccce
Confidence 46899999999742 2 1222 25679999975
No 122
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=55.64 E-value=5.6 Score=29.03 Aligned_cols=10 Identities=30% Similarity=0.776 Sum_probs=6.7
Q ss_pred hccCCCCCCC
Q 027011 42 NLVCATCGKP 51 (229)
Q Consensus 42 ~l~C~~Cg~~ 51 (229)
+|+||.||-.
T Consensus 50 ~Y~Cp~CGF~ 59 (61)
T COG2888 50 PYRCPKCGFE 59 (61)
T ss_pred ceECCCcCcc
Confidence 4777777753
No 123
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=55.48 E-value=30 Score=30.04 Aligned_cols=38 Identities=21% Similarity=0.495 Sum_probs=28.7
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHcC---CCCHHHHHHHHH
Q 027011 114 DKELLKELEAMGFPVARATRALHYSG---NANVEAAVNWVV 151 (229)
Q Consensus 114 d~~~l~qL~eMGF~~~~a~kAL~~Tg---n~~~E~A~~WL~ 151 (229)
.++++..|...||++..|.+|+..-+ +.+++..+-+-+
T Consensus 148 ~~e~~~aL~~LGy~~~~a~~ai~~~~~~~~~~~~~~ir~aL 188 (194)
T PRK14605 148 NSDILATLTALGYSSSEAAKAISSLGDNGDLPLEERIKLAL 188 (194)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhccCCCCHHHHHHHHH
Confidence 46789999999999999999998764 235565554433
No 124
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=55.08 E-value=6.7 Score=41.47 Aligned_cols=55 Identities=25% Similarity=0.416 Sum_probs=41.7
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCCCCcccccccccccc
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTG 66 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~~~~~E~~~a~K~t~ 66 (229)
-++-||..|+|||..+-..|.|..- |+. | -+|+|--||..+.+.--.+.|.-|.+
T Consensus 351 ~~khkCr~CakvfgS~SaLqiHlRS--HTG--E-----RPfqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 351 FFKHKCRFCAKVFGSDSALQIHLRS--HTG--E-----RPFQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred cccchhhhhHhhcCchhhhhhhhhc--cCC--C-----CCeeecccccccccccceeeeeeecc
Confidence 3677999999999999999999865 542 3 47999999998766544455554443
No 125
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=54.50 E-value=5.1 Score=41.99 Aligned_cols=41 Identities=24% Similarity=0.412 Sum_probs=30.6
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCC
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~ 52 (229)
...+||.+|.|-|+----...|-.. |+ + .++|.|+.|+|.+
T Consensus 920 qRPyqC~iCkKAFKHKHHLtEHkRL--HS---G----EKPfQCdKClKRF 960 (1007)
T KOG3623|consen 920 QRPYQCIICKKAFKHKHHLTEHKRL--HS---G----EKPFQCDKCLKRF 960 (1007)
T ss_pred CCCcccchhhHhhhhhhhhhhhhhh--cc---C----CCcchhhhhhhhc
Confidence 4568899999988876666666554 43 3 3899999999864
No 126
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=54.40 E-value=33 Score=30.02 Aligned_cols=25 Identities=20% Similarity=0.267 Sum_probs=22.3
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHc
Q 027011 114 DKELLKELEAMGFPVARATRALHYS 138 (229)
Q Consensus 114 d~~~l~qL~eMGF~~~~a~kAL~~T 138 (229)
-+++++.|+.+||++..|.+|+..-
T Consensus 155 ~~ea~~AL~~LGy~~~ea~~av~~~ 179 (203)
T PRK14602 155 FRDALAGLANLGYGEEEARPVLKEV 179 (203)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3678999999999999999999875
No 127
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=53.93 E-value=34 Score=29.66 Aligned_cols=36 Identities=14% Similarity=0.252 Sum_probs=27.0
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHcCC-CCHHHHHHH
Q 027011 114 DKELLKELEAMGFPVARATRALHYSGN-ANVEAAVNW 149 (229)
Q Consensus 114 d~~~l~qL~eMGF~~~~a~kAL~~Tgn-~~~E~A~~W 149 (229)
.+++++.|+.+||++..|.+|+..-.. .+++..+.+
T Consensus 145 ~~e~~~aL~~LGy~~~ea~~al~~v~~~~~~eelir~ 181 (186)
T PRK14600 145 NDDALAALISLGYEKTKAFNAIQKIKPNLSTQDIIRK 181 (186)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhcCCCHHHHHHH
Confidence 367899999999999999999987532 355554433
No 128
>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]
Probab=53.46 E-value=5.9 Score=41.07 Aligned_cols=34 Identities=24% Similarity=0.430 Sum_probs=25.6
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~ 52 (229)
.|-|..||.+| |-.|..+.++|++-.||.|+++|
T Consensus 292 ky~C~KC~~vl--------------gPF~qs~n~evkp~~C~~cqSkG 325 (854)
T KOG0477|consen 292 KYDCLKCGFVL--------------GPFVQSSNSEVKPGSCPECQSKG 325 (854)
T ss_pred hhhHHhhCCcc--------------CceeeccCceeCCCCCccccCCC
Confidence 56788888664 44555567789999999998873
No 129
>KOG1864 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=52.80 E-value=6.5 Score=39.83 Aligned_cols=53 Identities=8% Similarity=-0.009 Sum_probs=41.8
Q ss_pred hhccCCCCCCCCCCcccccccccccccccccchhhhccccccccc----Cccc---cCCcccccCCC
Q 027011 41 LNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEAIDVDM 100 (229)
Q Consensus 41 l~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~----P~Kl---v~~~e~lDls~ 100 (229)
..|.|..|... ..|.|+-+++..|.+|+++.+||+... =+|+ +..|..+.+-.
T Consensus 440 nky~c~~c~s~-------qeae~~l~~k~lp~~L~l~Lkrfk~~~~~~~~~kl~~~v~~plel~l~~ 499 (587)
T KOG1864|consen 440 NKYSCENCCSL-------QEAERRLKIKKLPYVLTLHLKRFKYSEQQNRYTKLLYRVVFPLELRLKD 499 (587)
T ss_pred CcccccccCch-------hhHHHhccccCCcceeeeehhccccccccccccccccccccccceeecc
Confidence 45999999887 679999999999999999999999995 3444 34455555543
No 130
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=52.42 E-value=10 Score=25.10 Aligned_cols=31 Identities=29% Similarity=0.309 Sum_probs=23.5
Q ss_pred eeeccccccccCCH---HHHHHHHHHhCCCCCCc
Q 027011 5 SLKCGDCGALLRSV---QEAQEHAELTSHSNFSE 35 (229)
Q Consensus 5 slkC~~Cg~~L~~~---~~aq~Ha~~T~H~nFse 35 (229)
.+.|..|+.++-+. .-++.|...|||..+-.
T Consensus 11 l~~CL~C~~~~c~~~~~~h~~~H~~~t~H~~~~~ 44 (50)
T smart00290 11 LWLCLTCGQVGCGRYQLGHALEHFEETGHPLVVK 44 (50)
T ss_pred eEEecCCCCcccCCCCCcHHHHHhhhhCCCEEEE
Confidence 46788888886533 45999999999986643
No 131
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=51.72 E-value=4.8 Score=42.42 Aligned_cols=67 Identities=13% Similarity=-0.045 Sum_probs=47.2
Q ss_pred CCCCCCch------hhhhhhccCCCCCCCCCCcccccccccccccccccchhhhccccccccc----Cccc---cCCccc
Q 027011 29 SHSNFSES------TEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV----PKAT---ADSEEA 95 (229)
Q Consensus 29 ~H~nFse~------~E~vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~----P~Kl---v~~~e~ 95 (229)
|-.|..|| .|..-.=.|=.|.+-| ..-|.|---|.|||.+|-++.|||..+- -+|+ -..|++
T Consensus 336 ~~knLqeSfr~yIqvE~l~GdN~Y~ae~~G-----lqdAkKGViFeSlPpVlhlqLKRFeyDfe~d~mvKINDryEFP~e 410 (1089)
T COG5077 336 GMKNLQESFRRYIQVETLDGDNRYNAEKHG-----LQDAKKGVIFESLPPVLHLQLKRFEYDFERDMMVKINDRYEFPLE 410 (1089)
T ss_pred chhhHHHHHHHhhhheeccCCccccccccc-----chhhccceeeccCchHHHHHHHHhccccccCceeeecccccCcch
Confidence 55566665 2333333555555542 2468899999999999999999999984 5555 157889
Q ss_pred ccCCC
Q 027011 96 IDVDM 100 (229)
Q Consensus 96 lDls~ 100 (229)
+|+.+
T Consensus 411 iDl~p 415 (1089)
T COG5077 411 IDLLP 415 (1089)
T ss_pred hcccc
Confidence 99887
No 132
>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=50.33 E-value=16 Score=34.97 Aligned_cols=23 Identities=13% Similarity=0.408 Sum_probs=18.6
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHH
Q 027011 114 DKELLKELEAMGFPVARATRALH 136 (229)
Q Consensus 114 d~~~l~qL~eMGF~~~~a~kAL~ 136 (229)
=.++|+.+..|||+++.++-.++
T Consensus 321 ~ddvidKv~~MGf~rDqV~a~v~ 343 (358)
T PF07223_consen 321 YDDVIDKVASMGFRRDQVRATVR 343 (358)
T ss_pred HHHHHHHHHHcCCcHHHHHHHHH
Confidence 34799999999999999974443
No 133
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=49.11 E-value=40 Score=29.38 Aligned_cols=24 Identities=21% Similarity=0.272 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHc
Q 027011 115 KELLKELEAMGFPVARATRALHYS 138 (229)
Q Consensus 115 ~~~l~qL~eMGF~~~~a~kAL~~T 138 (229)
.++++.|+.+||++..|.+|+..-
T Consensus 153 ~ea~~AL~~LGy~~~ea~~al~~i 176 (197)
T PRK14603 153 EDAVLALLALGFREAQVRSVVAEL 176 (197)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 578999999999999999999864
No 134
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=48.40 E-value=11 Score=30.66 Aligned_cols=12 Identities=33% Similarity=0.827 Sum_probs=9.8
Q ss_pred hhhccCCCCCCC
Q 027011 40 VLNLVCATCGKP 51 (229)
Q Consensus 40 vl~l~C~~Cg~~ 51 (229)
...+.||.||+.
T Consensus 84 ~~~~~CP~C~s~ 95 (115)
T COG0375 84 ELDYRCPKCGSI 95 (115)
T ss_pred hheeECCCCCCC
Confidence 566789999986
No 135
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=48.37 E-value=7.4 Score=25.44 Aligned_cols=41 Identities=10% Similarity=0.067 Sum_probs=20.0
Q ss_pred hccCCCCCCCCCCc-ccccccccccccccccchhhhcccccc
Q 027011 42 NLVCATCGKPCRSK-TETDLHRKRTGHTDFVDKTSEAAKPIS 82 (229)
Q Consensus 42 ~l~C~~Cg~~~~~~-~E~~~a~K~t~f~TFPd~Lvv~~~r~~ 82 (229)
+..||.||....-. --...-..-..+..+|=+|.+..+||.
T Consensus 2 ~~~Cp~Cg~~~~~~~g~~~r~i~~l~~~~~~~~L~i~~~R~~ 43 (47)
T PF14690_consen 2 PPRCPHCGSPSVHRHGYKTRRIRHLPIGGRPVYLRIRKRRYR 43 (47)
T ss_pred CccCCCcCCCceECCceEEEEEeecccCCEEEEEEEEeEEEE
Confidence 46899999862000 000111222334455666666666653
No 136
>PLN03086 PRLI-interacting factor K; Provisional
Probab=47.44 E-value=16 Score=37.12 Aligned_cols=33 Identities=30% Similarity=0.768 Sum_probs=24.5
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~ 50 (229)
-++|..||+.+. ....+.|-... | .++.|| ||+
T Consensus 453 H~~C~~Cgk~f~-~s~LekH~~~~-H----------kpv~Cp-Cg~ 485 (567)
T PLN03086 453 HVHCEKCGQAFQ-QGEMEKHMKVF-H----------EPLQCP-CGV 485 (567)
T ss_pred CccCCCCCCccc-hHHHHHHHHhc-C----------CCccCC-CCC
Confidence 357999999885 56678887762 4 357898 986
No 137
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.06 E-value=24 Score=31.08 Aligned_cols=24 Identities=29% Similarity=0.343 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHc
Q 027011 115 KELLKELEAMGFPVARATRALHYS 138 (229)
Q Consensus 115 ~~~l~qL~eMGF~~~~a~kAL~~T 138 (229)
+++++.|+.+||++..|.+|+..-
T Consensus 145 ~ea~~AL~~LGy~~~ea~~al~~v 168 (196)
T PRK13901 145 KELEQSIVNMGFDRKLVNSAIKEI 168 (196)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 578999999999999999999754
No 138
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=46.13 E-value=49 Score=28.83 Aligned_cols=24 Identities=29% Similarity=0.409 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHc
Q 027011 115 KELLKELEAMGFPVARATRALHYS 138 (229)
Q Consensus 115 ~~~l~qL~eMGF~~~~a~kAL~~T 138 (229)
.++++.|+.+||++..|.+|+..-
T Consensus 150 ~e~~~aL~~LGy~~~ea~~ai~~i 173 (195)
T PRK14604 150 RELSEILISLGYSAAEAAAAIAAL 173 (195)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 578999999999999999999765
No 139
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=46.02 E-value=3.7 Score=27.44 Aligned_cols=10 Identities=40% Similarity=1.072 Sum_probs=8.5
Q ss_pred hccCCCCCCC
Q 027011 42 NLVCATCGKP 51 (229)
Q Consensus 42 ~l~C~~Cg~~ 51 (229)
.++||.||-.
T Consensus 20 ~~vC~~Cg~~ 29 (52)
T smart00661 20 RFVCRKCGYE 29 (52)
T ss_pred EEECCcCCCe
Confidence 5899999974
No 140
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=45.99 E-value=1.9 Score=27.83 Aligned_cols=11 Identities=45% Similarity=0.911 Sum_probs=7.6
Q ss_pred hhhccCCCCCC
Q 027011 40 VLNLVCATCGK 50 (229)
Q Consensus 40 vl~l~C~~Cg~ 50 (229)
-.+++|++||.
T Consensus 20 r~R~vC~~Cg~ 30 (34)
T PF14803_consen 20 RERLVCPACGF 30 (34)
T ss_dssp S-EEEETTTTE
T ss_pred ccceECCCCCC
Confidence 45688888875
No 141
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=45.63 E-value=47 Score=31.70 Aligned_cols=40 Identities=28% Similarity=0.483 Sum_probs=35.3
Q ss_pred CCHHHHHHHH-hCCCCHHHHHHHHHHcCCCCHHHHHHHHHhC
Q 027011 113 VDKELLKELE-AMGFPVARATRALHYSGNANVEAAVNWVVEH 153 (229)
Q Consensus 113 vd~~~l~qL~-eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h 153 (229)
...++|.+|- .-|++-.-|++||...|| |+..|-.||-+-
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 4578899997 689999999999999997 999999999754
No 142
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=44.87 E-value=11 Score=28.08 Aligned_cols=27 Identities=22% Similarity=0.262 Sum_probs=21.7
Q ss_pred CHHHHHHHHHHcCCCCHHHHHHHHHhCC
Q 027011 127 PVARATRALHYSGNANVEAAVNWVVEHE 154 (229)
Q Consensus 127 ~~~~a~kAL~~Tgn~~~E~A~~WL~~h~ 154 (229)
+..+.+.||.+.+. +++.|++||++..
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 77888999999865 9999999999863
No 143
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=44.77 E-value=1e+02 Score=24.73 Aligned_cols=21 Identities=14% Similarity=0.324 Sum_probs=15.8
Q ss_pred HHHHHHhCCCCHHHHHHHHHH
Q 027011 117 LLKELEAMGFPVARATRALHY 137 (229)
Q Consensus 117 ~l~qL~eMGF~~~~a~kAL~~ 137 (229)
.+..|.++|||-...+.-|..
T Consensus 49 ~I~~lr~~G~sL~eI~~~l~~ 69 (133)
T cd04787 49 FILSARQLGFSLKDIKEILSH 69 (133)
T ss_pred HHHHHHHcCCCHHHHHHHHhh
Confidence 356678899998888776654
No 144
>PF10827 DUF2552: Protein of unknown function (DUF2552) ; InterPro: IPR020157 This entry contains proteins with no known function.
Probab=44.56 E-value=16 Score=27.72 Aligned_cols=16 Identities=25% Similarity=0.634 Sum_probs=14.1
Q ss_pred CCHHHHHHHHHhCCCC
Q 027011 141 ANVEAAVNWVVEHEND 156 (229)
Q Consensus 141 ~~~E~A~~WL~~h~dD 156 (229)
..++.|++||-+||++
T Consensus 59 ~tld~Ai~Wi~e~M~~ 74 (79)
T PF10827_consen 59 PTLDLAIAWIGEHMPH 74 (79)
T ss_pred ccHHHHHHHHHhcccc
Confidence 3699999999999986
No 145
>PF12737 Mating_C: C-terminal domain of homeodomain 1; InterPro: IPR024441 Mating in fungi is controlled by the loci that determine the mating type of an individual, and only individuals with differing mating types can mate. Basidiomycete fungi have evolved a unique mating system, termed tetrapolar or bifactorial incompatibility, in which mating type is determined by two unlinked loci; compatibility at both loci is required for mating to occur. The multi-allelic tetrapolar mating system is considered to be a novel innovation that could have only evolved once, and is thus unique to the mushroom fungi. This domain is found in the C-terminal of some mating-type proteins.
Probab=44.01 E-value=19 Score=35.16 Aligned_cols=30 Identities=23% Similarity=0.064 Sum_probs=25.0
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHhhcccCC
Q 027011 174 SKSSLTPEEIKLKAQELRYGIFYAVYFFSD 203 (229)
Q Consensus 174 ~~~~LTeEEkkaK~~ELr~ki~~~~~~~~~ 203 (229)
.-.+|+++|+.||++||++-.++++--+++
T Consensus 388 ~~~~l~~~~~~AK~reL~eLeAq~~aL~AE 417 (419)
T PF12737_consen 388 SPVALPEAEREAKRRELEELEAQARALRAE 417 (419)
T ss_pred CCcCCCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 355899999999999999999988866543
No 146
>KOG4702 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.40 E-value=21 Score=27.03 Aligned_cols=49 Identities=20% Similarity=0.263 Sum_probs=33.8
Q ss_pred HHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHhhccc
Q 027011 143 VEAAVNWVVEHENDPDIDEMPMVPVSGGGGASKSSLTPEEIKLKAQELRYGIFYAVYFF 201 (229)
Q Consensus 143 ~E~A~~WL~~h~dD~did~pl~~p~~s~s~~~~~~LTeEEkkaK~~ELr~ki~~~~~~~ 201 (229)
.-.++=|||+. |.+-+.... .-+.+|.|-|+....+|+++.||++--|+
T Consensus 17 FPV~~FwlfNQ---pe~Fee~v~-------~~krel~ppe~~~~~EE~~~~lRe~~a~~ 65 (77)
T KOG4702|consen 17 FPVGAFWLFNQ---PEIFEEFVR-------GYKRELSPPEATKRKEEYENFLREQMAFE 65 (77)
T ss_pred hhHHHHHHccC---hHHHHHHHH-------hccccCCChHHHhhHHHHHHHHHHHHHHH
Confidence 45577788775 332222211 12678888999999999999999986554
No 147
>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=43.03 E-value=8.6 Score=31.62 Aligned_cols=42 Identities=24% Similarity=0.501 Sum_probs=25.6
Q ss_pred eeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
-+|..||..|......+-.... ....+....+ =..||.||+-
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~v-p~~v~~~~~~---f~~C~~C~ki 133 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRV-PPYVYETYDE---FWRCPGCGKI 133 (147)
T ss_pred CccCCCCcEeeechhhcccccc-CccccccCCe---EEECCCCCCE
Confidence 3799999998776543322222 4444443322 3789999974
No 148
>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=42.71 E-value=17 Score=30.26 Aligned_cols=35 Identities=20% Similarity=0.464 Sum_probs=21.6
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
+.++|..|++....... ...... . ..-.||.||..
T Consensus 104 ~~~~C~~C~~~~~~~~~-~~~~~~-~-----------~~~~C~~C~~~ 138 (178)
T PF02146_consen 104 FRLRCSKCGKEYDREDI-VDSIDE-E-----------EPPRCPKCGGL 138 (178)
T ss_dssp EEEEETTTSBEEEGHHH-HHHHHT-T-----------SSCBCTTTSCB
T ss_pred ceeeecCCCccccchhh-cccccc-c-----------ccccccccCcc
Confidence 46899999998765432 222222 1 11299999874
No 149
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=41.95 E-value=11 Score=34.09 Aligned_cols=49 Identities=20% Similarity=0.325 Sum_probs=35.6
Q ss_pred CcceeeccccccccCCHHHHHHHHHHhCCCCCCch--hh-hhhhccCCCCCCC
Q 027011 2 AGVSLKCGDCGALLRSVQEAQEHAELTSHSNFSES--TE-AVLNLVCATCGKP 51 (229)
Q Consensus 2 ~~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~--~E-~vl~l~C~~Cg~~ 51 (229)
.-..|||+.|+|.|..---.+.|..+ -|..=... .| -.+-|+|..||-.
T Consensus 170 gvrpykc~~c~kaftqrcsleshl~k-vhgv~~~yaykerr~kl~vcedcg~t 221 (267)
T KOG3576|consen 170 GVRPYKCSLCEKAFTQRCSLESHLKK-VHGVQHQYAYKERRAKLYVCEDCGYT 221 (267)
T ss_pred CccccchhhhhHHHHhhccHHHHHHH-HcCchHHHHHHHhhhheeeecccCCC
Confidence 44679999999999888788888888 67643332 11 2344999999974
No 150
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=41.77 E-value=13 Score=26.59 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=15.4
Q ss_pred ccCCCCCCCCCCcccccccccccccccccc
Q 027011 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVD 72 (229)
Q Consensus 43 l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd 72 (229)
+.||.||.+ .+......|..+.||=
T Consensus 5 i~CP~CgnK-----TR~kir~DT~LkNfPl 29 (55)
T PF14205_consen 5 ILCPICGNK-----TRLKIREDTVLKNFPL 29 (55)
T ss_pred EECCCCCCc-----cceeeecCceeccccc
Confidence 569999876 2334445566666663
No 151
>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=41.07 E-value=17 Score=23.55 Aligned_cols=30 Identities=30% Similarity=0.748 Sum_probs=19.8
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
|.-|..||++. |..|... ..+-+|+.||..
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 35677888764 5667665 456789999874
No 152
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.32 E-value=4.2 Score=31.15 Aligned_cols=33 Identities=21% Similarity=0.596 Sum_probs=20.5
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
-.+|+|..||..+. ...| |+++ ..-.|+.||.+
T Consensus 10 tY~Y~c~~cg~~~d----vvq~--------~~dd----plt~ce~c~a~ 42 (82)
T COG2331 10 TYSYECTECGNRFD----VVQA--------MTDD----PLTTCEECGAR 42 (82)
T ss_pred ceEEeecccchHHH----HHHh--------cccC----ccccChhhChH
Confidence 46899999997642 2222 3333 22479999865
No 153
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=40.03 E-value=51 Score=28.32 Aligned_cols=27 Identities=22% Similarity=0.256 Sum_probs=24.1
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHcCC
Q 027011 114 DKELLKELEAMGFPVARATRALHYSGN 140 (229)
Q Consensus 114 d~~~l~qL~eMGF~~~~a~kAL~~Tgn 140 (229)
-++++..|..+||++..|.+|+..-+.
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~~~ 175 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKILK 175 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 368899999999999999999998764
No 154
>KOG0608 consensus Warts/lats-like serine threonine kinases [Cell cycle control, cell division, chromosome partitioning]
Probab=38.99 E-value=18 Score=37.94 Aligned_cols=42 Identities=21% Similarity=0.260 Sum_probs=38.3
Q ss_pred CCCCCHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Q 027011 110 EPEVDKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVV 151 (229)
Q Consensus 110 ~~~vd~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~ 151 (229)
..+++..++.-|+.-||++.-+..||..+|+.+++.|++++-
T Consensus 85 ~s~sn~qmlq~lv~ag~d~~~a~~al~~pns~sie~sie~~s 126 (1034)
T KOG0608|consen 85 GSESNSQMLQGLVGAGNDRHMALGALATPNSRSIEASIETIS 126 (1034)
T ss_pred ccccchhhhHhhhhccccchhhhhhhcCCCccccchhhhccc
Confidence 346788899999999999999999999999999999999983
No 155
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.97 E-value=28 Score=29.21 Aligned_cols=38 Identities=21% Similarity=0.441 Sum_probs=26.2
Q ss_pred CCcceeeccccccc---cCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 1 MAGVSLKCGDCGAL---LRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 1 ~~~~slkC~~Cg~~---L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
|-.+.|.|+.=+.. |.++++-+...++ .-++||.||+.
T Consensus 1 Mi~y~L~Cd~~HeFEGWF~ssaDfd~Q~~r-------------gLv~CPvCgs~ 41 (142)
T COG5319 1 MIRYALRCDKGHEFEGWFGSSADFDRQRER-------------GLVTCPVCGST 41 (142)
T ss_pred CceeeeeccCCCcccccccCchhHHHHHHc-------------CceeCCCCCcH
Confidence 34567888764444 6777777766666 33799999984
No 156
>KOG1296 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.79 E-value=3.5 Score=35.19 Aligned_cols=39 Identities=26% Similarity=0.641 Sum_probs=24.9
Q ss_pred ceeeccccccc------cCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 4 VSLKCGDCGAL------LRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 4 ~slkC~~Cg~~------L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
+.|||..||.+ .+-++..+.-+.| |..+|- .+|--|++-
T Consensus 29 ~kLkCtnCgE~~dkw~~I~l~E~~~~pg~R-gta~~v--------~KCK~C~Re 73 (161)
T KOG1296|consen 29 LKLKCTNCGELSDKWQYITLNEEVAMPGSR-GTASFV--------MKCKFCSRE 73 (161)
T ss_pred EEeccccccccCCceEEEEeeeeecCCCCc-chhhHh--------hhhhhhccc
Confidence 57999999988 3334444444445 444442 489899874
No 157
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=38.18 E-value=22 Score=31.72 Aligned_cols=14 Identities=21% Similarity=0.439 Sum_probs=11.3
Q ss_pred ceeeccccccccCC
Q 027011 4 VSLKCGDCGALLRS 17 (229)
Q Consensus 4 ~slkC~~Cg~~L~~ 17 (229)
++++|..|++....
T Consensus 118 ~~~~C~~C~~~~~~ 131 (244)
T PRK14138 118 EEYYCVRCGKRYTV 131 (244)
T ss_pred CeeEECCCCCcccH
Confidence 57899999998654
No 158
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=38.13 E-value=16 Score=38.84 Aligned_cols=39 Identities=21% Similarity=0.451 Sum_probs=32.3
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~ 52 (229)
+-.|+.||+.|....+.|.|.+. |.- -+++.|..|++-+
T Consensus 879 ~h~C~vCgk~FsSSsALqiH~rT--Htg-------~KPF~C~fC~~aF 917 (958)
T KOG1074|consen 879 AHVCNVCGKQFSSSAALEIHMRT--HTG-------PKPFFCHFCEEAF 917 (958)
T ss_pred hhhhccchhcccchHHHHHhhhc--CCC-------CCCccchhhhhhh
Confidence 35799999999999999999876 432 3679999999853
No 159
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=37.85 E-value=36 Score=27.48 Aligned_cols=29 Identities=17% Similarity=0.243 Sum_probs=23.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhcccCCC-ccchh
Q 027011 177 SLTPEEIKLKAQELRYGIFYAVYFFSDG-YCNCY 209 (229)
Q Consensus 177 ~LTeEEkkaK~~ELr~ki~~~~~~~~~~-~~~~~ 209 (229)
.||+|| +++|++-|.+..+--+|+ -|||.
T Consensus 101 ~ls~ee----le~L~~li~~~~~~~~~~~~~~~~ 130 (130)
T TIGR02698 101 PLSQTD----IEKLEKLLSEKKSTAVEEVPCNCI 130 (130)
T ss_pred CCCHHH----HHHHHHHHHhcccCCCccccCCCC
Confidence 577766 788999999998888887 49993
No 160
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=37.55 E-value=17 Score=30.63 Aligned_cols=43 Identities=21% Similarity=0.365 Sum_probs=25.3
Q ss_pred eecccccccc--CCHH--HHH-HHHHHhCCCCCCch-hhhhhhccCCCCCCC
Q 027011 6 LKCGDCGALL--RSVQ--EAQ-EHAELTSHSNFSES-TEAVLNLVCATCGKP 51 (229)
Q Consensus 6 lkC~~Cg~~L--~~~~--~aq-~Ha~~T~H~nFse~-~E~vl~l~C~~Cg~~ 51 (229)
+.|..||++. .+.. +.. ..++.+ .|.-. ...++--.|+.|+++
T Consensus 101 ~iC~~CGki~~i~~~~l~~~~~~~~~~~---gf~i~~~~l~~~GiC~~C~~~ 149 (169)
T PRK11639 101 FICDRCGAVKEECAEGVEDIMHTLAAKM---GFALRHNVIEAHGLCAACVEV 149 (169)
T ss_pred EEeCCCCCEEEecccHHHHHHHHHHHHc---CCEEeccEEEEEEEChhhcCc
Confidence 8999999994 3322 222 333332 55443 234445579999876
No 161
>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=37.44 E-value=43 Score=23.67 Aligned_cols=43 Identities=21% Similarity=0.337 Sum_probs=31.6
Q ss_pred CCCHHHHHHHH--hCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCC
Q 027011 112 EVDKELLKELE--AMGFPVARATRALHYSGNANVEAAVNWVVEHEN 155 (229)
Q Consensus 112 ~vd~~~l~qL~--eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~d 155 (229)
.+.++.+.|.. =-|=+++...|-|+.|+ -++..|+|-|++..|
T Consensus 7 ~vPedlI~q~q~VLqgksR~vIirELqrTn-LdVN~AvNNlLsRDd 51 (53)
T PF11547_consen 7 QVPEDLINQAQVVLQGKSRNVIIRELQRTN-LDVNLAVNNLLSRDD 51 (53)
T ss_dssp GS-HHHHHHHHHHSTTS-HHHHHHHHHHTT-T-HHHHHHHHHHHH-
T ss_pred cCCHHHHHHHHHHHcCCcHHHHHHHHHHhc-ccHHHHHHHHhcccc
Confidence 45667776643 46999999999999995 599999999998644
No 162
>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=37.35 E-value=18 Score=26.49 Aligned_cols=38 Identities=18% Similarity=0.249 Sum_probs=20.8
Q ss_pred ccCCCCCCCCCCcccccccccccccccccchhhhccccccccc
Q 027011 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAAKPISLEV 85 (229)
Q Consensus 43 l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~~r~~l~~ 85 (229)
|+||.||..- .| +...+.++ ..|-..+-|+.++|.+..
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 6899999751 11 11122222 234445667777777664
No 163
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.12 E-value=19 Score=26.60 Aligned_cols=11 Identities=55% Similarity=1.407 Sum_probs=8.9
Q ss_pred hhccCCCCCCC
Q 027011 41 LNLVCATCGKP 51 (229)
Q Consensus 41 l~l~C~~Cg~~ 51 (229)
+--.||.|||+
T Consensus 6 ~~v~CP~Cgkp 16 (65)
T COG3024 6 ITVPCPTCGKP 16 (65)
T ss_pred ccccCCCCCCc
Confidence 34589999998
No 164
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=37.00 E-value=6.5 Score=28.36 Aligned_cols=45 Identities=27% Similarity=0.470 Sum_probs=26.8
Q ss_pred ceeeccccccccCCHH-HHHHHHHHhCCCCCCchhhhhhhccCCCCCC
Q 027011 4 VSLKCGDCGALLRSVQ-EAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~-~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~ 50 (229)
++=-|.-|++-|.... +|. +-.- --+.=....+.++.-+||+||.
T Consensus 4 lrpnCE~C~~dLp~~s~~A~-ICSf-ECTFC~~C~e~~l~~~CPNCgG 49 (57)
T PF06906_consen 4 LRPNCECCDKDLPPDSPEAY-ICSF-ECTFCADCAETMLNGVCPNCGG 49 (57)
T ss_pred cCCCccccCCCCCCCCCcce-EEeE-eCcccHHHHHHHhcCcCcCCCC
Confidence 4445788888877655 332 1110 1111233468888999999987
No 165
>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=34.83 E-value=25 Score=30.42 Aligned_cols=15 Identities=20% Similarity=0.583 Sum_probs=11.6
Q ss_pred ceeeccccccccCCH
Q 027011 4 VSLKCGDCGALLRSV 18 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~ 18 (229)
..++|..|++.....
T Consensus 108 ~~~~C~~C~~~~~~~ 122 (218)
T cd01407 108 FRVRCTKCGKEYPRD 122 (218)
T ss_pred CcceeCCCcCCCcHH
Confidence 568999999986543
No 166
>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=33.93 E-value=57 Score=22.49 Aligned_cols=23 Identities=26% Similarity=0.404 Sum_probs=18.3
Q ss_pred CHHHHHHHHhC---CCCHHHHHHHHH
Q 027011 114 DKELLKELEAM---GFPVARATRALH 136 (229)
Q Consensus 114 d~~~l~qL~eM---GF~~~~a~kAL~ 136 (229)
.+.+.+||++- ||+.+.|.-|+.
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 35678899876 899999988875
No 167
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=33.52 E-value=24 Score=30.63 Aligned_cols=15 Identities=27% Similarity=0.760 Sum_probs=11.4
Q ss_pred hhhhhhccCCCCCCC
Q 027011 37 TEAVLNLVCATCGKP 51 (229)
Q Consensus 37 ~E~vl~l~C~~Cg~~ 51 (229)
.+--.+++||.||..
T Consensus 127 eA~~~~F~Cp~Cg~~ 141 (176)
T COG1675 127 EAMELGFTCPKCGED 141 (176)
T ss_pred HHHHhCCCCCCCCch
Confidence 344456999999986
No 168
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=33.49 E-value=51 Score=29.13 Aligned_cols=22 Identities=18% Similarity=0.335 Sum_probs=19.4
Q ss_pred HHHHHHhCCCCHHHHHHHHHHc
Q 027011 117 LLKELEAMGFPVARATRALHYS 138 (229)
Q Consensus 117 ~l~qL~eMGF~~~~a~kAL~~T 138 (229)
.++.|+.+||++..+++|+..-
T Consensus 159 ~v~AL~~LGy~~~e~~~av~~v 180 (201)
T COG0632 159 AVEALVALGYKEKEIKKAVKKV 180 (201)
T ss_pred HHHHHHHcCCCHHHHHHHHHHH
Confidence 3899999999999999998764
No 169
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=33.41 E-value=45 Score=25.06 Aligned_cols=26 Identities=19% Similarity=0.054 Sum_probs=22.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhcccC
Q 027011 177 SLTPEEIKLKAQELRYGIFYAVYFFS 202 (229)
Q Consensus 177 ~LTeEEkkaK~~ELr~ki~~~~~~~~ 202 (229)
.-|.||-.+++++|+++|+..+++-.
T Consensus 51 ~~s~eeq~~~i~~Le~~i~~k~~~L~ 76 (83)
T PF07544_consen 51 DRSVEEQEEEIEELEEQIRKKREVLQ 76 (83)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999987643
No 170
>PF14748 P5CR_dimer: Pyrroline-5-carboxylate reductase dimerisation; PDB: 2RCY_D 3TRI_A 2IZZ_B 2GR9_B 2GRA_B 2GER_C 1YQG_A 2AG8_A 3GT0_A 2AMF_E ....
Probab=33.36 E-value=96 Score=24.10 Aligned_cols=39 Identities=21% Similarity=0.286 Sum_probs=29.0
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCCCCC
Q 027011 115 KELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHENDP 157 (229)
Q Consensus 115 ~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~dD~ 157 (229)
+.+++..+.+|++++.|++.+..| +..+...+.++..+|
T Consensus 25 eal~~a~v~~Gl~~~~A~~lv~~t----~~G~a~ll~~~~~~~ 63 (107)
T PF14748_consen 25 EALADAAVAQGLPREEARKLVAQT----FIGAAKLLEESGRSP 63 (107)
T ss_dssp HHHHHHHHHTT--HHHHHHHHHHH----HHHHHHHHHHCSS-H
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH----HHHHHHHHHccCCCH
Confidence 456777889999999999999875 788999998765443
No 171
>PF08587 UBA_2: Ubiquitin associated domain (UBA) ; InterPro: IPR013896 This is a UBA (ubiquitin associated) protein []. Ubiquitin is involved in intracellular proteolysis. ; GO: 0004674 protein serine/threonine kinase activity; PDB: 3H4J_B.
Probab=33.06 E-value=22 Score=24.65 Aligned_cols=26 Identities=27% Similarity=0.512 Sum_probs=17.6
Q ss_pred CCHHHHHHHH-hCCCCHHHHHHHHHHc
Q 027011 113 VDKELLKELE-AMGFPVARATRALHYS 138 (229)
Q Consensus 113 vd~~~l~qL~-eMGF~~~~a~kAL~~T 138 (229)
+++++|..|. .|||+++...-||...
T Consensus 1 ide~vv~~Ls~tMGY~kdeI~eaL~~~ 27 (46)
T PF08587_consen 1 IDEDVVSKLSKTMGYDKDEIYEALESS 27 (46)
T ss_dssp T-HCCHHHHHCTT---HHHHHHHCCSS
T ss_pred CcHHHHHHHHHHhCCCHHHHHHHHHcC
Confidence 3566777776 7999999999999864
No 172
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=32.79 E-value=33 Score=24.53 Aligned_cols=24 Identities=29% Similarity=0.656 Sum_probs=17.7
Q ss_pred ceeeccccccccCCHHHHHHHHHH
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAEL 27 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~ 27 (229)
..-.|..|+.+++.......|.+.
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHH
T ss_pred CCCCCCcchhhccchhhHHHHHHH
Confidence 345799999999999999999988
No 173
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=32.36 E-value=12 Score=38.86 Aligned_cols=43 Identities=23% Similarity=0.478 Sum_probs=23.5
Q ss_pred eeeccccccccCCHH---HHHHH----HHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQ---EAQEH----AELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 5 slkC~~Cg~~L~~~~---~aq~H----a~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
.+.|.+||+++.=.+ -...| .-+.=|-++.+ -++..||.||+.
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~----~~p~~Cp~Cgs~ 484 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQE----PIPQSCPECGSE 484 (730)
T ss_pred eeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCC----CCCCCCCCCCCC
Confidence 467888877732111 01112 22222445554 378999999985
No 174
>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=32.23 E-value=23 Score=23.07 Aligned_cols=17 Identities=35% Similarity=0.770 Sum_probs=12.2
Q ss_pred cCCCCCCCCCCcccccccccccccc
Q 027011 44 VCATCGKPCRSKTETDLHRKRTGHT 68 (229)
Q Consensus 44 ~C~~Cg~~~~~~~E~~~a~K~t~f~ 68 (229)
.||.||.. +-.|++++.
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 556666654
No 175
>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=32.22 E-value=22 Score=23.10 Aligned_cols=11 Identities=18% Similarity=0.821 Sum_probs=9.1
Q ss_pred hhccCCCCCCC
Q 027011 41 LNLVCATCGKP 51 (229)
Q Consensus 41 l~l~C~~Cg~~ 51 (229)
++..||.|++.
T Consensus 4 i~v~CP~C~s~ 14 (36)
T PF03811_consen 4 IDVHCPRCQST 14 (36)
T ss_pred EeeeCCCCCCC
Confidence 56799999984
No 176
>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=31.97 E-value=27 Score=30.21 Aligned_cols=15 Identities=20% Similarity=0.649 Sum_probs=11.7
Q ss_pred ceeeccccccccCCH
Q 027011 4 VSLKCGDCGALLRSV 18 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~ 18 (229)
..++|..|+......
T Consensus 108 ~~~~C~~C~~~~~~~ 122 (224)
T cd01412 108 FRVRCSSCGYVGENN 122 (224)
T ss_pred CccccCCCCCCCCcc
Confidence 568999999987554
No 177
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=31.65 E-value=35 Score=28.77 Aligned_cols=45 Identities=18% Similarity=0.355 Sum_probs=23.9
Q ss_pred eeccccccccCCHHHHHHHHHHh-CCCCC-CchhhhhhhccCCCCCCC
Q 027011 6 LKCGDCGALLRSVQEAQEHAELT-SHSNF-SESTEAVLNLVCATCGKP 51 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~~T-~H~nF-se~~E~vl~l~C~~Cg~~ 51 (229)
.+|..||+.|........-...- .|..+ .+..+. .-..||.|...
T Consensus 115 ~~C~~CG~~f~~~~~i~~~~~~l~~~~~~~~~~~~~-~~~~C~~Cr~~ 161 (180)
T PRK12387 115 CNCRVCGRPFAVQKEIDYAIALLKHNGDSRAENHRE-SFETCPECKRQ 161 (180)
T ss_pred ccchhhCCccccHHHHHHHHHHHhhccchhHHHHHH-HHhhCHHHhcc
Confidence 47899999887655444332221 23222 222222 22579999764
No 178
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=31.61 E-value=4.6 Score=34.24 Aligned_cols=39 Identities=21% Similarity=0.598 Sum_probs=16.8
Q ss_pred ceeeccccccc------cCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 4 VSLKCGDCGAL------LRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 4 ~slkC~~Cg~~------L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
+.+||+.||.+ +...+..+.=+.| |..|| -++|..|++.
T Consensus 29 fkvkCt~CgE~~~k~V~i~~~e~~e~~gsr-G~aNf--------v~KCk~C~re 73 (161)
T PF05907_consen 29 FKVKCTSCGEVHPKWVYINRFEKHEIPGSR-GTANF--------VMKCKFCKRE 73 (161)
T ss_dssp EEEEETTSS--EEEEEEE-TT-BEE-TTSS--EESE--------EE--SSSS--
T ss_pred EEEEECCCCCccCcceEeecceEEecCCCc-cceEe--------EecCcCcCCc
Confidence 68999999987 2222111111122 33444 3699999885
No 179
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=31.30 E-value=60 Score=25.64 Aligned_cols=24 Identities=21% Similarity=0.570 Sum_probs=18.1
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHHHhCC
Q 027011 128 VARATRALHYSGNANVEAAVNWVVEHE 154 (229)
Q Consensus 128 ~~~a~kAL~~Tgn~~~E~A~~WL~~h~ 154 (229)
+.+.+++|. .| +++.|++|+.+|-
T Consensus 5 r~~I~~~I~-~g--~i~~Ai~w~~~~~ 28 (145)
T PF10607_consen 5 RKKIRQAIL-NG--DIDPAIEWLNENF 28 (145)
T ss_pred HHHHHHHHH-cC--CHHHHHHHHHHcC
Confidence 356677884 34 5999999998884
No 180
>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=31.28 E-value=19 Score=26.77 Aligned_cols=26 Identities=27% Similarity=0.402 Sum_probs=19.6
Q ss_pred ccCCCCCCCCCCcccccccccccccccccchhhhcc
Q 027011 43 LVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAA 78 (229)
Q Consensus 43 l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~ 78 (229)
-.|+.||++ ... ..|.-||+--+++.
T Consensus 79 ~~C~vC~k~--------l~~--~~f~~~p~~~v~H~ 104 (109)
T PF10367_consen 79 TKCSVCGKP--------LGN--SVFVVFPCGHVVHY 104 (109)
T ss_pred CCccCcCCc--------CCC--ceEEEeCCCeEEec
Confidence 479999997 222 67999999877764
No 181
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=31.20 E-value=29 Score=25.37 Aligned_cols=10 Identities=60% Similarity=1.441 Sum_probs=8.5
Q ss_pred hccCCCCCCC
Q 027011 42 NLVCATCGKP 51 (229)
Q Consensus 42 ~l~C~~Cg~~ 51 (229)
..+||.||++
T Consensus 6 ~v~CP~C~k~ 15 (62)
T PRK00418 6 TVNCPTCGKP 15 (62)
T ss_pred cccCCCCCCc
Confidence 3689999997
No 182
>PF12773 DZR: Double zinc ribbon
Probab=30.93 E-value=23 Score=23.47 Aligned_cols=12 Identities=25% Similarity=0.769 Sum_probs=8.9
Q ss_pred hhhccCCCCCCC
Q 027011 40 VLNLVCATCGKP 51 (229)
Q Consensus 40 vl~l~C~~Cg~~ 51 (229)
.....|+.||..
T Consensus 27 ~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 27 QSKKICPNCGAE 38 (50)
T ss_pred CCCCCCcCCcCC
Confidence 345789999985
No 183
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=30.87 E-value=1e+02 Score=23.33 Aligned_cols=36 Identities=22% Similarity=0.337 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHhCC
Q 027011 115 KELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVEHE 154 (229)
Q Consensus 115 ~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~h~ 154 (229)
..++..|..+|+|...|.|....-|. .|++=|.+|+
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 46789999999999999999999875 4667787763
No 184
>PF02347 GDC-P: Glycine cleavage system P-protein; InterPro: IPR020580 This family consists of glycine cleavage system P-proteins (1.4.4.2 from EC) from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex (2.1.2.10 from EC (GDC) also annotated as glycine cleavage system or glycine synthase. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. GDC consists of four proteins P, H, L and T []. The reaction catalysed by this protein is: Glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2 ; GO: 0004375 glycine dehydrogenase (decarboxylating) activity, 0055114 oxidation-reduction process; PDB: 1WYV_A 1WYT_C 1WYU_A.
Probab=30.82 E-value=45 Score=32.68 Aligned_cols=40 Identities=18% Similarity=0.148 Sum_probs=24.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhcccCCCccchhhHHHHHH
Q 027011 177 SLTPEEIKLKAQELRYGIFYAVYFFSDGYCNCYMLSYITN 216 (229)
Q Consensus 177 ~LTeEEkkaK~~ELr~ki~~~~~~~~~~~~~~~~~~~~~~ 216 (229)
+++|.|..+.+++|-+|=+-.+.|...|+|+.|.-+.|-.
T Consensus 46 ~~sE~e~~r~~~~la~kN~~~~~fiG~G~y~~~~P~~i~~ 85 (429)
T PF02347_consen 46 PLSEYELLRHLERLASKNKSYTSFIGAGSYTHYVPAVIDR 85 (429)
T ss_dssp ---HHHHHHHHHHHHTTS--TTS---CTTT-----HHHHH
T ss_pred CCCHHHHHHHHHHHHhcCCCCCccccccccCceeChhhcC
Confidence 5999999999999999888899999999999987766654
No 185
>KOG0435 consensus Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=30.58 E-value=34 Score=35.93 Aligned_cols=64 Identities=27% Similarity=0.537 Sum_probs=32.5
Q ss_pred eeccccccccCCHHH-HHH---HHHHhCCC-CCCchhhhhhhccCCCCCCCCCCcccccccccccccccccchhhhcc
Q 027011 6 LKCGDCGALLRSVQE-AQE---HAELTSHS-NFSESTEAVLNLVCATCGKPCRSKTETDLHRKRTGHTDFVDKTSEAA 78 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~-aq~---Ha~~T~H~-nFse~~E~vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~TFPd~Lvv~~ 78 (229)
+.|++||.+=.-..+ +-. ...-|+.- -.| ..++-.+..||.||++. -.-+.-+.||-|--.-..
T Consensus 437 vhc~~cG~vpVpes~LPV~LP~l~~~~~kG~Pls-~~~e~vn~~cP~cg~pA--------kRETDTMDTFvDSsWYYl 505 (876)
T KOG0435|consen 437 VHCDDCGAVPVPESELPVTLPELNDFTPKGPPLS-KADEWVNVDCPRCGEPA--------KRETDTMDTFVDSSWYYL 505 (876)
T ss_pred EEcCCCCcccCcHHHCCcccccccccCCCCCccc-chhhheeccCccCCCcc--------cccccccchhhccceeeE
Confidence 689999988222222 111 11112222 111 12455678999999972 122233556666544444
No 186
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=30.55 E-value=30 Score=31.47 Aligned_cols=34 Identities=24% Similarity=0.466 Sum_probs=21.5
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCC
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGK 50 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~ 50 (229)
++.+|..||+....+.....+ +....=+||.||.
T Consensus 121 ~~~~C~~C~~~~~~~~~~~~~-------------~~~~~p~C~~Cg~ 154 (250)
T COG0846 121 KRVRCSKCGNQYYDEDVIKFI-------------EDGLIPRCPKCGG 154 (250)
T ss_pred eeeEeCCCcCccchhhhhhhc-------------ccCCCCcCccCCC
Confidence 467899999887765511111 1112348999998
No 187
>PRK10204 hypothetical protein; Provisional
Probab=30.18 E-value=54 Score=23.39 Aligned_cols=19 Identities=37% Similarity=0.363 Sum_probs=16.5
Q ss_pred CCCCCHHHHHHHHHHHHHH
Q 027011 175 KSSLTPEEIKLKAQELRYG 193 (229)
Q Consensus 175 ~~~LTeEEkkaK~~ELr~k 193 (229)
...||-||+.+++.|||..
T Consensus 34 ~vtlt~eeA~aRl~~LRr~ 52 (55)
T PRK10204 34 LVTLTAEEALARLEELRRH 52 (55)
T ss_pred cccccHHHHHHHHHHHHHH
Confidence 4579999999999999874
No 188
>PHA02776 E7 protein; Provisional
Probab=30.02 E-value=8.3 Score=30.72 Aligned_cols=41 Identities=32% Similarity=0.508 Sum_probs=24.9
Q ss_pred eccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 7 KCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 7 kC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
.|..|++.+|=.-.+...+-|+-+.-+-++ +.++||.|-++
T Consensus 60 ~C~~C~~~lRL~V~st~~~IR~lqqLLl~~----L~ivCp~Ca~~ 100 (101)
T PHA02776 60 CCCGCDNNVRLVVECTEPDIQELHNLLLGS----LNIVCPICAPK 100 (101)
T ss_pred ECCCCCCeEEEEEEcChhhHHHHHHHhcCC----eEEECCCCCCC
Confidence 477788875544444444444444444443 67899999765
No 189
>KOG0099 consensus G protein subunit Galphas, small G protein superfamily [Signal transduction mechanisms]
Probab=29.93 E-value=48 Score=31.46 Aligned_cols=24 Identities=25% Similarity=0.310 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhh
Q 027011 175 KSSLTPEEIKLKAQELRYGIFYAV 198 (229)
Q Consensus 175 ~~~LTeEEkkaK~~ELr~ki~~~~ 198 (229)
+...+++||++|+.++++.|+++.
T Consensus 65 vnGF~~~EkreKI~dI~~Ni~eai 88 (379)
T KOG0099|consen 65 VNGFNDEEKREKIQDIKNNIKEAI 88 (379)
T ss_pred ecCCChHHHHHhhHHHHHHHHHHH
Confidence 456899999999999999999985
No 190
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=29.51 E-value=48 Score=19.52 Aligned_cols=20 Identities=20% Similarity=0.567 Sum_probs=14.3
Q ss_pred eeccccccccCCHHHHHHHHH
Q 027011 6 LKCGDCGALLRSVQEAQEHAE 26 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~ 26 (229)
++|..||..| +.+..+.|..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 5688888888 6666677754
No 191
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=28.96 E-value=14 Score=35.09 Aligned_cols=45 Identities=27% Similarity=0.547 Sum_probs=30.3
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCCCchhhhh---hhccCCCCCCC
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAV---LNLVCATCGKP 51 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~v---l~l~C~~Cg~~ 51 (229)
..+|+|.-||++|++--.. .-.||..-.|+.+.. .+++||.|..+
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 3579999999999874321 234666555554421 35999999875
No 192
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=28.63 E-value=32 Score=22.06 Aligned_cols=13 Identities=31% Similarity=1.094 Sum_probs=8.6
Q ss_pred cceeecccccccc
Q 027011 3 GVSLKCGDCGALL 15 (229)
Q Consensus 3 ~~slkC~~Cg~~L 15 (229)
+.+++|..||.++
T Consensus 23 g~~v~C~~C~~~f 35 (36)
T PF13717_consen 23 GRKVRCSKCGHVF 35 (36)
T ss_pred CcEEECCCCCCEe
Confidence 3467777777664
No 193
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=28.54 E-value=18 Score=33.67 Aligned_cols=14 Identities=29% Similarity=0.769 Sum_probs=12.0
Q ss_pred CCcceeeccccccc
Q 027011 1 MAGVSLKCGDCGAL 14 (229)
Q Consensus 1 ~~~~slkC~~Cg~~ 14 (229)
|..|+++|+.||.-
T Consensus 36 ~~Pf~i~C~~C~~~ 49 (324)
T PF04502_consen 36 MMPFNIWCNTCGEY 49 (324)
T ss_pred cCCccCcCCCCccc
Confidence 56789999999987
No 194
>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=28.16 E-value=65 Score=32.61 Aligned_cols=47 Identities=21% Similarity=0.427 Sum_probs=30.8
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCch--hhhhh--hccCCCCCCC
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSES--TEAVL--NLVCATCGKP 51 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~--~E~vl--~l~C~~Cg~~ 51 (229)
.-.+|..||..+|=+.-.+.+.+. .-..++.. .+.+. +.+||.||..
T Consensus 83 ~mv~~~~~~~~~RaD~l~e~~~~~-~~~~~~~~~~~~~i~~~~i~~p~~g~~ 133 (551)
T TIGR00389 83 WMVDCKSCKERFRADHLIEEKLGK-RLWGFSGPELNEVMEKYDINCPNCGGE 133 (551)
T ss_pred ceeecCCCCCEecchHHHHHHhhh-hcccCCHHHHHHHHHHcCCCCCCCCCC
Confidence 347899999999988877776553 11233332 23333 3689999974
No 195
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=28.14 E-value=28 Score=30.09 Aligned_cols=38 Identities=26% Similarity=0.628 Sum_probs=20.9
Q ss_pred eccccccccCCHHHHHHHHHHhC--CC-CCCchhhhhhhccCCCCCCC
Q 027011 7 KCGDCGALLRSVQEAQEHAELTS--HS-NFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 7 kC~~Cg~~L~~~~~aq~Ha~~T~--H~-nFse~~E~vl~l~C~~Cg~~ 51 (229)
+|.+||..|.-...-.--+.. . |. +|.+ =+.||.||+.
T Consensus 99 RCp~CN~~L~~vs~eev~~~V-p~~~~~~~~~------f~~C~~Cgki 139 (165)
T COG1656 99 RCPECNGELEKVSREEVKEKV-PEKVYRNYEE------FYRCPKCGKI 139 (165)
T ss_pred cCcccCCEeccCcHHHHhhcc-chhhhhcccc------eeECCCCccc
Confidence 689999887655443311111 1 11 1222 2679999985
No 196
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=28.13 E-value=30 Score=28.48 Aligned_cols=45 Identities=22% Similarity=0.437 Sum_probs=26.5
Q ss_pred eeeccccccc--cCCH--HHHHHHHHHhCCCCCCchh-hhhhhccCCCCCCC
Q 027011 5 SLKCGDCGAL--LRSV--QEAQEHAELTSHSNFSEST-EAVLNLVCATCGKP 51 (229)
Q Consensus 5 slkC~~Cg~~--L~~~--~~aq~Ha~~T~H~nFse~~-E~vl~l~C~~Cg~~ 51 (229)
-+.|.+||++ +.+. ...+...+. +..|.=.. ...+--.|+.|++.
T Consensus 93 HliC~~CG~v~e~~~~~i~~~~~~~~~--~~Gf~i~~~~l~~~G~C~~C~~~ 142 (145)
T COG0735 93 HLICLDCGKVIEFEDDEIEALQEEIAK--KLGFKLKDHTLEIYGICPDCQAK 142 (145)
T ss_pred EEEecCCCCEEEecchhHHHHHHHHHH--hcCCeeeeeEEEEEEECcchHhh
Confidence 4789999999 4443 334444443 44565432 23334569999874
No 197
>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=27.97 E-value=43 Score=29.07 Aligned_cols=14 Identities=21% Similarity=0.432 Sum_probs=10.8
Q ss_pred ceeeccccccccCC
Q 027011 4 VSLKCGDCGALLRS 17 (229)
Q Consensus 4 ~slkC~~Cg~~L~~ 17 (229)
+.++|..|+.....
T Consensus 94 ~~~~C~~C~~~~~~ 107 (206)
T cd01410 94 FIEVCKSCGPEYVR 107 (206)
T ss_pred CcccCCCCCCccch
Confidence 56789999987543
No 198
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=27.88 E-value=18 Score=28.59 Aligned_cols=14 Identities=43% Similarity=0.911 Sum_probs=11.8
Q ss_pred hhhhhccCCCCCCC
Q 027011 38 EAVLNLVCATCGKP 51 (229)
Q Consensus 38 E~vl~l~C~~Cg~~ 51 (229)
-.+|.|+|..||+.
T Consensus 64 Kv~Lr~~Ct~Cgka 77 (94)
T COG1631 64 KVDLRLRCTECGKA 77 (94)
T ss_pred eEEEEEEehhhccc
Confidence 36788999999984
No 199
>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=27.61 E-value=22 Score=25.52 Aligned_cols=9 Identities=56% Similarity=1.486 Sum_probs=4.9
Q ss_pred ccCCCCCCC
Q 027011 43 LVCATCGKP 51 (229)
Q Consensus 43 l~C~~Cg~~ 51 (229)
.+||.||++
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 479999997
No 200
>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=26.24 E-value=31 Score=22.52 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=7.4
Q ss_pred ccCCCCCCC
Q 027011 43 LVCATCGKP 51 (229)
Q Consensus 43 l~C~~Cg~~ 51 (229)
++||.||..
T Consensus 1 m~Cp~Cg~~ 9 (43)
T PF08271_consen 1 MKCPNCGSK 9 (43)
T ss_dssp ESBTTTSSS
T ss_pred CCCcCCcCC
Confidence 589999885
No 201
>PF03249 TSA: Type specific antigen; InterPro: IPR004933 There are several antigenic variants in Rickettsia tsutsugamushi, and a type-specific antigen (TSA) of 56-kilodaltons located on the rickettsial surface is responsible for the variation [, ]. TSA proteins are probably integral membrane proteins. ; GO: 0016021 integral to membrane
Probab=26.07 E-value=1.2e+02 Score=29.98 Aligned_cols=36 Identities=39% Similarity=0.377 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHHHHHHHhhcccCCCccchhhHHHHHHHHHHHH
Q 027011 178 LTPEEIKLKAQELRYGIFYAVYFFSDGYCNCYMLSYITNAFLDTI 222 (229)
Q Consensus 178 LTeEEkkaK~~ELr~ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (229)
-+-|.-+.|.+||-+-|.+-|+-| | .||.|||.+.|
T Consensus 265 ASveqiq~kmqeln~~le~~r~sf-d--------g~i~nafa~qi 300 (503)
T PF03249_consen 265 ASVEQIQNKMQELNDILEELRESF-D--------GYIGNAFANQI 300 (503)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHhh-h--------hhHHHHhhhhh
Confidence 357899999999999999999855 2 47899999877
No 202
>PF10832 DUF2559: Protein of unknown function (DUF2559); InterPro: IPR022541 This family of proteins appear to be restricted to Proteobacteria. The sequences are annotated as YhfG however currently no function is known.
Probab=26.05 E-value=65 Score=23.03 Aligned_cols=20 Identities=30% Similarity=0.302 Sum_probs=17.0
Q ss_pred CCCCCHHHHHHHHHHHHHHH
Q 027011 175 KSSLTPEEIKLKAQELRYGI 194 (229)
Q Consensus 175 ~~~LTeEEkkaK~~ELr~ki 194 (229)
...||.|++.+++.|||..-
T Consensus 33 ~vtL~~e~a~~RL~eLRrhY 52 (54)
T PF10832_consen 33 LVTLTAEQALARLEELRRHY 52 (54)
T ss_pred ceeccHHHHHHHHHHHHHHh
Confidence 44799999999999999753
No 203
>PF06348 DUF1059: Protein of unknown function (DUF1059); InterPro: IPR009409 This entry consists of short hypothetical archaeal and bacterial proteins of unknown function.
Probab=25.81 E-value=44 Score=23.54 Aligned_cols=26 Identities=42% Similarity=0.787 Sum_probs=20.4
Q ss_pred eeeccc----cccccCCHHH------HHHHHHHhCCC
Q 027011 5 SLKCGD----CGALLRSVQE------AQEHAELTSHS 31 (229)
Q Consensus 5 slkC~~----Cg~~L~~~~~------aq~Ha~~T~H~ 31 (229)
+|.|.+ |+..+++..+ ++.||.. -|.
T Consensus 3 ~f~C~d~g~~C~~~~~a~tedEll~~~~~Ha~~-~Hg 38 (57)
T PF06348_consen 3 SFDCRDVGPDCGFVIRAETEDELLEAVVEHARE-VHG 38 (57)
T ss_pred EEEccccCCCCCeEEeeCCHHHHHHHHHHHHHH-hcC
Confidence 789986 9999988543 7899998 553
No 204
>PF15178 TOM_sub5: Mitochondrial import receptor subunit TOM5 homolog
Probab=25.76 E-value=62 Score=22.72 Aligned_cols=15 Identities=40% Similarity=0.625 Sum_probs=11.8
Q ss_pred CCCCCHHHHHHHHHH
Q 027011 175 KSSLTPEEIKLKAQE 189 (229)
Q Consensus 175 ~~~LTeEEkkaK~~E 189 (229)
.++++|||.++|+++
T Consensus 8 ~pk~DPeE~k~kmR~ 22 (51)
T PF15178_consen 8 GPKMDPEEMKRKMRE 22 (51)
T ss_pred CCCCCHHHHHHHHHH
Confidence 357999998888764
No 205
>PRK07634 pyrroline-5-carboxylate reductase; Reviewed
Probab=25.45 E-value=84 Score=26.87 Aligned_cols=34 Identities=9% Similarity=0.188 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHh
Q 027011 115 KELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVE 152 (229)
Q Consensus 115 ~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~ 152 (229)
+.+.+.++.+||+++.|++.+..+ +..+.+-+.+
T Consensus 186 ~a~~~~~~~~Gl~~~~a~~~~~~~----~~g~~~~~~~ 219 (245)
T PRK07634 186 ESLIEATKSYGVDEETAKHLVIQM----ISGSASMLEQ 219 (245)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH----HHHHHHHHhC
Confidence 345677899999999999999865 6667776654
No 206
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=25.44 E-value=80 Score=17.63 Aligned_cols=21 Identities=19% Similarity=0.374 Sum_probs=14.3
Q ss_pred eeccccccccCCHHHHHHHHHH
Q 027011 6 LKCGDCGALLRSVQEAQEHAEL 27 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~~ 27 (229)
++|..|.-.-+ ......|..+
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 58888987776 7777788665
No 207
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=25.35 E-value=30 Score=22.65 Aligned_cols=11 Identities=36% Similarity=0.915 Sum_probs=6.2
Q ss_pred ceeeccccccc
Q 027011 4 VSLKCGDCGAL 14 (229)
Q Consensus 4 ~slkC~~Cg~~ 14 (229)
.-|+|+.||.+
T Consensus 5 ~~YkC~~CGni 15 (36)
T PF06397_consen 5 EFYKCEHCGNI 15 (36)
T ss_dssp EEEE-TTT--E
T ss_pred cEEEccCCCCE
Confidence 45899999987
No 208
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=25.32 E-value=1e+02 Score=25.09 Aligned_cols=42 Identities=21% Similarity=0.206 Sum_probs=34.5
Q ss_pred CCCCCHHHHHHHH-hCCCCHHHHHHHHHHcCCCCHHHHHHHHHh
Q 027011 110 EPEVDKELLKELE-AMGFPVARATRALHYSGNANVEAAVNWVVE 152 (229)
Q Consensus 110 ~~~vd~~~l~qL~-eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~ 152 (229)
...|..+.|+.+| +|-.+++.|++.|+.+.+ ++-+|+.-|.+
T Consensus 76 kV~IkkeDlelImnELei~k~~aer~LrE~~G-dvv~Alral~s 118 (119)
T KOG3450|consen 76 KVTIKKEDLELIMNELEISKAAAERSLREHMG-DVVEALRALTS 118 (119)
T ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHHHHhcc-cHHHHHHHHhc
Confidence 4567888888766 888999999999999877 88888876654
No 209
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=25.05 E-value=35 Score=28.86 Aligned_cols=9 Identities=44% Similarity=1.357 Sum_probs=7.9
Q ss_pred ccCCCCCCC
Q 027011 43 LVCATCGKP 51 (229)
Q Consensus 43 l~C~~Cg~~ 51 (229)
++||.||.+
T Consensus 1 m~cp~c~~~ 9 (154)
T PRK00464 1 MRCPFCGHP 9 (154)
T ss_pred CcCCCCCCC
Confidence 589999987
No 210
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=24.29 E-value=1.3e+02 Score=31.17 Aligned_cols=27 Identities=22% Similarity=0.175 Sum_probs=23.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHhhc
Q 027011 173 ASKSSLTPEEIKLKAQELRYGIFYAVY 199 (229)
Q Consensus 173 ~~~~~LTeEEkkaK~~ELr~ki~~~~~ 199 (229)
++...+|++++++++++|+++|++|.+
T Consensus 22 ~~~~~~~~~~~~~~i~~L~~~i~~~~~ 48 (689)
T PRK14351 22 EPVEELSEDEAEEQAEQLREAIREHDH 48 (689)
T ss_pred cccccCCHHHHHHHHHHHHHHHHHHHH
Confidence 345689999999999999999999974
No 211
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=24.03 E-value=1.4e+02 Score=26.74 Aligned_cols=35 Identities=20% Similarity=0.280 Sum_probs=26.3
Q ss_pred CCHHHHHHHH-hCCCCHHHHHHHHHHcCCCCHHHHHH
Q 027011 113 VDKELLKELE-AMGFPVARATRALHYSGNANVEAAVN 148 (229)
Q Consensus 113 vd~~~l~qL~-eMGF~~~~a~kAL~~Tgn~~~E~A~~ 148 (229)
++...++.++ ..|-+++.|.|||+.+.| ++-.||-
T Consensus 170 ve~kDIeLVmsQanvSR~kAVkALk~~~~-DiVnAIM 205 (209)
T KOG2239|consen 170 VEAKDIELVMSQANVSRAKAVKALKNNNN-DIVNAIM 205 (209)
T ss_pred CchhhHHHHHHHhhhhHHHHHHHHHhccc-hHHHHHH
Confidence 4555666654 578999999999999866 7766664
No 212
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=24.01 E-value=25 Score=22.55 Aligned_cols=10 Identities=40% Similarity=1.305 Sum_probs=7.4
Q ss_pred hccCCCCCCC
Q 027011 42 NLVCATCGKP 51 (229)
Q Consensus 42 ~l~C~~Cg~~ 51 (229)
.++||.|+.+
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 4789999986
No 213
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=23.98 E-value=76 Score=28.82 Aligned_cols=15 Identities=27% Similarity=0.468 Sum_probs=11.6
Q ss_pred cceeeccccccccCC
Q 027011 3 GVSLKCGDCGALLRS 17 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~ 17 (229)
-..++|..|++...-
T Consensus 126 ~~~~~C~~C~~~~~~ 140 (285)
T PRK05333 126 LDGVRCMGCGARHPR 140 (285)
T ss_pred cCEEEECCCCCcCCH
Confidence 357899999988653
No 214
>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=23.98 E-value=23 Score=34.98 Aligned_cols=46 Identities=20% Similarity=0.291 Sum_probs=28.3
Q ss_pred eeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
+.|+.||..=--.=+.+.+..+||.+.=+..-.....|.|-.||++
T Consensus 147 i~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 147 IGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred EeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 6788888874333333444445666554443222346999999997
No 215
>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=23.89 E-value=55 Score=24.75 Aligned_cols=27 Identities=30% Similarity=0.572 Sum_probs=18.8
Q ss_pred hhhhhccCCCCCCCCCCcccccccccccccc
Q 027011 38 EAVLNLVCATCGKPCRSKTETDLHRKRTGHT 68 (229)
Q Consensus 38 E~vl~l~C~~Cg~~~~~~~E~~~a~K~t~f~ 68 (229)
+.+.+++|..|++. ...+.++|+.+-.
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 56788999999964 2345677776644
No 216
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.72 E-value=1.1e+02 Score=28.22 Aligned_cols=39 Identities=28% Similarity=0.307 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHhhcccCCCccc--hhhHHHHHHHHHHH
Q 027011 183 IKLKAQELRYGIFYAVYFFSDGYCN--CYMLSYITNAFLDT 221 (229)
Q Consensus 183 kkaK~~ELr~ki~~~~~~~~~~~~~--~~~~~~~~~~~~~~ 221 (229)
=..|+++|.++--.-|+-|+||-|- -|+.||+--..+|+
T Consensus 52 y~~KIq~Lsk~Y~~iR~trgDGNCfyra~~~s~lE~ll~d~ 92 (256)
T KOG3991|consen 52 YTTKIQELSKKYTVIRKTRGDGNCFYRAFAYSYLELLLLDR 92 (256)
T ss_pred HHHHHHHHHHHhhhhheecCCCceehHHHHHHHHHHHHhch
Confidence 4689999999999999999999773 46777776555543
No 217
>COG3404 Methenyl tetrahydrofolate cyclohydrolase [Amino acid transport and metabolism]
Probab=23.57 E-value=88 Score=28.00 Aligned_cols=36 Identities=17% Similarity=-0.081 Sum_probs=27.6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhhcccCCCccchhh
Q 027011 175 KSSLTPEEIKLKAQELRYGIFYAVYFFSDGYCNCYM 210 (229)
Q Consensus 175 ~~~LTeEEkkaK~~ELr~ki~~~~~~~~~~~~~~~~ 210 (229)
.|+-|+|||+++.+.||.-++.++.---|---+|+-
T Consensus 93 lPK~teEEK~~R~~~lQ~Alk~Aa~vP~~ia~~~~~ 128 (208)
T COG3404 93 LPKSTEEEKAARRKALQNALKEAAKVPLDIATLMVD 128 (208)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHhChHHHHHHHHH
Confidence 456799999999999999999998765454444443
No 218
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=23.32 E-value=89 Score=23.20 Aligned_cols=20 Identities=15% Similarity=0.243 Sum_probs=17.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHh
Q 027011 177 SLTPEEIKLKAQELRYGIFYA 197 (229)
Q Consensus 177 ~LTeEEkkaK~~ELr~ki~~~ 197 (229)
||+|+|++ .++||.+.|+..
T Consensus 2 ~LSe~E~r-~L~eiEr~L~~~ 21 (82)
T PF11239_consen 2 PLSEHEQR-RLEEIERQLRAD 21 (82)
T ss_pred CCCHHHHH-HHHHHHHHHHhc
Confidence 79999988 899999999763
No 219
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=23.15 E-value=30 Score=26.47 Aligned_cols=23 Identities=35% Similarity=0.889 Sum_probs=16.9
Q ss_pred ccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 8 CGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 8 C~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
|.+||.+|.-. + ..+.|+.||..
T Consensus 3 C~~Cg~~l~~~----------~-----------~~~~C~~C~~~ 25 (104)
T TIGR01384 3 CPKCGSLMTPK----------N-----------GVYVCPSCGYE 25 (104)
T ss_pred CcccCcccccC----------C-----------CeEECcCCCCc
Confidence 89999999421 0 14899999975
No 220
>TIGR01926 peroxid_rel uncharacterized peroxidase-related enzyme. This protein family with length of about 200 amino acids. One member, from Myxococcus xanthus, is a selenoprotein, with an otherwise conserved Cys replaced by Sec. This family is drawn narrowly enough to suggest that These proteins contain a domain described by TIGR00778, with a CxxCxxxHxxxxxxxG motif. Some members of that family are known to act as peroxidases or correlate with resistance to oxidative stress.
Probab=22.97 E-value=1.4e+02 Score=24.32 Aligned_cols=29 Identities=21% Similarity=0.282 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHHhCCCCHHHHHHHHHHcC
Q 027011 111 PEVDKELLKELEAMGFPVARATRALHYSG 139 (229)
Q Consensus 111 ~~vd~~~l~qL~eMGF~~~~a~kAL~~Tg 139 (229)
..++++.++.|.+.||+.....-.+...|
T Consensus 130 ~~v~~~~~~~l~~~g~s~~eivel~~~i~ 158 (177)
T TIGR01926 130 AKVNEADFAALRAAGFSDLDILDLIHSVA 158 (177)
T ss_pred ccCCHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 36889999999999999999887766654
No 221
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=22.88 E-value=45 Score=21.84 Aligned_cols=9 Identities=33% Similarity=0.870 Sum_probs=7.3
Q ss_pred ccCCCCCCC
Q 027011 43 LVCATCGKP 51 (229)
Q Consensus 43 l~C~~Cg~~ 51 (229)
-.||.||.+
T Consensus 4 ~pCP~CGG~ 12 (37)
T smart00778 4 GPCPNCGGS 12 (37)
T ss_pred cCCCCCCCc
Confidence 369999886
No 222
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.79 E-value=41 Score=28.02 Aligned_cols=14 Identities=36% Similarity=0.916 Sum_probs=11.9
Q ss_pred hhhhhccCCCCCCC
Q 027011 38 EAVLNLVCATCGKP 51 (229)
Q Consensus 38 E~vl~l~C~~Cg~~ 51 (229)
..++...||.||.|
T Consensus 24 AkML~~hCp~Cg~P 37 (131)
T COG1645 24 AKMLAKHCPKCGTP 37 (131)
T ss_pred hHHHHhhCcccCCc
Confidence 35788999999997
No 223
>PRK05367 glycine dehydrogenase; Provisional
Probab=22.76 E-value=2.1e+02 Score=30.89 Aligned_cols=50 Identities=14% Similarity=0.217 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhcccCCCccchhhHHHHHHHHHHHHHHHh
Q 027011 177 SLTPEEIKLKAQELRYGIFYAVYFFSDGYCNCYMLSYITNAFLDTIFWFL 226 (229)
Q Consensus 177 ~LTeEEkkaK~~ELr~ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 (229)
+++|-|..+.+++|-+|=+..+.|.--||+++|.-+-|....+..--|+-
T Consensus 57 ~~sE~e~~~~~~~la~~N~~~~~~ig~G~y~~~~P~vi~~~i~~~~~~~t 106 (954)
T PRK05367 57 ALSEAEALAELRAIASKNKVFRSYIGQGYYGTHTPPVILRNILENPAWYT 106 (954)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCcccCCCCCCCcCcHHHHHHHHhCcchhh
Confidence 68999999999999888887889999999999888877555555445554
No 224
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=22.61 E-value=48 Score=26.87 Aligned_cols=12 Identities=42% Similarity=0.991 Sum_probs=9.2
Q ss_pred hhhccCCCCCCC
Q 027011 40 VLNLVCATCGKP 51 (229)
Q Consensus 40 vl~l~C~~Cg~~ 51 (229)
|-.|+|++|+..
T Consensus 10 vt~l~C~~C~t~ 21 (113)
T PF09862_consen 10 VTRLKCPSCGTE 21 (113)
T ss_pred EEEEEcCCCCCE
Confidence 456889999874
No 225
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=22.59 E-value=39 Score=22.68 Aligned_cols=8 Identities=38% Similarity=1.128 Sum_probs=7.1
Q ss_pred cCCCCCCC
Q 027011 44 VCATCGKP 51 (229)
Q Consensus 44 ~C~~Cg~~ 51 (229)
+||.||.+
T Consensus 1 ~CP~Cg~~ 8 (47)
T PF04606_consen 1 RCPHCGSK 8 (47)
T ss_pred CcCCCCCe
Confidence 59999996
No 226
>PF04558 tRNA_synt_1c_R1: Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 ; InterPro: IPR007639 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This is a domain found N-terminal to the catalytic domain of glutaminyl-tRNA synthetase (6.1.1.18 from EC) in eukaryotes but not in Escherichia coli. This domain is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3TL4_X.
Probab=22.51 E-value=43 Score=28.53 Aligned_cols=49 Identities=14% Similarity=0.104 Sum_probs=26.7
Q ss_pred CHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q 027011 142 NVEAAVNWVVEHENDPDIDEMPMVPVSGGGGASKSSLTPEEIKLKAQELRYGIF 195 (229)
Q Consensus 142 ~~E~A~~WL~~h~dD~did~pl~~p~~s~s~~~~~~LTeEEkkaK~~ELr~ki~ 195 (229)
-+++|+.||.+|..++-....+.-.-+. .-.+||||.++.+.+.-+.-+
T Consensus 86 Ql~AA~~Yl~~~~~~~~d~~~Fe~~cGV-----GV~VT~E~I~~~V~~~i~~~k 134 (164)
T PF04558_consen 86 QLDAALKYLKSNPSEPIDVAEFEKACGV-----GVVVTPEQIEAAVEKYIEENK 134 (164)
T ss_dssp HHHHHHHHHHHHGG-G--HHHHHHTTTT-----T----HHHHHHHHHHHHHHTH
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHcCC-----CeEECHHHHHHHHHHHHHHhH
Confidence 4789999999997732111112111111 236899999998887765443
No 227
>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=22.50 E-value=36 Score=27.19 Aligned_cols=10 Identities=30% Similarity=0.913 Sum_probs=8.2
Q ss_pred ccCCCCCCCC
Q 027011 43 LVCATCGKPC 52 (229)
Q Consensus 43 l~C~~Cg~~~ 52 (229)
.+||+||++|
T Consensus 10 R~Cp~CG~kF 19 (108)
T PF09538_consen 10 RTCPSCGAKF 19 (108)
T ss_pred ccCCCCcchh
Confidence 4899999876
No 228
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=22.32 E-value=55 Score=31.73 Aligned_cols=32 Identities=22% Similarity=0.449 Sum_probs=28.0
Q ss_pred ceeeccccccccCCHHHHHHHHHHhCCCCCCc
Q 027011 4 VSLKCGDCGALLRSVQEAQEHAELTSHSNFSE 35 (229)
Q Consensus 4 ~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse 35 (229)
.+++|--|.|.+++-+-...|..+-+|.--..
T Consensus 194 ~r~~CLyCekifrdkntLkeHMrkK~HrrinP 225 (423)
T KOG2482|consen 194 ERLRCLYCEKIFRDKNTLKEHMRKKRHRRINP 225 (423)
T ss_pred hhheeeeeccccCCcHHHHHHHHhccCcccCC
Confidence 37899999999999999999999989975443
No 229
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=21.92 E-value=45 Score=28.45 Aligned_cols=47 Identities=21% Similarity=0.411 Sum_probs=22.9
Q ss_pred eeeccccccccCCHHH------HHHHHHHhCCCCCCchhh---hhhhccCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQE------AQEHAELTSHSNFSESTE---AVLNLVCATCGKP 51 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~------aq~Ha~~T~H~nFse~~E---~vl~l~C~~Cg~~ 51 (229)
-.+|..|+|-|=+... --.|..++.|...+=-.+ ....|.|-.||.+
T Consensus 14 vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~~ 69 (152)
T PF09416_consen 14 VVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGSR 69 (152)
T ss_dssp EEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT---
T ss_pred EeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCCC
Confidence 4689999988644443 468999999986532211 1124789999985
No 230
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=21.90 E-value=1.2e+02 Score=23.71 Aligned_cols=22 Identities=32% Similarity=0.351 Sum_probs=19.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHhh
Q 027011 177 SLTPEEIKLKAQELRYGIFYAV 198 (229)
Q Consensus 177 ~LTeEEkkaK~~ELr~ki~~~~ 198 (229)
.||++++++=.+|||+..+..-
T Consensus 2 SLn~~Q~~~T~~ELq~nf~~~~ 23 (89)
T PF10078_consen 2 SLNPEQRRATRQELQANFELSG 23 (89)
T ss_pred CCCHHHHHHHHHHHHHHHHHcC
Confidence 5899999999999999887653
No 231
>PF12907 zf-met2: Zinc-binding
Probab=21.67 E-value=57 Score=21.83 Aligned_cols=27 Identities=26% Similarity=0.441 Sum_probs=21.8
Q ss_pred eeeccccc---cccCCHHHHHHHHHHhCCCC
Q 027011 5 SLKCGDCG---ALLRSVQEAQEHAELTSHSN 32 (229)
Q Consensus 5 slkC~~Cg---~~L~~~~~aq~Ha~~T~H~n 32 (229)
+++|..|- -...+....+.|++. -|..
T Consensus 1 ~i~C~iC~qtF~~t~~~~~L~eH~en-KHpK 30 (40)
T PF12907_consen 1 NIICKICRQTFMQTTNEPQLKEHAEN-KHPK 30 (40)
T ss_pred CcCcHHhhHHHHhcCCHHHHHHHHHc-cCCC
Confidence 47899999 457777889999998 7875
No 232
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=21.56 E-value=1.9e+02 Score=26.93 Aligned_cols=38 Identities=29% Similarity=0.306 Sum_probs=31.9
Q ss_pred CHHHHHHHHhCCCCHHHHHHHHHHcCCCCHHHHHHHHHh
Q 027011 114 DKELLKELEAMGFPVARATRALHYSGNANVEAAVNWVVE 152 (229)
Q Consensus 114 d~~~l~qL~eMGF~~~~a~kAL~~Tgn~~~E~A~~WL~~ 152 (229)
.++.++-|.+-|.+...+..++..+|| ++-.|++|+.+
T Consensus 174 ~~~~~~~L~~~~~~~~~a~~~~~l~~G-~p~~A~~~~~~ 211 (319)
T PRK08769 174 AHEALAWLLAQGVSERAAQEALDAARG-HPGLAAQWLRE 211 (319)
T ss_pred HHHHHHHHHHcCCChHHHHHHHHHcCC-CHHHHHHHhcC
Confidence 456778888889999999999999887 78899998743
No 233
>PF08838 DUF1811: Protein of unknown function (DUF1811); InterPro: IPR014938 This entry consists uncharacterised bacterial proteins. Some of the proteins are annotated as being transcriptional regulators (see Q4MQL7 from SWISSPROT, Q65MA2 from SWISSPROT). The structure of one of the proteins has revealed a beta-barrel like structure with helix-turn-helix like motif. ; PDB: 2YXY_A 1SF9_A.
Probab=21.48 E-value=87 Score=25.12 Aligned_cols=23 Identities=17% Similarity=0.166 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhc
Q 027011 177 SLTPEEIKLKAQELRYGIFYAVY 199 (229)
Q Consensus 177 ~LTeEEkkaK~~ELr~ki~~~~~ 199 (229)
.+|++|-+...+.|++|.|+|..
T Consensus 6 eMs~~EL~~Ei~~L~ekarKAEq 28 (102)
T PF08838_consen 6 EMSEEELRQEIARLKEKARKAEQ 28 (102)
T ss_dssp C--HHHHHHHHHHHHHHHHHHHH
T ss_pred hcCHHHHHHHHHHHHHHHHHHHH
Confidence 58999999999999999999875
No 234
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=21.38 E-value=1.5e+02 Score=21.92 Aligned_cols=21 Identities=19% Similarity=0.417 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCCHHHHHHHHH
Q 027011 116 ELLKELEAMGFPVARATRALH 136 (229)
Q Consensus 116 ~~l~qL~eMGF~~~~a~kAL~ 136 (229)
.+++.+..|||+..+++..|.
T Consensus 13 aA~dam~~lG~~~~~v~~vl~ 33 (65)
T PF10440_consen 13 AALDAMRQLGFSKKQVRPVLK 33 (65)
T ss_pred HHHHHHHHcCCCHHHHHHHHH
Confidence 468889999999999875443
No 235
>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=21.30 E-value=45 Score=30.82 Aligned_cols=31 Identities=32% Similarity=0.590 Sum_probs=19.7
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPCR 53 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~~ 53 (229)
=.||..|+.++-..+ .++ - -++||.||...|
T Consensus 26 ~~~c~~c~~~~~~~~-----l~~------------~-~~vc~~c~~h~r 56 (285)
T TIGR00515 26 WTKCPKCGQVLYTKE-----LER------------N-LEVCPKCDHHMR 56 (285)
T ss_pred eeECCCCcchhhHHH-----HHh------------h-CCCCCCCCCcCc
Confidence 468999998764322 111 1 169999998754
No 236
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=21.20 E-value=1.1e+02 Score=19.64 Aligned_cols=25 Identities=20% Similarity=0.477 Sum_probs=16.1
Q ss_pred cceeeccccccccCC----HHHHHHHHHH
Q 027011 3 GVSLKCGDCGALLRS----VQEAQEHAEL 27 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~----~~~aq~Ha~~ 27 (229)
....+|..|+++++. ......|..+
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 356789999999776 4667778754
No 237
>PRK06260 threonine synthase; Validated
Probab=21.19 E-value=55 Score=30.94 Aligned_cols=26 Identities=31% Similarity=0.644 Sum_probs=18.2
Q ss_pred eeeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCC
Q 027011 5 SLKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKP 51 (229)
Q Consensus 5 slkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~ 51 (229)
.|+|..||+.+... ...++||.||.+
T Consensus 3 ~~~C~~cg~~~~~~---------------------~~~~~Cp~cg~~ 28 (397)
T PRK06260 3 WLKCIECGKEYDPD---------------------EIIYTCPECGGL 28 (397)
T ss_pred EEEECCCCCCCCCC---------------------CccccCCCCCCe
Confidence 58999999765321 124789999865
No 238
>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=21.14 E-value=1.5e+02 Score=24.87 Aligned_cols=41 Identities=27% Similarity=0.591 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHhCCCCH-HHHHHHHHHcCCC----CHHHHHHHHHh
Q 027011 112 EVDKELLKELEAMGFPV-ARATRALHYSGNA----NVEAAVNWVVE 152 (229)
Q Consensus 112 ~vd~~~l~qL~eMGF~~-~~a~kAL~~Tgn~----~~E~A~~WL~~ 152 (229)
.+.++++..|..+|||- ...+.+|.+-|.. .+=+|+.||.+
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 35677889999999999 9999999998874 36679999964
No 239
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=21.09 E-value=53 Score=29.36 Aligned_cols=13 Identities=15% Similarity=0.649 Sum_probs=10.4
Q ss_pred ceeeccccccccC
Q 027011 4 VSLKCGDCGALLR 16 (229)
Q Consensus 4 ~slkC~~Cg~~L~ 16 (229)
+.++|..|++.+.
T Consensus 116 ~~~~C~~C~~~~~ 128 (242)
T PTZ00408 116 LKVRCTATGHVFD 128 (242)
T ss_pred ceEEECCCCcccC
Confidence 5689999998764
No 240
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=20.98 E-value=70 Score=28.54 Aligned_cols=30 Identities=20% Similarity=0.360 Sum_probs=23.3
Q ss_pred cceeeccccccccCCHHHHHHHHHHhCCCCC
Q 027011 3 GVSLKCGDCGALLRSVQEAQEHAELTSHSNF 33 (229)
Q Consensus 3 ~~slkC~~Cg~~L~~~~~aq~Ha~~T~H~nF 33 (229)
..+++|..|+|+|++..=...|... -|...
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~n-KH~e~ 104 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFN-KHPEK 104 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHH-H-HHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhh-cCHHH
Confidence 4578999999999999999999988 78643
No 241
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=20.81 E-value=52 Score=24.61 Aligned_cols=19 Identities=16% Similarity=0.462 Sum_probs=13.0
Q ss_pred ccCCCCCCCCCCccccccccccccccc
Q 027011 43 LVCATCGKPCRSKTETDLHRKRTGHTD 69 (229)
Q Consensus 43 l~C~~Cg~~~~~~~E~~~a~K~t~f~T 69 (229)
+.||.||.+ ..+.+++..+
T Consensus 2 m~CP~Cg~~--------a~irtSr~~s 20 (72)
T PRK09678 2 FHCPLCQHA--------AHARTSRYIT 20 (72)
T ss_pred ccCCCCCCc--------cEEEEChhcC
Confidence 589999996 3555555443
No 242
>PF14282 FlxA: FlxA-like protein
Probab=20.69 E-value=1.2e+02 Score=23.86 Aligned_cols=21 Identities=29% Similarity=0.203 Sum_probs=18.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHH
Q 027011 176 SSLTPEEIKLKAQELRYGIFY 196 (229)
Q Consensus 176 ~~LTeEEkkaK~~ELr~ki~~ 196 (229)
..|++|+|+.|.+.|+..|..
T Consensus 42 ~~~~~e~k~~q~q~Lq~QI~~ 62 (106)
T PF14282_consen 42 SDLDAEQKQQQIQLLQAQIQQ 62 (106)
T ss_pred cCCCHHHHHHHHHHHHHHHHH
Confidence 478999999999999988864
No 243
>PF07688 KaiA: KaiA domain; InterPro: IPR011648 KaiA is a component of the kaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. The kaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction. In the complex, KaiA enhances the phosphorylation status of kaiC. In contrast, the presence of kaiB in the complex decreases the phosphorylation status of kaiC, suggesting that kaiB acts by antagonising the interaction between kaiA and kaiC. The activity of KaiA activates kaiBC expression, while KaiC represses it. The overall fold of the KaiA monomer is that of a four-helix bundle, which forms a dimer in the known structure []. KaiA functions as a homodimer. Each monomer is composed of three functional domains: the N-terminal amplitude-amplifier domain, the central period-adjuster domain and the C-termianl clock-oscillator domain. The N-terminal domain of KaiA, from cyanobacteria, acts as a psuedo-receiver domain, but lacks the conserved aspartyl residue required for phosphotransfer in response regulators []. The C-terminal domain is responsible for dimer formation, binding to KaiC, enhancing KaiC phosphorylation and generating the circadian oscillations []. The KaiA protein from Anabaena sp. (strain PCC 7120) lacks the N-terminal CheY-like domain.; GO: 0006468 protein phosphorylation, 0007623 circadian rhythm; PDB: 1V2Z_A 1Q6B_B 1Q6A_A 1SV1_B 1SUY_B 1R5Q_A 1M2E_A 1R8J_B 1M2F_A.
Probab=20.60 E-value=1.8e+02 Score=27.20 Aligned_cols=46 Identities=26% Similarity=0.302 Sum_probs=38.1
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHh--hcccCCCccchhhHHHHHHHHHH
Q 027011 175 KSSLTPEEIKLKAQELRYGIFYA--VYFFSDGYCNCYMLSYITNAFLD 220 (229)
Q Consensus 175 ~~~LTeEEkkaK~~ELr~ki~~~--~~~~~~~~~~~~~~~~~~~~~~~ 220 (229)
-..|+++|+++=++.|+..-|.- -||..|.--|--.=+|+..||.-
T Consensus 179 ~~~l~~~e~~~ll~~l~~~Yr~i~l~YF~~~~~~n~~id~fvn~~Ffa 226 (283)
T PF07688_consen 179 LRNLPPEERQELLRQLKSDYRDILLNYFSDDKALNQAIDSFVNTAFFA 226 (283)
T ss_dssp CCCCTCHHHHHHHHHHHHHHHHHHHHTTSTTS-HHHHHHHHHHHHHHT
T ss_pred HHhCCHHHHHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHhc
Confidence 45799999999999999888875 49999999998888888888753
No 244
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=20.41 E-value=58 Score=30.21 Aligned_cols=36 Identities=25% Similarity=0.630 Sum_probs=26.8
Q ss_pred eeccccccccCCHHHHHHHHHHhCCCCCCchhhhhhhccCCCCCCCC
Q 027011 6 LKCGDCGALLRSVQEAQEHAELTSHSNFSESTEAVLNLVCATCGKPC 52 (229)
Q Consensus 6 lkC~~Cg~~L~~~~~aq~Ha~~T~H~nFse~~E~vl~l~C~~Cg~~~ 52 (229)
|.|++||-.+.-..-.+ |..+.-.. .|+|--||+.+
T Consensus 4 FtCnvCgEsvKKp~vek-H~srCrn~----------~fSCIDC~k~F 39 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEK-HMSRCRNA----------YFSCIDCGKTF 39 (276)
T ss_pred EehhhhhhhccccchHH-HHHhccCC----------eeEEeeccccc
Confidence 68999999988776655 98883332 36788898865
Done!