Query 025608
Match_columns 250
No_of_seqs 152 out of 1361
Neff 9.3
Searched_HMMs 46136
Date Fri Mar 29 07:35:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025608.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025608hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1812 Predicted E3 ubiquitin 100.0 1.1E-36 2.4E-41 264.0 11.6 199 40-242 145-347 (384)
2 KOG1814 Predicted E3 ubiquitin 100.0 7.6E-36 1.6E-40 249.9 9.8 208 36-245 179-416 (445)
3 KOG1815 Predicted E3 ubiquitin 100.0 1.7E-29 3.6E-34 224.8 9.6 203 39-250 68-277 (444)
4 KOG0006 E3 ubiquitin-protein l 99.9 1.3E-25 2.9E-30 182.5 8.3 204 35-245 215-444 (446)
5 smart00647 IBR In Between Ring 99.2 1.2E-11 2.6E-16 80.7 3.8 63 112-174 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.2 3.1E-12 6.7E-17 83.5 0.9 63 112-174 1-64 (64)
7 smart00647 IBR In Between Ring 98.5 1.5E-07 3.3E-12 61.1 4.6 41 198-238 15-60 (64)
8 PF13639 zf-RING_2: Ring finge 98.5 6.5E-08 1.4E-12 57.9 2.1 41 43-90 2-42 (44)
9 PF15227 zf-C3HC4_4: zinc fing 98.5 7.2E-08 1.6E-12 56.9 1.7 41 44-90 1-41 (42)
10 PF01485 IBR: IBR domain; Int 98.5 6.2E-08 1.3E-12 62.9 1.4 41 198-238 15-60 (64)
11 PF14634 zf-RING_5: zinc-RING 98.5 1.7E-07 3.7E-12 56.1 3.2 41 43-90 1-41 (44)
12 PF00097 zf-C3HC4: Zinc finger 98.5 1.5E-07 3.3E-12 55.4 2.9 40 44-90 1-40 (41)
13 PLN03208 E3 ubiquitin-protein 98.4 3.6E-07 7.9E-12 71.4 4.1 69 36-109 13-90 (193)
14 PF13445 zf-RING_UBOX: RING-ty 98.4 3.5E-07 7.6E-12 54.0 2.9 42 44-89 1-43 (43)
15 PF13923 zf-C3HC4_2: Zinc fing 98.3 4.7E-07 1E-11 52.7 2.7 38 44-90 1-38 (39)
16 KOG0320 Predicted E3 ubiquitin 98.2 1E-06 2.2E-11 67.2 3.8 57 37-103 127-183 (187)
17 cd00162 RING RING-finger (Real 98.2 2.8E-06 6.1E-11 50.5 3.7 44 43-96 1-44 (45)
18 PF13920 zf-C3HC4_3: Zinc fing 98.0 6.8E-06 1.5E-10 50.5 3.0 45 42-98 3-48 (50)
19 PHA02926 zinc finger-like prot 97.9 1.6E-05 3.4E-10 63.1 3.8 57 39-98 168-230 (242)
20 KOG0823 Predicted E3 ubiquitin 97.8 1.2E-05 2.5E-10 64.2 2.3 60 38-106 44-103 (230)
21 smart00184 RING Ring finger. E 97.7 3.4E-05 7.4E-10 44.0 3.2 38 44-90 1-38 (39)
22 KOG2177 Predicted E3 ubiquitin 97.7 4.1E-05 8.9E-10 65.1 5.0 108 39-174 11-122 (386)
23 PHA02929 N1R/p28-like protein; 97.7 4.4E-05 9.5E-10 62.3 4.1 51 39-98 172-227 (238)
24 KOG2164 Predicted E3 ubiquitin 97.6 2.7E-05 5.7E-10 68.9 2.0 59 41-106 186-244 (513)
25 KOG0317 Predicted E3 ubiquitin 97.6 4.2E-05 9.1E-10 62.9 2.4 52 40-103 238-289 (293)
26 smart00504 Ubox Modified RING 97.5 0.00015 3.3E-09 46.6 3.8 51 42-104 2-52 (63)
27 KOG4628 Predicted E3 ubiquitin 97.3 0.00019 4E-09 61.5 3.5 46 42-93 230-275 (348)
28 KOG4367 Predicted Zn-finger pr 97.3 0.00011 2.3E-09 63.8 2.0 86 146-242 172-259 (699)
29 TIGR00599 rad18 DNA repair pro 97.2 0.00028 6.2E-09 61.8 3.7 66 39-116 24-90 (397)
30 COG5540 RING-finger-containing 97.2 0.00024 5.1E-09 58.9 2.7 56 36-99 318-373 (374)
31 TIGR00570 cdk7 CDK-activating 97.1 0.0012 2.5E-08 55.8 5.8 53 42-102 4-58 (309)
32 PF12678 zf-rbx1: RING-H2 zinc 96.7 0.00097 2.1E-08 44.3 2.1 41 43-90 21-71 (73)
33 PF11793 FANCL_C: FANCL C-term 96.7 0.00073 1.6E-08 44.5 1.4 57 41-99 2-67 (70)
34 KOG0287 Postreplication repair 96.6 0.0015 3.2E-08 55.1 2.4 62 42-115 24-86 (442)
35 KOG1002 Nucleotide excision re 96.4 0.0022 4.8E-08 57.1 2.9 59 35-100 530-588 (791)
36 COG5574 PEX10 RING-finger-cont 96.4 0.0027 5.8E-08 51.9 3.1 53 40-102 214-266 (271)
37 PF11789 zf-Nse: Zinc-finger o 96.4 0.0027 5.8E-08 40.0 2.3 50 38-94 8-57 (57)
38 KOG1814 Predicted E3 ubiquitin 96.2 0.0011 2.5E-08 57.2 -0.0 40 199-238 271-313 (445)
39 KOG0978 E3 ubiquitin ligase in 96.1 0.0026 5.7E-08 59.2 1.6 56 39-105 641-696 (698)
40 KOG1428 Inhibitor of type V ad 96.1 0.012 2.5E-07 58.6 5.6 181 42-236 3487-3684(3738)
41 PF14835 zf-RING_6: zf-RING of 95.7 0.0012 2.5E-08 42.1 -1.7 47 42-101 8-54 (65)
42 KOG1039 Predicted E3 ubiquitin 95.4 0.014 3E-07 50.3 3.1 95 37-133 157-264 (344)
43 KOG4185 Predicted E3 ubiquitin 95.1 0.073 1.6E-06 45.3 6.6 122 41-172 3-131 (296)
44 KOG0823 Predicted E3 ubiquitin 94.8 0.0085 1.9E-07 48.1 0.3 26 224-249 65-91 (230)
45 PF04564 U-box: U-box domain; 94.8 0.018 4E-07 38.1 1.8 52 40-102 3-54 (73)
46 COG5243 HRD1 HRD ubiquitin lig 94.7 0.059 1.3E-06 46.3 5.0 48 43-99 289-346 (491)
47 PF10571 UPF0547: Uncharacteri 94.6 0.016 3.5E-07 30.1 0.9 23 202-228 1-24 (26)
48 PF05883 Baculo_RING: Baculovi 94.4 0.047 1E-06 40.3 3.2 37 39-76 24-67 (134)
49 KOG1815 Predicted E3 ubiquitin 94.3 0.036 7.8E-07 50.0 2.9 40 198-237 155-197 (444)
50 PF14634 zf-RING_5: zinc-RING 93.8 0.048 1E-06 32.2 2.0 41 204-250 2-44 (44)
51 KOG2660 Locus-specific chromos 93.5 0.042 9E-07 46.5 1.8 48 39-97 13-60 (331)
52 COG5432 RAD18 RING-finger-cont 93.5 0.06 1.3E-06 44.7 2.6 62 42-115 26-88 (391)
53 KOG1812 Predicted E3 ubiquitin 93.3 0.056 1.2E-06 47.7 2.4 84 84-173 232-346 (384)
54 KOG2879 Predicted E3 ubiquitin 93.3 0.11 2.4E-06 42.8 3.9 55 35-98 233-287 (298)
55 smart00744 RINGv The RING-vari 93.3 0.13 2.8E-06 31.2 3.2 41 44-90 2-47 (49)
56 PRK14890 putative Zn-ribbon RN 93.2 0.067 1.4E-06 33.5 1.9 47 202-249 8-55 (59)
57 KOG4739 Uncharacterized protei 93.1 0.038 8.2E-07 44.8 1.0 47 41-99 3-49 (233)
58 PF07975 C1_4: TFIIH C1-like d 93.0 0.028 6.1E-07 34.3 0.0 25 148-172 19-43 (51)
59 PF00097 zf-C3HC4: Zinc finger 92.9 0.021 4.5E-07 33.1 -0.7 26 223-248 16-41 (41)
60 PF13719 zinc_ribbon_5: zinc-r 92.7 0.073 1.6E-06 30.2 1.4 31 128-160 2-35 (37)
61 COG5152 Uncharacterized conser 92.3 0.075 1.6E-06 41.7 1.6 35 39-76 194-228 (259)
62 PF15227 zf-C3HC4_4: zinc fing 92.3 0.041 8.8E-07 32.2 0.0 29 220-248 12-42 (42)
63 KOG1952 Transcription factor N 92.3 0.25 5.4E-06 47.0 5.1 53 38-90 188-241 (950)
64 PF13240 zinc_ribbon_2: zinc-r 92.1 0.073 1.6E-06 26.8 0.9 20 228-249 1-20 (23)
65 PF12773 DZR: Double zinc ribb 92.0 0.14 3E-06 31.0 2.2 39 201-249 12-50 (50)
66 KOG4692 Predicted E3 ubiquitin 91.9 0.29 6.3E-06 41.9 4.7 37 37-76 418-454 (489)
67 smart00661 RPOL9 RNA polymeras 91.8 0.13 2.8E-06 31.4 2.0 26 203-228 2-30 (52)
68 KOG2817 Predicted E3 ubiquitin 91.7 0.22 4.8E-06 43.3 3.9 59 41-105 334-392 (394)
69 KOG0006 E3 ubiquitin-protein l 91.7 0.17 3.8E-06 42.6 3.1 92 61-170 341-437 (446)
70 PF13923 zf-C3HC4_2: Zinc fing 91.5 0.064 1.4E-06 30.7 0.3 27 220-248 12-39 (39)
71 PF12861 zf-Apc11: Anaphase-pr 91.5 0.18 3.9E-06 34.2 2.5 33 60-98 50-82 (85)
72 KOG0317 Predicted E3 ubiquitin 91.4 0.045 9.8E-07 45.4 -0.6 29 219-249 251-280 (293)
73 PF13248 zf-ribbon_3: zinc-rib 91.2 0.11 2.4E-06 26.9 1.0 11 202-212 3-13 (26)
74 PF13717 zinc_ribbon_4: zinc-r 91.0 0.16 3.4E-06 28.6 1.5 31 128-160 2-35 (36)
75 cd00162 RING RING-finger (Real 90.9 0.12 2.5E-06 29.9 1.0 41 204-250 2-43 (45)
76 KOG0828 Predicted E3 ubiquitin 90.7 0.15 3.3E-06 45.4 2.0 53 38-98 568-634 (636)
77 PHA00626 hypothetical protein 90.6 0.18 3.9E-06 31.1 1.6 26 203-228 2-33 (59)
78 COG2888 Predicted Zn-ribbon RN 90.4 0.18 3.9E-06 31.5 1.6 48 201-249 9-57 (61)
79 KOG0802 E3 ubiquitin ligase [P 90.4 0.28 6E-06 45.5 3.5 44 41-91 291-336 (543)
80 PF14835 zf-RING_6: zf-RING of 89.9 0.22 4.7E-06 31.8 1.6 37 202-249 8-47 (65)
81 PF07975 C1_4: TFIIH C1-like d 89.9 0.13 2.9E-06 31.3 0.7 31 217-249 19-50 (51)
82 PRK14714 DNA polymerase II lar 89.9 0.23 5E-06 49.4 2.6 43 202-250 668-717 (1337)
83 KOG3039 Uncharacterized conser 89.8 0.15 3.3E-06 41.4 1.1 60 37-105 217-277 (303)
84 PRK00398 rpoP DNA-directed RNA 89.7 0.27 5.8E-06 29.3 1.9 28 202-229 4-32 (46)
85 PRK04023 DNA polymerase II lar 89.5 0.28 6E-06 47.8 2.8 41 200-250 625-671 (1121)
86 PRK00432 30S ribosomal protein 89.5 0.25 5.4E-06 30.1 1.6 26 201-228 20-47 (50)
87 KOG4265 Predicted E3 ubiquitin 89.4 0.31 6.8E-06 41.8 2.7 50 37-98 286-336 (349)
88 PF14570 zf-RING_4: RING/Ubox 89.3 0.15 3.2E-06 30.7 0.5 45 204-250 1-45 (48)
89 KOG0297 TNF receptor-associate 89.1 0.31 6.7E-06 43.3 2.6 38 38-77 18-55 (391)
90 KOG4159 Predicted E3 ubiquitin 88.8 0.59 1.3E-05 41.4 4.1 48 39-98 82-129 (398)
91 PLN03086 PRLI-interacting fact 88.6 0.94 2E-05 41.9 5.5 58 84-160 406-463 (567)
92 TIGR00622 ssl1 transcription f 88.2 0.23 5E-06 35.6 1.0 41 129-171 56-102 (112)
93 COG5220 TFB3 Cdk activating ki 88.0 0.11 2.5E-06 41.9 -0.7 49 43-97 12-63 (314)
94 KOG0978 E3 ubiquitin ligase in 87.8 0.16 3.4E-06 47.7 -0.0 47 195-250 637-686 (698)
95 KOG1785 Tyrosine kinase negati 87.6 0.21 4.6E-06 43.4 0.6 44 43-94 371-414 (563)
96 KOG4445 Uncharacterized conser 87.4 0.51 1.1E-05 39.6 2.6 44 36-79 110-153 (368)
97 PF14570 zf-RING_4: RING/Ubox 87.4 0.73 1.6E-05 27.7 2.7 44 44-96 1-46 (48)
98 TIGR02098 MJ0042_CXXC MJ0042 f 87.3 0.31 6.7E-06 27.6 1.0 30 129-160 3-35 (38)
99 COG1198 PriA Primosomal protei 87.2 1.3 2.8E-05 42.4 5.6 33 203-235 446-484 (730)
100 KOG2807 RNA polymerase II tran 87.2 0.12 2.7E-06 43.6 -0.9 23 149-171 344-366 (378)
101 KOG0824 Predicted E3 ubiquitin 87.1 0.46 9.9E-06 39.9 2.3 53 39-102 5-57 (324)
102 KOG0311 Predicted E3 ubiquitin 86.9 0.13 2.7E-06 44.1 -1.1 46 40-95 42-87 (381)
103 KOG1734 Predicted RING-contain 86.8 0.27 5.8E-06 40.6 0.7 57 39-102 222-285 (328)
104 KOG1645 RING-finger-containing 86.8 0.57 1.2E-05 41.0 2.7 52 42-100 5-58 (463)
105 smart00661 RPOL9 RNA polymeras 86.8 0.42 9.2E-06 29.0 1.5 28 130-159 2-29 (52)
106 PF09297 zf-NADH-PPase: NADH p 86.6 0.84 1.8E-05 24.8 2.5 26 202-227 4-30 (32)
107 PF13639 zf-RING_2: Ring finge 86.5 0.17 3.7E-06 29.7 -0.4 41 204-248 3-43 (44)
108 PF14952 zf-tcix: Putative tre 86.2 0.42 9.1E-06 27.9 1.1 26 199-228 9-37 (44)
109 KOG2879 Predicted E3 ubiquitin 85.9 0.36 7.8E-06 39.9 1.1 43 201-249 239-283 (298)
110 PF09788 Tmemb_55A: Transmembr 85.9 0.47 1E-05 38.9 1.7 19 125-143 120-138 (256)
111 COG5175 MOT2 Transcriptional r 85.9 0.87 1.9E-05 38.9 3.3 62 39-110 13-77 (480)
112 PF10601 zf-LITAF-like: LITAF- 85.7 0.13 2.8E-06 34.0 -1.3 47 202-250 8-66 (73)
113 KOG2906 RNA polymerase III sub 85.6 0.51 1.1E-05 32.7 1.5 28 202-229 2-32 (105)
114 PF06677 Auto_anti-p27: Sjogre 85.3 0.69 1.5E-05 26.8 1.8 22 202-225 18-41 (41)
115 KOG0804 Cytoplasmic Zn-finger 85.3 0.4 8.7E-06 42.4 1.1 39 38-76 172-211 (493)
116 PF09538 FYDLN_acid: Protein o 85.3 0.56 1.2E-05 33.6 1.7 27 201-228 9-36 (108)
117 PRK00398 rpoP DNA-directed RNA 85.2 0.72 1.6E-05 27.4 1.9 29 128-160 3-31 (46)
118 PRK14559 putative protein seri 85.0 0.72 1.6E-05 43.6 2.7 10 227-236 42-51 (645)
119 PF03833 PolC_DP2: DNA polymer 85.0 0.28 6E-06 46.9 0.0 41 200-250 654-700 (900)
120 PLN03208 E3 ubiquitin-protein 84.6 0.51 1.1E-05 37.3 1.3 33 199-236 16-48 (193)
121 PRK14873 primosome assembly pr 84.5 2 4.3E-05 40.9 5.5 25 202-226 393-418 (665)
122 PF04641 Rtf2: Rtf2 RING-finge 84.5 2.1 4.5E-05 35.8 5.1 71 38-118 110-182 (260)
123 PF15616 TerY-C: TerY-C metal 84.4 0.9 2E-05 33.6 2.5 24 201-230 77-100 (131)
124 KOG0320 Predicted E3 ubiquitin 83.9 0.37 8.1E-06 37.3 0.3 45 201-250 131-175 (187)
125 PHA03096 p28-like protein; Pro 82.4 1.8 4E-05 36.6 3.9 39 42-80 179-222 (284)
126 PF10367 Vps39_2: Vacuolar sor 81.9 1.2 2.5E-05 31.5 2.2 31 41-72 78-108 (109)
127 PF12861 zf-Apc11: Anaphase-pr 81.4 1.2 2.6E-05 30.3 2.0 45 202-249 33-78 (85)
128 KOG3800 Predicted E3 ubiquitin 80.3 2.4 5.1E-05 35.6 3.7 50 43-100 2-53 (300)
129 PF02150 RNA_POL_M_15KD: RNA p 80.0 0.67 1.5E-05 25.9 0.3 28 129-159 2-29 (35)
130 PRK09710 lar restriction allev 79.1 1.9 4E-05 27.6 2.1 31 199-229 4-38 (64)
131 KOG1813 Predicted E3 ubiquitin 79.0 1 2.3E-05 37.7 1.3 37 37-76 237-273 (313)
132 COG1998 RPS31 Ribosomal protei 79.0 1.5 3.3E-05 26.3 1.7 25 202-227 20-46 (51)
133 TIGR00595 priA primosomal prot 78.7 4.2 9E-05 37.5 5.2 25 203-227 224-249 (505)
134 PHA02929 N1R/p28-like protein; 78.7 1.8 3.9E-05 35.6 2.5 48 200-249 173-223 (238)
135 KOG3579 Predicted E3 ubiquitin 78.5 1.3 2.9E-05 36.8 1.8 53 37-94 264-321 (352)
136 PF07191 zinc-ribbons_6: zinc- 78.3 1.5 3.2E-05 28.6 1.6 32 203-236 3-40 (70)
137 COG5222 Uncharacterized conser 77.4 7.8 0.00017 32.7 5.9 44 41-94 274-317 (427)
138 KOG4172 Predicted E3 ubiquitin 77.0 1 2.2E-05 27.7 0.5 45 42-97 8-53 (62)
139 PF14803 Nudix_N_2: Nudix N-te 76.6 1.2 2.6E-05 24.7 0.7 28 130-159 2-31 (34)
140 PHA02926 zinc finger-like prot 76.4 1.8 4E-05 34.9 1.9 51 199-249 168-226 (242)
141 PRK00420 hypothetical protein; 76.2 1.9 4.2E-05 31.0 1.9 23 202-226 24-48 (112)
142 COG5151 SSL1 RNA polymerase II 75.9 1.1 2.3E-05 37.9 0.5 42 128-171 362-409 (421)
143 KOG0827 Predicted E3 ubiquitin 75.8 1.7 3.7E-05 37.9 1.7 45 42-90 5-50 (465)
144 PF08746 zf-RING-like: RING-li 75.6 2.4 5.3E-05 24.8 1.9 42 44-90 1-42 (43)
145 TIGR01384 TFS_arch transcripti 75.5 1.9 4.1E-05 30.5 1.7 25 203-229 2-27 (104)
146 PF05290 Baculo_IE-1: Baculovi 75.4 13 0.00029 27.4 6.0 57 35-97 74-131 (140)
147 COG1997 RPL43A Ribosomal prote 75.3 3.1 6.8E-05 28.3 2.5 29 200-228 34-63 (89)
148 PRK14559 putative protein seri 75.3 2.4 5.1E-05 40.2 2.7 11 202-212 42-52 (645)
149 COG0777 AccD Acetyl-CoA carbox 75.1 1 2.3E-05 37.4 0.3 31 198-228 25-57 (294)
150 PF14354 Lar_restr_allev: Rest 75.1 2.8 6E-05 26.4 2.2 27 200-226 2-37 (61)
151 KOG3002 Zn finger protein [Gen 74.8 2.5 5.4E-05 36.0 2.5 48 37-98 44-91 (299)
152 TIGR00622 ssl1 transcription f 74.7 3.5 7.6E-05 29.6 2.8 46 202-249 56-110 (112)
153 KOG3970 Predicted E3 ubiquitin 74.5 5.9 0.00013 32.0 4.3 53 43-98 52-105 (299)
154 PF07282 OrfB_Zn_ribbon: Putat 74.2 2.6 5.5E-05 27.3 1.9 28 200-227 27-55 (69)
155 PF08271 TF_Zn_Ribbon: TFIIB z 74.1 3 6.4E-05 24.3 2.0 24 203-226 2-27 (43)
156 COG1645 Uncharacterized Zn-fin 73.8 2.1 4.4E-05 31.6 1.5 23 202-226 29-52 (131)
157 PF03119 DNA_ligase_ZBD: NAD-d 73.5 3.6 7.8E-05 21.7 2.0 20 203-222 1-20 (28)
158 COG5574 PEX10 RING-finger-cont 72.7 0.95 2.1E-05 37.3 -0.5 41 202-249 216-258 (271)
159 PRK04023 DNA polymerase II lar 72.6 3.3 7.2E-05 40.7 2.9 33 127-169 625-662 (1121)
160 KOG1001 Helicase-like transcri 72.3 1.4 3E-05 41.9 0.4 52 42-104 455-506 (674)
161 PF12906 RINGv: RING-variant d 72.2 3.2 6.8E-05 24.8 1.8 33 44-77 1-38 (47)
162 PRK14714 DNA polymerase II lar 71.8 4.3 9.2E-05 41.0 3.5 29 129-167 668-701 (1337)
163 PRK08665 ribonucleotide-diphos 71.4 2.3 5E-05 41.1 1.7 26 202-229 725-751 (752)
164 PF14149 YhfH: YhfH-like prote 71.1 0.42 9.2E-06 26.9 -2.0 31 194-224 6-37 (37)
165 TIGR01206 lysW lysine biosynth 70.6 3.4 7.4E-05 25.5 1.7 30 129-160 3-32 (54)
166 PF14569 zf-UDP: Zinc-binding 70.5 2.4 5.3E-05 28.1 1.1 43 149-219 27-69 (80)
167 TIGR03655 anti_R_Lar restricti 70.4 4.3 9.3E-05 24.8 2.2 29 202-230 2-38 (53)
168 COG5219 Uncharacterized conser 69.8 2 4.3E-05 41.8 0.9 53 39-98 1467-1523(1525)
169 PRK05654 acetyl-CoA carboxylas 69.5 1.1 2.3E-05 38.2 -0.9 31 198-228 24-56 (292)
170 KOG2114 Vacuolar assembly/sort 69.4 7.7 0.00017 37.5 4.5 40 42-95 841-880 (933)
171 PF07754 DUF1610: Domain of un 69.4 3.3 7.2E-05 21.0 1.2 22 229-250 1-24 (24)
172 TIGR02300 FYDLN_acid conserved 69.1 3.3 7.1E-05 30.4 1.6 27 201-228 9-36 (129)
173 PRK05580 primosome assembly pr 67.3 11 0.00024 36.2 5.3 14 106-119 351-364 (679)
174 PRK14892 putative transcriptio 67.3 3.9 8.4E-05 28.8 1.7 30 199-228 19-52 (99)
175 COG0375 HybF Zn finger protein 67.1 2.4 5.2E-05 30.6 0.6 24 226-249 70-93 (115)
176 PF02318 FYVE_2: FYVE-type zin 66.9 6.2 0.00013 28.6 2.8 33 41-73 54-88 (118)
177 PF14446 Prok-RING_1: Prokaryo 66.7 7.4 0.00016 24.0 2.6 33 42-74 6-39 (54)
178 PF02701 zf-Dof: Dof domain, z 66.0 2.3 5E-05 26.9 0.3 32 201-248 5-36 (63)
179 smart00834 CxxC_CXXC_SSSS Puta 66.0 5.6 0.00012 22.5 2.0 29 129-159 6-35 (41)
180 TIGR00515 accD acetyl-CoA carb 65.7 1.4 3E-05 37.4 -1.0 31 198-228 23-55 (285)
181 COG5109 Uncharacterized conser 65.7 7.4 0.00016 33.1 3.3 56 41-102 336-391 (396)
182 PRK12380 hydrogenase nickel in 65.6 13 0.00029 26.7 4.3 48 106-159 39-95 (113)
183 CHL00174 accD acetyl-CoA carbo 65.4 1.3 2.9E-05 37.5 -1.1 30 199-228 36-67 (296)
184 PRK11827 hypothetical protein; 65.4 4.6 0.0001 25.5 1.6 28 201-228 8-36 (60)
185 KOG1940 Zn-finger protein [Gen 65.2 4.4 9.5E-05 34.0 1.9 51 36-95 153-204 (276)
186 PRK12380 hydrogenase nickel in 64.8 3.9 8.4E-05 29.5 1.3 23 227-249 71-93 (113)
187 KOG0825 PHD Zn-finger protein 64.7 1.9 4E-05 41.1 -0.4 21 61-81 120-140 (1134)
188 PF01155 HypA: Hydrogenase exp 64.7 1.4 3.1E-05 31.8 -0.9 23 227-249 71-93 (113)
189 PRK03824 hypA hydrogenase nick 64.3 13 0.00029 27.6 4.2 35 107-143 40-83 (135)
190 PF06906 DUF1272: Protein of u 64.2 5.1 0.00011 24.8 1.6 47 43-100 7-54 (57)
191 COG5432 RAD18 RING-finger-cont 64.1 2.5 5.5E-05 35.4 0.3 27 220-248 37-65 (391)
192 TIGR00100 hypA hydrogenase nic 63.4 4.3 9.2E-05 29.4 1.3 22 228-249 72-93 (115)
193 KOG2906 RNA polymerase III sub 62.9 4 8.7E-05 28.4 1.1 29 129-159 2-30 (105)
194 TIGR01053 LSD1 zinc finger dom 62.8 7.9 0.00017 20.9 2.0 25 202-226 2-27 (31)
195 KOG3053 Uncharacterized conser 62.5 5.7 0.00012 32.8 2.0 51 43-95 22-79 (293)
196 PRK12286 rpmF 50S ribosomal pr 62.4 5.4 0.00012 25.0 1.5 24 198-226 24-48 (57)
197 PF06827 zf-FPG_IleRS: Zinc fi 62.1 5.2 0.00011 21.2 1.2 23 202-224 2-27 (30)
198 TIGR00100 hypA hydrogenase nic 61.0 18 0.0004 26.1 4.3 48 106-159 39-95 (115)
199 COG1594 RPB9 DNA-directed RNA 59.9 5.6 0.00012 28.7 1.5 30 129-160 3-32 (113)
200 TIGR00686 phnA alkylphosphonat 59.6 5.3 0.00011 28.4 1.2 26 130-160 4-29 (109)
201 KOG3268 Predicted E3 ubiquitin 59.4 10 0.00022 29.5 2.8 62 36-99 160-229 (234)
202 PF01599 Ribosomal_S27: Riboso 59.4 6 0.00013 23.7 1.2 25 202-226 19-46 (47)
203 KOG2462 C2H2-type Zn-finger pr 59.2 12 0.00026 31.2 3.4 52 199-250 159-223 (279)
204 PRK03681 hypA hydrogenase nick 59.2 20 0.00044 25.8 4.3 49 106-159 39-96 (114)
205 smart00531 TFIIE Transcription 59.0 12 0.00027 28.2 3.3 33 125-159 96-132 (147)
206 KOG2034 Vacuolar sorting prote 58.9 14 0.00031 35.9 4.3 37 43-80 819-855 (911)
207 TIGR02443 conserved hypothetic 58.8 9.2 0.0002 24.0 2.0 27 202-228 10-41 (59)
208 PF14353 CpXC: CpXC protein 58.5 7.2 0.00015 28.6 1.9 48 85-143 1-51 (128)
209 PRK13130 H/ACA RNA-protein com 58.1 6.1 0.00013 24.6 1.2 13 200-212 4-16 (56)
210 COG3813 Uncharacterized protei 58.0 7.7 0.00017 25.3 1.6 57 43-114 7-65 (84)
211 PF14445 Prok-RING_2: Prokaryo 57.8 2 4.4E-05 25.9 -0.9 36 41-76 7-42 (57)
212 TIGR00570 cdk7 CDK-activating 57.2 6.5 0.00014 33.6 1.6 34 129-167 4-37 (309)
213 KOG4684 Uncharacterized conser 57.1 7.8 0.00017 31.1 1.9 19 125-143 135-153 (275)
214 PF05605 zf-Di19: Drought indu 57.0 19 0.00042 21.9 3.4 40 41-97 2-41 (54)
215 PRK08115 ribonucleotide-diphos 56.9 5.3 0.00012 39.0 1.2 24 202-227 828-853 (858)
216 KOG2807 RNA polymerase II tran 56.4 4.5 9.7E-05 34.6 0.5 45 200-249 329-374 (378)
217 PF05129 Elf1: Transcription e 56.2 6.7 0.00014 26.5 1.2 29 200-228 21-56 (81)
218 KOG0801 Predicted E3 ubiquitin 56.1 2.9 6.4E-05 31.9 -0.5 27 41-67 177-203 (205)
219 PF06943 zf-LSD1: LSD1 zinc fi 56.1 13 0.00028 19.0 2.0 23 204-226 1-24 (25)
220 PF12760 Zn_Tnp_IS1595: Transp 55.6 31 0.00068 20.2 4.0 27 200-226 17-45 (46)
221 PRK10220 hypothetical protein; 54.1 8.1 0.00018 27.5 1.4 26 130-160 5-30 (111)
222 PF02591 DUF164: Putative zinc 53.9 11 0.00024 23.2 1.9 20 192-211 37-56 (56)
223 KOG2932 E3 ubiquitin ligase in 53.9 9.2 0.0002 32.5 1.9 35 39-75 88-122 (389)
224 PF08274 PhnA_Zn_Ribbon: PhnA 52.9 4.8 0.0001 21.6 0.1 26 130-160 4-29 (30)
225 PF09526 DUF2387: Probable met 52.7 12 0.00026 24.6 2.0 26 202-227 9-39 (71)
226 PF10122 Mu-like_Com: Mu-like 52.3 5.7 0.00012 24.1 0.4 11 203-213 6-16 (51)
227 PF08792 A2L_zn_ribbon: A2L zi 51.7 15 0.00031 20.2 1.9 25 202-226 4-29 (33)
228 PRK03681 hypA hydrogenase nick 51.5 8.5 0.00018 27.8 1.2 22 228-249 72-94 (114)
229 PF06844 DUF1244: Protein of u 51.4 14 0.00031 23.7 2.1 17 65-81 11-27 (68)
230 PRK06266 transcription initiat 51.2 15 0.00032 28.8 2.7 31 126-159 115-145 (178)
231 PF07649 C1_3: C1-like domain; 51.1 5.5 0.00012 21.1 0.2 21 228-249 2-22 (30)
232 smart00249 PHD PHD zinc finger 51.0 7.6 0.00016 22.2 0.8 33 44-76 2-34 (47)
233 TIGR00599 rad18 DNA repair pro 51.0 5.9 0.00013 35.2 0.4 41 202-249 27-67 (397)
234 TIGR00373 conserved hypothetic 50.8 14 0.0003 28.4 2.3 31 126-159 107-137 (158)
235 PF01363 FYVE: FYVE zinc finge 50.1 7.3 0.00016 25.0 0.6 35 200-236 8-43 (69)
236 PF13453 zf-TFIIB: Transcripti 49.8 6.5 0.00014 22.6 0.3 25 131-157 2-26 (41)
237 PF14447 Prok-RING_4: Prokaryo 48.7 5.2 0.00011 24.7 -0.2 31 59-100 22-52 (55)
238 smart00659 RPOLCX RNA polymera 48.3 15 0.00032 21.6 1.7 12 200-211 18-29 (44)
239 PF02891 zf-MIZ: MIZ/SP-RING z 48.1 19 0.00041 21.7 2.2 47 42-95 3-49 (50)
240 PF00643 zf-B_box: B-box zinc 47.9 3.5 7.5E-05 23.6 -1.1 24 149-172 14-37 (42)
241 COG5236 Uncharacterized conser 47.7 11 0.00024 32.5 1.5 51 36-96 56-106 (493)
242 PF07503 zf-HYPF: HypF finger; 47.3 9.8 0.00021 21.2 0.8 31 66-98 1-32 (35)
243 PF09723 Zn-ribbon_8: Zinc rib 46.5 18 0.00039 20.9 1.9 28 129-158 6-34 (42)
244 PF03604 DNA_RNApol_7kD: DNA d 46.2 17 0.00037 19.8 1.6 22 135-159 5-26 (32)
245 KOG0826 Predicted E3 ubiquitin 45.7 25 0.00054 30.2 3.3 54 41-105 300-353 (357)
246 smart00734 ZnF_Rad18 Rad18-lik 45.7 10 0.00023 19.4 0.7 20 86-107 2-21 (26)
247 PRK00564 hypA hydrogenase nick 45.5 13 0.00027 27.0 1.4 22 228-249 73-95 (117)
248 smart00531 TFIIE Transcription 45.4 50 0.0011 24.9 4.7 43 82-145 96-138 (147)
249 COG1996 RPC10 DNA-directed RNA 45.3 12 0.00027 22.5 1.1 10 240-249 22-31 (49)
250 PRK03824 hypA hydrogenase nick 44.7 13 0.00028 27.8 1.3 9 241-249 106-114 (135)
251 cd00021 BBOX B-Box-type zinc f 44.6 10 0.00022 21.0 0.6 26 148-173 10-35 (39)
252 smart00714 LITAF Possible memb 44.3 11 0.00025 24.1 0.9 47 202-250 4-60 (67)
253 PF14369 zf-RING_3: zinc-finge 42.7 28 0.0006 19.3 2.2 30 128-160 2-31 (35)
254 COG1579 Zn-ribbon protein, pos 42.5 27 0.00058 28.8 2.9 57 101-159 167-230 (239)
255 TIGR01031 rpmF_bact ribosomal 42.4 16 0.00035 22.6 1.3 23 199-226 24-47 (55)
256 KOG1571 Predicted E3 ubiquitin 42.3 42 0.00092 29.2 4.2 29 36-67 300-328 (355)
257 COG2051 RPS27A Ribosomal prote 42.3 16 0.00034 23.5 1.2 31 128-161 19-49 (67)
258 COG0266 Nei Formamidopyrimidin 42.2 17 0.00037 30.6 1.8 24 202-225 246-272 (273)
259 COG3024 Uncharacterized protei 41.6 11 0.00024 24.0 0.5 16 200-215 6-21 (65)
260 COG2824 PhnA Uncharacterized Z 41.2 20 0.00042 25.4 1.7 25 202-228 4-30 (112)
261 PF09788 Tmemb_55A: Transmembr 41.1 24 0.00052 29.2 2.4 64 84-159 122-186 (256)
262 COG1096 Predicted RNA-binding 40.5 17 0.00038 28.5 1.5 24 202-227 150-174 (188)
263 COG1439 Predicted nucleic acid 40.2 17 0.00036 28.4 1.4 10 227-236 154-163 (177)
264 PRK14811 formamidopyrimidine-D 40.0 20 0.00043 30.1 1.9 21 202-222 236-258 (269)
265 PF02318 FYVE_2: FYVE-type zin 39.9 25 0.00054 25.4 2.2 36 200-236 53-89 (118)
266 PF03107 C1_2: C1 domain; Int 39.5 15 0.00032 19.5 0.7 21 228-249 2-22 (30)
267 PRK09521 exosome complex RNA-b 39.2 20 0.00044 28.2 1.8 25 202-227 150-175 (189)
268 KOG3039 Uncharacterized conser 39.0 25 0.00055 28.9 2.3 42 37-81 38-80 (303)
269 PLN03086 PRLI-interacting fact 39.0 17 0.00037 33.9 1.4 30 199-228 431-463 (567)
270 PF09889 DUF2116: Uncharacteri 38.8 15 0.00033 23.1 0.8 13 202-214 4-16 (59)
271 PF01428 zf-AN1: AN1-like Zinc 38.2 11 0.00024 21.9 0.1 25 150-176 13-37 (43)
272 PLN00209 ribosomal protein S27 38.2 31 0.00067 23.4 2.2 30 129-161 37-66 (86)
273 PRK10445 endonuclease VIII; Pr 38.1 22 0.00048 29.7 1.9 13 202-214 236-248 (263)
274 PF01783 Ribosomal_L32p: Ribos 38.1 12 0.00026 23.2 0.2 21 200-225 25-46 (56)
275 PF04981 NMD3: NMD3 family ; 37.9 18 0.00038 29.7 1.2 14 200-213 34-47 (236)
276 PHA02862 5L protein; Provision 37.7 43 0.00093 25.3 3.1 46 43-99 4-54 (156)
277 KOG4275 Predicted E3 ubiquitin 37.4 13 0.00028 31.4 0.4 30 42-74 301-331 (350)
278 COG3357 Predicted transcriptio 37.4 73 0.0016 22.0 3.9 60 95-159 17-85 (97)
279 KOG1941 Acetylcholine receptor 37.2 18 0.00039 31.8 1.2 46 42-94 366-412 (518)
280 PRK14810 formamidopyrimidine-D 37.1 23 0.0005 29.8 1.9 13 202-214 245-257 (272)
281 PF01780 Ribosomal_L37ae: Ribo 37.1 16 0.00034 25.2 0.7 27 202-228 36-63 (90)
282 PRK01103 formamidopyrimidine/5 36.7 25 0.00054 29.6 2.0 13 202-214 246-258 (274)
283 PF10426 zf-RAG1: Recombinatio 36.4 5.5 0.00012 21.3 -1.2 22 85-106 2-23 (30)
284 KOG0309 Conserved WD40 repeat- 36.1 28 0.0006 33.5 2.3 46 40-94 1027-1072(1081)
285 PF14471 DUF4428: Domain of un 36.1 36 0.00079 20.6 2.1 30 43-74 1-30 (51)
286 smart00064 FYVE Protein presen 36.0 33 0.00071 21.8 2.1 36 42-77 11-47 (68)
287 PHA02825 LAP/PHD finger-like p 35.9 49 0.0011 25.4 3.2 49 41-100 8-61 (162)
288 PRK05978 hypothetical protein; 35.9 21 0.00045 27.1 1.3 10 200-209 32-41 (148)
289 KOG2164 Predicted E3 ubiquitin 35.9 12 0.00026 34.0 -0.0 43 201-248 186-231 (513)
290 PF00628 PHD: PHD-finger; Int 35.8 17 0.00036 21.6 0.6 33 44-76 2-34 (51)
291 PF10083 DUF2321: Uncharacteri 35.7 18 0.00039 27.5 0.9 14 201-214 39-52 (158)
292 KOG2462 C2H2-type Zn-finger pr 35.5 49 0.0011 27.8 3.4 33 126-160 213-253 (279)
293 TIGR02605 CxxC_CxxC_SSSS putat 35.3 35 0.00076 20.4 2.0 28 129-158 6-34 (52)
294 PF01396 zf-C4_Topoisom: Topoi 35.1 22 0.00048 20.2 1.0 20 202-222 2-24 (39)
295 PLN02189 cellulose synthase 34.8 28 0.0006 34.8 2.2 61 129-220 35-95 (1040)
296 PF11809 DUF3330: Domain of un 34.7 18 0.00038 23.3 0.6 42 37-78 7-51 (70)
297 cd00065 FYVE FYVE domain; Zinc 34.2 29 0.00062 21.1 1.5 35 43-77 4-39 (57)
298 KOG3970 Predicted E3 ubiquitin 33.8 18 0.0004 29.3 0.7 75 157-249 20-101 (299)
299 smart00336 BBOX B-Box-type zin 33.8 21 0.00046 20.0 0.8 24 149-172 14-37 (42)
300 PRK00415 rps27e 30S ribosomal 33.3 32 0.00069 21.7 1.6 31 128-161 11-41 (59)
301 smart00154 ZnF_AN1 AN1-like Zi 33.2 23 0.00049 20.2 0.9 18 150-167 12-29 (39)
302 PLN02638 cellulose synthase A 33.1 21 0.00046 35.8 1.1 43 149-219 35-77 (1079)
303 PRK11032 hypothetical protein; 33.0 35 0.00077 26.2 2.1 28 216-249 121-149 (160)
304 TIGR00577 fpg formamidopyrimid 32.9 29 0.00064 29.1 1.9 13 202-214 246-258 (272)
305 PRK13945 formamidopyrimidine-D 32.5 30 0.00066 29.2 1.9 13 202-214 255-267 (282)
306 PF12675 DUF3795: Protein of u 32.1 79 0.0017 20.9 3.5 36 199-234 32-71 (78)
307 PTZ00083 40S ribosomal protein 31.5 50 0.0011 22.4 2.4 30 129-161 36-65 (85)
308 KOG2930 SCF ubiquitin ligase, 31.3 45 0.00097 23.6 2.2 23 61-90 80-102 (114)
309 cd00350 rubredoxin_like Rubred 31.3 39 0.00085 18.3 1.6 20 230-249 5-24 (33)
310 KOG3161 Predicted E3 ubiquitin 31.1 15 0.00033 34.4 -0.1 35 42-76 12-47 (861)
311 PTZ00255 60S ribosomal protein 31.0 53 0.0011 22.6 2.5 31 199-229 34-65 (90)
312 TIGR00280 L37a ribosomal prote 30.9 45 0.00097 23.0 2.1 30 200-229 34-64 (91)
313 PF04216 FdhE: Protein involve 30.7 24 0.00052 29.9 1.0 27 202-228 173-207 (290)
314 PF03966 Trm112p: Trm112p-like 30.6 45 0.00098 21.4 2.1 10 202-211 54-63 (68)
315 PRK12495 hypothetical protein; 30.6 47 0.001 26.9 2.5 28 200-236 41-68 (226)
316 COG5175 MOT2 Transcriptional r 30.6 13 0.00028 32.0 -0.6 46 203-250 16-61 (480)
317 COG3492 Uncharacterized protei 30.5 50 0.0011 22.7 2.2 17 65-81 42-58 (104)
318 PF13834 DUF4193: Domain of un 30.2 23 0.0005 24.8 0.6 33 37-70 66-98 (99)
319 KOG4362 Transcriptional regula 29.9 12 0.00025 35.5 -1.1 56 39-103 19-74 (684)
320 PF00412 LIM: LIM domain; Int 29.2 46 0.001 20.1 1.9 34 39-74 24-57 (58)
321 TIGR00595 priA primosomal prot 29.1 33 0.00072 31.7 1.7 37 201-249 213-260 (505)
322 PF05191 ADK_lid: Adenylate ki 28.8 45 0.00097 18.6 1.6 27 130-158 3-29 (36)
323 PF08209 Sgf11: Sgf11 (transcr 28.4 19 0.00042 19.7 0.0 9 242-250 4-12 (33)
324 PF13821 DUF4187: Domain of un 28.3 15 0.00033 22.7 -0.5 14 224-237 25-38 (55)
325 PF14319 Zn_Tnp_IS91: Transpos 28.3 1.2E+02 0.0027 21.6 4.2 50 106-167 19-69 (111)
326 PRK13264 3-hydroxyanthranilate 28.1 27 0.00058 27.4 0.8 25 190-214 146-170 (177)
327 TIGR03847 conserved hypothetic 28.0 43 0.00094 26.0 1.8 12 200-211 155-166 (177)
328 PRK03976 rpl37ae 50S ribosomal 27.9 53 0.0011 22.6 2.1 30 200-229 35-65 (90)
329 TIGR03037 anthran_nbaC 3-hydro 27.9 29 0.00063 26.7 0.9 21 189-209 139-159 (159)
330 PRK00241 nudC NADH pyrophospha 27.8 41 0.0009 28.0 1.9 28 200-227 98-126 (256)
331 cd04476 RPA1_DBD_C RPA1_DBD_C: 27.6 37 0.0008 26.0 1.5 26 201-227 34-60 (166)
332 PF01873 eIF-5_eIF-2B: Domain 27.4 55 0.0012 24.1 2.3 27 201-227 93-123 (125)
333 PF13913 zf-C2HC_2: zinc-finge 26.8 36 0.00078 17.1 0.9 18 86-105 3-20 (25)
334 PF01667 Ribosomal_S27e: Ribos 26.6 41 0.00089 20.9 1.2 32 128-162 7-38 (55)
335 PLN02400 cellulose synthase 26.6 39 0.00085 34.0 1.7 18 149-166 54-71 (1085)
336 PRK00762 hypA hydrogenase nick 26.5 38 0.00082 24.8 1.3 23 226-249 70-99 (124)
337 COG3529 Predicted nucleic-acid 26.4 23 0.00049 22.3 0.1 26 203-228 12-42 (66)
338 PF11682 DUF3279: Protein of u 26.4 42 0.00092 24.8 1.5 15 202-216 111-125 (128)
339 COG5540 RING-finger-containing 26.4 24 0.00051 30.0 0.2 43 202-249 324-368 (374)
340 COG2260 Predicted Zn-ribbon RN 26.4 39 0.00085 21.1 1.1 13 201-213 5-17 (59)
341 PF08882 Acetone_carb_G: Aceto 26.0 39 0.00085 24.2 1.2 14 218-231 23-36 (112)
342 smart00109 C1 Protein kinase C 25.8 58 0.0012 18.7 1.8 23 227-249 12-34 (49)
343 PF09151 DUF1936: Domain of un 25.7 36 0.00078 18.2 0.7 10 202-211 2-11 (36)
344 KOG2923 Uncharacterized conser 25.2 47 0.001 21.2 1.3 21 194-214 37-57 (67)
345 PF11023 DUF2614: Protein of u 25.1 35 0.00076 24.5 0.8 11 159-169 86-96 (114)
346 cd00729 rubredoxin_SM Rubredox 25.0 55 0.0012 17.9 1.5 6 244-249 20-25 (34)
347 cd02335 ZZ_ADA2 Zinc finger, Z 25.0 81 0.0018 18.7 2.3 33 43-75 2-35 (49)
348 KOG2789 Putative Zn-finger pro 24.9 25 0.00054 31.0 0.1 40 35-75 68-107 (482)
349 PF14205 Cys_rich_KTR: Cystein 24.6 66 0.0014 19.9 1.8 10 127-138 3-12 (55)
350 COG2816 NPY1 NTP pyrophosphohy 24.4 79 0.0017 26.7 2.9 30 199-228 109-139 (279)
351 PF11781 RRN7: RNA polymerase 24.4 56 0.0012 18.2 1.4 24 202-227 9-34 (36)
352 cd02249 ZZ Zinc finger, ZZ typ 24.2 70 0.0015 18.7 1.9 32 43-75 2-34 (46)
353 PRK00418 DNA gyrase inhibitor; 24.0 42 0.00092 21.4 1.0 13 200-212 5-17 (62)
354 PF04438 zf-HIT: HIT zinc fing 23.7 25 0.00053 18.8 -0.1 18 227-249 3-20 (30)
355 PLN02915 cellulose synthase A 23.4 42 0.0009 33.7 1.3 18 149-166 33-50 (1044)
356 PF01927 Mut7-C: Mut7-C RNAse 23.4 92 0.002 23.4 2.9 52 107-160 67-134 (147)
357 COG4847 Uncharacterized protei 23.2 76 0.0017 22.0 2.1 41 39-80 4-44 (103)
358 PF05715 zf-piccolo: Piccolo Z 23.2 45 0.00098 21.0 0.9 37 130-168 4-40 (61)
359 PF10272 Tmpp129: Putative tra 23.2 1.1E+02 0.0025 26.8 3.8 36 64-101 313-354 (358)
360 PF14169 YdjO: Cold-inducible 23.0 72 0.0016 20.1 1.9 29 130-159 20-48 (59)
361 PF10497 zf-4CXXC_R1: Zinc-fin 22.5 1.8E+02 0.004 20.5 4.1 28 63-90 37-66 (105)
362 COG1656 Uncharacterized conser 22.4 78 0.0017 24.4 2.3 14 128-143 97-110 (165)
363 COG1040 ComFC Predicted amidop 22.4 17 0.00037 29.6 -1.3 25 202-237 25-49 (225)
364 TIGR00311 aIF-2beta translatio 22.3 51 0.0011 24.5 1.3 28 200-227 96-127 (133)
365 PRK03988 translation initiatio 22.3 56 0.0012 24.5 1.5 28 200-227 101-132 (138)
366 COG5151 SSL1 RNA polymerase II 22.2 19 0.00042 30.6 -1.0 46 202-249 363-417 (421)
367 PF09943 DUF2175: Uncharacteri 22.2 1.1E+02 0.0023 21.6 2.8 40 41-81 2-41 (101)
368 PF02148 zf-UBP: Zn-finger in 22.2 82 0.0018 19.8 2.1 31 44-76 1-35 (63)
369 PF00098 zf-CCHC: Zinc knuckle 21.9 58 0.0013 15.0 1.0 16 160-175 2-17 (18)
370 PF00569 ZZ: Zinc finger, ZZ t 21.8 1.1E+02 0.0024 17.9 2.5 33 41-73 4-37 (46)
371 PF14690 zf-ISL3: zinc-finger 21.8 55 0.0012 18.9 1.2 13 202-214 3-15 (47)
372 smart00653 eIF2B_5 domain pres 21.5 60 0.0013 23.3 1.5 27 200-226 79-109 (110)
373 PF04216 FdhE: Protein involve 21.4 39 0.00085 28.6 0.6 10 200-209 196-205 (290)
374 KOG2691 RNA polymerase II subu 21.3 67 0.0015 22.8 1.6 28 129-158 5-34 (113)
375 PRK00423 tfb transcription ini 21.2 83 0.0018 27.0 2.6 28 201-228 11-40 (310)
376 PLN02436 cellulose synthase A 21.2 70 0.0015 32.3 2.3 34 130-166 38-71 (1094)
377 PRK12496 hypothetical protein; 20.8 66 0.0014 24.8 1.7 27 202-237 128-154 (164)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-36 Score=263.96 Aligned_cols=199 Identities=37% Similarity=0.877 Sum_probs=169.6
Q ss_pred CceecccCcccc-cCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccCChHHHHHHHHHH
Q 025608 40 RSFVCEICVETK-LRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKAL 118 (250)
Q Consensus 40 ~~~~C~iC~~~~-~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~ 118 (250)
...+|.||+.+. ..+.++....|+|.||.+|+++|++.+ ..+...++||..+|...++.+....+|++.+.++|.+.+
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~-~~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~ 223 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK-LLSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRL 223 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh-hccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHH
Confidence 456899999554 444667678999999999999999998 445688999999999999999999999999999999999
Q ss_pred HhhccCCCCeecCCCCCCCCceecCc---cCccCcccCCcccchhccccCcccCCCCCchhHhhhccCCCchHHHHHHHH
Q 025608 119 CESLIPGAQKFYCPFKDCSALLIDDA---GEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKL 195 (250)
Q Consensus 119 ~~~~~~~~~~~~Cp~~~C~~~~~~~~---~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~ 195 (250)
.+.++...+.++||.|+|...+.... ........|+.|+..||.+|+.+||.+++|++++++....... +..+..+
T Consensus 224 ~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d-~~~~~~l 302 (384)
T KOG1812|consen 224 KEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVD-DITLKYL 302 (384)
T ss_pred HHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCccccc-HHHHHHH
Confidence 99999988878999999998877653 2345667899999999999999999999999999987644322 2222333
Q ss_pred HhcCCCccCCCCCcceeccCCCcceEEeccccccccccccccCCCCC
Q 025608 196 AQNQKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHG 242 (250)
Q Consensus 196 ~~~~~~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~ 242 (250)
+ ..|+.||+|+..|++.+|||||+|+||++|||.|+.+|.++.+.
T Consensus 303 a--~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~ 347 (384)
T KOG1812|consen 303 A--KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGE 347 (384)
T ss_pred H--HhcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCcc
Confidence 3 78899999999999999999999999999999999999866664
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.6e-36 Score=249.93 Aligned_cols=208 Identities=26% Similarity=0.649 Sum_probs=169.4
Q ss_pred cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcC-cccccCCCCCCCCCCCHHHHhccCChHHHHHH
Q 025608 36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQEN-VTSIGCPVTDCGGSLEPEYCRDILPEEAFDKW 114 (250)
Q Consensus 36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~-~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~ 114 (250)
......+.|.|||+......-+..++|+|.||+.|++.|+...|.+| ...++||+.+|+..-....++.+|+.+++++|
T Consensus 179 ~F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arY 258 (445)
T KOG1814|consen 179 KFVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARY 258 (445)
T ss_pred HHHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHH
Confidence 44566789999999998877788889999999999999999999997 58999999999999999999999999999999
Q ss_pred HHHHHhhccCC-CCeecCCCCCCCCceecCccCccCcccCCcccchhccccCcccCCCCCchhHh--------hhccCCC
Q 025608 115 GKALCESLIPG-AQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQ--------KLHKDEP 185 (250)
Q Consensus 115 ~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~--------~~~~~~~ 185 (250)
++++.+.++.. .+.++||.+.|+.+...+++ ...+.|..|+..||..|+..||++..|.--. .+.....
T Consensus 259 e~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~--~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~ 336 (445)
T KOG1814|consen 259 EKLMLQKTLELMSDVVYCPRACCQLPVKQDPG--RALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADE 336 (445)
T ss_pred HHHHHHHHHHhhcccccCChhhccCccccCch--hhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCH
Confidence 99999888876 56679999999999855544 3668999999999999999999999996431 1111111
Q ss_pred ch------------HHHHHHHHH----hcCCCccCCCCCcceeccCCCcceEE-ecccccccccccccc---CCCCCcCC
Q 025608 186 ES------------EDIILMKLA----QNQKWNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLS---TVSHGYYC 245 (250)
Q Consensus 186 ~~------------~~~~~~~~~----~~~~~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~---~~~h~~~~ 245 (250)
.+ ...++++++ -..+.++||+|+++|+|++|||+|+| +|++.|||+|...+. ++.|+.+=
T Consensus 337 a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~ 416 (445)
T KOG1814|consen 337 ARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEP 416 (445)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCCChhhhhcCC
Confidence 10 011122222 12466999999999999999999999 999999999987773 56786543
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=1.7e-29 Score=224.77 Aligned_cols=203 Identities=27% Similarity=0.593 Sum_probs=165.0
Q ss_pred CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcc-cccCCCCCCCCCCCHHHHhccCCh-HHHHHHHH
Q 025608 39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVT-SIGCPVTDCGGSLEPEYCRDILPE-EAFDKWGK 116 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~-~i~CP~~~C~~~l~~~~i~~~l~~-~~~~~~~~ 116 (250)
....+|.||++..+. ......|+|.||..||..|+...|.++.. .|+||..+|...+..+.|..++++ +..++|.+
T Consensus 68 ~~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~ 145 (444)
T KOG1815|consen 68 KGDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQR 145 (444)
T ss_pred CccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHHH
Confidence 455789999998876 34456999999999999999999988632 399999999999999999999988 59999999
Q ss_pred HHHhhccCCCC-eecCCCCCCCCceecCccCccCcccCCcccchhccccCcccCCCCCchhHhhhccCCCchHHHHHHHH
Q 025608 117 ALCESLIPGAQ-KFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKL 195 (250)
Q Consensus 117 ~~~~~~~~~~~-~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~ 195 (250)
.+..+++.... ..|||+|+|+..+... ......+.| .|+..||+.|..+||++.+|.....|.+......+...
T Consensus 146 ~i~~syve~~~~lkwCP~~~C~~av~~~-~~~~~~v~C-~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~--- 220 (444)
T KOG1815|consen 146 YILRSYVEDNVPLKWCPAPGCGLAVKFG-SLESVEVDC-GCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETIN--- 220 (444)
T ss_pred HHHHHHHhcCCccccCCCCCCCceeecc-CCCccceeC-CCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhh---
Confidence 99999998755 4599999999988864 233466888 56669999999999999999998887665433322211
Q ss_pred HhcCCCccCCCCCcceeccCCCcceEE-e--ccccccccccccccCCCCCcC-CCCCCC
Q 025608 196 AQNQKWNRCPNCKFYVEKKDGCSYIRC-R--CGHAFCYHCGVQLSTVSHGYY-CPSCNK 250 (250)
Q Consensus 196 ~~~~~~~~CP~C~~~i~k~~GCnhm~C-~--C~~~FC~~C~~~~~~~~h~~~-~~~~~~ 250 (250)
....+.++||+|.++|+|++|||||+| . |+++|||+|+..|. .|++. .+.|||
T Consensus 221 wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~--~h~~~~~~~c~~ 277 (444)
T KOG1815|consen 221 WILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLS--DHGSSTGYSCNR 277 (444)
T ss_pred hhhccCccCCCcccchhccCCccccccccCCcCCeeceeeecccc--cccccceeeeee
Confidence 234556889999999999999999999 5 99999999999996 44333 667764
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=1.3e-25 Score=182.52 Aligned_cols=204 Identities=27% Similarity=0.614 Sum_probs=152.6
Q ss_pred ccCCCCceecccCcccccCCCceecCCCC--CcchHHHHHHHHHHHhhcCc--------ccccCCCCCCCCCCCHH-HHh
Q 025608 35 RSETSRSFVCEICVETKLRNESFSIKGCS--HMYCVDCTVKYVDSKLQENV--------TSIGCPVTDCGGSLEPE-YCR 103 (250)
Q Consensus 35 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~--------~~i~CP~~~C~~~l~~~-~i~ 103 (250)
...+.+..+|-.|-+.-.+ ...++|. |..|.+|++.|....+++.. ..+.||. +|...+-.+ .--
T Consensus 215 i~~N~~ni~C~~Ctdv~~~---vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF 290 (446)
T KOG0006|consen 215 IATNSRNITCITCTDVRSP---VLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHF 290 (446)
T ss_pred hhcccccceeEEecCCccc---eEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhh
Confidence 4566778899999875443 2234888 99999999999999987743 4678885 777665444 345
Q ss_pred ccCChHHHHHHHHHHHhhccCCCCeecCCCCCCCCceecCccCccCcccCCc-ccchhccccCcccCCCCCchhHhh---
Q 025608 104 DILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPN-CHRLFCAQCKVAWHAGIECADFQK--- 179 (250)
Q Consensus 104 ~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~H~~~~C~~~~~--- 179 (250)
.+|+.+.+.+|++...+..+...+.+.||.|+|+..+...++ ..++.|+. |++.||..|...+|.|. |.+.-.
T Consensus 291 ~ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD--~rkvtC~~gCgf~FCR~C~e~yh~ge-C~~~~~as~ 367 (446)
T KOG0006|consen 291 RILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPD--QRKVTCEGGCGFAFCRECKEAYHEGE-CSAVFEASG 367 (446)
T ss_pred eecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCC--CCcccCCCCchhHhHHHHHhhhcccc-ceeeecccc
Confidence 789999999999999999999999999999999998887763 57899987 99999999999999884 442110
Q ss_pred -----hccCCCchHHHH---HHHHHhcCCCccCCCCCcceeccCCCcceEE-e--ccccccccccccccCCCCCcCC
Q 025608 180 -----LHKDEPESEDII---LMKLAQNQKWNRCPNCKFYVEKKDGCSYIRC-R--CGHAFCYHCGVQLSTVSHGYYC 245 (250)
Q Consensus 180 -----~~~~~~~~~~~~---~~~~~~~~~~~~CP~C~~~i~k~~GCnhm~C-~--C~~~FC~~C~~~~~~~~h~~~~ 245 (250)
..-++...+.+. .....-+..+|+||+|.++.||+|||-||.| . ||.+|||.|+-+|+-.--+-+|
T Consensus 368 t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~CmgdHW 444 (446)
T KOG0006|consen 368 TTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVCMGDHW 444 (446)
T ss_pred ccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhhccccc
Confidence 011111111111 1112223567999999999999999999999 4 9999999999999644333333
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.21 E-value=1.2e-11 Score=80.65 Aligned_cols=63 Identities=37% Similarity=0.839 Sum_probs=53.1
Q ss_pred HHHHHHHHhhccCC-CCeecCCCCCCCCceecCccCccCcccCCcccchhccccCcccCCCCCc
Q 025608 112 DKWGKALCESLIPG-AQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIEC 174 (250)
Q Consensus 112 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 174 (250)
++|++++.+.++.. .+..|||+|+|+.++....+.....+.|+.|+..||+.|+.+||.+.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 46888888888876 4566999999999888864334578999999999999999999999987
No 6
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=99.21 E-value=3.1e-12 Score=83.47 Aligned_cols=63 Identities=30% Similarity=0.774 Sum_probs=41.4
Q ss_pred HHHHHHHHhhccCCCCe-ecCCCCCCCCceecCccCccCcccCCcccchhccccCcccCCCCCc
Q 025608 112 DKWGKALCESLIPGAQK-FYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIEC 174 (250)
Q Consensus 112 ~~~~~~~~~~~~~~~~~-~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 174 (250)
++|++++.+.++..... .+||+|+|+.++..+++.....+.|+.|+..||+.|+.+||.|.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 46777777777765544 5999999999999987655445999999999999999999999886
No 7
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.52 E-value=1.5e-07 Score=61.07 Aligned_cols=41 Identities=32% Similarity=1.010 Sum_probs=36.7
Q ss_pred cCCCccCC--CCCcceeccC--CCcceEE-eccccccccccccccC
Q 025608 198 NQKWNRCP--NCKFYVEKKD--GCSYIRC-RCGHAFCYHCGVQLST 238 (250)
Q Consensus 198 ~~~~~~CP--~C~~~i~k~~--GCnhm~C-~C~~~FC~~C~~~~~~ 238 (250)
+..++.|| +|+.+|...+ |..+|+| .|++.|||.|+.+|+.
T Consensus 15 ~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~ 60 (64)
T smart00647 15 NPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHS 60 (64)
T ss_pred CCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCC
Confidence 35778999 9999999975 9999999 9999999999999953
No 8
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.50 E-value=6.5e-08 Score=57.93 Aligned_cols=41 Identities=27% Similarity=0.652 Sum_probs=32.5
Q ss_pred ecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608 43 VCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV 90 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 90 (250)
+|+||++++..++.+..++|+|.||.+|+..|++.. ..||.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~-------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN-------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS-------SB-TT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC-------CcCCc
Confidence 599999999755555556899999999999999853 28886
No 9
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.47 E-value=7.2e-08 Score=56.94 Aligned_cols=41 Identities=22% Similarity=0.577 Sum_probs=28.0
Q ss_pred cccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608 44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV 90 (250)
Q Consensus 44 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 90 (250)
|+||++.+..+. .++|||.||.+|+.++++..- ...+.||.
T Consensus 1 CpiC~~~~~~Pv---~l~CGH~FC~~Cl~~~~~~~~---~~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLFKDPV---SLPCGHSFCRSCLERLWKEPS---GSGFSCPE 41 (42)
T ss_dssp ETTTTSB-SSEE---E-SSSSEEEHHHHHHHHCCSS---SST---SS
T ss_pred CCccchhhCCcc---ccCCcCHHHHHHHHHHHHccC---CcCCCCcC
Confidence 899999887643 359999999999999997432 22388986
No 10
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=98.46 E-value=6.2e-08 Score=62.89 Aligned_cols=41 Identities=39% Similarity=1.162 Sum_probs=29.5
Q ss_pred cCCCccCCC--CCcceeccCCCcc--eEE-eccccccccccccccC
Q 025608 198 NQKWNRCPN--CKFYVEKKDGCSY--IRC-RCGHAFCYHCGVQLST 238 (250)
Q Consensus 198 ~~~~~~CP~--C~~~i~k~~GCnh--m~C-~C~~~FC~~C~~~~~~ 238 (250)
...++.||+ |+.++++.+|.++ |+| .|++.|||.|+.+|+.
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp ---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 345589988 9999999999999 999 7999999999999953
No 11
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.46 E-value=1.7e-07 Score=56.08 Aligned_cols=41 Identities=29% Similarity=0.773 Sum_probs=35.0
Q ss_pred ecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608 43 VCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV 90 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 90 (250)
+|+||++.+.....+.+++|+|.||..|+.... ...+.||.
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~~~~~CP~ 41 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------GKSVKCPI 41 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------CCCCCCcC
Confidence 499999999656667788999999999999988 35688997
No 12
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.45 E-value=1.5e-07 Score=55.41 Aligned_cols=40 Identities=33% Similarity=0.831 Sum_probs=32.7
Q ss_pred cccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608 44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV 90 (250)
Q Consensus 44 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 90 (250)
|+||++.+..+. .+++|+|.||.+|+.+++.. ...+.||.
T Consensus 1 C~iC~~~~~~~~--~~~~C~H~fC~~C~~~~~~~-----~~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFEDPV--ILLPCGHSFCRDCLRKWLEN-----SGSVKCPL 40 (41)
T ss_dssp ETTTSSBCSSEE--EETTTSEEEEHHHHHHHHHH-----TSSSBTTT
T ss_pred CCcCCccccCCC--EEecCCCcchHHHHHHHHHh-----cCCccCCc
Confidence 799999876543 35799999999999999997 35567886
No 13
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.38 E-value=3.6e-07 Score=71.36 Aligned_cols=69 Identities=20% Similarity=0.507 Sum_probs=50.4
Q ss_pred cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhh---------cCcccccCCCCCCCCCCCHHHHhccC
Q 025608 36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQ---------ENVTSIGCPVTDCGGSLEPEYCRDIL 106 (250)
Q Consensus 36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~---------~~~~~i~CP~~~C~~~l~~~~i~~~l 106 (250)
....+.++|+||++.+..+. ...|+|.||..|+..|+...-. .......||. |...++...+..+.
T Consensus 13 ~~~~~~~~CpICld~~~dPV---vT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiy 87 (193)
T PLN03208 13 VDSGGDFDCNICLDQVRDPV---VTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIY 87 (193)
T ss_pred ccCCCccCCccCCCcCCCcE---EcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEee
Confidence 34456789999999876443 3589999999999999764311 1234679998 99999988877665
Q ss_pred ChH
Q 025608 107 PEE 109 (250)
Q Consensus 107 ~~~ 109 (250)
+..
T Consensus 88 grg 90 (193)
T PLN03208 88 GRG 90 (193)
T ss_pred ccC
Confidence 443
No 14
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.37 E-value=3.5e-07 Score=54.05 Aligned_cols=42 Identities=29% Similarity=0.672 Sum_probs=24.4
Q ss_pred cccCcccc-cCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCC
Q 025608 44 CEICVETK-LRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCP 89 (250)
Q Consensus 44 C~iC~~~~-~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 89 (250)
|+||.+ + ..+..+.+++|||.||.+|+.+.+.... ...|+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~---~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD---RNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC---CCeeeCc
Confidence 899999 6 4455566779999999999999998443 3568887
No 15
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.32 E-value=4.7e-07 Score=52.66 Aligned_cols=38 Identities=32% Similarity=0.927 Sum_probs=28.9
Q ss_pred cccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608 44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV 90 (250)
Q Consensus 44 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 90 (250)
|+||++.+.. .+.+++|||.||.+|+.+|++.. .+||.
T Consensus 1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~-------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKN-------PKCPV 38 (39)
T ss_dssp ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCT-------SB-TT
T ss_pred CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCc-------CCCcC
Confidence 7999987765 33457999999999999998852 57775
No 16
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.24 E-value=1e-06 Score=67.17 Aligned_cols=57 Identities=18% Similarity=0.607 Sum_probs=43.5
Q ss_pred CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh
Q 025608 37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR 103 (250)
Q Consensus 37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~ 103 (250)
.....+.|+||++.+.....+ ...|||.||..|++..+. ...+||. |+..|+..++-
T Consensus 127 ~~~~~~~CPiCl~~~sek~~v-sTkCGHvFC~~Cik~alk-------~~~~CP~--C~kkIt~k~~~ 183 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKVPV-STKCGHVFCSQCIKDALK-------NTNKCPT--CRKKITHKQFH 183 (187)
T ss_pred ccccccCCCceecchhhcccc-ccccchhHHHHHHHHHHH-------hCCCCCC--cccccchhhhe
Confidence 445568999999998765544 359999999999999887 3468998 66667666543
No 17
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.15 E-value=2.8e-06 Score=50.48 Aligned_cols=44 Identities=32% Similarity=0.809 Sum_probs=33.2
Q ss_pred ecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCC
Q 025608 43 VCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGS 96 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 96 (250)
+|+||++.+. ....+.+|+|.||.+|+..|+.. ....||. |+..
T Consensus 1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~------~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKS------GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhhh--CceEecCCCChhcHHHHHHHHHh------CcCCCCC--CCCc
Confidence 4899999873 33445579999999999999885 3457887 6643
No 18
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=97.98 E-value=6.8e-06 Score=50.52 Aligned_cols=45 Identities=27% Similarity=0.803 Sum_probs=33.9
Q ss_pred eecccCcccccCCCceecCCCCCc-chHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608 42 FVCEICVETKLRNESFSIKGCSHM-YCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE 98 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 98 (250)
..|.||++.... ..+.+|+|. ||.+|+.+++. ....||. |...++
T Consensus 3 ~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~-------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 3 EECPICFENPRD---VVLLPCGHLCFCEECAERLLK-------RKKKCPI--CRQPIE 48 (50)
T ss_dssp SB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHH-------TTSBBTT--TTBB-S
T ss_pred CCCccCCccCCc---eEEeCCCChHHHHHHhHHhcc-------cCCCCCc--CChhhc
Confidence 569999997543 345699999 99999999998 3468998 776654
No 19
>PHA02926 zinc finger-like protein; Provisional
Probab=97.85 E-value=1.6e-05 Score=63.07 Aligned_cols=57 Identities=26% Similarity=0.708 Sum_probs=40.1
Q ss_pred CCceecccCcccccC-----CCce-ecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608 39 SRSFVCEICVETKLR-----NESF-SIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE 98 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~-----~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 98 (250)
++..+|+||++.... +..| .+.+|+|.||..|+..|..... +....-.||. |...+.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~-~~~~~rsCPi--CR~~f~ 230 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRR-ETGASDNCPI--CRTRFR 230 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhcc-ccCcCCcCCC--Ccceee
Confidence 445689999997521 2222 3669999999999999998653 2234457998 776543
No 20
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.80 E-value=1.2e-05 Score=64.22 Aligned_cols=60 Identities=22% Similarity=0.624 Sum_probs=46.9
Q ss_pred CCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccC
Q 025608 38 TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDIL 106 (250)
Q Consensus 38 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l 106 (250)
+...|+|.||++....+. +.-|||.||..||-+|+..+.. .-.||. |+..++.+.+--+.
T Consensus 44 ~~~~FdCNICLd~akdPV---vTlCGHLFCWpClyqWl~~~~~----~~~cPV--CK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPV---VTLCGHLFCWPCLYQWLQTRPN----SKECPV--CKAEVSIDTVVPLY 103 (230)
T ss_pred CCCceeeeeeccccCCCE---EeecccceehHHHHHHHhhcCC----CeeCCc--cccccccceEEeee
Confidence 577899999999776544 3489999999999999996644 236788 88888887766554
No 21
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=97.75 E-value=3.4e-05 Score=44.00 Aligned_cols=38 Identities=29% Similarity=0.795 Sum_probs=28.2
Q ss_pred cccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608 44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV 90 (250)
Q Consensus 44 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 90 (250)
|+||++... ....++|+|.||..|+..|+. .....||.
T Consensus 1 C~iC~~~~~---~~~~~~C~H~~c~~C~~~~~~------~~~~~CP~ 38 (39)
T smart00184 1 CPICLEELK---DPVVLPCGHTFCRSCIRKWLK------SGNNTCPI 38 (39)
T ss_pred CCcCccCCC---CcEEecCCChHHHHHHHHHHH------hCcCCCCC
Confidence 789988732 244569999999999999988 12356775
No 22
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.74 E-value=4.1e-05 Score=65.11 Aligned_cols=108 Identities=19% Similarity=0.447 Sum_probs=67.8
Q ss_pred CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccCChHHHHHHHHHH
Q 025608 39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKAL 118 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~ 118 (250)
.+.+.|+||++.+..+ .+++|+|.||..|+...+. ..+.||. |.. ... .+.....+.......
T Consensus 11 ~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-------~~~~Cp~--cr~-~~~----~~~~n~~l~~~~~~~ 73 (386)
T KOG2177|consen 11 QEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-------GPLSCPV--CRP-PSR----NLRPNVLLANLVERL 73 (386)
T ss_pred cccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-------CCcCCcc--cCC-chh----ccCccHHHHHHHHHH
Confidence 4567899999999876 4569999999999999998 4589998 663 211 222333333333333
Q ss_pred HhhccCCCC---eecCCCCCCCCceecCccCccCcccCCcccchhccccC-cccCCCCCc
Q 025608 119 CESLIPGAQ---KFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCK-VAWHAGIEC 174 (250)
Q Consensus 119 ~~~~~~~~~---~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~-~~~H~~~~C 174 (250)
....+.... ...|+. . .....+.|..|...+|..|. ...|.++.-
T Consensus 74 ~~~~~~~~~~~~~~~c~~----------~-~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~ 122 (386)
T KOG2177|consen 74 RQLRLSRPLGSKEELCEK----------H-GEELKLFCEEDEKLLCVLCRESGEHRGHPV 122 (386)
T ss_pred HhcCCcccccccchhhhh----------c-CCcceEEecccccccCCCCCCcccccCCcc
Confidence 322111111 113331 1 11145778899999999998 566777643
No 23
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.69 E-value=4.4e-05 Score=62.27 Aligned_cols=51 Identities=27% Similarity=0.703 Sum_probs=37.3
Q ss_pred CCceecccCcccccCCC-----ceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608 39 SRSFVCEICVETKLRNE-----SFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE 98 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 98 (250)
....+|+||++.+..+. +..+.+|+|.||.+|+..|+.. .-.||. |...+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-------~~tCPl--CR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-------KNTCPV--CRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-------CCCCCC--CCCEee
Confidence 34568999999875432 2345689999999999999863 237998 776543
No 24
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.62 E-value=2.7e-05 Score=68.86 Aligned_cols=59 Identities=20% Similarity=0.589 Sum_probs=46.1
Q ss_pred ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccC
Q 025608 41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDIL 106 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l 106 (250)
...||||++..+... +..|||.||..||.+|+... .-..+-.||. |...+.+.++..+.
T Consensus 186 ~~~CPICL~~~~~p~---~t~CGHiFC~~CiLqy~~~s--~~~~~~~CPi--C~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPV---RTNCGHIFCGPCILQYWNYS--AIKGPCSCPI--CRSTITLKDLLPVF 244 (513)
T ss_pred CCcCCcccCCCCccc---ccccCceeeHHHHHHHHhhh--cccCCccCCc--hhhhccccceeeee
Confidence 678999998766543 34799999999999999977 2235778998 99888887665543
No 25
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.57 E-value=4.2e-05 Score=62.92 Aligned_cols=52 Identities=23% Similarity=0.758 Sum_probs=40.1
Q ss_pred CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh
Q 025608 40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR 103 (250)
Q Consensus 40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~ 103 (250)
....|.+|++....+. ..+|||.||.+|+..|....- .||. |...+.+..+-
T Consensus 238 a~~kC~LCLe~~~~pS---aTpCGHiFCWsCI~~w~~ek~-------eCPl--CR~~~~pskvi 289 (293)
T KOG0317|consen 238 ATRKCSLCLENRSNPS---ATPCGHIFCWSCILEWCSEKA-------ECPL--CREKFQPSKVI 289 (293)
T ss_pred CCCceEEEecCCCCCC---cCcCcchHHHHHHHHHHcccc-------CCCc--ccccCCCccee
Confidence 3457999999875543 459999999999999998542 2998 88887776543
No 26
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=97.48 E-value=0.00015 Score=46.57 Aligned_cols=51 Identities=25% Similarity=0.258 Sum_probs=39.5
Q ss_pred eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhc
Q 025608 42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRD 104 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 104 (250)
+.|+||.+.+..+ ...+|||.||++|+.+|+.. ...||. |+..++.+++..
T Consensus 2 ~~Cpi~~~~~~~P---v~~~~G~v~~~~~i~~~~~~-------~~~cP~--~~~~~~~~~l~~ 52 (63)
T smart00504 2 FLCPISLEVMKDP---VILPSGQTYERRAIEKWLLS-------HGTDPV--TGQPLTHEDLIP 52 (63)
T ss_pred cCCcCCCCcCCCC---EECCCCCEEeHHHHHHHHHH-------CCCCCC--CcCCCChhhcee
Confidence 4699999987754 23599999999999999985 247897 777777665543
No 27
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.33 E-value=0.00019 Score=61.45 Aligned_cols=46 Identities=28% Similarity=0.628 Sum_probs=38.3
Q ss_pred eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCC
Q 025608 42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDC 93 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C 93 (250)
.+|.||+|++...+-...++|.|.|...|+..|+... .-.||.+++
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~------r~~CPvCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT------RTFCPVCKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc------CccCCCCCC
Confidence 6899999999877777778999999999999999955 125998333
No 28
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.33 E-value=0.00011 Score=63.77 Aligned_cols=86 Identities=17% Similarity=0.393 Sum_probs=54.1
Q ss_pred CccCcccCCcccchhccccCcccCCCCCchhHhhhccCCCchHHHHHHHHHhcCCCccCCCCCcceeccCCCcc-eEE-e
Q 025608 146 EAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSY-IRC-R 223 (250)
Q Consensus 146 ~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~C~~~i~k~~GCnh-m~C-~ 223 (250)
+....+.|..|...+|.-|+..-|++..=-....+.....++. .....-.++.+|- ..+|=|| |.| .
T Consensus 172 ~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grv----s~~~s~r~~~~ct-------~h~~e~~smyc~~ 240 (699)
T KOG4367|consen 172 PKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRV----SRRLSPRKVSTCT-------DHELENHSMYCVQ 240 (699)
T ss_pred hhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCce----eeccchhhhhhcc-------CCCCCCceEEEEe
Confidence 3456789999999999999998888753222223333222221 1111111223342 1244455 999 9
Q ss_pred ccccccccccccccCCCCC
Q 025608 224 CGHAFCYHCGVQLSTVSHG 242 (250)
Q Consensus 224 C~~~FC~~C~~~~~~~~h~ 242 (250)
|+...||.|+.+.+..+|-
T Consensus 241 ck~pvc~~clee~khs~he 259 (699)
T KOG4367|consen 241 CKMPVCYQCLEEGKHSSHE 259 (699)
T ss_pred cCChHHHHHHHhhcccchh
Confidence 9999999999999877773
No 29
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.24 E-value=0.00028 Score=61.77 Aligned_cols=66 Identities=21% Similarity=0.507 Sum_probs=45.7
Q ss_pred CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH-hccCChHHHHHHHH
Q 025608 39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC-RDILPEEAFDKWGK 116 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i-~~~l~~~~~~~~~~ 116 (250)
...+.|+||.+.+..+. +.+|+|.||..|+..++... ..||. |...+....+ .+.+-.++++.|..
T Consensus 24 e~~l~C~IC~d~~~~Pv---itpCgH~FCs~CI~~~l~~~-------~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~~~~ 90 (397)
T TIGR00599 24 DTSLRCHICKDFFDVPV---LTSCSHTFCSLCIRRCLSNQ-------PKCPL--CRAEDQESKLRSNWLVSEIVESFKN 90 (397)
T ss_pred ccccCCCcCchhhhCcc---CCCCCCchhHHHHHHHHhCC-------CCCCC--CCCccccccCccchHHHHHHHHHHH
Confidence 44568999999886543 45999999999999998631 37997 8877665433 23333455555543
No 30
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.21 E-value=0.00024 Score=58.87 Aligned_cols=56 Identities=29% Similarity=0.719 Sum_probs=43.6
Q ss_pred cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608 36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP 99 (250)
Q Consensus 36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~ 99 (250)
.+.....+|.||++++.-.+-...++|.|.|.+.|+.+|+... ..+||. |...+++
T Consensus 318 ~ea~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y------~~~CPv--Crt~iPP 373 (374)
T COG5540 318 VEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGY------SNKCPV--CRTAIPP 373 (374)
T ss_pred HhcCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhh------cccCCc--cCCCCCC
Confidence 4556678999999999644445667999999999999999833 458998 8776653
No 31
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.10 E-value=0.0012 Score=55.76 Aligned_cols=53 Identities=25% Similarity=0.478 Sum_probs=36.7
Q ss_pred eecccCccccc-CCCc-eecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608 42 FVCEICVETKL-RNES-FSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC 102 (250)
Q Consensus 42 ~~C~iC~~~~~-~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 102 (250)
..||+|..+.. .+.+ +....|||.||.+|+...+. . .+..||. |+..+....+
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~----~--~~~~CP~--C~~~lrk~~f 58 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV----R--GSGSCPE--CDTPLRKNNF 58 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc----C--CCCCCCC--CCCccchhhc
Confidence 35999998642 2222 22227999999999999974 2 2348996 8887776553
No 32
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=96.75 E-value=0.00097 Score=44.34 Aligned_cols=41 Identities=22% Similarity=0.600 Sum_probs=29.4
Q ss_pred ecccCcccccCC----------CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608 43 VCEICVETKLRN----------ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV 90 (250)
Q Consensus 43 ~C~iC~~~~~~~----------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 90 (250)
.|.||++++... -.+....|+|.|...|+.+|++.. -.||.
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-------~~CP~ 71 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-------NTCPL 71 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-------SB-TT
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-------CcCCC
Confidence 399999998221 223355899999999999999733 17886
No 33
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.72 E-value=0.00073 Score=44.51 Aligned_cols=57 Identities=19% Similarity=0.412 Sum_probs=26.7
Q ss_pred ceecccCccccc-CCCcee----cCCCCCcchHHHHHHHHHHHhhcCc--cc--ccCCCCCCCCCCCH
Q 025608 41 SFVCEICVETKL-RNESFS----IKGCSHMYCVDCTVKYVDSKLQENV--TS--IGCPVTDCGGSLEP 99 (250)
Q Consensus 41 ~~~C~iC~~~~~-~~~~~~----~~~C~H~fC~~Cl~~~~~~~i~~~~--~~--i~CP~~~C~~~l~~ 99 (250)
..+|+||++... ....+. ...|+..|...||.+|+...-.+.. .+ =.||. |...|+.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeeeE
Confidence 357999998864 322222 3478899999999999987655432 12 26997 8877654
No 34
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.56 E-value=0.0015 Score=55.08 Aligned_cols=62 Identities=26% Similarity=0.516 Sum_probs=46.0
Q ss_pred eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhc-cCChHHHHHHH
Q 025608 42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRD-ILPEEAFDKWG 115 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~~ 115 (250)
+-|.||++.|..+.+ .+|+|.||.-|++.|+..+ -.||. |...+....++. .+-.++++.|.
T Consensus 24 LRC~IC~eyf~ip~i---tpCsHtfCSlCIR~~L~~~-------p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 24 LRCGICFEYFNIPMI---TPCSHTFCSLCIRKFLSYK-------PQCPT--CCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHhHHHHHhcCcee---ccccchHHHHHHHHHhccC-------CCCCc--eecccchhhhhhhhHHHHHHHHHH
Confidence 359999999876543 4899999999999999843 35887 888888777753 33445555554
No 35
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.45 E-value=0.0022 Score=57.13 Aligned_cols=59 Identities=27% Similarity=0.667 Sum_probs=44.2
Q ss_pred ccCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608 35 RSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE 100 (250)
Q Consensus 35 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 100 (250)
..++....+|.+|-++.. +.+ ...|.|.||+-|++.|+.....+. .+.||. |...|+.+
T Consensus 530 ~~enk~~~~C~lc~d~ae--d~i-~s~ChH~FCrlCi~eyv~~f~~~~--nvtCP~--C~i~LsiD 588 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDPAE--DYI-ESSCHHKFCRLCIKEYVESFMENN--NVTCPV--CHIGLSID 588 (791)
T ss_pred CccccCceeecccCChhh--hhH-hhhhhHHHHHHHHHHHHHhhhccc--CCCCcc--cccccccc
Confidence 345667788999988654 323 349999999999999999775543 399998 77666655
No 36
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.43 E-value=0.0027 Score=51.85 Aligned_cols=53 Identities=25% Similarity=0.612 Sum_probs=38.0
Q ss_pred CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608 40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC 102 (250)
Q Consensus 40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 102 (250)
..+.|.||++.... +...+|||.||..|+...+..+ ..-.||. |.....+..+
T Consensus 214 ~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~-----k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKK-----KYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred cccceeeeecccCC---cccccccchhhHHHHHHHHHhh-----ccccCch--hhhhccchhh
Confidence 35679999986543 4566999999999999954322 2336998 8877666655
No 37
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.40 E-value=0.0027 Score=39.97 Aligned_cols=50 Identities=24% Similarity=0.529 Sum_probs=31.7
Q ss_pred CCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCC
Q 025608 38 TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCG 94 (250)
Q Consensus 38 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 94 (250)
....+.|+|-...+..+ .....|+|.|-++-+..|+ .+...+.||..+|.
T Consensus 8 ~~~~~~CPiT~~~~~~P--V~s~~C~H~fek~aI~~~i-----~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDP--VKSKKCGHTFEKEAILQYI-----QRNGSKRCPVAGCN 57 (57)
T ss_dssp SB--SB-TTTSSB-SSE--EEESSS--EEEHHHHHHHC-----TTTS-EE-SCCC-S
T ss_pred cEeccCCCCcCChhhCC--cCcCCCCCeecHHHHHHHH-----HhcCCCCCCCCCCC
Confidence 34456899999887644 4456999999999999999 23467899998884
No 38
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.23 E-value=0.0011 Score=57.20 Aligned_cols=40 Identities=28% Similarity=0.724 Sum_probs=37.0
Q ss_pred CCCccCCC--CCcceeccCCCcceEE-eccccccccccccccC
Q 025608 199 QKWNRCPN--CKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLST 238 (250)
Q Consensus 199 ~~~~~CP~--C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~ 238 (250)
.+++.||+ |..++....|.+-..| +|+..||..|...|++
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG 313 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG 313 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC
Confidence 46799998 9999988899999999 9999999999999965
No 39
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.10 E-value=0.0026 Score=59.16 Aligned_cols=56 Identities=20% Similarity=0.596 Sum_probs=42.4
Q ss_pred CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608 39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI 105 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~ 105 (250)
.....|++|.+... + ..+..|+|.||-+|++..+...- =+||. |+..|...++..+
T Consensus 641 K~~LkCs~Cn~R~K--d-~vI~kC~H~FC~~Cvq~r~etRq------RKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 641 KELLKCSVCNTRWK--D-AVITKCGHVFCEECVQTRYETRQ------RKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCchh--h-HHHHhcchHHHHHHHHHHHHHhc------CCCCC--CCCCCCccccccc
Confidence 45678999984322 2 23459999999999999988553 38997 9998988887654
No 40
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.05 E-value=0.012 Score=58.55 Aligned_cols=181 Identities=19% Similarity=0.415 Sum_probs=101.1
Q ss_pred eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCc---ccccCCCCCCCCCCCHHHHhccCChHHHHHHHHHH
Q 025608 42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENV---TSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKAL 118 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~---~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~ 118 (250)
-.|.|||.+.-.......+.|+|.|...|.+.-++..-.+.+ ..|.||. |...++--.++.+|++ +.+.|+...
T Consensus 3487 DmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP-iKel~edV~ 3563 (3738)
T KOG1428|consen 3487 DMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP-IKELYEDVR 3563 (3738)
T ss_pred ceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH-HHHHHHHHH
Confidence 359999987643333445699999999999999987766542 4689998 9999999888888864 233333322
Q ss_pred Hhh-------ccCCCCeecCCCCCCCCceecCc-cCccCcccCCcccchhccccCcccCCCC-CchhHhhhccCCCchHH
Q 025608 119 CES-------LIPGAQKFYCPFKDCSALLIDDA-GEAIRESECPNCHRLFCAQCKVAWHAGI-ECADFQKLHKDEPESED 189 (250)
Q Consensus 119 ~~~-------~~~~~~~~~Cp~~~C~~~~~~~~-~~~~~~~~C~~C~~~~C~~C~~~~H~~~-~C~~~~~~~~~~~~~~~ 189 (250)
.++ .+...+.+.=| += -+..++ +...++. .++.|.+|++.+-+|. .|+.... .+....++
T Consensus 3564 ~KA~MRLEYeGL~ks~AiT~P--~~--~FYNdPa~YAmnRY-----~Y~vC~KCrKAYFGGEaRCdAe~~--~ddydP~E 3632 (3738)
T KOG1428|consen 3564 RKALMRLEYEGLHKSEAITTP--GV--RFYNDPAGYAMNRY-----AYYVCYKCRKAYFGGEARCDAEAG--GDDYDPRE 3632 (3738)
T ss_pred HHHhhhhhhccccccccccCC--Cc--eeccChhhhhhhhh-----hhhhhhhhhhhhcCchhhcchhcC--CCCCCHHH
Confidence 221 22233333333 11 122221 1111211 3678889999887774 5665332 11122221
Q ss_pred HHHHHHHhcCCCccCCCCCc-cee-ccCCCcc---eEEeccccccccccccc
Q 025608 190 IILMKLAQNQKWNRCPNCKF-YVE-KKDGCSY---IRCRCGHAFCYHCGVQL 236 (250)
Q Consensus 190 ~~~~~~~~~~~~~~CP~C~~-~i~-k~~GCnh---m~C~C~~~FC~~C~~~~ 236 (250)
+.-..--.-.+.+.||+=|+ .+| |-.=|-. ..|-=-+|||-.|-.++
T Consensus 3633 LiCG~CSDvS~aQmCPkHGtdfLEYKCRyCCSvAVfFCFGTTHFCn~CHDDF 3684 (3738)
T KOG1428|consen 3633 LICGACSDVSRAQMCPKHGTDFLEYKCRYCCSVAVFFCFGTTHFCNACHDDF 3684 (3738)
T ss_pred hhhccccccccceecccccchhhhhhhheeeeEeEEEEcccccccchhhhHH
Confidence 11111111235688998666 332 1111111 33433578898886665
No 41
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=95.70 E-value=0.0012 Score=42.05 Aligned_cols=47 Identities=26% Similarity=0.721 Sum_probs=21.1
Q ss_pred eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHH
Q 025608 42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEY 101 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~ 101 (250)
.-|++|.+.+..+ +.+..|.|.||..|+...+. -.||. |..+--..+
T Consensus 8 LrCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~~~~---------~~CPv--C~~Paw~qD 54 (65)
T PF14835_consen 8 LRCSICFDILKEP--VCLGGCEHIFCSSCIRDCIG---------SECPV--CHTPAWIQD 54 (65)
T ss_dssp TS-SSS-S--SS---B---SSS--B-TTTGGGGTT---------TB-SS--S--B-S-SS
T ss_pred cCCcHHHHHhcCC--ceeccCccHHHHHHhHHhcC---------CCCCC--cCChHHHHH
Confidence 3599999886644 34569999999999966332 24998 765543333
No 42
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.36 E-value=0.014 Score=50.33 Aligned_cols=95 Identities=21% Similarity=0.391 Sum_probs=55.6
Q ss_pred CCCCceecccCcccccCCC-----ceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH---HH--Hh-cc
Q 025608 37 ETSRSFVCEICVETKLRNE-----SFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP---EY--CR-DI 105 (250)
Q Consensus 37 ~~~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~---~~--i~-~~ 105 (250)
......+|.||++...... +-.+..|.|.||..|++.|-...-.+....-.||. |...... .. +. .-
T Consensus 157 ~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~--CRv~s~~v~pS~~Wv~t~~ 234 (344)
T KOG1039|consen 157 QKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPF--CRVPSSFVNPSSFWVETKE 234 (344)
T ss_pred CccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCc--ccCccccccccceeeeecc
Confidence 3456678999999876443 22356899999999999998544333344558998 6643322 11 11 11
Q ss_pred CChHHHHHHHHHHHhhcc--CCCCeecCCC
Q 025608 106 LPEEAFDKWGKALCESLI--PGAQKFYCPF 133 (250)
Q Consensus 106 l~~~~~~~~~~~~~~~~~--~~~~~~~Cp~ 133 (250)
-...+.+.|++.+..... .......||.
T Consensus 235 ~k~~li~e~~~~~s~~~c~yf~~~~g~cPf 264 (344)
T KOG1039|consen 235 EKQKLIEEYEAEMSAKDCKYFSQGLGSCPF 264 (344)
T ss_pred cccccHHHHHHHhhccchhhhcCCCCCCCC
Confidence 233456666655543211 1234457885
No 43
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.06 E-value=0.073 Score=45.28 Aligned_cols=122 Identities=20% Similarity=0.407 Sum_probs=65.5
Q ss_pred ceecccCcccccC---CCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCC--CCHHHHhccCChH-HHHHH
Q 025608 41 SFVCEICVETKLR---NESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGS--LEPEYCRDILPEE-AFDKW 114 (250)
Q Consensus 41 ~~~C~iC~~~~~~---~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~--l~~~~i~~~l~~~-~~~~~ 114 (250)
..+|.||-++++. +..++.+.|+|.+|..|+...+.. ..+.||. |... +....++.+-..- .++..
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~------~~i~cpf--cR~~~~~~~~~~~~l~kNf~ll~~~ 74 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN------SRILCPF--CRETTEIPDGDVKSLQKNFALLQAI 74 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC------ceeeccC--CCCcccCCchhHhhhhhhHHHHHHH
Confidence 3579999999864 345667899999999999988772 3567776 7766 4445555443222 22222
Q ss_pred HHHHHhhccCCCCeecCCCCCCCCceecCccCccCcccCCcccchhccccCc-ccCCCC
Q 025608 115 GKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKV-AWHAGI 172 (250)
Q Consensus 115 ~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~-~~H~~~ 172 (250)
... ...++.......+| +.|+......-......-.|+.-...+|..|.. ..|.++
T Consensus 75 ~~~-~~~~~~~~~~~~~~-~~c~~~~~nl~~~vc~~~~~~~~~~~~c~t~~~~~~~~~~ 131 (296)
T KOG4185|consen 75 EHM-KKTTVEEKGEADSP-PKCKEHPYNLAEFVCVEPDCSSKDKLMCRTCEEFGIHKGH 131 (296)
T ss_pred HHH-hcccccccCcccCC-cccccCcccccceeecCCCcchhhhhhhhhccchhhhhhh
Confidence 222 12222222222344 135433222211111112355666778888876 334443
No 44
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.85 E-value=0.0085 Score=48.10 Aligned_cols=26 Identities=42% Similarity=1.034 Sum_probs=22.5
Q ss_pred ccccccccccccc-cCCCCCcCCCCCC
Q 025608 224 CGHAFCYHCGVQL-STVSHGYYCPSCN 249 (250)
Q Consensus 224 C~~~FC~~C~~~~-~~~~h~~~~~~~~ 249 (250)
|||-|||-|+-.| ....+...||.|+
T Consensus 65 CGHLFCWpClyqWl~~~~~~~~cPVCK 91 (230)
T KOG0823|consen 65 CGHLFCWPCLYQWLQTRPNSKECPVCK 91 (230)
T ss_pred cccceehHHHHHHHhhcCCCeeCCccc
Confidence 9999999999999 4556777799996
No 45
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=94.82 E-value=0.018 Score=38.14 Aligned_cols=52 Identities=17% Similarity=0.206 Sum_probs=35.7
Q ss_pred CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608 40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC 102 (250)
Q Consensus 40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 102 (250)
..|.|+|+.+-+..+. ..++||.|.++++.+|+.. ....||. ++..++.+++
T Consensus 3 ~~f~CpIt~~lM~dPV---i~~~G~tyer~~I~~~l~~------~~~~~P~--t~~~l~~~~l 54 (73)
T PF04564_consen 3 DEFLCPITGELMRDPV---ILPSGHTYERSAIERWLEQ------NGGTDPF--TRQPLSESDL 54 (73)
T ss_dssp GGGB-TTTSSB-SSEE---EETTSEEEEHHHHHHHHCT------TSSB-TT--T-SB-SGGGS
T ss_pred cccCCcCcCcHhhCce---eCCcCCEEcHHHHHHHHHc------CCCCCCC--CCCcCCcccc
Confidence 4578999998877643 3488999999999999995 3457787 6777776544
No 46
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=94.73 E-value=0.059 Score=46.29 Aligned_cols=48 Identities=19% Similarity=0.582 Sum_probs=35.2
Q ss_pred ecccCcccc-cCC---------CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608 43 VCEICVETK-LRN---------ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP 99 (250)
Q Consensus 43 ~C~iC~~~~-~~~---------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~ 99 (250)
.|.||+++. .++ ..++.++|||.+...|++.|++.+ =.||. |+.++-.
T Consensus 289 ~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq-------QTCPI--Cr~p~if 346 (491)
T COG5243 289 TCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ-------QTCPI--CRRPVIF 346 (491)
T ss_pred eEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc-------cCCCc--ccCcccc
Confidence 599999993 322 123467999999999999999944 36888 7665433
No 47
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=94.61 E-value=0.016 Score=30.12 Aligned_cols=23 Identities=35% Similarity=0.831 Sum_probs=13.0
Q ss_pred ccCCCCCcceeccCCCcceEE-eccccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~F 228 (250)
|.||.|+..|... -..| .||+.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCCCCCCCC
Confidence 4677777766432 2445 466555
No 48
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=94.39 E-value=0.047 Score=40.28 Aligned_cols=37 Identities=19% Similarity=0.552 Sum_probs=27.5
Q ss_pred CCceecccCcccccC-CCceecCCCC------CcchHHHHHHHHH
Q 025608 39 SRSFVCEICVETKLR-NESFSIKGCS------HMYCVDCTVKYVD 76 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~-~~~~~~~~C~------H~fC~~Cl~~~~~ 76 (250)
...++|.||++.... +-++.+ .++ |.||.+|+++|-.
T Consensus 24 ~~~~EC~IC~~~I~~~~GvV~v-t~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 24 RCTVECQICFDRIDNNDGVVYV-TDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred ccCeeehhhhhhhhcCCCEEEE-ecCCeehHHHHHHHHHHHHHHh
Confidence 346799999999876 333333 554 8899999999953
No 49
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.26 E-value=0.036 Score=50.01 Aligned_cols=40 Identities=33% Similarity=0.822 Sum_probs=34.0
Q ss_pred cCCCccCC--CCCcceec-cCCCcceEEecccccccccccccc
Q 025608 198 NQKWNRCP--NCKFYVEK-KDGCSYIRCRCGHAFCYHCGVQLS 237 (250)
Q Consensus 198 ~~~~~~CP--~C~~~i~k-~~GCnhm~C~C~~~FC~~C~~~~~ 237 (250)
...++-|| .|+..+.. .+...-+.|.|++.|||.|+.+++
T Consensus 155 ~~~lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H 197 (444)
T KOG1815|consen 155 NVPLKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESH 197 (444)
T ss_pred CCccccCCCCCCCceeeccCCCccceeCCCCchhHhhcccccc
Confidence 34467787 59998887 788999999999999999999985
No 50
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=93.82 E-value=0.048 Score=32.19 Aligned_cols=41 Identities=32% Similarity=0.716 Sum_probs=29.3
Q ss_pred CCCCCcceeccCCCcceEE--eccccccccccccccCCCCCcCCCCCCC
Q 025608 204 CPNCKFYVEKKDGCSYIRC--RCGHAFCYHCGVQLSTVSHGYYCPSCNK 250 (250)
Q Consensus 204 CP~C~~~i~k~~GCnhm~C--~C~~~FC~~C~~~~~~~~h~~~~~~~~~ 250 (250)
||.|......... .- .||+.||..|...+. .....||.|++
T Consensus 2 C~~C~~~~~~~~~----~~l~~CgH~~C~~C~~~~~--~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERR----PRLTSCGHIFCEKCLKKLK--GKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCC----eEEcccCCHHHHHHHHhhc--CCCCCCcCCCC
Confidence 6667665522222 33 799999999999996 45556999986
No 51
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=93.52 E-value=0.042 Score=46.49 Aligned_cols=48 Identities=29% Similarity=0.750 Sum_probs=35.7
Q ss_pred CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCC
Q 025608 39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSL 97 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 97 (250)
....+|.+|-.-+-+. +....|-|.||++||-+|+.. ...||. |+..+
T Consensus 13 n~~itC~LC~GYliDA--TTI~eCLHTFCkSCivk~l~~-------~~~CP~--C~i~i 60 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDA--TTITECLHTFCKSCIVKYLEE-------SKYCPT--CDIVI 60 (331)
T ss_pred ccceehhhccceeecc--hhHHHHHHHHHHHHHHHHHHH-------hccCCc--cceec
Confidence 3445799998877544 334599999999999999995 357997 55433
No 52
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=93.50 E-value=0.06 Score=44.73 Aligned_cols=62 Identities=21% Similarity=0.368 Sum_probs=41.1
Q ss_pred eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh-ccCChHHHHHHH
Q 025608 42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR-DILPEEAFDKWG 115 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~~~ 115 (250)
.-|-||-+.+..+- ..+|+|.||.-|++.|+..+ --||. |........++ ..+..++.+.|.
T Consensus 26 lrC~IC~~~i~ip~---~TtCgHtFCslCIR~hL~~q-------p~CP~--Cr~~~~esrlr~~s~~~ei~es~~ 88 (391)
T COG5432 26 LRCRICDCRISIPC---ETTCGHTFCSLCIRRHLGTQ-------PFCPV--CREDPCESRLRGSSGSREINESHA 88 (391)
T ss_pred HHhhhhhheeecce---ecccccchhHHHHHHHhcCC-------CCCcc--ccccHHhhhcccchhHHHHHHhhh
Confidence 35999998776543 35999999999999999844 24777 76554444333 223444455443
No 53
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.34 E-value=0.056 Score=47.74 Aligned_cols=84 Identities=18% Similarity=0.443 Sum_probs=55.1
Q ss_pred ccccCCCCCCCCCCCHHHHhc----c----------------C---ChHHHHHHHHHHHhh--------ccCCCCeecCC
Q 025608 84 TSIGCPVTDCGGSLEPEYCRD----I----------------L---PEEAFDKWGKALCES--------LIPGAQKFYCP 132 (250)
Q Consensus 84 ~~i~CP~~~C~~~l~~~~i~~----~----------------l---~~~~~~~~~~~~~~~--------~~~~~~~~~Cp 132 (250)
..+.||.++|...+...++.. . + +....+.|+++.... ++. .....||
T Consensus 232 ~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la-~~wr~Cp 310 (384)
T KOG1812|consen 232 DRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYLA-KRWRQCP 310 (384)
T ss_pred hcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHHH-HhcCcCc
Confidence 455888888887666554321 0 0 123355555544221 222 4466899
Q ss_pred CCCCCCceecCccCccCcccCCcccchhccccCcccCCCCC
Q 025608 133 FKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIE 173 (250)
Q Consensus 133 ~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~ 173 (250)
.|+..+....+ -+.++|. ||..||+.|..+|..+..
T Consensus 311 --kC~~~ie~~~G--Cnhm~Cr-C~~~fcy~C~~~~~~~~~ 346 (384)
T KOG1812|consen 311 --KCKFMIELSEG--CNHMTCR-CGHQFCYMCGGDWKTHNG 346 (384)
T ss_pred --ccceeeeecCC--cceEEee-ccccchhhcCcchhhCCc
Confidence 99998877665 6889998 999999999999865543
No 54
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.31 E-value=0.11 Score=42.82 Aligned_cols=55 Identities=29% Similarity=0.627 Sum_probs=39.0
Q ss_pred ccCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608 35 RSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE 98 (250)
Q Consensus 35 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 98 (250)
....+-..+|++|.+.-+.+ .....|+|.+|--|+....... ..+.||. |+....
T Consensus 233 ss~~t~~~~C~~Cg~~PtiP--~~~~~C~HiyCY~Ci~ts~~~~-----asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 233 SSTGTSDTECPVCGEPPTIP--HVIGKCGHIYCYYCIATSRLWD-----ASFTCPL--CGENVE 287 (298)
T ss_pred cccccCCceeeccCCCCCCC--eeeccccceeehhhhhhhhcch-----hhcccCc--cCCCCc
Confidence 34445566899999865544 3345799999999998876633 3478997 776544
No 55
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=93.28 E-value=0.13 Score=31.20 Aligned_cols=41 Identities=15% Similarity=0.560 Sum_probs=29.2
Q ss_pred cccCcccccCCCceecCCCC-----CcchHHHHHHHHHHHhhcCcccccCCC
Q 025608 44 CEICVETKLRNESFSIKGCS-----HMYCVDCTVKYVDSKLQENVTSIGCPV 90 (250)
Q Consensus 44 C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 90 (250)
|-||++.....+.+ ..+|. |.+..+||.+|+..... .+||.
T Consensus 2 CrIC~~~~~~~~~l-~~PC~C~G~~~~vH~~Cl~~W~~~~~~-----~~C~i 47 (49)
T smart00744 2 CRICHDEGDEGDPL-VSPCRCKGSLKYVHQECLERWINESGN-----KTCEI 47 (49)
T ss_pred ccCCCCCCCCCCee-EeccccCCchhHHHHHHHHHHHHHcCC-----CcCCC
Confidence 88999844444444 34775 78999999999985532 37776
No 56
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=93.22 E-value=0.067 Score=33.46 Aligned_cols=47 Identities=26% Similarity=0.755 Sum_probs=37.6
Q ss_pred ccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
..|-.|+..|.-.+.--++.| +||..-=|+|-+-.+ .++.|.||+|+
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk-~~~~Y~CP~CG 55 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRK-QSNPYTCPKCG 55 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHh-cCCceECCCCC
Confidence 578899998887787789999 999886677766553 46778999997
No 57
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.14 E-value=0.038 Score=44.80 Aligned_cols=47 Identities=23% Similarity=0.651 Sum_probs=34.7
Q ss_pred ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608 41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP 99 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~ 99 (250)
.+.|..|+.--+ .+.|.+.+|.|.||..|.+.-... .||. |+..+-.
T Consensus 3 ~VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~~~---------~C~l--Ckk~ir~ 49 (233)
T KOG4739|consen 3 FVHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASSPD---------VCPL--CKKSIRI 49 (233)
T ss_pred eEEeccccccCC-CCceeeeechhhhhhhhcccCCcc---------cccc--ccceeee
Confidence 357999987655 566778899999999998754331 7887 8766544
No 58
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=93.01 E-value=0.028 Score=34.27 Aligned_cols=25 Identities=32% Similarity=0.865 Sum_probs=16.1
Q ss_pred cCcccCCcccchhccccCcccCCCC
Q 025608 148 IRESECPNCHRLFCAQCKVAWHAGI 172 (250)
Q Consensus 148 ~~~~~C~~C~~~~C~~C~~~~H~~~ 172 (250)
.....|+.|+..||..|..-.|..+
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CCeEECCCCCCccccCcChhhhccc
Confidence 3668999999999999999888664
No 59
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=92.86 E-value=0.021 Score=33.06 Aligned_cols=26 Identities=38% Similarity=0.889 Sum_probs=20.5
Q ss_pred eccccccccccccccCCCCCcCCCCC
Q 025608 223 RCGHAFCYHCGVQLSTVSHGYYCPSC 248 (250)
Q Consensus 223 ~C~~~FC~~C~~~~~~~~h~~~~~~~ 248 (250)
.||+.||..|+..|-...-...||.|
T Consensus 16 ~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 16 PCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp TTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred cCCCcchHHHHHHHHHhcCCccCCcC
Confidence 79999999999998543556669877
No 60
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=92.67 E-value=0.073 Score=30.21 Aligned_cols=31 Identities=26% Similarity=0.698 Sum_probs=23.4
Q ss_pred eecCCCCCCCCceecCcc---CccCcccCCcccchh
Q 025608 128 KFYCPFKDCSALLIDDAG---EAIRESECPNCHRLF 160 (250)
Q Consensus 128 ~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~ 160 (250)
.+.|| .|+..+..+++ .....++|+.|+..|
T Consensus 2 ~i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 35798 99998887743 345689999998765
No 61
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=92.35 E-value=0.075 Score=41.66 Aligned_cols=35 Identities=23% Similarity=0.636 Sum_probs=28.0
Q ss_pred CCceecccCcccccCCCceecCCCCCcchHHHHHHHHH
Q 025608 39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVD 76 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 76 (250)
.-+|.|.||-.++..+.+ ..|||.||..|...-+.
T Consensus 194 ~IPF~C~iCKkdy~spvv---t~CGH~FC~~Cai~~y~ 228 (259)
T COG5152 194 KIPFLCGICKKDYESPVV---TECGHSFCSLCAIRKYQ 228 (259)
T ss_pred CCceeehhchhhccchhh---hhcchhHHHHHHHHHhc
Confidence 446789999999976543 48999999999876655
No 62
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=92.29 E-value=0.041 Score=32.23 Aligned_cols=29 Identities=38% Similarity=1.017 Sum_probs=18.7
Q ss_pred eEEeccccccccccccccCCCCC--cCCCCC
Q 025608 220 IRCRCGHAFCYHCGVQLSTVSHG--YYCPSC 248 (250)
Q Consensus 220 m~C~C~~~FC~~C~~~~~~~~h~--~~~~~~ 248 (250)
++=.||+.||..|+..+....+. +.||.|
T Consensus 12 v~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 12 VSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp EE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred cccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 34469999999999888444443 578876
No 63
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=92.25 E-value=0.25 Score=46.97 Aligned_cols=53 Identities=28% Similarity=0.653 Sum_probs=41.4
Q ss_pred CCCceecccCcccccC-CCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608 38 TSRSFVCEICVETKLR-NESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV 90 (250)
Q Consensus 38 ~~~~~~C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 90 (250)
....++|.||++.+.. ..++....|-|.|...|+++|..+.-.++...-+||.
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~ 241 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPA 241 (950)
T ss_pred hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCc
Confidence 3667899999999854 3456666778999999999999985445556678997
No 64
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=92.13 E-value=0.073 Score=26.77 Aligned_cols=20 Identities=30% Similarity=1.050 Sum_probs=9.6
Q ss_pred ccccccccccCCCCCcCCCCCC
Q 025608 228 FCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 228 FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
||-.||.++.....+ ||+|+
T Consensus 1 ~Cp~CG~~~~~~~~f--C~~CG 20 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKF--CPNCG 20 (23)
T ss_pred CCcccCCCCCCcCcc--hhhhC
Confidence 344555555443444 55554
No 65
>PF12773 DZR: Double zinc ribbon
Probab=92.01 E-value=0.14 Score=31.01 Aligned_cols=39 Identities=28% Similarity=0.682 Sum_probs=20.3
Q ss_pred CccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCC
Q 025608 201 WNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 201 ~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
.+.||+|++.+..... . ..+|-.|+........+ |++|+
T Consensus 12 ~~fC~~CG~~l~~~~~-~-------~~~C~~Cg~~~~~~~~f--C~~CG 50 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQ-S-------KKICPNCGAENPPNAKF--CPNCG 50 (50)
T ss_pred ccCChhhcCChhhccC-C-------CCCCcCCcCCCcCCcCc--cCccc
Confidence 4677777776661111 1 13455555555433334 77774
No 66
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.91 E-value=0.29 Score=41.90 Aligned_cols=37 Identities=30% Similarity=0.580 Sum_probs=27.6
Q ss_pred CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHH
Q 025608 37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVD 76 (250)
Q Consensus 37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 76 (250)
..++.-.|+||+-. +...+| .+|+|.-|.+|+.+++-
T Consensus 418 p~sEd~lCpICyA~-pi~Avf--~PC~H~SC~~CI~qHlm 454 (489)
T KOG4692|consen 418 PDSEDNLCPICYAG-PINAVF--APCSHRSCYGCITQHLM 454 (489)
T ss_pred CCcccccCcceecc-cchhhc--cCCCCchHHHHHHHHHh
Confidence 33555569999953 333334 59999999999999987
No 67
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=91.83 E-value=0.13 Score=31.37 Aligned_cols=26 Identities=31% Similarity=0.708 Sum_probs=20.3
Q ss_pred cCCCCCcceeccCC--CcceEE-eccccc
Q 025608 203 RCPNCKFYVEKKDG--CSYIRC-RCGHAF 228 (250)
Q Consensus 203 ~CP~C~~~i~k~~G--Cnhm~C-~C~~~F 228 (250)
-||.||.++...++ -+++.| .||+++
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 69999997776643 468999 899875
No 68
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.73 E-value=0.22 Score=43.32 Aligned_cols=59 Identities=17% Similarity=0.350 Sum_probs=46.5
Q ss_pred ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608 41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI 105 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~ 105 (250)
.|.|||=-+.-+.++.+..+.|||.++++=+.+..+ +|...++||. |+........+++
T Consensus 334 vF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~sfKCPY--CP~e~~~~~~kql 392 (394)
T KOG2817|consen 334 VFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQSFKCPY--CPVEQLASDTKQL 392 (394)
T ss_pred eeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCeeeeCCC--CCcccCHHhcccc
Confidence 568999887777777788889999999988777665 5556899998 9887777665543
No 69
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=91.67 E-value=0.17 Score=42.59 Aligned_cols=92 Identities=21% Similarity=0.561 Sum_probs=56.5
Q ss_pred CCCCcchHHHHHHHHHHHhhcC---cccccCCCCCCCCCCCHHHHhccCChHHHHHHHHHHHhhccCCCCeecCCCCCCC
Q 025608 61 GCSHMYCVDCTVKYVDSKLQEN---VTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCS 137 (250)
Q Consensus 61 ~C~H~fC~~Cl~~~~~~~i~~~---~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~ 137 (250)
.|+-.||+.|+..|-.-.-... ... ..|.-.++... ....+|..+..+. .......|| .|.
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~as~t-----~tc~y~vde~~-------a~~arwd~as~~T--Ik~tTkpCP--kCh 404 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEASGT-----TTCAYRVDERA-------AEQARWDAASKET--IKKTTKPCP--KCH 404 (446)
T ss_pred CchhHhHHHHHhhhccccceeeeccccc-----cceeeecChhh-------hhhhhhhhhhhhh--hhhccCCCC--Ccc
Confidence 5889999999999876322211 111 12332333222 3345666654432 233445788 888
Q ss_pred CceecCccCccCcccCCc--ccchhccccCcccCC
Q 025608 138 ALLIDDAGEAIRESECPN--CHRLFCAQCKVAWHA 170 (250)
Q Consensus 138 ~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H~ 170 (250)
.....+.+ ...+.|+. ||..||+.|+-.|..
T Consensus 405 vptErnGG--CmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 405 VPTERNGG--CMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred CccccCCc--eEEeecCCCCCCceeEeccCChhhh
Confidence 77777655 35577854 999999999998853
No 70
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=91.50 E-value=0.064 Score=30.71 Aligned_cols=27 Identities=33% Similarity=0.860 Sum_probs=20.3
Q ss_pred eEE-eccccccccccccccCCCCCcCCCCC
Q 025608 220 IRC-RCGHAFCYHCGVQLSTVSHGYYCPSC 248 (250)
Q Consensus 220 m~C-~C~~~FC~~C~~~~~~~~h~~~~~~~ 248 (250)
+.- .||+.||+.|..+|... ...||.|
T Consensus 12 ~~~~~CGH~fC~~C~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 12 VVVTPCGHSFCKECIEKYLEK--NPKCPVC 39 (39)
T ss_dssp EEECTTSEEEEHHHHHHHHHC--TSB-TTT
T ss_pred CEECCCCCchhHHHHHHHHHC--cCCCcCC
Confidence 355 89999999999999544 2568877
No 71
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=91.47 E-value=0.18 Score=34.24 Aligned_cols=33 Identities=24% Similarity=0.709 Sum_probs=25.3
Q ss_pred CCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608 60 KGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE 98 (250)
Q Consensus 60 ~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 98 (250)
-.|+|.|...|+.+|+.++-. .=.||. |.+.+.
T Consensus 50 g~C~H~FH~hCI~kWl~~~~~----~~~CPm--CR~~w~ 82 (85)
T PF12861_consen 50 GKCSHNFHMHCILKWLSTQSS----KGQCPM--CRQPWK 82 (85)
T ss_pred ccCccHHHHHHHHHHHccccC----CCCCCC--cCCeee
Confidence 379999999999999997622 227887 776654
No 72
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=91.38 E-value=0.045 Score=45.45 Aligned_cols=29 Identities=34% Similarity=0.878 Sum_probs=23.2
Q ss_pred ceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608 219 YIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 219 hm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
|-+| .||+-|||-|...|- +-.-+||-|-
T Consensus 251 ~pSaTpCGHiFCWsCI~~w~--~ek~eCPlCR 280 (293)
T KOG0317|consen 251 NPSATPCGHIFCWSCILEWC--SEKAECPLCR 280 (293)
T ss_pred CCCcCcCcchHHHHHHHHHH--ccccCCCccc
Confidence 5678 899999999999994 3344699884
No 73
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=91.21 E-value=0.11 Score=26.94 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=5.7
Q ss_pred ccCCCCCccee
Q 025608 202 NRCPNCKFYVE 212 (250)
Q Consensus 202 ~~CP~C~~~i~ 212 (250)
+.||+|+..+.
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 45566555443
No 74
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.98 E-value=0.16 Score=28.65 Aligned_cols=31 Identities=29% Similarity=0.640 Sum_probs=22.7
Q ss_pred eecCCCCCCCCceecCcc---CccCcccCCcccchh
Q 025608 128 KFYCPFKDCSALLIDDAG---EAIRESECPNCHRLF 160 (250)
Q Consensus 128 ~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~ 160 (250)
.+.|| .|++.+..++. .....++|+.|+..|
T Consensus 2 ~i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 35788 89988887633 345678999998764
No 75
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=90.93 E-value=0.12 Score=29.90 Aligned_cols=41 Identities=29% Similarity=0.638 Sum_probs=26.8
Q ss_pred CCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCCC
Q 025608 204 CPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCNK 250 (250)
Q Consensus 204 CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~~ 250 (250)
||-|...+ =+-+.- .||+.||+.|+..|... ....||.|++
T Consensus 2 C~iC~~~~-----~~~~~~~~C~H~~c~~C~~~~~~~-~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEF-----REPVVLLPCGHVFCRSCIDKWLKS-GKNTCPLCRT 43 (45)
T ss_pred CCcCchhh-----hCceEecCCCChhcHHHHHHHHHh-CcCCCCCCCC
Confidence 55555544 122334 59999999999988532 3446999974
No 76
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.73 E-value=0.15 Score=45.44 Aligned_cols=53 Identities=25% Similarity=0.657 Sum_probs=37.1
Q ss_pred CCCceecccCcccccCCCc--------------eecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608 38 TSRSFVCEICVETKLRNES--------------FSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE 98 (250)
Q Consensus 38 ~~~~~~C~iC~~~~~~~~~--------------~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 98 (250)
...+..|.||+.+.+.... ..+.+|.|.|.++||.+|+... .+.||. |...|+
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~y------kl~CPv--CR~pLP 634 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTY------KLICPV--CRCPLP 634 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhh------cccCCc--cCCCCC
Confidence 4556689999987642111 1145999999999999999832 378998 554443
No 77
>PHA00626 hypothetical protein
Probab=90.60 E-value=0.18 Score=31.06 Aligned_cols=26 Identities=27% Similarity=0.607 Sum_probs=20.2
Q ss_pred cCCCCCc-ceeccCCCcc----eEE-eccccc
Q 025608 203 RCPNCKF-YVEKKDGCSY----IRC-RCGHAF 228 (250)
Q Consensus 203 ~CP~C~~-~i~k~~GCnh----m~C-~C~~~F 228 (250)
.||+|+. -|.|.+-|+. ..| .||+.|
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 5999999 5778776654 778 888876
No 78
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.45 E-value=0.18 Score=31.50 Aligned_cols=48 Identities=23% Similarity=0.612 Sum_probs=39.4
Q ss_pred CccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608 201 WNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 201 ~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
.-.|-.|+..|.-.++=-++.| +||...=|+|-+-. ..++-|.||+|+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CR-k~g~~Y~Cp~CG 57 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCR-KLGNPYRCPKCG 57 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhHH-HcCCceECCCcC
Confidence 4578889999988888888999 99988888887666 357788999996
No 79
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.41 E-value=0.28 Score=45.52 Aligned_cols=44 Identities=20% Similarity=0.509 Sum_probs=33.7
Q ss_pred ceecccCcccccCC--CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCC
Q 025608 41 SFVCEICVETKLRN--ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVT 91 (250)
Q Consensus 41 ~~~C~iC~~~~~~~--~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~ 91 (250)
.-.|.||.+..... .....++|+|.|+..|++.|++.+ -.||.+
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~-------qtCP~C 336 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ-------QTCPTC 336 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHHh-------CcCCcc
Confidence 45799999998642 113456999999999999999962 368873
No 80
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=89.91 E-value=0.22 Score=31.84 Aligned_cols=37 Identities=35% Similarity=0.805 Sum_probs=16.7
Q ss_pred ccCCCCCcceecc---CCCcceEEeccccccccccccccCCCCCcCCCCCC
Q 025608 202 NRCPNCKFYVEKK---DGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 202 ~~CP~C~~~i~k~---~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
.+|++|...+... +||.|+ ||+.|-++.- ++.||.|+
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~-------fCs~Ci~~~~----~~~CPvC~ 47 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHI-------FCSSCIRDCI----GSECPVCH 47 (65)
T ss_dssp TS-SSS-S--SS-B---SSS---------B-TTTGGGGT----TTB-SSS-
T ss_pred cCCcHHHHHhcCCceeccCccH-------HHHHHhHHhc----CCCCCCcC
Confidence 6899999876543 666665 6666655532 24588886
No 81
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=89.88 E-value=0.13 Score=31.34 Aligned_cols=31 Identities=39% Similarity=1.061 Sum_probs=19.6
Q ss_pred CcceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608 217 CSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 217 Cnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
=....| +|+.+||+-|-.=++..-|. ||-|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~--CPGC~ 50 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHN--CPGCE 50 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-S--SSTT-
T ss_pred CCeEECCCCCCccccCcChhhhccccC--CcCCC
Confidence 345778 89999999998888877888 99885
No 82
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=89.85 E-value=0.23 Score=49.43 Aligned_cols=43 Identities=35% Similarity=0.895 Sum_probs=32.4
Q ss_pred ccCCCCCcceeccCCCcceEE-eccccc-----cccccccccCC-CCCcCCCCCCC
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGHAF-----CYHCGVQLSTV-SHGYYCPSCNK 250 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~F-----C~~C~~~~~~~-~h~~~~~~~~~ 250 (250)
++||+|+..+... .| .||.+. |-.|+....+. +-...||+|+.
T Consensus 668 rkCPkCG~~t~~~------fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGt 717 (1337)
T PRK14714 668 RRCPSCGTETYEN------RCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDV 717 (1337)
T ss_pred EECCCCCCccccc------cCcccCCcCCCceeCccCCCccCCCccccccCCCCCC
Confidence 8999999976532 99 899775 99999987322 11567999984
No 83
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.80 E-value=0.15 Score=41.36 Aligned_cols=60 Identities=15% Similarity=0.331 Sum_probs=45.8
Q ss_pred CCCCceecccCcccccCCC-ceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608 37 ETSRSFVCEICVETKLRNE-SFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI 105 (250)
Q Consensus 37 ~~~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~ 105 (250)
..++.+.|+||-++++... ...+.+++|.|+.+|..++|. ..+.+|. ++..+..++|..|
T Consensus 217 a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir-------~D~v~pv--~d~plkdrdiI~L 277 (303)
T KOG3039|consen 217 AASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR-------KDMVDPV--TDKPLKDRDIIGL 277 (303)
T ss_pred hhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc-------ccccccC--CCCcCcccceEee
Confidence 3457788999999987543 234779999999999999987 2356787 8888887776544
No 84
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.75 E-value=0.27 Score=29.31 Aligned_cols=28 Identities=29% Similarity=0.593 Sum_probs=19.6
Q ss_pred ccCCCCCcceeccCCCcceEE-ecccccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFC 229 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC 229 (250)
-.||+|+..++-.++=..++| .||..+=
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 478888887766654447888 7887653
No 85
>PRK04023 DNA polymerase II large subunit; Validated
Probab=89.54 E-value=0.28 Score=47.76 Aligned_cols=41 Identities=32% Similarity=0.873 Sum_probs=32.7
Q ss_pred CCccCCCCCcceeccCCCcceEE-ecccc-----ccccccccccCCCCCcCCCCCCC
Q 025608 200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHA-----FCYHCGVQLSTVSHGYYCPSCNK 250 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~~~~~~h~~~~~~~~~ 250 (250)
..+.||.||... ....| .||.+ ||-.|+.... .+.||+|+.
T Consensus 625 g~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~----~y~CPKCG~ 671 (1121)
T PRK04023 625 GRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVE----EDECEKCGR 671 (1121)
T ss_pred cCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCC----CCcCCCCCC
Confidence 458999999985 56899 89965 9999977664 367999974
No 86
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=89.45 E-value=0.25 Score=30.08 Aligned_cols=26 Identities=23% Similarity=0.639 Sum_probs=19.5
Q ss_pred CccCCCCCc-ceeccCCCcceEE-eccccc
Q 025608 201 WNRCPNCKF-YVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 201 ~~~CP~C~~-~i~k~~GCnhm~C-~C~~~F 228 (250)
.+.||+|+. .+.... +.++| +||+.+
T Consensus 20 ~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 379999998 433333 79999 999875
No 87
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.38 E-value=0.31 Score=41.83 Aligned_cols=50 Identities=24% Similarity=0.634 Sum_probs=35.0
Q ss_pred CCCCceecccCcccccCCCceecCCCCCc-chHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608 37 ETSRSFVCEICVETKLRNESFSIKGCSHM-YCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE 98 (250)
Q Consensus 37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 98 (250)
++....+|-||+++..+ +.+++|.|. .|.+|.+...- + . =.||. |.+.+.
T Consensus 286 ~~~~gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~-q--~----n~CPI--CRqpi~ 336 (349)
T KOG4265|consen 286 ESESGKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRY-Q--T----NNCPI--CRQPIE 336 (349)
T ss_pred cccCCCeeEEEecCCcc---eEEecchhhehhHhHHHHHHH-h--h----cCCCc--cccchH
Confidence 33445689999986543 445699999 89999987762 1 1 25898 876654
No 88
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=89.34 E-value=0.15 Score=30.71 Aligned_cols=45 Identities=24% Similarity=0.718 Sum_probs=21.0
Q ss_pred CCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608 204 CPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK 250 (250)
Q Consensus 204 CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~ 250 (250)
||-|-..+ ...|=+..=|.|+++.|..|...+..... --||.|.+
T Consensus 1 cp~C~e~~-d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~-g~CPgCr~ 45 (48)
T PF14570_consen 1 CPLCDEEL-DETDKDFYPCECGFQICRFCYHDILENEG-GRCPGCRE 45 (48)
T ss_dssp -TTTS-B---CCCTT--SSTTS----HHHHHHHTTSS--SB-TTT--
T ss_pred CCCccccc-ccCCCccccCcCCCcHHHHHHHHHHhccC-CCCCCCCC
Confidence 45555554 33444566678999999999988864222 24999874
No 89
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=89.06 E-value=0.31 Score=43.25 Aligned_cols=38 Identities=18% Similarity=0.612 Sum_probs=30.0
Q ss_pred CCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHH
Q 025608 38 TSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDS 77 (250)
Q Consensus 38 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 77 (250)
..+...|++|...+..+... ..|+|.||..|+..+...
T Consensus 18 ~~~~l~C~~C~~vl~~p~~~--~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDPVQT--TTCGHRFCAGCLLESLSN 55 (391)
T ss_pred CcccccCccccccccCCCCC--CCCCCcccccccchhhcc
Confidence 34556799999988755322 499999999999999885
No 90
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.79 E-value=0.59 Score=41.36 Aligned_cols=48 Identities=25% Similarity=0.726 Sum_probs=35.3
Q ss_pred CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608 39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE 98 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 98 (250)
...|+|.||++.+..+.. .+|||.||..|+.+-+. ..-.||. |...+.
T Consensus 82 ~sef~c~vc~~~l~~pv~---tpcghs~c~~Cl~r~ld-------~~~~cp~--Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPPVV---TPCGHSFCLECLDRSLD-------QETECPL--CRDELV 129 (398)
T ss_pred cchhhhhhhHhhcCCCcc---ccccccccHHHHHHHhc-------cCCCCcc--cccccc
Confidence 667899999988876532 39999999999777222 3346886 876665
No 91
>PLN03086 PRLI-interacting factor K; Provisional
Probab=88.65 E-value=0.94 Score=41.88 Aligned_cols=58 Identities=16% Similarity=0.403 Sum_probs=36.5
Q ss_pred ccccCCCCCCCCCCCHHHHhccCChHHHHHHHHHHHhhccCCCCeecCCCCCCCCceecCccCccCcccCCcccchh
Q 025608 84 TSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLF 160 (250)
Q Consensus 84 ~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 160 (250)
..+.||. |...+....+..++.. =....+.||..+|+..+.....+ +.+.|+.|+..|
T Consensus 406 ~~V~C~N--C~~~i~l~~l~lHe~~---------------C~r~~V~Cp~~~Cg~v~~r~el~--~H~~C~~Cgk~f 463 (567)
T PLN03086 406 DTVECRN--CKHYIPSRSIALHEAY---------------CSRHNVVCPHDGCGIVLRVEEAK--NHVHCEKCGQAF 463 (567)
T ss_pred CeEECCC--CCCccchhHHHHHHhh---------------CCCcceeCCcccccceeeccccc--cCccCCCCCCcc
Confidence 4668886 8877777665533211 12345678876798888665432 446788887665
No 92
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.21 E-value=0.23 Score=35.60 Aligned_cols=41 Identities=22% Similarity=0.579 Sum_probs=29.6
Q ss_pred ecCCCCCCCCceecCc------cCccCcccCCcccchhccccCcccCCC
Q 025608 129 FYCPFKDCSALLIDDA------GEAIRESECPNCHRLFCAQCKVAWHAG 171 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~------~~~~~~~~C~~C~~~~C~~C~~~~H~~ 171 (250)
..|- +|+..+.... .....+..|+.|+..||..|..-+|+.
T Consensus 56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh
Confidence 3577 8887665431 122356789999999999999988854
No 93
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=87.98 E-value=0.11 Score=41.92 Aligned_cols=49 Identities=24% Similarity=0.597 Sum_probs=35.4
Q ss_pred ecccCcccc-cCCCce--ecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCC
Q 025608 43 VCEICVETK-LRNESF--SIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSL 97 (250)
Q Consensus 43 ~C~iC~~~~-~~~~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 97 (250)
.||||..+. -.+++. ....|-|.+|-+|+.+.+. ..+-.||..+|+.+|
T Consensus 12 ~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs------~GpAqCP~~gC~kIL 63 (314)
T COG5220 12 RCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS------RGPAQCPYKGCGKIL 63 (314)
T ss_pred cCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc------CCCCCCCCccHHHHH
Confidence 599999875 223332 2334999999999988776 246689999998644
No 94
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=87.84 E-value=0.16 Score=47.74 Aligned_cols=47 Identities=28% Similarity=0.733 Sum_probs=33.8
Q ss_pred HHhcCCCccCCCCCcceeccCCCcceEE---eccccccccccccccCCCCCcCCCCCCC
Q 025608 195 LAQNQKWNRCPNCKFYVEKKDGCSYIRC---RCGHAFCYHCGVQLSTVSHGYYCPSCNK 250 (250)
Q Consensus 195 ~~~~~~~~~CP~C~~~i~k~~GCnhm~C---~C~~~FC~~C~~~~~~~~h~~~~~~~~~ 250 (250)
+..-....+||-|... .=-+ +|+|.||+-|-++.....+. -||.||.
T Consensus 637 lk~yK~~LkCs~Cn~R--------~Kd~vI~kC~H~FC~~Cvq~r~etRqR-KCP~Cn~ 686 (698)
T KOG0978|consen 637 LKEYKELLKCSVCNTR--------WKDAVITKCGHVFCEECVQTRYETRQR-KCPKCNA 686 (698)
T ss_pred HHHHHhceeCCCccCc--------hhhHHHHhcchHHHHHHHHHHHHHhcC-CCCCCCC
Confidence 3333556899999852 1112 69999999999998655555 6999995
No 95
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=87.59 E-value=0.21 Score=43.43 Aligned_cols=44 Identities=32% Similarity=0.879 Sum_probs=32.2
Q ss_pred ecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCC
Q 025608 43 VCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCG 94 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 94 (250)
-|.||.+...+ +...+|||..|..||..|-.+. + .-.||.+.|.
T Consensus 371 LCKICaendKd---vkIEPCGHLlCt~CLa~WQ~sd---~--gq~CPFCRcE 414 (563)
T KOG1785|consen 371 LCKICAENDKD---VKIEPCGHLLCTSCLAAWQDSD---E--GQTCPFCRCE 414 (563)
T ss_pred HHHHhhccCCC---cccccccchHHHHHHHhhcccC---C--CCCCCceeeE
Confidence 49999875433 4567999999999999996532 1 2368886664
No 96
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=87.38 E-value=0.51 Score=39.60 Aligned_cols=44 Identities=20% Similarity=0.508 Sum_probs=35.9
Q ss_pred cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHh
Q 025608 36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKL 79 (250)
Q Consensus 36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i 79 (250)
..+.....|.||+--|..+.-|...+|.|.|...||.+|+....
T Consensus 110 ~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 110 ENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred cCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence 45566677999998888777677789999999999999987443
No 97
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=87.37 E-value=0.73 Score=27.72 Aligned_cols=44 Identities=20% Similarity=0.554 Sum_probs=20.0
Q ss_pred cccCcccccC--CCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCC
Q 025608 44 CEICVETKLR--NESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGS 96 (250)
Q Consensus 44 C~iC~~~~~~--~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 96 (250)
|++|.+++.. .++... +|+..+|+.|+.+-..+ ..=+||. |+..
T Consensus 1 cp~C~e~~d~~d~~~~PC-~Cgf~IC~~C~~~i~~~------~~g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPC-ECGFQICRFCYHDILEN------EGGRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SS-TTS----HHHHHHHTTS------S-SB-TT--T--B
T ss_pred CCCcccccccCCCccccC-cCCCcHHHHHHHHHHhc------cCCCCCC--CCCC
Confidence 7889988732 233333 78899999999887661 1236886 6643
No 98
>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=87.34 E-value=0.31 Score=27.61 Aligned_cols=30 Identities=17% Similarity=0.514 Sum_probs=20.7
Q ss_pred ecCCCCCCCCceecCcc---CccCcccCCcccchh
Q 025608 129 FYCPFKDCSALLIDDAG---EAIRESECPNCHRLF 160 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~ 160 (250)
+.|| .|+..+..+++ .....+.|+.|+..|
T Consensus 3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 5788 89987777632 122368899998764
No 99
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=87.25 E-value=1.3 Score=42.41 Aligned_cols=33 Identities=33% Similarity=0.873 Sum_probs=19.2
Q ss_pred cCCCCCcceeccCCCcceEE-ecccc-----cccccccc
Q 025608 203 RCPNCKFYVEKKDGCSYIRC-RCGHA-----FCYHCGVQ 235 (250)
Q Consensus 203 ~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~ 235 (250)
.||+|..++.-...=+.|.| .||++ .|-.||..
T Consensus 446 ~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 446 ECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 67777775544433367777 67665 45555444
No 100
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=87.24 E-value=0.12 Score=43.60 Aligned_cols=23 Identities=30% Similarity=0.868 Sum_probs=19.8
Q ss_pred CcccCCcccchhccccCcccCCC
Q 025608 149 RESECPNCHRLFCAQCKVAWHAG 171 (250)
Q Consensus 149 ~~~~C~~C~~~~C~~C~~~~H~~ 171 (250)
...+|+.|+..||..|..-.|..
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred CcEEchhccceeeccchHHHHhh
Confidence 55889999999999999877754
No 101
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.12 E-value=0.46 Score=39.89 Aligned_cols=53 Identities=21% Similarity=0.380 Sum_probs=38.1
Q ss_pred CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608 39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC 102 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 102 (250)
...-+|.||+.+-..+ ..+.|.|.||--|++.-...- ...|+. |...++.+.+
T Consensus 5 ~~~~eC~IC~nt~n~P---v~l~C~HkFCyiCiKGsy~nd------k~~Cav--CR~pids~i~ 57 (324)
T KOG0824|consen 5 TKKKECLICYNTGNCP---VNLYCFHKFCYICIKGSYKND------KKTCAV--CRFPIDSTID 57 (324)
T ss_pred ccCCcceeeeccCCcC---ccccccchhhhhhhcchhhcC------CCCCce--ecCCCCcchh
Confidence 4455799999876554 346999999999999876622 224887 8877766543
No 102
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.88 E-value=0.13 Score=44.07 Aligned_cols=46 Identities=30% Similarity=0.734 Sum_probs=32.3
Q ss_pred CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCC
Q 025608 40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGG 95 (250)
Q Consensus 40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 95 (250)
..+.|+||++-+...- ....|.|.||.+|+-..+... .=.||. |..
T Consensus 42 ~~v~c~icl~llk~tm--ttkeClhrfc~~ci~~a~r~g------n~ecpt--cRk 87 (381)
T KOG0311|consen 42 IQVICPICLSLLKKTM--TTKECLHRFCFDCIWKALRSG------NNECPT--CRK 87 (381)
T ss_pred hhhccHHHHHHHHhhc--ccHHHHHHHHHHHHHHHHHhc------CCCCch--HHh
Confidence 3457999998775432 234999999999998877732 125776 654
No 103
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.80 E-value=0.27 Score=40.59 Aligned_cols=57 Identities=16% Similarity=0.320 Sum_probs=40.5
Q ss_pred CCceecccCcccccCCC-------ceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608 39 SRSFVCEICVETKLRNE-------SFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC 102 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~-------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 102 (250)
.....|.||-..+..+. -...++|+|.|...|++.|...- +. =.||. |++.++...+
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivG----Kk-qtCPY--CKekVdl~rm 285 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVG----KK-QTCPY--CKEKVDLKRM 285 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeec----CC-CCCch--HHHHhhHhhh
Confidence 34446999998775433 22345999999999999998732 22 26997 8888777654
No 104
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.78 E-value=0.57 Score=41.00 Aligned_cols=52 Identities=25% Similarity=0.698 Sum_probs=38.3
Q ss_pred eecccCcccccC--CCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608 42 FVCEICVETKLR--NESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE 100 (250)
Q Consensus 42 ~~C~iC~~~~~~--~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 100 (250)
.+|+||++.+.. +.-...+.|+|.|=.+|+++|+. ......||. |...-...
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-----k~~~~~cp~--c~~katkr 58 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-----KKTKMQCPL--CSGKATKR 58 (463)
T ss_pred ccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-----hhhhhhCcc--cCChhHHH
Confidence 479999999753 33344669999999999999993 345678998 66544433
No 105
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=86.77 E-value=0.42 Score=29.05 Aligned_cols=28 Identities=32% Similarity=0.832 Sum_probs=19.9
Q ss_pred cCCCCCCCCceecCccCccCcccCCcccch
Q 025608 130 YCPFKDCSALLIDDAGEAIRESECPNCHRL 159 (250)
Q Consensus 130 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 159 (250)
+|| .|+..+..........+.|+.||+.
T Consensus 2 FCp--~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP--KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCC--CCCCccccccCCCCCEEECCcCCCe
Confidence 688 8999887765433346788888854
No 106
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=86.60 E-value=0.84 Score=24.80 Aligned_cols=26 Identities=31% Similarity=0.623 Sum_probs=16.1
Q ss_pred ccCCCCCcceeccCCCcceEE-ecccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~ 227 (250)
+-||.||.+.....+=-.+.| .|+..
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred cccCcCCccccCCCCcCEeECCCCcCE
Confidence 678999998888877677888 88764
No 107
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=86.46 E-value=0.17 Score=29.68 Aligned_cols=41 Identities=32% Similarity=0.705 Sum_probs=25.2
Q ss_pred CCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCC
Q 025608 204 CPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSC 248 (250)
Q Consensus 204 CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~ 248 (250)
||=|...+.. +=.-+.-.||+.|++.|+..|-... ..||.|
T Consensus 3 C~IC~~~~~~--~~~~~~l~C~H~fh~~Ci~~~~~~~--~~CP~C 43 (44)
T PF13639_consen 3 CPICLEEFED--GEKVVKLPCGHVFHRSCIKEWLKRN--NSCPVC 43 (44)
T ss_dssp ETTTTCBHHT--TSCEEEETTSEEEEHHHHHHHHHHS--SB-TTT
T ss_pred CcCCChhhcC--CCeEEEccCCCeeCHHHHHHHHHhC--CcCCcc
Confidence 4445554433 2222333799999999999995322 379988
No 108
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=86.20 E-value=0.42 Score=27.87 Aligned_cols=26 Identities=31% Similarity=0.888 Sum_probs=18.3
Q ss_pred CCCccCCCCCcceeccCCCcceEE---eccccc
Q 025608 199 QKWNRCPNCKFYVEKKDGCSYIRC---RCGHAF 228 (250)
Q Consensus 199 ~~~~~CP~C~~~i~k~~GCnhm~C---~C~~~F 228 (250)
..+++||+||++- |+--+.| .|++.|
T Consensus 9 RGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 9 RGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred hccccCCcCcCcc----CcccccccCCccchhh
Confidence 3569999999974 6666666 465544
No 109
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.91 E-value=0.36 Score=39.94 Aligned_cols=43 Identities=30% Similarity=0.797 Sum_probs=29.0
Q ss_pred CccCCCCCc--ceeccCCCcceEEeccccccccccccccCCCCCcCCCCCC
Q 025608 201 WNRCPNCKF--YVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 201 ~~~CP~C~~--~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
...||-|+. .|....| .|++-+||.|.+.--..+-++-||.||
T Consensus 239 ~~~C~~Cg~~PtiP~~~~------~C~HiyCY~Ci~ts~~~~asf~Cp~Cg 283 (298)
T KOG2879|consen 239 DTECPVCGEPPTIPHVIG------KCGHIYCYYCIATSRLWDASFTCPLCG 283 (298)
T ss_pred CceeeccCCCCCCCeeec------cccceeehhhhhhhhcchhhcccCccC
Confidence 389999999 4555555 366677788866554334455688887
No 110
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=85.88 E-value=0.47 Score=38.88 Aligned_cols=19 Identities=21% Similarity=0.581 Sum_probs=15.0
Q ss_pred CCCeecCCCCCCCCceecC
Q 025608 125 GAQKFYCPFKDCSALLIDD 143 (250)
Q Consensus 125 ~~~~~~Cp~~~C~~~~~~~ 143 (250)
+..++-||.|+|+.++.-.
T Consensus 120 sS~rIaCPRp~CkRiI~L~ 138 (256)
T PF09788_consen 120 SSQRIACPRPNCKRIINLG 138 (256)
T ss_pred ccccccCCCCCCcceEEeC
Confidence 4667899999999877654
No 111
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=85.85 E-value=0.87 Score=38.87 Aligned_cols=62 Identities=24% Similarity=0.547 Sum_probs=40.4
Q ss_pred CCceecccCccccc--CCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc-CChHH
Q 025608 39 SRSFVCEICVETKL--RNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI-LPEEA 110 (250)
Q Consensus 39 ~~~~~C~iC~~~~~--~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~-l~~~~ 110 (250)
.+.+ |++|+++.. +..++.. +||-.+|+-||...-+ .++ =+||. |....+.+-++-. |++++
T Consensus 13 eed~-cplcie~mditdknf~pc-~cgy~ic~fc~~~irq-~ln-----grcpa--crr~y~denv~~~~~s~ee 77 (480)
T COG5175 13 EEDY-CPLCIEPMDITDKNFFPC-PCGYQICQFCYNNIRQ-NLN-----GRCPA--CRRKYDDENVRYVTLSPEE 77 (480)
T ss_pred cccc-CcccccccccccCCcccC-CcccHHHHHHHHHHHh-hcc-----CCChH--hhhhccccceeEEecCHHH
Confidence 3444 999999874 4454444 8888999999975433 222 27997 8877776665432 44443
No 112
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=85.66 E-value=0.13 Score=34.02 Aligned_cols=47 Identities=28% Similarity=0.528 Sum_probs=28.2
Q ss_pred ccCCCCCccee----c-cCCCcceEE-ecccccccc------ccccccCCCCCcCCCCCCC
Q 025608 202 NRCPNCKFYVE----K-KDGCSYIRC-RCGHAFCYH------CGVQLSTVSHGYYCPSCNK 250 (250)
Q Consensus 202 ~~CP~C~~~i~----k-~~GCnhm~C-~C~~~FC~~------C~~~~~~~~h~~~~~~~~~ 250 (250)
..||.|+..++ + .+.-.++.+ ..---+||. |....+...|+ ||+||+
T Consensus 8 ~~CP~C~~~~~T~v~~~~g~~t~~~~~~l~~~~~~~~~~iP~~~~~~kd~~H~--Cp~C~~ 66 (73)
T PF10601_consen 8 IYCPYCQQQVQTRVEYKSGTMTYICAALLCLFGCWPCCCIPFCCDSCKDVYHY--CPNCGA 66 (73)
T ss_pred eECCCCCCEEEEEEEEEeChHHHHHHHHHHHHHHHHHhhHhhccccccCceEE--CCCCCC
Confidence 68999998554 2 355556555 222222243 34444666888 999985
No 113
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=85.65 E-value=0.51 Score=32.69 Aligned_cols=28 Identities=32% Similarity=0.762 Sum_probs=21.7
Q ss_pred ccCCCCCcc--eeccCCCcceEE-ecccccc
Q 025608 202 NRCPNCKFY--VEKKDGCSYIRC-RCGHAFC 229 (250)
Q Consensus 202 ~~CP~C~~~--i~k~~GCnhm~C-~C~~~FC 229 (250)
.-||.|+.+ |+..+.||.+.| .|.+.|=
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 369999994 445556999999 9999874
No 114
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=85.33 E-value=0.69 Score=26.85 Aligned_cols=22 Identities=45% Similarity=1.126 Sum_probs=17.3
Q ss_pred ccCCCCCcceec-cCCCcceEE-ecc
Q 025608 202 NRCPNCKFYVEK-KDGCSYIRC-RCG 225 (250)
Q Consensus 202 ~~CP~C~~~i~k-~~GCnhm~C-~C~ 225 (250)
..||.|++++.+ .+| .+.| .|+
T Consensus 18 ~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCC--CEECCCCC
Confidence 699999999888 455 5777 664
No 115
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=85.33 E-value=0.4 Score=42.38 Aligned_cols=39 Identities=21% Similarity=0.474 Sum_probs=29.5
Q ss_pred CCCceecccCcccccCCC-ceecCCCCCcchHHHHHHHHH
Q 025608 38 TSRSFVCEICVETKLRNE-SFSIKGCSHMYCVDCTVKYVD 76 (250)
Q Consensus 38 ~~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~ 76 (250)
-.+..+|+||++....+. .+....|+|.|...|+..|..
T Consensus 172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~ 211 (493)
T KOG0804|consen 172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD 211 (493)
T ss_pred cccCCCcchhHhhcCccccceeeeecccccchHHHhhccc
Confidence 355668999999875442 233458999999999998865
No 116
>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=85.26 E-value=0.56 Score=33.56 Aligned_cols=27 Identities=30% Similarity=0.715 Sum_probs=20.5
Q ss_pred CccCCCCCcceeccCCCcceEE-eccccc
Q 025608 201 WNRCPNCKFYVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 201 ~~~CP~C~~~i~k~~GCnhm~C-~C~~~F 228 (250)
-+.||+||...--..- +-++| +||+.|
T Consensus 9 KR~Cp~CG~kFYDLnk-~PivCP~CG~~~ 36 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNK-DPIVCPKCGTEF 36 (108)
T ss_pred cccCCCCcchhccCCC-CCccCCCCCCcc
Confidence 3789999986655544 77888 888876
No 117
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.23 E-value=0.72 Score=27.40 Aligned_cols=29 Identities=21% Similarity=0.497 Sum_probs=21.6
Q ss_pred eecCCCCCCCCceecCccCccCcccCCcccchh
Q 025608 128 KFYCPFKDCSALLIDDAGEAIRESECPNCHRLF 160 (250)
Q Consensus 128 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 160 (250)
.+.|| +|++.+..++... .+.||.||..+
T Consensus 3 ~y~C~--~CG~~~~~~~~~~--~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCA--RCGREVELDEYGT--GVRCPYCGYRI 31 (46)
T ss_pred EEECC--CCCCEEEECCCCC--ceECCCCCCeE
Confidence 45788 9999888775432 58899998764
No 118
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=85.04 E-value=0.72 Score=43.55 Aligned_cols=10 Identities=40% Similarity=1.016 Sum_probs=5.7
Q ss_pred cccccccccc
Q 025608 227 AFCYHCGVQL 236 (250)
Q Consensus 227 ~FC~~C~~~~ 236 (250)
.||-.||.+.
T Consensus 42 ~fC~~CG~~~ 51 (645)
T PRK14559 42 AHCPNCGAET 51 (645)
T ss_pred ccccccCCcc
Confidence 3666665554
No 119
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=84.97 E-value=0.28 Score=46.90 Aligned_cols=41 Identities=37% Similarity=1.002 Sum_probs=0.0
Q ss_pred CCccCCCCCcceeccCCCcceEE-ecccc-----ccccccccccCCCCCcCCCCCCC
Q 025608 200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHA-----FCYHCGVQLSTVSHGYYCPSCNK 250 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~~~~~~h~~~~~~~~~ 250 (250)
..++||+|+.... ..+| .||.+ +|..|+....+. .||+|++
T Consensus 654 ~~r~Cp~Cg~~t~------~~~Cp~CG~~T~~~~~Cp~C~~~~~~~----~C~~C~~ 700 (900)
T PF03833_consen 654 GRRRCPKCGKETF------YNRCPECGSHTEPVYVCPDCGIEVEED----ECPKCGR 700 (900)
T ss_dssp ---------------------------------------------------------
T ss_pred ecccCcccCCcch------hhcCcccCCccccceeccccccccCcc----ccccccc
Confidence 3489999999754 5689 89988 999999998543 6999974
No 120
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=84.60 E-value=0.51 Score=37.29 Aligned_cols=33 Identities=27% Similarity=0.532 Sum_probs=24.4
Q ss_pred CCCccCCCCCcceeccCCCcceEEeccccccccccccc
Q 025608 199 QKWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQL 236 (250)
Q Consensus 199 ~~~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~ 236 (250)
...-.||=|.-.+... +.=.||+.|||.|...|
T Consensus 16 ~~~~~CpICld~~~dP-----VvT~CGH~FC~~CI~~w 48 (193)
T PLN03208 16 GGDFDCNICLDQVRDP-----VVTLCGHLFCWPCIHKW 48 (193)
T ss_pred CCccCCccCCCcCCCc-----EEcCCCchhHHHHHHHH
Confidence 3446899998865321 22289999999999988
No 121
>PRK14873 primosome assembly protein PriA; Provisional
Probab=84.55 E-value=2 Score=40.89 Aligned_cols=25 Identities=28% Similarity=0.614 Sum_probs=13.8
Q ss_pred ccCCCCCcceeccCCCcceEE-eccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGH 226 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~ 226 (250)
-.||+|..++.-..+=+.+.| .||+
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcC
Confidence 367777765554333345666 5654
No 122
>PF04641 Rtf2: Rtf2 RING-finger
Probab=84.53 E-value=2.1 Score=35.77 Aligned_cols=71 Identities=20% Similarity=0.431 Sum_probs=51.5
Q ss_pred CCCceecccCcccccCC-CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccCC-hHHHHHHH
Q 025608 38 TSRSFVCEICVETKLRN-ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILP-EEAFDKWG 115 (250)
Q Consensus 38 ~~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~-~~~~~~~~ 115 (250)
....|.|||-..++... .+..+.+|||.|....++..- . .-.||. |+..+...+|-.|-+ .+.++.+.
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~----~~~Cp~--c~~~f~~~DiI~Lnp~~ee~~~l~ 179 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----K----SKKCPV--CGKPFTEEDIIPLNPPEEELEKLR 179 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----c----cccccc--cCCccccCCEEEecCCccHHHHHH
Confidence 56778899999998653 455678999999999999882 1 224998 999999888776654 23455554
Q ss_pred HHH
Q 025608 116 KAL 118 (250)
Q Consensus 116 ~~~ 118 (250)
..+
T Consensus 180 ~~~ 182 (260)
T PF04641_consen 180 ERM 182 (260)
T ss_pred HHH
Confidence 444
No 123
>PF15616 TerY-C: TerY-C metal binding domain
Probab=84.44 E-value=0.9 Score=33.61 Aligned_cols=24 Identities=33% Similarity=0.935 Sum_probs=14.7
Q ss_pred CccCCCCCcceeccCCCcceEEeccccccc
Q 025608 201 WNRCPNCKFYVEKKDGCSYIRCRCGHAFCY 230 (250)
Q Consensus 201 ~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~ 230 (250)
.--||.|+...- ...|.||.-|||
T Consensus 77 ~PgCP~CGn~~~------fa~C~CGkl~Ci 100 (131)
T PF15616_consen 77 APGCPHCGNQYA------FAVCGCGKLFCI 100 (131)
T ss_pred CCCCCCCcChhc------EEEecCCCEEEe
Confidence 378999998522 334455555554
No 124
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.88 E-value=0.37 Score=37.28 Aligned_cols=45 Identities=33% Similarity=0.783 Sum_probs=32.9
Q ss_pred CccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608 201 WNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK 250 (250)
Q Consensus 201 ~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~ 250 (250)
.-.||.|...+.+..- +.=+||+-||-.|.+..-...|. ||-|+|
T Consensus 131 ~~~CPiCl~~~sek~~---vsTkCGHvFC~~Cik~alk~~~~--CP~C~k 175 (187)
T KOG0320|consen 131 TYKCPICLDSVSEKVP---VSTKCGHVFCSQCIKDALKNTNK--CPTCRK 175 (187)
T ss_pred ccCCCceecchhhccc---cccccchhHHHHHHHHHHHhCCC--CCCccc
Confidence 4689999987766542 21278889999998888555666 998874
No 125
>PHA03096 p28-like protein; Provisional
Probab=82.37 E-value=1.8 Score=36.55 Aligned_cols=39 Identities=18% Similarity=0.453 Sum_probs=30.0
Q ss_pred eecccCcccccCC----Cce-ecCCCCCcchHHHHHHHHHHHhh
Q 025608 42 FVCEICVETKLRN----ESF-SIKGCSHMYCVDCTVKYVDSKLQ 80 (250)
Q Consensus 42 ~~C~iC~~~~~~~----~~~-~~~~C~H~fC~~Cl~~~~~~~i~ 80 (250)
.+|+||++..... ..| .+..|.|.||..|++.|......
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~ 222 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY 222 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh
Confidence 5699999887432 223 26699999999999999997653
No 126
>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=81.89 E-value=1.2 Score=31.50 Aligned_cols=31 Identities=23% Similarity=0.498 Sum_probs=24.9
Q ss_pred ceecccCcccccCCCceecCCCCCcchHHHHH
Q 025608 41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTV 72 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~ 72 (250)
...|++|...+..+ .|...+|+|.|...|++
T Consensus 78 ~~~C~vC~k~l~~~-~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNS-VFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCc-eEEEeCCCeEEeccccc
Confidence 34599999998764 46667999999999975
No 127
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=81.43 E-value=1.2 Score=30.29 Aligned_cols=45 Identities=38% Similarity=0.875 Sum_probs=35.1
Q ss_pred ccCCCCCcceeccCCCcceEEecccccccccccccc-CCCCCcCCCCCC
Q 025608 202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLS-TVSHGYYCPSCN 249 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~-~~~h~~~~~~~~ 249 (250)
..||.|+.+ .+.|--+...|++.|=..|..+|- +.+..-.||-|-
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR 78 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCR 78 (85)
T ss_pred cCCCCccCC---CCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcC
Confidence 478999997 567888888999999999999993 323344698874
No 128
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=80.26 E-value=2.4 Score=35.57 Aligned_cols=50 Identities=24% Similarity=0.616 Sum_probs=34.1
Q ss_pred ecccCcccc-cCCCc-eecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608 43 VCEICVETK-LRNES-FSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE 100 (250)
Q Consensus 43 ~C~iC~~~~-~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 100 (250)
.|++|-.+. ..+++ +...+|+|..|-+|+-..+.. .+-.|| .|..++-..
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~------g~~~Cp--eC~~iLRk~ 53 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL------GPAQCP--ECMVILRKN 53 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc------CCCCCC--cccchhhhc
Confidence 388888764 23333 334599999999999988772 244688 488766443
No 129
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=80.05 E-value=0.67 Score=25.87 Aligned_cols=28 Identities=29% Similarity=0.726 Sum_probs=19.0
Q ss_pred ecCCCCCCCCceecCccCccCcccCCcccch
Q 025608 129 FYCPFKDCSALLIDDAGEAIRESECPNCHRL 159 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 159 (250)
.+|| .|++.+.+..+..... .|+.|++.
T Consensus 2 ~FCp--~C~nlL~p~~~~~~~~-~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKEDKEKRV-ACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEETTTTE-EESSSS-E
T ss_pred eeCC--CCCccceEcCCCccCc-CCCCCCCc
Confidence 3688 9999998876544443 68777764
No 130
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=79.08 E-value=1.9 Score=27.56 Aligned_cols=31 Identities=19% Similarity=0.400 Sum_probs=20.2
Q ss_pred CCCccCCCCCccee---ccCCCcceEE-ecccccc
Q 025608 199 QKWNRCPNCKFYVE---KKDGCSYIRC-RCGHAFC 229 (250)
Q Consensus 199 ~~~~~CP~C~~~i~---k~~GCnhm~C-~C~~~FC 229 (250)
..+|+||.|+..+. ..+|=-.+.| .|+..-.
T Consensus 4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~~~ 38 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAISGYYRAKCNGCESRTG 38 (64)
T ss_pred ccccCCCCCCCceeEEEecCceEEEEcCCCCcCcc
Confidence 45699999998443 3355444667 7877533
No 131
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.05 E-value=1 Score=37.71 Aligned_cols=37 Identities=27% Similarity=0.531 Sum_probs=29.8
Q ss_pred CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHH
Q 025608 37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVD 76 (250)
Q Consensus 37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 76 (250)
...-+|.|-||-.++..+.+ ..|+|+||..|....++
T Consensus 237 ~~~~Pf~c~icr~~f~~pVv---t~c~h~fc~~ca~~~~q 273 (313)
T KOG1813|consen 237 IELLPFKCFICRKYFYRPVV---TKCGHYFCEVCALKPYQ 273 (313)
T ss_pred cccCCccccccccccccchh---hcCCceeehhhhccccc
Confidence 44556789999999876554 38999999999888776
No 132
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=79.04 E-value=1.5 Score=26.30 Aligned_cols=25 Identities=24% Similarity=0.620 Sum_probs=16.0
Q ss_pred ccCCCCCc-ceeccCCCcceEE-ecccc
Q 025608 202 NRCPNCKF-YVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 202 ~~CP~C~~-~i~k~~GCnhm~C-~C~~~ 227 (250)
+.||+|+. +++-..+ +...| +||+.
T Consensus 20 ~~CPrCG~gvfmA~H~-dR~~CGkCgyT 46 (51)
T COG1998 20 RFCPRCGPGVFMADHK-DRWACGKCGYT 46 (51)
T ss_pred ccCCCCCCcchhhhcC-ceeEeccccce
Confidence 89999995 2222211 27888 88863
No 133
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.68 E-value=4.2 Score=37.47 Aligned_cols=25 Identities=32% Similarity=0.782 Sum_probs=11.3
Q ss_pred cCCCCCcceeccCCCcceEE-ecccc
Q 025608 203 RCPNCKFYVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 203 ~CP~C~~~i~k~~GCnhm~C-~C~~~ 227 (250)
.||+|.+++.-...=+.+.| .||+.
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQ 249 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCc
Confidence 55555554432222234555 55543
No 134
>PHA02929 N1R/p28-like protein; Provisional
Probab=78.67 E-value=1.8 Score=35.61 Aligned_cols=48 Identities=29% Similarity=0.532 Sum_probs=33.7
Q ss_pred CCccCCCCCcceeccCCCcc---eEEeccccccccccccccCCCCCcCCCCCC
Q 025608 200 KWNRCPNCKFYVEKKDGCSY---IRCRCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnh---m~C~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
.-..||=|.-.+...+.=+. +.-.|+|.||..|..+|... ...||.|-
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--~~tCPlCR 223 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--KNTCPVCR 223 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--CCCCCCCC
Confidence 34789999997765443221 33378999999999999543 23699995
No 135
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.54 E-value=1.3 Score=36.84 Aligned_cols=53 Identities=21% Similarity=0.589 Sum_probs=40.1
Q ss_pred CCCCceecccCcccccCCCceecCCCC----CcchHHHHHHHHHHHhhcCcccccCCC-CCCC
Q 025608 37 ETSRSFVCEICVETKLRNESFSIKGCS----HMYCVDCTVKYVDSKLQENVTSIGCPV-TDCG 94 (250)
Q Consensus 37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~----H~fC~~Cl~~~~~~~i~~~~~~i~CP~-~~C~ 94 (250)
.....+-|.+|-+.+.+..++ .|. |.||-.|-+..|+.+-.. ..|.||. .+|.
T Consensus 264 A~~apLcCTLC~ERLEDTHFV---QCPSVp~HKFCFPCSResIK~Qg~s--gevYCPSGdkCP 321 (352)
T KOG3579|consen 264 APSAPLCCTLCHERLEDTHFV---QCPSVPSHKFCFPCSRESIKQQGAS--GEVYCPSGDKCP 321 (352)
T ss_pred CCCCceeehhhhhhhccCcee---ecCCCcccceecccCHHHHHhhcCC--CceeCCCCCcCc
Confidence 345568899999988765433 665 999999999999987444 4889997 3565
No 136
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=78.32 E-value=1.5 Score=28.61 Aligned_cols=32 Identities=34% Similarity=0.905 Sum_probs=20.1
Q ss_pred cCCCCCcceeccCCCcceEE-ecccc-----ccccccccc
Q 025608 203 RCPNCKFYVEKKDGCSYIRC-RCGHA-----FCYHCGVQL 236 (250)
Q Consensus 203 ~CP~C~~~i~k~~GCnhm~C-~C~~~-----FC~~C~~~~ 236 (250)
.||.|...++..+ .+.+| .|+.. +|--|++++
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHH
Confidence 7999999988888 78888 88765 466776665
No 137
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.44 E-value=7.8 Score=32.70 Aligned_cols=44 Identities=23% Similarity=0.631 Sum_probs=32.2
Q ss_pred ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCC
Q 025608 41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCG 94 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 94 (250)
.+.|++|-.-+..+ .....|+|.||.+|+..-+.. ..++||. |.
T Consensus 274 ~LkCplc~~Llrnp--~kT~cC~~~fc~eci~~al~d------sDf~Cpn--C~ 317 (427)
T COG5222 274 SLKCPLCHCLLRNP--MKTPCCGHTFCDECIGTALLD------SDFKCPN--CS 317 (427)
T ss_pred cccCcchhhhhhCc--ccCccccchHHHHHHhhhhhh------ccccCCC--cc
Confidence 37899998765433 223589999999999887662 3578998 54
No 138
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.05 E-value=1 Score=27.68 Aligned_cols=45 Identities=27% Similarity=0.722 Sum_probs=30.7
Q ss_pred eecccCcccccCCCceecCCCCCc-chHHHHHHHHHHHhhcCcccccCCCCCCCCCC
Q 025608 42 FVCEICVETKLRNESFSIKGCSHM-YCVDCTVKYVDSKLQENVTSIGCPVTDCGGSL 97 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 97 (250)
-+|.||++.--++. +-.|||. +|-+|-.+.++. ..=.||. |..++
T Consensus 8 dECTICye~pvdsV---lYtCGHMCmCy~Cg~rl~~~------~~g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEHPVDSV---LYTCGHMCMCYACGLRLKKA------LHGCCPI--CRAPI 53 (62)
T ss_pred cceeeeccCcchHH---HHHcchHHhHHHHHHHHHHc------cCCcCcc--hhhHH
Confidence 47999998543333 3389999 899998887773 1125776 66543
No 139
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=76.61 E-value=1.2 Score=24.73 Aligned_cols=28 Identities=29% Similarity=0.807 Sum_probs=15.3
Q ss_pred cCCCCCCCCceecC--ccCccCcccCCcccch
Q 025608 130 YCPFKDCSALLIDD--AGEAIRESECPNCHRL 159 (250)
Q Consensus 130 ~Cp~~~C~~~~~~~--~~~~~~~~~C~~C~~~ 159 (250)
+|| .|++.+... .+++-.+..|+.||..
T Consensus 2 fC~--~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCP--QCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-T--TT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccc--cccChhhhhcCCCCCccceECCCCCCE
Confidence 688 888766653 4455677889888853
No 140
>PHA02926 zinc finger-like protein; Provisional
Probab=76.39 E-value=1.8 Score=34.90 Aligned_cols=51 Identities=25% Similarity=0.408 Sum_probs=30.6
Q ss_pred CCCccCCCCCcceeccCCCcc-eEE---eccccccccccccccCCCC----CcCCCCCC
Q 025608 199 QKWNRCPNCKFYVEKKDGCSY-IRC---RCGHAFCYHCGVQLSTVSH----GYYCPSCN 249 (250)
Q Consensus 199 ~~~~~CP~C~~~i~k~~GCnh-m~C---~C~~~FC~~C~~~~~~~~h----~~~~~~~~ 249 (250)
..-+.|+=|.-.+-+...-+. ..= .|+|.||+.|...|....+ ...||-|-
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR 226 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICR 226 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCc
Confidence 334789999875532211111 111 6788899999999954322 23499884
No 141
>PRK00420 hypothetical protein; Validated
Probab=76.23 E-value=1.9 Score=30.98 Aligned_cols=23 Identities=35% Similarity=0.797 Sum_probs=16.6
Q ss_pred ccCCCCCcceec-cCCCcceEE-eccc
Q 025608 202 NRCPNCKFYVEK-KDGCSYIRC-RCGH 226 (250)
Q Consensus 202 ~~CP~C~~~i~k-~~GCnhm~C-~C~~ 226 (250)
..||.|+.++.+ .+| ...| .||.
T Consensus 24 ~~CP~Cg~pLf~lk~g--~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFELKDG--EVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceecCCC--ceECCCCCC
Confidence 899999999887 444 5555 5554
No 142
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=75.91 E-value=1.1 Score=37.89 Aligned_cols=42 Identities=21% Similarity=0.509 Sum_probs=29.1
Q ss_pred eecCCCCCCCCceecCc------cCccCcccCCcccchhccccCcccCCC
Q 025608 128 KFYCPFKDCSALLIDDA------GEAIRESECPNCHRLFCAQCKVAWHAG 171 (250)
Q Consensus 128 ~~~Cp~~~C~~~~~~~~------~~~~~~~~C~~C~~~~C~~C~~~~H~~ 171 (250)
...|- .|+..+...+ ....-+..|+.|+..||..|..-.|..
T Consensus 362 s~~Cf--~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~ 409 (421)
T COG5151 362 STHCF--VCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHET 409 (421)
T ss_pred Cccce--eccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHH
Confidence 34676 6777666432 122456789999999999999876643
No 143
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.81 E-value=1.7 Score=37.91 Aligned_cols=45 Identities=22% Similarity=0.774 Sum_probs=31.1
Q ss_pred eecccCcccccCCCce-ecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608 42 FVCEICVETKLRNESF-SIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV 90 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 90 (250)
..|.||-+-++.+.-. ..-.|||.|...|+..|++..-.+ -.||.
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~----R~cpi 50 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN----RGCPI 50 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc----CCCCc
Confidence 4699996656654333 333599999999999999844221 35776
No 144
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=75.57 E-value=2.4 Score=24.80 Aligned_cols=42 Identities=29% Similarity=0.586 Sum_probs=20.1
Q ss_pred cccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608 44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPV 90 (250)
Q Consensus 44 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 90 (250)
|.+|-+-......-...+|+-.+...|+++|+...-. + +||.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~----~-~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSN----P-KCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS------B-TT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCC----C-CCcC
Confidence 5667665544333223478888999999999985522 2 6875
No 145
>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=75.46 E-value=1.9 Score=30.49 Aligned_cols=25 Identities=28% Similarity=0.642 Sum_probs=19.4
Q ss_pred cCCCCCcceeccCCCcceEE-ecccccc
Q 025608 203 RCPNCKFYVEKKDGCSYIRC-RCGHAFC 229 (250)
Q Consensus 203 ~CP~C~~~i~k~~GCnhm~C-~C~~~FC 229 (250)
-||.||.++...+ +.+.| .|++.+=
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCcccccCC--CeEECcCCCCccc
Confidence 5999999887655 48889 8987754
No 146
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=75.36 E-value=13 Score=27.45 Aligned_cols=57 Identities=23% Similarity=0.402 Sum_probs=42.5
Q ss_pred ccCCCCceecccCcccccCCCcee-cCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCC
Q 025608 35 RSETSRSFVCEICVETKLRNESFS-IKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSL 97 (250)
Q Consensus 35 ~~~~~~~~~C~iC~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 97 (250)
...+....+|.||-+....+.+.. -.-||=.+|.-|-...|+... ..-+||. |+..+
T Consensus 74 vF~d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~----~ypvCPv--CkTSF 131 (140)
T PF05290_consen 74 VFLDPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN----LYPVCPV--CKTSF 131 (140)
T ss_pred eecCCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc----cCCCCCc--ccccc
Confidence 345568899999999887666543 457889999999999999553 2348998 76544
No 147
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=75.32 E-value=3.1 Score=28.27 Aligned_cols=29 Identities=28% Similarity=0.638 Sum_probs=25.4
Q ss_pred CCccCCCCCcceeccCCCcceEE-eccccc
Q 025608 200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~F 228 (250)
....||.|+....+..+=.--.| .||+.|
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 34799999999999988888889 899877
No 148
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=75.29 E-value=2.4 Score=40.17 Aligned_cols=11 Identities=36% Similarity=0.842 Sum_probs=7.0
Q ss_pred ccCCCCCccee
Q 025608 202 NRCPNCKFYVE 212 (250)
Q Consensus 202 ~~CP~C~~~i~ 212 (250)
+-||+||..+.
T Consensus 42 ~fC~~CG~~~~ 52 (645)
T PRK14559 42 AHCPNCGAETG 52 (645)
T ss_pred ccccccCCccc
Confidence 57777776543
No 149
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=75.14 E-value=1 Score=37.43 Aligned_cols=31 Identities=29% Similarity=0.835 Sum_probs=25.7
Q ss_pred cCCCccCCCCCcceecc-CCCcceEE-eccccc
Q 025608 198 NQKWNRCPNCKFYVEKK-DGCSYIRC-RCGHAF 228 (250)
Q Consensus 198 ~~~~~~CP~C~~~i~k~-~GCnhm~C-~C~~~F 228 (250)
.+.|.+||.|+.++-+. -+=|...| +|++||
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCccc
Confidence 56789999999977766 47788889 999987
No 150
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=75.08 E-value=2.8 Score=26.36 Aligned_cols=27 Identities=33% Similarity=0.863 Sum_probs=16.4
Q ss_pred CCccCCCCCccee--ccC-C--C---cceEE-eccc
Q 025608 200 KWNRCPNCKFYVE--KKD-G--C---SYIRC-RCGH 226 (250)
Q Consensus 200 ~~~~CP~C~~~i~--k~~-G--C---nhm~C-~C~~ 226 (250)
.+++||.||.... +.. + - -.|.| .||.
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 3589999996322 222 2 1 45778 7776
No 151
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=74.81 E-value=2.5 Score=36.03 Aligned_cols=48 Identities=21% Similarity=0.471 Sum_probs=34.5
Q ss_pred CCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608 37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE 98 (250)
Q Consensus 37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 98 (250)
.....++||||++.+.++. +.. +=||..|.+|-. ...-+||. |...+.
T Consensus 44 ~~~~lleCPvC~~~l~~Pi-~QC-~nGHlaCssC~~----------~~~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 44 LDLDLLDCPVCFNPLSPPI-FQC-DNGHLACSSCRT----------KVSNKCPT--CRLPIG 91 (299)
T ss_pred cchhhccCchhhccCcccc-eec-CCCcEehhhhhh----------hhcccCCc--cccccc
Confidence 3466779999999987654 211 336999999986 13358997 887776
No 152
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=74.73 E-value=3.5 Score=29.61 Aligned_cols=46 Identities=28% Similarity=0.653 Sum_probs=36.5
Q ss_pred ccCCCCCcceecc--------CCCcceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608 202 NRCPNCKFYVEKK--------DGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 202 ~~CP~C~~~i~k~--------~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
+.|-.|...+... ..=....| +|+..||.-|-.=++..-|. ||.|.
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~--CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHC--CPGCI 110 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccC--CcCCC
Confidence 5699998866532 12346789 99999999999999888888 99986
No 153
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.54 E-value=5.9 Score=31.98 Aligned_cols=53 Identities=15% Similarity=0.446 Sum_probs=39.7
Q ss_pred ecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhc-CcccccCCCCCCCCCCC
Q 025608 43 VCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQE-NVTSIGCPVTDCGGSLE 98 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~-~~~~i~CP~~~C~~~l~ 98 (250)
.|.+|-.++...+.+.+ -|-|.|...|+..+..+--.+ .-....||. |.+.+-
T Consensus 52 NC~LC~t~La~gdt~RL-vCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~eiF 105 (299)
T KOG3970|consen 52 NCRLCNTPLASGDTTRL-VCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEIF 105 (299)
T ss_pred CCceeCCccccCcceee-hhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCccC
Confidence 59999999887776655 999999999999987744333 235678986 775543
No 154
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=74.15 E-value=2.6 Score=27.26 Aligned_cols=28 Identities=25% Similarity=0.685 Sum_probs=21.5
Q ss_pred CCccCCCCCcceeccCCCcceEE-ecccc
Q 025608 200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~ 227 (250)
..+.||.|+....+...=..++| .||..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 45899999999888555556778 78765
No 155
>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=74.14 E-value=3 Score=24.29 Aligned_cols=24 Identities=29% Similarity=0.726 Sum_probs=12.6
Q ss_pred cCCCCCcc-eeccCCCcceEE-eccc
Q 025608 203 RCPNCKFY-VEKKDGCSYIRC-RCGH 226 (250)
Q Consensus 203 ~CP~C~~~-i~k~~GCnhm~C-~C~~ 226 (250)
.||.|+.. +.-+..=..+.| .||.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 47777773 333344445566 6654
No 156
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=73.80 E-value=2.1 Score=31.65 Aligned_cols=23 Identities=39% Similarity=0.928 Sum_probs=16.9
Q ss_pred ccCCCCCcceeccCCCcceEE-eccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGH 226 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~ 226 (250)
..||.||.++.+..| .+.| .|++
T Consensus 29 ~hCp~Cg~PLF~KdG--~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPLFRKDG--EVFCPVCGY 52 (131)
T ss_pred hhCcccCCcceeeCC--eEECCCCCc
Confidence 799999998887665 4555 5553
No 157
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=73.45 E-value=3.6 Score=21.65 Aligned_cols=20 Identities=35% Similarity=0.811 Sum_probs=13.3
Q ss_pred cCCCCCcceeccCCCcceEE
Q 025608 203 RCPNCKFYVEKKDGCSYIRC 222 (250)
Q Consensus 203 ~CP~C~~~i~k~~GCnhm~C 222 (250)
.||.|+..+.+.+|=-.+.|
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C 20 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRC 20 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE
T ss_pred CcCCCCCEeEcCCCCEeEEC
Confidence 49999999999988777777
No 158
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.67 E-value=0.95 Score=37.34 Aligned_cols=41 Identities=34% Similarity=0.760 Sum_probs=28.4
Q ss_pred ccCCCCCcceeccCCCcceEE-ecccccccccccc-ccCCCCCcCCCCCC
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQ-LSTVSHGYYCPSCN 249 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~-~~~~~h~~~~~~~~ 249 (250)
.+|+=|--..+ --.| .||+-|||.|+.- | +-..+-.||-|-
T Consensus 216 ~kC~lC~e~~~------~ps~t~CgHlFC~~Cl~~~~-t~~k~~~CplCR 258 (271)
T COG5574 216 YKCFLCLEEPE------VPSCTPCGHLFCLSCLLISW-TKKKYEFCPLCR 258 (271)
T ss_pred cceeeeecccC------CcccccccchhhHHHHHHHH-HhhccccCchhh
Confidence 56777776655 3567 8999999999887 7 323333388773
No 159
>PRK04023 DNA polymerase II large subunit; Validated
Probab=72.61 E-value=3.3 Score=40.71 Aligned_cols=33 Identities=24% Similarity=0.657 Sum_probs=23.5
Q ss_pred CeecCCCCCCCCceecCccCccCcccCCcccc-----hhccccCcccC
Q 025608 127 QKFYCPFKDCSALLIDDAGEAIRESECPNCHR-----LFCAQCKVAWH 169 (250)
Q Consensus 127 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~-----~~C~~C~~~~H 169 (250)
....|| +|+... ..+.||.||. .+|..|+....
T Consensus 625 g~RfCp--sCG~~t--------~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 625 GRRKCP--SCGKET--------FYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred cCccCC--CCCCcC--------CcccCCCCCCCCCcceeCccccCcCC
Confidence 345898 887762 4478999985 58888876543
No 160
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=72.30 E-value=1.4 Score=41.93 Aligned_cols=52 Identities=29% Similarity=0.733 Sum_probs=36.9
Q ss_pred eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhc
Q 025608 42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRD 104 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 104 (250)
+.|.+|.+ .+. +....|+|.||.+|+...+...-.. .||. |...+....+..
T Consensus 455 ~~c~ic~~---~~~-~~it~c~h~~c~~c~~~~i~~~~~~-----~~~~--cr~~l~~~~l~s 506 (674)
T KOG1001|consen 455 HWCHICCD---LDS-FFITRCGHDFCVECLKKSIQQSENA-----PCPL--CRNVLKEKKLLS 506 (674)
T ss_pred cccccccc---ccc-ceeecccchHHHHHHHhccccccCC-----CCcH--HHHHHHHHHHhh
Confidence 78999998 223 2334999999999999999844221 6776 877766655543
No 161
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=72.25 E-value=3.2 Score=24.80 Aligned_cols=33 Identities=24% Similarity=0.678 Sum_probs=22.6
Q ss_pred cccCcccccCCCceecCCCC-----CcchHHHHHHHHHH
Q 025608 44 CEICVETKLRNESFSIKGCS-----HMYCVDCTVKYVDS 77 (250)
Q Consensus 44 C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~ 77 (250)
|-||+++...+..+ ..+|. ..+..+||..|+..
T Consensus 1 CrIC~~~~~~~~~l-i~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPL-ISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-E-E-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCce-ecccccCCCcchhHHHHHHHHHHh
Confidence 67899887655522 23665 35789999999997
No 162
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=71.76 E-value=4.3 Score=40.97 Aligned_cols=29 Identities=31% Similarity=0.890 Sum_probs=20.4
Q ss_pred ecCCCCCCCCceecCccCccCcccCCcccchh-----ccccCcc
Q 025608 129 FYCPFKDCSALLIDDAGEAIRESECPNCHRLF-----CAQCKVA 167 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~-----C~~C~~~ 167 (250)
+.|| +|+.... ...||.||... |..|+..
T Consensus 668 rkCP--kCG~~t~--------~~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 668 RRCP--SCGTETY--------ENRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EECC--CCCCccc--------cccCcccCCcCCCceeCccCCCc
Confidence 6899 8887522 23788888665 7777764
No 163
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=71.39 E-value=2.3 Score=41.10 Aligned_cols=26 Identities=38% Similarity=1.129 Sum_probs=23.0
Q ss_pred ccCCCCCcceeccCCCcceEE-ecccccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFC 229 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC 229 (250)
..||.|+..+...+||. +| .||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence 46999999999999998 99 9998655
No 164
>PF14149 YhfH: YhfH-like protein
Probab=71.15 E-value=0.42 Score=26.92 Aligned_cols=31 Identities=26% Similarity=0.630 Sum_probs=22.3
Q ss_pred HHHhcCCCccCCCCCcceeccCCCcceEE-ec
Q 025608 194 KLAQNQKWNRCPNCKFYVEKKDGCSYIRC-RC 224 (250)
Q Consensus 194 ~~~~~~~~~~CP~C~~~i~k~~GCnhm~C-~C 224 (250)
++..+...|.||.||..|+-..-|-..+| .|
T Consensus 6 eFfrnLp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 6 EFFRNLPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred HHHHhCCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 44556667999999998887666666666 54
No 165
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=70.63 E-value=3.4 Score=25.54 Aligned_cols=30 Identities=30% Similarity=0.542 Sum_probs=22.2
Q ss_pred ecCCCCCCCCceecCccCccCcccCCcccchh
Q 025608 129 FYCPFKDCSALLIDDAGEAIRESECPNCHRLF 160 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 160 (250)
+.|| .|++.+..........+.|+.||..+
T Consensus 3 ~~CP--~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECP--DCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCC--CCCCEEecCCCccCCEEeCCCCCCEE
Confidence 4788 89988777654445678899988764
No 166
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=70.51 E-value=2.4 Score=28.09 Aligned_cols=43 Identities=21% Similarity=0.549 Sum_probs=16.2
Q ss_pred CcccCCcccchhccccCcccCCCCCchhHhhhccCCCchHHHHHHHHHhcCCCccCCCCCcceeccCCCcc
Q 025608 149 RESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSY 219 (250)
Q Consensus 149 ~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~C~~~i~k~~GCnh 219 (250)
..+.|..|+...|..|.. | ..+...+.||.|+....+..|+-.
T Consensus 27 ~FVAC~eC~fPvCr~CyE----------Y------------------Erkeg~q~CpqCkt~ykr~kgsp~ 69 (80)
T PF14569_consen 27 VFVACHECAFPVCRPCYE----------Y------------------ERKEGNQVCPQCKTRYKRHKGSPR 69 (80)
T ss_dssp B--S-SSS-----HHHHH----------H------------------HHHTS-SB-TTT--B----TT---
T ss_pred EEEEEcccCCccchhHHH----------H------------------HhhcCcccccccCCCcccccCCCC
Confidence 668899999999877763 1 112344899999998887777643
No 167
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=70.40 E-value=4.3 Score=24.84 Aligned_cols=29 Identities=24% Similarity=0.330 Sum_probs=18.1
Q ss_pred ccCCCCCccee------ccCCCcce-EE-eccccccc
Q 025608 202 NRCPNCKFYVE------KKDGCSYI-RC-RCGHAFCY 230 (250)
Q Consensus 202 ~~CP~C~~~i~------k~~GCnhm-~C-~C~~~FC~ 230 (250)
++||.|+-.-+ .+.+..++ .| .|++..-+
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 79999998433 22345555 47 77776543
No 168
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=69.80 E-value=2 Score=41.83 Aligned_cols=53 Identities=21% Similarity=0.454 Sum_probs=36.4
Q ss_pred CCceecccCccccc-C-CCce--ecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCC
Q 025608 39 SRSFVCEICVETKL-R-NESF--SIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLE 98 (250)
Q Consensus 39 ~~~~~C~iC~~~~~-~-~~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~ 98 (250)
++.-+|+||+.... . ...+ +...|.|.|...|+-+|+.+.-+ =.||. |...++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~-----s~CPl--CRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSAR-----SNCPL--CRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCC-----CCCCc--cccccc
Confidence 34447999998765 1 2222 24478899999999999996533 26897 765543
No 169
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=69.46 E-value=1.1 Score=38.18 Aligned_cols=31 Identities=29% Similarity=0.836 Sum_probs=24.4
Q ss_pred cCCCccCCCCCcceecc-CCCcceEE-eccccc
Q 025608 198 NQKWNRCPNCKFYVEKK-DGCSYIRC-RCGHAF 228 (250)
Q Consensus 198 ~~~~~~CP~C~~~i~k~-~GCnhm~C-~C~~~F 228 (250)
++.|.+||+|+..+-+. -.=|.+.| .|++||
T Consensus 24 ~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 24 EGLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 44589999999977655 35567899 999998
No 170
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=69.43 E-value=7.7 Score=37.46 Aligned_cols=40 Identities=25% Similarity=0.346 Sum_probs=30.6
Q ss_pred eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCC
Q 025608 42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGG 95 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 95 (250)
..|..|--++..+.+. ..|+|.|...|+. ...-.||. |..
T Consensus 841 skCs~C~~~LdlP~Vh--F~CgHsyHqhC~e----------~~~~~CP~--C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLDLPFVH--FLCGHSYHQHCLE----------DKEDKCPK--CLP 880 (933)
T ss_pred eeecccCCccccceee--eecccHHHHHhhc----------cCcccCCc--cch
Confidence 4799998877666544 4899999999998 23458987 764
No 171
>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=69.35 E-value=3.3 Score=20.98 Aligned_cols=22 Identities=27% Similarity=0.839 Sum_probs=12.5
Q ss_pred cccccccccCC--CCCcCCCCCCC
Q 025608 229 CYHCGVQLSTV--SHGYYCPSCNK 250 (250)
Q Consensus 229 C~~C~~~~~~~--~h~~~~~~~~~ 250 (250)
|-.|+..+.+. .-.|.||+|+.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 44565555322 23467898874
No 172
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=69.08 E-value=3.3 Score=30.36 Aligned_cols=27 Identities=19% Similarity=0.166 Sum_probs=19.7
Q ss_pred CccCCCCCcceeccCCCcceEE-eccccc
Q 025608 201 WNRCPNCKFYVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 201 ~~~CP~C~~~i~k~~GCnhm~C-~C~~~F 228 (250)
-+.||+|+...--..- +-++| +||+.|
T Consensus 9 Kr~Cp~cg~kFYDLnk-~p~vcP~cg~~~ 36 (129)
T TIGR02300 9 KRICPNTGSKFYDLNR-RPAVSPYTGEQF 36 (129)
T ss_pred cccCCCcCccccccCC-CCccCCCcCCcc
Confidence 3789999886554444 67888 888875
No 173
>PRK05580 primosome assembly protein PriA; Validated
Probab=67.33 E-value=11 Score=36.15 Aligned_cols=14 Identities=14% Similarity=0.133 Sum_probs=7.0
Q ss_pred CChHHHHHHHHHHH
Q 025608 106 LPEEAFDKWGKALC 119 (250)
Q Consensus 106 l~~~~~~~~~~~~~ 119 (250)
++...++..++.+.
T Consensus 351 ls~~l~~~i~~~l~ 364 (679)
T PRK05580 351 LSPPLLEAIKQRLE 364 (679)
T ss_pred CCHHHHHHHHHHHH
Confidence 45555555555443
No 174
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=67.25 E-value=3.9 Score=28.76 Aligned_cols=30 Identities=30% Similarity=0.587 Sum_probs=21.3
Q ss_pred CCCccCCCCCcce---eccCCCcceEE-eccccc
Q 025608 199 QKWNRCPNCKFYV---EKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 199 ~~~~~CP~C~~~i---~k~~GCnhm~C-~C~~~F 228 (250)
..+..||+|+... ....|=-|+.| .||+.+
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 3457999999532 23346679999 999875
No 175
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=67.12 E-value=2.4 Score=30.63 Aligned_cols=24 Identities=29% Similarity=0.958 Sum_probs=19.7
Q ss_pred ccccccccccccCCCCCcCCCCCC
Q 025608 226 HAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 226 ~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
.-+|+.|+..+....|.+.||.|.
T Consensus 70 ~~~C~~C~~~~~~e~~~~~CP~C~ 93 (115)
T COG0375 70 ECWCLDCGQEVELEELDYRCPKCG 93 (115)
T ss_pred EEEeccCCCeecchhheeECCCCC
Confidence 357888888888888888899996
No 176
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=66.88 E-value=6.2 Score=28.63 Aligned_cols=33 Identities=24% Similarity=0.377 Sum_probs=21.2
Q ss_pred ceecccCcccccC--CCceecCCCCCcchHHHHHH
Q 025608 41 SFVCEICVETKLR--NESFSIKGCSHMYCVDCTVK 73 (250)
Q Consensus 41 ~~~C~iC~~~~~~--~~~~~~~~C~H~fC~~Cl~~ 73 (250)
.-.|.+|..++.. ........|.|.+|..|-..
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 3479999987642 22244669999999998544
No 177
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=66.73 E-value=7.4 Score=24.01 Aligned_cols=33 Identities=21% Similarity=0.399 Sum_probs=26.9
Q ss_pred eecccCccccc-CCCceecCCCCCcchHHHHHHH
Q 025608 42 FVCEICVETKL-RNESFSIKGCSHMYCVDCTVKY 74 (250)
Q Consensus 42 ~~C~iC~~~~~-~~~~~~~~~C~H~fC~~Cl~~~ 74 (250)
..|++|-+.+. .+++.....|+-.+.++||...
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 45999999995 5666777899999999999653
No 178
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=66.03 E-value=2.3 Score=26.86 Aligned_cols=32 Identities=34% Similarity=0.638 Sum_probs=20.1
Q ss_pred CccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCC
Q 025608 201 WNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSC 248 (250)
Q Consensus 201 ~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~ 248 (250)
...||.|... ++.|||.=.-......|+ |-.|
T Consensus 5 ~~~CPRC~S~--------------nTKFcYyNNy~~~QPR~~--Ck~C 36 (63)
T PF02701_consen 5 PLPCPRCDST--------------NTKFCYYNNYNLSQPRYF--CKSC 36 (63)
T ss_pred CCCCCCcCCC--------------CCEEEeecCCCCCCcchh--hHHH
Confidence 4789999876 456777665555544444 4444
No 179
>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=65.96 E-value=5.6 Score=22.53 Aligned_cols=29 Identities=21% Similarity=0.442 Sum_probs=18.9
Q ss_pred ecCCCCCCCCceecCcc-CccCcccCCcccch
Q 025608 129 FYCPFKDCSALLIDDAG-EAIRESECPNCHRL 159 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~-~~~~~~~C~~C~~~ 159 (250)
+.|+ .|+..+..... .......||.||..
T Consensus 6 y~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCE--DCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEcC--CCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 5788 89986654421 12456789998863
No 180
>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=65.75 E-value=1.4 Score=37.35 Aligned_cols=31 Identities=26% Similarity=0.714 Sum_probs=23.9
Q ss_pred cCCCccCCCCCcceecc-CCCcceEE-eccccc
Q 025608 198 NQKWNRCPNCKFYVEKK-DGCSYIRC-RCGHAF 228 (250)
Q Consensus 198 ~~~~~~CP~C~~~i~k~-~GCnhm~C-~C~~~F 228 (250)
++.|.+||+|+..+-+. -.=|...| .|++||
T Consensus 23 ~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 23 EGVWTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred CCCeeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 34589999999977765 34566889 899986
No 181
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=65.65 E-value=7.4 Score=33.13 Aligned_cols=56 Identities=21% Similarity=0.341 Sum_probs=40.7
Q ss_pred ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHH
Q 025608 41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYC 102 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i 102 (250)
.|.||+=-+.-+.++.+.+++|+|.+=.+=+.. -..+|...++||. |+..-.+..+
T Consensus 336 ~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~----LS~nG~~~FKCPY--CP~~~~~~~~ 391 (396)
T COG5109 336 LFICPVLKELCTDENPPVMLECGHVISKEALSV----LSQNGVLSFKCPY--CPEMSKYENI 391 (396)
T ss_pred eeeccccHhhhcccCCCeeeeccceeeHHHHHH----HhhcCcEEeeCCC--CCcchhhhhh
Confidence 567999777777777788889999986554443 3346778999997 8876655544
No 182
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=65.61 E-value=13 Score=26.70 Aligned_cols=48 Identities=23% Similarity=0.533 Sum_probs=29.4
Q ss_pred CChHHHHHHHHHHHhhccCC---------CCeecCCCCCCCCceecCccCccCcccCCcccch
Q 025608 106 LPEEAFDKWGKALCESLIPG---------AQKFYCPFKDCSALLIDDAGEAIRESECPNCHRL 159 (250)
Q Consensus 106 l~~~~~~~~~~~~~~~~~~~---------~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 159 (250)
+.++.++.....+.+.++.. +...+|+ +|+..+.... ..+.||.||..
T Consensus 39 v~pe~L~f~f~~~~~~T~~egA~L~I~~vp~~~~C~--~Cg~~~~~~~----~~~~CP~Cgs~ 95 (113)
T PRK12380 39 VEESAVRFSFEIVCHGTVAQGCDLHIVYKPAQAWCW--DCSQVVEIHQ----HDAQCPHCHGE 95 (113)
T ss_pred cCHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCEEecCC----cCccCcCCCCC
Confidence 45666766666665544432 2345898 8987766643 33558888743
No 183
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=65.44 E-value=1.3 Score=37.51 Aligned_cols=30 Identities=30% Similarity=0.588 Sum_probs=22.9
Q ss_pred CCCccCCCCCcceecc-CCCcceEE-eccccc
Q 025608 199 QKWNRCPNCKFYVEKK-DGCSYIRC-RCGHAF 228 (250)
Q Consensus 199 ~~~~~CP~C~~~i~k~-~GCnhm~C-~C~~~F 228 (250)
..|.+||+|+..+.+. -.=|...| .|++||
T Consensus 36 ~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 36 HLWVQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred CCeeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 3578999999976655 35667888 899886
No 184
>PRK11827 hypothetical protein; Provisional
Probab=65.38 E-value=4.6 Score=25.55 Aligned_cols=28 Identities=21% Similarity=0.265 Sum_probs=21.3
Q ss_pred CccCCCCCcceeccCCCcceEE-eccccc
Q 025608 201 WNRCPNCKFYVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 201 ~~~CP~C~~~i~k~~GCnhm~C-~C~~~F 228 (250)
+..||.|+..++-..+=+.+.| .|+-.|
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeec
Confidence 3689999998887666677888 777544
No 185
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=65.20 E-value=4.4 Score=34.03 Aligned_cols=51 Identities=29% Similarity=0.621 Sum_probs=37.4
Q ss_pred cCCCCceecccCcccccCC-CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCC
Q 025608 36 SETSRSFVCEICVETKLRN-ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGG 95 (250)
Q Consensus 36 ~~~~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 95 (250)
.+....+.||||.+.+... .....++|+|..-..|++.+.. ++ ..||. |..
T Consensus 153 ~e~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~----~~---y~CP~--C~~ 204 (276)
T KOG1940|consen 153 VERSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMIC----EG---YTCPI--CSK 204 (276)
T ss_pred hhhcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhc----cC---CCCCc--ccc
Confidence 4445556699999987533 3344679999999999988876 22 78998 776
No 186
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=64.83 E-value=3.9 Score=29.52 Aligned_cols=23 Identities=30% Similarity=0.931 Sum_probs=12.5
Q ss_pred cccccccccccCCCCCcCCCCCC
Q 025608 227 AFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 227 ~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
.+|..|+..+.....++.||+|+
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cg 93 (113)
T PRK12380 71 AWCWDCSQVVEIHQHDAQCPHCH 93 (113)
T ss_pred EEcccCCCEEecCCcCccCcCCC
Confidence 34444555554434455588776
No 187
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=64.73 E-value=1.9 Score=41.09 Aligned_cols=21 Identities=14% Similarity=0.205 Sum_probs=14.1
Q ss_pred CCCCcchHHHHHHHHHHHhhc
Q 025608 61 GCSHMYCVDCTVKYVDSKLQE 81 (250)
Q Consensus 61 ~C~H~fC~~Cl~~~~~~~i~~ 81 (250)
.|+|.+|..||..+....+..
T Consensus 120 ~~~~~~CP~Ci~s~~DqL~~~ 140 (1134)
T KOG0825|consen 120 THVENQCPNCLKSCNDQLEES 140 (1134)
T ss_pred hhhhhhhhHHHHHHHHHhhcc
Confidence 467777777777776655544
No 188
>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=64.72 E-value=1.4 Score=31.76 Aligned_cols=23 Identities=30% Similarity=0.879 Sum_probs=14.7
Q ss_pred cccccccccccCCCCCcCCCCCC
Q 025608 227 AFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 227 ~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
.+|..|+..|....+.+.||+|+
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cg 93 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFDFSCPRCG 93 (113)
T ss_dssp EEETTTS-EEECHHCCHH-SSSS
T ss_pred EECCCCCCEEecCCCCCCCcCCc
Confidence 56666777776556667899987
No 189
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=64.32 E-value=13 Score=27.63 Aligned_cols=35 Identities=14% Similarity=0.130 Sum_probs=21.3
Q ss_pred ChHHHHHHHHHHHhhccCCC---------CeecCCCCCCCCceecC
Q 025608 107 PEEAFDKWGKALCESLIPGA---------QKFYCPFKDCSALLIDD 143 (250)
Q Consensus 107 ~~~~~~~~~~~~~~~~~~~~---------~~~~Cp~~~C~~~~~~~ 143 (250)
.++.++.....+.+..+... ...+|+ +|+..+...
T Consensus 40 ~pe~L~fafe~l~~gt~~ega~L~i~~~p~~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 40 DKEIVEFALNELLKGTILEGAEIIFEEEEAVLKCR--NCGNEWSLK 83 (135)
T ss_pred hHHHHHHHHHHHHcCCcccCCEEEEEecceEEECC--CCCCEEecc
Confidence 45666666666555443222 345999 999877664
No 190
>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=64.22 E-value=5.1 Score=24.79 Aligned_cols=47 Identities=28% Similarity=0.614 Sum_probs=31.6
Q ss_pred ecccCcccccCCCcee-cCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608 43 VCEICVETKLRNESFS-IKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE 100 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 100 (250)
.|..|-.+++++..-. .-+=...||.+|....+. -.||. |++.|...
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~---------~~CPN--CgGelv~R 54 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLN---------GVCPN--CGGELVRR 54 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc---------CcCcC--CCCccccC
Confidence 5999999887655211 112247899999887664 26887 88877544
No 191
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=64.08 E-value=2.5 Score=35.39 Aligned_cols=27 Identities=41% Similarity=0.971 Sum_probs=20.5
Q ss_pred eEE--eccccccccccccccCCCCCcCCCCC
Q 025608 220 IRC--RCGHAFCYHCGVQLSTVSHGYYCPSC 248 (250)
Q Consensus 220 m~C--~C~~~FC~~C~~~~~~~~h~~~~~~~ 248 (250)
+-| .||+.||++|-+.+-+..-+ ||.|
T Consensus 37 ip~~TtCgHtFCslCIR~hL~~qp~--CP~C 65 (391)
T COG5432 37 IPCETTCGHTFCSLCIRRHLGTQPF--CPVC 65 (391)
T ss_pred cceecccccchhHHHHHHHhcCCCC--Cccc
Confidence 557 79999999998888443334 8887
No 192
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=63.36 E-value=4.3 Score=29.40 Aligned_cols=22 Identities=32% Similarity=0.777 Sum_probs=12.1
Q ss_pred ccccccccccCCCCCcCCCCCC
Q 025608 228 FCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 228 FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
+|-.|+..+....+++.||+|+
T Consensus 72 ~C~~Cg~~~~~~~~~~~CP~Cg 93 (115)
T TIGR00100 72 ECEDCSEEVSPEIDLYRCPKCH 93 (115)
T ss_pred EcccCCCEEecCCcCccCcCCc
Confidence 4444445554434456677775
No 193
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=62.94 E-value=4 Score=28.36 Aligned_cols=29 Identities=31% Similarity=0.911 Sum_probs=21.1
Q ss_pred ecCCCCCCCCceecCccCccCcccCCcccch
Q 025608 129 FYCPFKDCSALLIDDAGEAIRESECPNCHRL 159 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 159 (250)
.+|| .|++.+++..+.....+.|+.|.+.
T Consensus 2 ~FCP--~Cgn~Live~g~~~~rf~C~tCpY~ 30 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESGESCNRFSCRTCPYV 30 (105)
T ss_pred cccC--CCCCEEEEecCCeEeeEEcCCCCce
Confidence 3688 9999999887665566667666544
No 194
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=62.78 E-value=7.9 Score=20.92 Aligned_cols=25 Identities=28% Similarity=0.661 Sum_probs=21.9
Q ss_pred ccCCCCCcceeccCCCcceEE-eccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGH 226 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~ 226 (250)
..|+.|+.++.-..|=..+.| .|.+
T Consensus 2 ~~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 2 VVCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred cCcCCCCcEeecCCCCCeEECCCCCe
Confidence 369999999999999999999 8865
No 195
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=62.51 E-value=5.7 Score=32.75 Aligned_cols=51 Identities=24% Similarity=0.576 Sum_probs=36.8
Q ss_pred ecccCcccccCCCce-ecCCCC-----CcchHHHHHHHHHHHhhc-CcccccCCCCCCCC
Q 025608 43 VCEICVETKLRNESF-SIKGCS-----HMYCVDCTVKYVDSKLQE-NVTSIGCPVTDCGG 95 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~-~~~~C~-----H~fC~~Cl~~~~~~~i~~-~~~~i~CP~~~C~~ 95 (250)
-|=|||.+..+.... -.-+|. |.+..+|+..|+...-.+ ...++.||+ |..
T Consensus 22 ~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqT 79 (293)
T KOG3053|consen 22 CCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQT 79 (293)
T ss_pred eEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcc
Confidence 599999876544322 133665 779999999999866553 468999998 653
No 196
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=62.37 E-value=5.4 Score=24.97 Aligned_cols=24 Identities=29% Similarity=0.524 Sum_probs=17.4
Q ss_pred cCCCccCCCCCcceeccCCCcceEE-eccc
Q 025608 198 NQKWNRCPNCKFYVEKKDGCSYIRC-RCGH 226 (250)
Q Consensus 198 ~~~~~~CP~C~~~i~k~~GCnhm~C-~C~~ 226 (250)
...+..||+||.+... |-.| .||+
T Consensus 24 ~~~l~~C~~CG~~~~~-----H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECPNCGEPKLP-----HRVCPSCGY 48 (57)
T ss_pred CCcceECCCCCCccCC-----eEECCCCCc
Confidence 3455789999998764 6667 6664
No 197
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=62.13 E-value=5.2 Score=21.18 Aligned_cols=23 Identities=43% Similarity=1.050 Sum_probs=10.8
Q ss_pred ccCCCCCcceecc--CCCcceEE-ec
Q 025608 202 NRCPNCKFYVEKK--DGCSYIRC-RC 224 (250)
Q Consensus 202 ~~CP~C~~~i~k~--~GCnhm~C-~C 224 (250)
++||.|+.+|++. +|=+...| +|
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rC 27 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRC 27 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTT
T ss_pred CcCccCCCcceEeEecCCCCeECcCC
Confidence 4788888877654 33333444 44
No 198
>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=61.02 E-value=18 Score=26.06 Aligned_cols=48 Identities=19% Similarity=0.392 Sum_probs=28.6
Q ss_pred CChHHHHHHHHHHHhhccCC---------CCeecCCCCCCCCceecCccCccCcccCCcccch
Q 025608 106 LPEEAFDKWGKALCESLIPG---------AQKFYCPFKDCSALLIDDAGEAIRESECPNCHRL 159 (250)
Q Consensus 106 l~~~~~~~~~~~~~~~~~~~---------~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 159 (250)
+.++.++.....+.+.++.. +...+|+ +|+..+.... ..+.||.||..
T Consensus 39 V~p~~L~faf~~~~~~t~~ega~L~I~~~p~~~~C~--~Cg~~~~~~~----~~~~CP~Cgs~ 95 (115)
T TIGR00100 39 VNPSQLQFAFEVVREGTVAEGAKLNIEDEPVECECE--DCSEEVSPEI----DLYRCPKCHGI 95 (115)
T ss_pred cCHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCEEecCC----cCccCcCCcCC
Confidence 35666666555555433322 2345898 8987766643 23668888754
No 199
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=59.88 E-value=5.6 Score=28.69 Aligned_cols=30 Identities=23% Similarity=0.542 Sum_probs=22.3
Q ss_pred ecCCCCCCCCceecCccCccCcccCCcccchh
Q 025608 129 FYCPFKDCSALLIDDAGEAIRESECPNCHRLF 160 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 160 (250)
.+|| .|++++.+........+.|+.||+..
T Consensus 3 ~FCp--~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCP--KCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccC--CccCeeEEeEcCCCcEEECCCCCcch
Confidence 3788 99999998644334578888888763
No 200
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=59.58 E-value=5.3 Score=28.36 Aligned_cols=26 Identities=27% Similarity=0.715 Sum_probs=19.4
Q ss_pred cCCCCCCCCceecCccCccCcccCCcccchh
Q 025608 130 YCPFKDCSALLIDDAGEAIRESECPNCHRLF 160 (250)
Q Consensus 130 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 160 (250)
.|| .|+..+.+.++ ..+.||.|+..|
T Consensus 4 ~CP--~C~seytY~dg---~~~iCpeC~~EW 29 (109)
T TIGR00686 4 PCP--KCNSEYTYHDG---TQLICPSCLYEW 29 (109)
T ss_pred cCC--cCCCcceEecC---CeeECccccccc
Confidence 477 88887777665 447898888775
No 201
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.40 E-value=10 Score=29.48 Aligned_cols=62 Identities=18% Similarity=0.438 Sum_probs=41.0
Q ss_pred cCCCCceecccCccccc----CCCceecCCCCCcchHHHHHHHHHHHhhcC-cccc---cCCCCCCCCCCCH
Q 025608 36 SETSRSFVCEICVETKL----RNESFSIKGCSHMYCVDCTVKYVDSKLQEN-VTSI---GCPVTDCGGSLEP 99 (250)
Q Consensus 36 ~~~~~~~~C~iC~~~~~----~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~-~~~i---~CP~~~C~~~l~~ 99 (250)
..+.+...|.||+...- ++.+-...+|+..|..-||..|+..-+... .+.| .||. |..++..
T Consensus 160 ekdd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pial 229 (234)
T KOG3268|consen 160 EKDDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIAL 229 (234)
T ss_pred CcchhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCccee
Confidence 34455667999985432 223334569999999999999998766553 2222 6887 7766554
No 202
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=59.36 E-value=6 Score=23.67 Aligned_cols=25 Identities=28% Similarity=0.610 Sum_probs=16.1
Q ss_pred ccCC--CCCcceeccCCCcceEE-eccc
Q 025608 202 NRCP--NCKFYVEKKDGCSYIRC-RCGH 226 (250)
Q Consensus 202 ~~CP--~C~~~i~k~~GCnhm~C-~C~~ 226 (250)
+.|| .|+.-+.--.=-|..+| +|++
T Consensus 19 k~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hcCCCcccCCceEeeecCCCccCCCccc
Confidence 8999 89995432222468888 8875
No 203
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=59.18 E-value=12 Score=31.23 Aligned_cols=52 Identities=25% Similarity=0.485 Sum_probs=29.3
Q ss_pred CCCccCCCCCcceeccCC--------CcceEE-ecccccc--ccccccc--cCCCCCcCCCCCCC
Q 025608 199 QKWNRCPNCKFYVEKKDG--------CSYIRC-RCGHAFC--YHCGVQL--STVSHGYYCPSCNK 250 (250)
Q Consensus 199 ~~~~~CP~C~~~i~k~~G--------Cnhm~C-~C~~~FC--~~C~~~~--~~~~h~~~~~~~~~ 250 (250)
...+.||.|+......+. =---.| .||..|= |+=..-+ +|+..-|.|++|+|
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~k 223 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGK 223 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccc
Confidence 455889999886664421 112235 6666663 2211111 35566778888876
No 204
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=59.15 E-value=20 Score=25.82 Aligned_cols=49 Identities=16% Similarity=0.438 Sum_probs=29.4
Q ss_pred CChHHHHHHHHHHHhhccCC---------CCeecCCCCCCCCceecCccCccCcccCCcccch
Q 025608 106 LPEEAFDKWGKALCESLIPG---------AQKFYCPFKDCSALLIDDAGEAIRESECPNCHRL 159 (250)
Q Consensus 106 l~~~~~~~~~~~~~~~~~~~---------~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 159 (250)
+.++.++.....+.+.++.. +...+|+ +|+..+..... ..+.||.||..
T Consensus 39 V~p~~L~f~f~~~~~~t~~egA~L~i~~~p~~~~C~--~Cg~~~~~~~~---~~~~CP~Cgs~ 96 (114)
T PRK03681 39 VETSSLAFCFDLVCRGTVAEGCKLHLEEQEAECWCE--TCQQYVTLLTQ---RVRRCPQCHGD 96 (114)
T ss_pred cCHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCeeecCCc---cCCcCcCcCCC
Confidence 35666666666665544432 2345899 89977665431 22568888754
No 205
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=58.96 E-value=12 Score=28.21 Aligned_cols=33 Identities=18% Similarity=0.461 Sum_probs=20.2
Q ss_pred CCCeecCCCCCCCCceecCcc----CccCcccCCcccch
Q 025608 125 GAQKFYCPFKDCSALLIDDAG----EAIRESECPNCHRL 159 (250)
Q Consensus 125 ~~~~~~Cp~~~C~~~~~~~~~----~~~~~~~C~~C~~~ 159 (250)
....+.|| .|+..+...+. .....+.||.||..
T Consensus 96 ~~~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 96 NNAYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred CCcEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 34566999 78876665311 11233888888765
No 206
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=58.94 E-value=14 Score=35.87 Aligned_cols=37 Identities=30% Similarity=0.575 Sum_probs=30.1
Q ss_pred ecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhh
Q 025608 43 VCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQ 80 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~ 80 (250)
+|.+|...+-... |...+|||.|.++|+...+.....
T Consensus 819 ~C~~C~~~ll~~p-F~vf~CgH~FH~~Cl~~~v~~~~~ 855 (911)
T KOG2034|consen 819 SCDHCGRPLLIKP-FYVFPCGHCFHRDCLIRHVLSLLS 855 (911)
T ss_pred chHHhcchhhcCc-ceeeeccchHHHHHHHHHHHcccc
Confidence 6999998886544 556799999999999999885543
No 207
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=58.79 E-value=9.2 Score=24.01 Aligned_cols=27 Identities=26% Similarity=0.669 Sum_probs=20.4
Q ss_pred ccCCCCCc----ceeccCCCcceEE-eccccc
Q 025608 202 NRCPNCKF----YVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 202 ~~CP~C~~----~i~k~~GCnhm~C-~C~~~F 228 (250)
-.||+|+. .+-+..|=.++.| .||+.-
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 47999987 3345577788999 999853
No 208
>PF14353 CpXC: CpXC protein
Probab=58.47 E-value=7.2 Score=28.62 Aligned_cols=48 Identities=29% Similarity=0.482 Sum_probs=28.1
Q ss_pred cccCCCCCCCCCCCHHHHhcc---CChHHHHHHHHHHHhhccCCCCeecCCCCCCCCceecC
Q 025608 85 SIGCPVTDCGGSLEPEYCRDI---LPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDD 143 (250)
Q Consensus 85 ~i~CP~~~C~~~l~~~~i~~~---l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~ 143 (250)
.|.||. |+..+..+....+ .++++.++.. . .+-..+.|| .|+..+...
T Consensus 1 ~itCP~--C~~~~~~~v~~~I~~~~~p~l~e~il----~---g~l~~~~CP--~Cg~~~~~~ 51 (128)
T PF14353_consen 1 EITCPH--CGHEFEFEVWTSINADEDPELKEKIL----D---GSLFSFTCP--SCGHKFRLE 51 (128)
T ss_pred CcCCCC--CCCeeEEEEEeEEcCcCCHHHHHHHH----c---CCcCEEECC--CCCCceecC
Confidence 378997 8887776654332 3344333332 1 234566899 888766543
No 209
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=58.14 E-value=6.1 Score=24.62 Aligned_cols=13 Identities=38% Similarity=1.020 Sum_probs=10.6
Q ss_pred CCccCCCCCccee
Q 025608 200 KWNRCPNCKFYVE 212 (250)
Q Consensus 200 ~~~~CP~C~~~i~ 212 (250)
.++.||+|+++..
T Consensus 4 ~mr~C~~CgvYTL 16 (56)
T PRK13130 4 KIRKCPKCGVYTL 16 (56)
T ss_pred cceECCCCCCEEc
Confidence 4689999999765
No 210
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.99 E-value=7.7 Score=25.32 Aligned_cols=57 Identities=26% Similarity=0.606 Sum_probs=36.3
Q ss_pred ecccCcccccCCCceecCCC--CCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhccCChHHHHHH
Q 025608 43 VCEICVETKLRNESFSIKGC--SHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKW 114 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~ 114 (250)
.|..|-.+++++..-.+ -| .|.||.+|...-+. =.||. |++.|...-++ +...+.+|
T Consensus 7 nCECCDrDLpp~s~dA~-ICtfEcTFCadCae~~l~---------g~CPn--CGGelv~RP~R---Paa~L~r~ 65 (84)
T COG3813 7 NCECCDRDLPPDSTDAR-ICTFECTFCADCAENRLH---------GLCPN--CGGELVARPIR---PAAKLARY 65 (84)
T ss_pred CCcccCCCCCCCCCcee-EEEEeeehhHhHHHHhhc---------CcCCC--CCchhhcCcCC---hHHHHhhC
Confidence 48889888876543222 34 48999999875443 26887 99887665544 33444444
No 211
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=57.82 E-value=2 Score=25.86 Aligned_cols=36 Identities=17% Similarity=0.367 Sum_probs=29.3
Q ss_pred ceecccCcccccCCCceecCCCCCcchHHHHHHHHH
Q 025608 41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVD 76 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 76 (250)
.++|.+|-+.++..+.-...-||-.-|.+||+.-.-
T Consensus 7 ry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~deYY 42 (57)
T PF14445_consen 7 RYSCDLCNSSHPISELRQCVLCGRWACNSCWQDEYY 42 (57)
T ss_pred hHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhhHh
Confidence 467999999988777666668999999999987443
No 212
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=57.24 E-value=6.5 Score=33.57 Aligned_cols=34 Identities=18% Similarity=0.413 Sum_probs=21.2
Q ss_pred ecCCCCCCCCceecCccCccCcccCCcccchhccccCcc
Q 025608 129 FYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVA 167 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~ 167 (250)
..|| .|..-....+.-. ..+. .||..||..|...
T Consensus 4 ~~CP--~Ck~~~y~np~~k-l~i~--~CGH~~C~sCv~~ 37 (309)
T TIGR00570 4 QGCP--RCKTTKYRNPSLK-LMVN--VCGHTLCESCVDL 37 (309)
T ss_pred CCCC--cCCCCCccCcccc-cccC--CCCCcccHHHHHH
Confidence 3688 7877544443322 2222 6899999999763
No 213
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=57.06 E-value=7.8 Score=31.05 Aligned_cols=19 Identities=26% Similarity=0.662 Sum_probs=14.9
Q ss_pred CCCeecCCCCCCCCceecC
Q 025608 125 GAQKFYCPFKDCSALLIDD 143 (250)
Q Consensus 125 ~~~~~~Cp~~~C~~~~~~~ 143 (250)
+..++-||.|.|..++--+
T Consensus 135 sSqRIACPRpnCkRiInL~ 153 (275)
T KOG4684|consen 135 SSQRIACPRPNCKRIINLD 153 (275)
T ss_pred ccceeccCCCCcceeeecC
Confidence 4667789999999877654
No 214
>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=56.96 E-value=19 Score=21.91 Aligned_cols=40 Identities=20% Similarity=0.546 Sum_probs=23.5
Q ss_pred ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCC
Q 025608 41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSL 97 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l 97 (250)
.|.||.|...+.. .=|..++...=.+....+.||. |...+
T Consensus 2 ~f~CP~C~~~~~~---------------~~L~~H~~~~H~~~~~~v~CPi--C~~~~ 41 (54)
T PF05605_consen 2 SFTCPYCGKGFSE---------------SSLVEHCEDEHRSESKNVVCPI--CSSRV 41 (54)
T ss_pred CcCCCCCCCccCH---------------HHHHHHHHhHCcCCCCCccCCC--chhhh
Confidence 5789999874332 2244555543333345799998 76543
No 215
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=56.93 E-value=5.3 Score=38.97 Aligned_cols=24 Identities=46% Similarity=1.149 Sum_probs=21.0
Q ss_pred ccCCCCCc-ceeccCCCcceEE-ecccc
Q 025608 202 NRCPNCKF-YVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 202 ~~CP~C~~-~i~k~~GCnhm~C-~C~~~ 227 (250)
-.||-|+. .|+..|||| +| +||.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 58999999 899999999 68 88765
No 216
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=56.37 E-value=4.5 Score=34.55 Aligned_cols=45 Identities=29% Similarity=0.698 Sum_probs=33.2
Q ss_pred CCccCCCCCcceeccCCCcceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608 200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
+...|-.|+-. .-+=.-..| .|+.+||--|-.=++..-|. ||.|+
T Consensus 329 ~~~~Cf~C~~~---~~~~~~y~C~~Ck~~FCldCDv~iHesLh~--CpgCe 374 (378)
T KOG2807|consen 329 GSRFCFACQGE---LLSSGRYRCESCKNVFCLDCDVFIHESLHN--CPGCE 374 (378)
T ss_pred CCcceeeeccc---cCCCCcEEchhccceeeccchHHHHhhhhc--CCCcC
Confidence 33558777221 122234889 99999999999888888888 99996
No 217
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=56.21 E-value=6.7 Score=26.48 Aligned_cols=29 Identities=38% Similarity=0.945 Sum_probs=16.9
Q ss_pred CCccCCCCC------cceeccCCCcceEE-eccccc
Q 025608 200 KWNRCPNCK------FYVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 200 ~~~~CP~C~------~~i~k~~GCnhm~C-~C~~~F 228 (250)
..-.||.|+ +.|.+..|=-+++| .||..|
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 447999999 24556678889999 998776
No 218
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.13 E-value=2.9 Score=31.85 Aligned_cols=27 Identities=22% Similarity=0.442 Sum_probs=18.5
Q ss_pred ceecccCcccccCCCceecCCCCCcch
Q 025608 41 SFVCEICVETKLRNESFSIKGCSHMYC 67 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC 67 (250)
.-+|.||++++...+.+..++|...|.
T Consensus 177 kGECvICLEdL~~GdtIARLPCLCIYH 203 (205)
T KOG0801|consen 177 KGECVICLEDLEAGDTIARLPCLCIYH 203 (205)
T ss_pred CCcEEEEhhhccCCCceeccceEEEee
Confidence 346888888887666666667775553
No 219
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=56.08 E-value=13 Score=19.03 Aligned_cols=23 Identities=26% Similarity=0.748 Sum_probs=18.8
Q ss_pred CCCCCcceeccCCCcceEE-eccc
Q 025608 204 CPNCKFYVEKKDGCSYIRC-RCGH 226 (250)
Q Consensus 204 CP~C~~~i~k~~GCnhm~C-~C~~ 226 (250)
|-+|+.++.-..|-.++.| .|.+
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 5578888888889889998 8865
No 220
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=55.63 E-value=31 Score=20.22 Aligned_cols=27 Identities=22% Similarity=0.434 Sum_probs=14.9
Q ss_pred CCccCCCCCcc-eeccCCCcceEE-eccc
Q 025608 200 KWNRCPNCKFY-VEKKDGCSYIRC-RCGH 226 (250)
Q Consensus 200 ~~~~CP~C~~~-i~k~~GCnhm~C-~C~~ 226 (250)
+-..||+|+.. +-+..+=....| .|++
T Consensus 17 ~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 33679999983 223333334555 5554
No 221
>PRK10220 hypothetical protein; Provisional
Probab=54.07 E-value=8.1 Score=27.47 Aligned_cols=26 Identities=23% Similarity=0.667 Sum_probs=19.1
Q ss_pred cCCCCCCCCceecCccCccCcccCCcccchh
Q 025608 130 YCPFKDCSALLIDDAGEAIRESECPNCHRLF 160 (250)
Q Consensus 130 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 160 (250)
.|| .|+.-+.+.++ ..+.||.|+..|
T Consensus 5 ~CP--~C~seytY~d~---~~~vCpeC~hEW 30 (111)
T PRK10220 5 HCP--KCNSEYTYEDN---GMYICPECAHEW 30 (111)
T ss_pred cCC--CCCCcceEcCC---CeEECCcccCcC
Confidence 577 88887777665 447888888774
No 222
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=53.92 E-value=11 Score=23.21 Aligned_cols=20 Identities=25% Similarity=0.554 Sum_probs=14.3
Q ss_pred HHHHHhcCCCccCCCCCcce
Q 025608 192 LMKLAQNQKWNRCPNCKFYV 211 (250)
Q Consensus 192 ~~~~~~~~~~~~CP~C~~~i 211 (250)
+.++.....+..||+|+.++
T Consensus 37 ~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 37 LNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred HHHHHcCCCeEECcCCCccC
Confidence 34455556789999999753
No 223
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=53.90 E-value=9.2 Score=32.50 Aligned_cols=35 Identities=20% Similarity=0.493 Sum_probs=24.2
Q ss_pred CCceecccCcccccCCCceecCCCCCcchHHHHHHHH
Q 025608 39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYV 75 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 75 (250)
....-|.-|- ++....=++.+|.|.||.+|.+..-
T Consensus 88 p~VHfCd~Cd--~PI~IYGRmIPCkHvFCl~CAr~~~ 122 (389)
T KOG2932|consen 88 PRVHFCDRCD--FPIAIYGRMIPCKHVFCLECARSDS 122 (389)
T ss_pred cceEeecccC--CcceeeecccccchhhhhhhhhcCc
Confidence 3345688885 3433334588999999999987643
No 224
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=52.94 E-value=4.8 Score=21.60 Aligned_cols=26 Identities=27% Similarity=0.691 Sum_probs=11.7
Q ss_pred cCCCCCCCCceecCccCccCcccCCcccchh
Q 025608 130 YCPFKDCSALLIDDAGEAIRESECPNCHRLF 160 (250)
Q Consensus 130 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 160 (250)
.|| .|++-....++ ..+.|+.|+..|
T Consensus 4 ~Cp--~C~se~~y~D~---~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCP--LCGSEYTYEDG---ELLVCPECGHEW 29 (30)
T ss_dssp --T--TT-----EE-S---SSEEETTTTEEE
T ss_pred CCC--CCCCcceeccC---CEEeCCcccccC
Confidence 466 77765555443 457788887653
No 225
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=52.71 E-value=12 Score=24.56 Aligned_cols=26 Identities=31% Similarity=0.999 Sum_probs=20.1
Q ss_pred ccCCCCCc----ceeccCCCcceEE-ecccc
Q 025608 202 NRCPNCKF----YVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 202 ~~CP~C~~----~i~k~~GCnhm~C-~C~~~ 227 (250)
-.||+|+. .+-+..|=.++.| .||+.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 47999998 2335677888999 99985
No 226
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=52.28 E-value=5.7 Score=24.11 Aligned_cols=11 Identities=36% Similarity=0.902 Sum_probs=5.2
Q ss_pred cCCCCCcceec
Q 025608 203 RCPNCKFYVEK 213 (250)
Q Consensus 203 ~CP~C~~~i~k 213 (250)
+|++|+..+-+
T Consensus 6 RC~~CnklLa~ 16 (51)
T PF10122_consen 6 RCGHCNKLLAK 16 (51)
T ss_pred eccchhHHHhh
Confidence 44444444444
No 227
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=51.73 E-value=15 Score=20.18 Aligned_cols=25 Identities=24% Similarity=0.526 Sum_probs=11.5
Q ss_pred ccCCCCCcceeccCCCcceEE-eccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGH 226 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~ 226 (250)
+.|+.|+....-..-=+.+.| .|+.
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCc
Confidence 566666663222122224555 5554
No 228
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=51.52 E-value=8.5 Score=27.78 Aligned_cols=22 Identities=23% Similarity=0.744 Sum_probs=11.8
Q ss_pred ccccccccccCC-CCCcCCCCCC
Q 025608 228 FCYHCGVQLSTV-SHGYYCPSCN 249 (250)
Q Consensus 228 FC~~C~~~~~~~-~h~~~~~~~~ 249 (250)
+|..|+..+... .++..||+|+
T Consensus 72 ~C~~Cg~~~~~~~~~~~~CP~Cg 94 (114)
T PRK03681 72 WCETCQQYVTLLTQRVRRCPQCH 94 (114)
T ss_pred EcccCCCeeecCCccCCcCcCcC
Confidence 444444455332 2346688886
No 229
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=51.44 E-value=14 Score=23.67 Aligned_cols=17 Identities=24% Similarity=0.634 Sum_probs=12.6
Q ss_pred cchHHHHHHHHHHHhhc
Q 025608 65 MYCVDCTVKYVDSKLQE 81 (250)
Q Consensus 65 ~fC~~Cl~~~~~~~i~~ 81 (250)
-||+.||.+|....-.+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 38999999999987665
No 230
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=51.19 E-value=15 Score=28.82 Aligned_cols=31 Identities=26% Similarity=0.673 Sum_probs=20.1
Q ss_pred CCeecCCCCCCCCceecCccCccCcccCCcccch
Q 025608 126 AQKFYCPFKDCSALLIDDAGEAIRESECPNCHRL 159 (250)
Q Consensus 126 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 159 (250)
...+.|| .|+.-+...+.- ...+.||.||..
T Consensus 115 ~~~Y~Cp--~C~~rytf~eA~-~~~F~Cp~Cg~~ 145 (178)
T PRK06266 115 NMFFFCP--NCHIRFTFDEAM-EYGFRCPQCGEM 145 (178)
T ss_pred CCEEECC--CCCcEEeHHHHh-hcCCcCCCCCCC
Confidence 4456898 688666655322 245889888865
No 231
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=51.12 E-value=5.5 Score=21.10 Aligned_cols=21 Identities=29% Similarity=0.782 Sum_probs=9.0
Q ss_pred ccccccccccCCCCCcCCCCCC
Q 025608 228 FCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 228 FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
.|-.|+.+..+ ...|.|+.|+
T Consensus 2 ~C~~C~~~~~~-~~~Y~C~~Cd 22 (30)
T PF07649_consen 2 RCDACGKPIDG-GWFYRCSECD 22 (30)
T ss_dssp --TTTS----S---EEE-TTT-
T ss_pred cCCcCCCcCCC-CceEECccCC
Confidence 46788888865 6788898886
No 232
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.97 E-value=5.9 Score=35.17 Aligned_cols=41 Identities=29% Similarity=0.687 Sum_probs=27.6
Q ss_pred ccCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCC
Q 025608 202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
..||-|.-.+..- +.=.||+.||..|...|-... ..||.|.
T Consensus 27 l~C~IC~d~~~~P-----vitpCgH~FCs~CI~~~l~~~--~~CP~Cr 67 (397)
T TIGR00599 27 LRCHICKDFFDVP-----VLTSCSHTFCSLCIRRCLSNQ--PKCPLCR 67 (397)
T ss_pred cCCCcCchhhhCc-----cCCCCCCchhHHHHHHHHhCC--CCCCCCC
Confidence 6888887755321 111789999999988874322 3599986
No 234
>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=50.81 E-value=14 Score=28.41 Aligned_cols=31 Identities=19% Similarity=0.458 Sum_probs=19.9
Q ss_pred CCeecCCCCCCCCceecCccCccCcccCCcccch
Q 025608 126 AQKFYCPFKDCSALLIDDAGEAIRESECPNCHRL 159 (250)
Q Consensus 126 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 159 (250)
..-+.|| .|..-+...+.- ...+.||.||..
T Consensus 107 ~~~Y~Cp--~c~~r~tf~eA~-~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICP--NMCVRFTFNEAM-ELNFTCPRCGAM 137 (158)
T ss_pred CCeEECC--CCCcEeeHHHHH-HcCCcCCCCCCE
Confidence 4455898 788665554322 245889988865
No 235
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=50.07 E-value=7.3 Score=25.04 Aligned_cols=35 Identities=23% Similarity=0.448 Sum_probs=18.7
Q ss_pred CCccCCCCCcceeccCCCcceEE-eccccccccccccc
Q 025608 200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQL 236 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~ 236 (250)
....|+.|+...- --=..-.| .||.-||..|....
T Consensus 8 ~~~~C~~C~~~F~--~~~rrhhCr~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 8 EASNCMICGKKFS--LFRRRHHCRNCGRVVCSSCSSQR 43 (69)
T ss_dssp G-SB-TTT--B-B--SSS-EEE-TTT--EEECCCS-EE
T ss_pred CCCcCcCcCCcCC--CceeeEccCCCCCEECCchhCCE
Confidence 3478999998762 23556789 99999999998765
No 236
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=49.76 E-value=6.5 Score=22.57 Aligned_cols=25 Identities=28% Similarity=0.662 Sum_probs=11.4
Q ss_pred CCCCCCCCceecCccCccCcccCCccc
Q 025608 131 CPFKDCSALLIDDAGEAIRESECPNCH 157 (250)
Q Consensus 131 Cp~~~C~~~~~~~~~~~~~~~~C~~C~ 157 (250)
|| .|+..+.......+..-.|+.|+
T Consensus 2 CP--~C~~~l~~~~~~~~~id~C~~C~ 26 (41)
T PF13453_consen 2 CP--RCGTELEPVRLGDVEIDVCPSCG 26 (41)
T ss_pred cC--CCCcccceEEECCEEEEECCCCC
Confidence 66 67665444322223333444443
No 237
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=48.69 E-value=5.2 Score=24.73 Aligned_cols=31 Identities=32% Similarity=0.805 Sum_probs=22.4
Q ss_pred cCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608 59 IKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE 100 (250)
Q Consensus 59 ~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 100 (250)
+++|+|.+|..||-..- -=.||. |+..++..
T Consensus 22 ~~pCgH~I~~~~f~~~r---------YngCPf--C~~~~~~~ 52 (55)
T PF14447_consen 22 VLPCGHLICDNCFPGER---------YNGCPF--CGTPFEFD 52 (55)
T ss_pred cccccceeeccccChhh---------ccCCCC--CCCcccCC
Confidence 56999999999985421 225888 88777654
No 238
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=48.27 E-value=15 Score=21.60 Aligned_cols=12 Identities=25% Similarity=0.797 Sum_probs=7.2
Q ss_pred CCccCCCCCcce
Q 025608 200 KWNRCPNCKFYV 211 (250)
Q Consensus 200 ~~~~CP~C~~~i 211 (250)
...+||.||..|
T Consensus 18 ~~irC~~CG~rI 29 (44)
T smart00659 18 DVVRCRECGYRI 29 (44)
T ss_pred CceECCCCCceE
Confidence 336777777644
No 239
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=48.08 E-value=19 Score=21.71 Aligned_cols=47 Identities=19% Similarity=0.516 Sum_probs=23.6
Q ss_pred eecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCC
Q 025608 42 FVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGG 95 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 95 (250)
+.|++-+.....+ .+...|.|.-|- -+..|+......+ ...||. |++
T Consensus 3 L~CPls~~~i~~P--~Rg~~C~H~~CF-Dl~~fl~~~~~~~--~W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRIP--VRGKNCKHLQCF-DLESFLESNQRTP--KWKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-SSE--EEETT--SS--E-EHHHHHHHHHHS-----B-TT--T--
T ss_pred eeCCCCCCEEEeC--ccCCcCcccceE-CHHHHHHHhhccC--CeECcC--CcC
Confidence 4588877665432 456799999773 3777888765543 378997 653
No 240
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=47.91 E-value=3.5 Score=23.63 Aligned_cols=24 Identities=29% Similarity=0.755 Sum_probs=21.0
Q ss_pred CcccCCcccchhccccCcccCCCC
Q 025608 149 RESECPNCHRLFCAQCKVAWHAGI 172 (250)
Q Consensus 149 ~~~~C~~C~~~~C~~C~~~~H~~~ 172 (250)
..+.|..|+..+|..|....|.++
T Consensus 14 ~~~~C~~C~~~~C~~C~~~~H~~H 37 (42)
T PF00643_consen 14 LSLFCEDCNEPLCSECTVSGHKGH 37 (42)
T ss_dssp EEEEETTTTEEEEHHHHHTSTTTS
T ss_pred eEEEecCCCCccCccCCCCCCCCC
Confidence 568899999999999998778775
No 241
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=47.72 E-value=11 Score=32.48 Aligned_cols=51 Identities=24% Similarity=0.646 Sum_probs=33.0
Q ss_pred cCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCC
Q 025608 36 SETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGS 96 (250)
Q Consensus 36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 96 (250)
..+.+...|.||.+..+-+ .+.+|+|.+|.-|-.+.-..-. .-.||. |...
T Consensus 56 dtDEen~~C~ICA~~~TYs---~~~PC~H~~CH~Ca~RlRALY~-----~K~C~~--CrTE 106 (493)
T COG5236 56 DTDEENMNCQICAGSTTYS---ARYPCGHQICHACAVRLRALYM-----QKGCPL--CRTE 106 (493)
T ss_pred ccccccceeEEecCCceEE---EeccCCchHHHHHHHHHHHHHh-----ccCCCc--cccc
Confidence 3344555699998766532 3569999999999876533221 225776 6543
No 242
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=47.31 E-value=9.8 Score=21.19 Aligned_cols=31 Identities=29% Similarity=0.673 Sum_probs=16.1
Q ss_pred chHHHHHHHHHHHhhc-CcccccCCCCCCCCCCC
Q 025608 66 YCVDCTVKYVDSKLQE-NVTSIGCPVTDCGGSLE 98 (250)
Q Consensus 66 fC~~Cl~~~~~~~i~~-~~~~i~CP~~~C~~~l~ 98 (250)
+|.+|++.|....-.. .-..+.|+. |+-.++
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~--CGPr~~ 32 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTN--CGPRYS 32 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTT--CC-SCC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCC--CCCCEE
Confidence 5889999886643221 346788987 775443
No 243
>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=46.53 E-value=18 Score=20.89 Aligned_cols=28 Identities=18% Similarity=0.457 Sum_probs=17.8
Q ss_pred ecCCCCCCCCceecC-ccCccCcccCCcccc
Q 025608 129 FYCPFKDCSALLIDD-AGEAIRESECPNCHR 158 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~-~~~~~~~~~C~~C~~ 158 (250)
+.|+ +|+..+... ...+.....||.||.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCE--ECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeC--CCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 4787 888655543 111245678998886
No 244
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=46.24 E-value=17 Score=19.78 Aligned_cols=22 Identities=27% Similarity=0.652 Sum_probs=13.3
Q ss_pred CCCCceecCccCccCcccCCcccch
Q 025608 135 DCSALLIDDAGEAIRESECPNCHRL 159 (250)
Q Consensus 135 ~C~~~~~~~~~~~~~~~~C~~C~~~ 159 (250)
+|+..+..... ..+.|+.||..
T Consensus 5 ~Cg~~~~~~~~---~~irC~~CG~R 26 (32)
T PF03604_consen 5 ECGAEVELKPG---DPIRCPECGHR 26 (32)
T ss_dssp SSSSSE-BSTS---STSSBSSSS-S
T ss_pred cCCCeeEcCCC---CcEECCcCCCe
Confidence 77777665443 34788888864
No 245
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=45.72 E-value=25 Score=30.24 Aligned_cols=54 Identities=20% Similarity=0.455 Sum_probs=36.2
Q ss_pred ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHhcc
Q 025608 41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCRDI 105 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~ 105 (250)
.-.|+||......+.+. .--|=.||-.|+.+|+... =+||..+++ .+.+++.++
T Consensus 300 ~~~CpvClk~r~Nptvl--~vSGyVfCY~Ci~~Yv~~~-------~~CPVT~~p--~~v~~l~rl 353 (357)
T KOG0826|consen 300 REVCPVCLKKRQNPTVL--EVSGYVFCYPCIFSYVVNY-------GHCPVTGYP--ASVDHLIRL 353 (357)
T ss_pred cccChhHHhccCCCceE--EecceEEeHHHHHHHHHhc-------CCCCccCCc--chHHHHHHH
Confidence 34699999887655433 3457889999999999822 268885554 444444433
No 246
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=45.69 E-value=10 Score=19.45 Aligned_cols=20 Identities=25% Similarity=0.544 Sum_probs=15.3
Q ss_pred ccCCCCCCCCCCCHHHHhccCC
Q 025608 86 IGCPVTDCGGSLEPEYCRDILP 107 (250)
Q Consensus 86 i~CP~~~C~~~l~~~~i~~~l~ 107 (250)
+.||. |...+....+..+|+
T Consensus 2 v~CPi--C~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCPV--CFREVPENLINSHLD 21 (26)
T ss_pred CcCCC--CcCcccHHHHHHHHH
Confidence 57997 888887777777665
No 247
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.54 E-value=13 Score=27.01 Aligned_cols=22 Identities=18% Similarity=0.463 Sum_probs=10.9
Q ss_pred ccccccccccCCC-CCcCCCCCC
Q 025608 228 FCYHCGVQLSTVS-HGYYCPSCN 249 (250)
Q Consensus 228 FC~~C~~~~~~~~-h~~~~~~~~ 249 (250)
+|-.|+..+.... ++..||+|+
T Consensus 73 ~C~~Cg~~~~~~~~~~~~CP~Cg 95 (117)
T PRK00564 73 ECKDCSHVFKPNALDYGVCEKCH 95 (117)
T ss_pred EhhhCCCccccCCccCCcCcCCC
Confidence 3444445553322 333488886
No 248
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=45.42 E-value=50 Score=24.86 Aligned_cols=43 Identities=26% Similarity=0.481 Sum_probs=29.2
Q ss_pred CcccccCCCCCCCCCCCHHHHhccCChHHHHHHHHHHHhhccCCCCeecCCCCCCCCceecCcc
Q 025608 82 NVTSIGCPVTDCGGSLEPEYCRDILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAG 145 (250)
Q Consensus 82 ~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~ 145 (250)
+...+.||. |+..++..++..+.+ ....+.|| .|++.+...+.
T Consensus 96 ~~~~Y~Cp~--C~~~y~~~ea~~~~d-----------------~~~~f~Cp--~Cg~~l~~~dn 138 (147)
T smart00531 96 NNAYYKCPN--CQSKYTFLEANQLLD-----------------MDGTFTCP--RCGEELEEDDN 138 (147)
T ss_pred CCcEEECcC--CCCEeeHHHHHHhcC-----------------CCCcEECC--CCCCEEEEcCc
Confidence 346789997 988887655443322 23458999 99998877643
No 249
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=45.30 E-value=12 Score=22.53 Aligned_cols=10 Identities=40% Similarity=1.175 Sum_probs=5.8
Q ss_pred CCCcCCCCCC
Q 025608 240 SHGYYCPSCN 249 (250)
Q Consensus 240 ~h~~~~~~~~ 249 (250)
.-+.-||+|+
T Consensus 22 ~~~irCp~Cg 31 (49)
T COG1996 22 TRGIRCPYCG 31 (49)
T ss_pred cCceeCCCCC
Confidence 4445577775
No 250
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.71 E-value=13 Score=27.76 Aligned_cols=9 Identities=33% Similarity=0.851 Sum_probs=6.0
Q ss_pred CCcCCCCCC
Q 025608 241 HGYYCPSCN 249 (250)
Q Consensus 241 h~~~~~~~~ 249 (250)
.++.||+|+
T Consensus 106 ~~~~CP~Cg 114 (135)
T PRK03824 106 AFLKCPKCG 114 (135)
T ss_pred cCcCCcCCC
Confidence 445588886
No 251
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=44.62 E-value=10 Score=21.02 Aligned_cols=26 Identities=23% Similarity=0.519 Sum_probs=20.7
Q ss_pred cCcccCCcccchhccccCcccCCCCC
Q 025608 148 IRESECPNCHRLFCAQCKVAWHAGIE 173 (250)
Q Consensus 148 ~~~~~C~~C~~~~C~~C~~~~H~~~~ 173 (250)
...+.|..|+..+|..|....|.++.
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred ceEEEeCccChhhhhhcChhhcCCCC
Confidence 35678999999999999876677653
No 252
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=44.30 E-value=11 Score=24.11 Aligned_cols=47 Identities=30% Similarity=0.718 Sum_probs=24.9
Q ss_pred ccCCCCCccee----cc-CCCcceEE--ecccccc---ccccccccCCCCCcCCCCCCC
Q 025608 202 NRCPNCKFYVE----KK-DGCSYIRC--RCGHAFC---YHCGVQLSTVSHGYYCPSCNK 250 (250)
Q Consensus 202 ~~CP~C~~~i~----k~-~GCnhm~C--~C~~~FC---~~C~~~~~~~~h~~~~~~~~~ 250 (250)
..||.|+..++ .. ++-.++.+ .+-.-+| ..|....++..|+ ||+||+
T Consensus 4 i~Cp~C~~~~~T~v~~~~g~~t~~~~~ll~~~~~~~~iP~~~~~~kd~~H~--Cp~C~~ 60 (67)
T smart00714 4 LFCPRCQNNVTTRVETETGVCAWLICCLLFLLCFCCCLPCCLDSFKDVNHY--CPNCGA 60 (67)
T ss_pred eECCCCCCEEEEEEEEEeChHHHHHHHHHHHHHHHHHHHHhcccccCccEE--CCCCCC
Confidence 46888877443 22 33444444 2211001 1234445677898 999985
No 253
>PF14369 zf-RING_3: zinc-finger
Probab=42.69 E-value=28 Score=19.30 Aligned_cols=30 Identities=23% Similarity=0.802 Sum_probs=18.1
Q ss_pred eecCCCCCCCCceecCccCccCcccCCcccchh
Q 025608 128 KFYCPFKDCSALLIDDAGEAIRESECPNCHRLF 160 (250)
Q Consensus 128 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 160 (250)
.+||= .|...+....... ..+.||.|+..|
T Consensus 2 ~ywCh--~C~~~V~~~~~~~-~~~~CP~C~~gF 31 (35)
T PF14369_consen 2 RYWCH--QCNRFVRIAPSPD-SDVACPRCHGGF 31 (35)
T ss_pred CEeCc--cCCCEeEeCcCCC-CCcCCcCCCCcE
Confidence 46777 7888777643221 224688887543
No 254
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=42.45 E-value=27 Score=28.81 Aligned_cols=57 Identities=16% Similarity=0.247 Sum_probs=34.8
Q ss_pred HHhccCChHHHHHHHHHHHhh-ccCCC--CeecCCCCCCCCceecCcc----CccCcccCCcccch
Q 025608 101 YCRDILPEEAFDKWGKALCES-LIPGA--QKFYCPFKDCSALLIDDAG----EAIRESECPNCHRL 159 (250)
Q Consensus 101 ~i~~~l~~~~~~~~~~~~~~~-~~~~~--~~~~Cp~~~C~~~~~~~~~----~~~~~~~C~~C~~~ 159 (250)
.+..-++++++..|.+..... .+.-. ..--|. +|.-.+..... .....++||.||..
T Consensus 167 ~L~~~l~~ell~~yeri~~~~kg~gvvpl~g~~C~--GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 167 ELKEKLDPELLSEYERIRKNKKGVGVVPLEGRVCG--GCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred HHHHhcCHHHHHHHHHHHhcCCCceEEeecCCccc--CCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 345557899999999887654 11111 122676 78766654310 12356889999865
No 255
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=42.40 E-value=16 Score=22.60 Aligned_cols=23 Identities=30% Similarity=0.667 Sum_probs=15.4
Q ss_pred CCCccCCCCCcceeccCCCcceEE-eccc
Q 025608 199 QKWNRCPNCKFYVEKKDGCSYIRC-RCGH 226 (250)
Q Consensus 199 ~~~~~CP~C~~~i~k~~GCnhm~C-~C~~ 226 (250)
..+..||+||.+.. .|-.| .||+
T Consensus 24 p~l~~C~~cG~~~~-----~H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEFKL-----PHRVCPSCGY 47 (55)
T ss_pred CcceECCCCCCccc-----CeeECCccCe
Confidence 45578999998655 25566 6653
No 256
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.30 E-value=42 Score=29.20 Aligned_cols=29 Identities=21% Similarity=0.602 Sum_probs=20.5
Q ss_pred cCCCCceecccCcccccCCCceecCCCCCcch
Q 025608 36 SETSRSFVCEICVETKLRNESFSIKGCSHMYC 67 (250)
Q Consensus 36 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC 67 (250)
...+....|.||.++... +...+|||.-|
T Consensus 300 ~~~~~p~lcVVcl~e~~~---~~fvpcGh~cc 328 (355)
T KOG1571|consen 300 RELPQPDLCVVCLDEPKS---AVFVPCGHVCC 328 (355)
T ss_pred cccCCCCceEEecCCccc---eeeecCCcEEE
Confidence 344555679999987654 44569999955
No 257
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=42.26 E-value=16 Score=23.55 Aligned_cols=31 Identities=23% Similarity=0.453 Sum_probs=20.5
Q ss_pred eecCCCCCCCCceecCccCccCcccCCcccchhc
Q 025608 128 KFYCPFKDCSALLIDDAGEAIRESECPNCHRLFC 161 (250)
Q Consensus 128 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C 161 (250)
.+.|| +|++....-.. ....+.|..||...+
T Consensus 19 ~VkCp--dC~N~q~vFsh-ast~V~C~~CG~~l~ 49 (67)
T COG2051 19 RVKCP--DCGNEQVVFSH-ASTVVTCLICGTTLA 49 (67)
T ss_pred EEECC--CCCCEEEEecc-CceEEEecccccEEE
Confidence 35899 99975443321 135588999988765
No 258
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=42.23 E-value=17 Score=30.58 Aligned_cols=24 Identities=33% Similarity=0.664 Sum_probs=17.5
Q ss_pred ccCCCCCcceecc--CCCcceEE-ecc
Q 025608 202 NRCPNCKFYVEKK--DGCSYIRC-RCG 225 (250)
Q Consensus 202 ~~CP~C~~~i~k~--~GCnhm~C-~C~ 225 (250)
++|+.|+.+|+|. +|=+-..| .|+
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 8999999999976 55555555 453
No 259
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.64 E-value=11 Score=24.00 Aligned_cols=16 Identities=25% Similarity=0.304 Sum_probs=12.8
Q ss_pred CCccCCCCCcceeccC
Q 025608 200 KWNRCPNCKFYVEKKD 215 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~ 215 (250)
..++||.|+.+++..+
T Consensus 6 ~~v~CP~Cgkpv~w~~ 21 (65)
T COG3024 6 ITVPCPTCGKPVVWGE 21 (65)
T ss_pred ccccCCCCCCcccccc
Confidence 4589999999988643
No 260
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=41.21 E-value=20 Score=25.44 Aligned_cols=25 Identities=32% Similarity=0.976 Sum_probs=19.4
Q ss_pred ccCCCCCc-ceeccCCCcceEE-eccccc
Q 025608 202 NRCPNCKF-YVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 202 ~~CP~C~~-~i~k~~GCnhm~C-~C~~~F 228 (250)
-.||+|.. +.-..++ +|.| .|.++|
T Consensus 4 p~cp~c~sEytYed~~--~~~cpec~~ew 30 (112)
T COG2824 4 PPCPKCNSEYTYEDGG--QLICPECAHEW 30 (112)
T ss_pred CCCCccCCceEEecCc--eEeCchhcccc
Confidence 58999977 6666666 8888 888776
No 261
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=41.07 E-value=24 Score=29.20 Aligned_cols=64 Identities=19% Similarity=0.499 Sum_probs=37.5
Q ss_pred ccccCCCCCCCCCCCHHHHhc-cCChHHHHHHHHHHHhhccCCCCeecCCCCCCCCceecCccCccCcccCCcccch
Q 025608 84 TSIGCPVTDCGGSLEPEYCRD-ILPEEAFDKWGKALCESLIPGAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRL 159 (250)
Q Consensus 84 ~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 159 (250)
..|.||-++|+.+|+...... -++++. ......-++.|+ .|...|..+.-.....++||+|.+.
T Consensus 122 ~rIaCPRp~CkRiI~L~~~~~~p~~~~~----------~~~p~~~rv~Cg--hC~~~Fl~~~~~~~tlARCPHCrKv 186 (256)
T PF09788_consen 122 QRIACPRPNCKRIINLGPSHQGPVTPPV----------PTQPGSCRVICG--HCSNTFLFNTLTSNTLARCPHCRKV 186 (256)
T ss_pred ccccCCCCCCcceEEeCCccCCCCCCCC----------CCCCCceeEECC--CCCCcEeccCCCCCccccCCCCcee
Confidence 356777778888877765421 111110 000123457898 8998888774443456789887644
No 262
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=40.50 E-value=17 Score=28.55 Aligned_cols=24 Identities=29% Similarity=0.879 Sum_probs=19.8
Q ss_pred ccCCCCCcceeccCCCcceEE-ecccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~ 227 (250)
-.|++|+..+++ .=+.|+| +||..
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCCE
Confidence 689999999999 4478889 88863
No 263
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=40.19 E-value=17 Score=28.41 Aligned_cols=10 Identities=50% Similarity=1.125 Sum_probs=5.9
Q ss_pred cccccccccc
Q 025608 227 AFCYHCGVQL 236 (250)
Q Consensus 227 ~FC~~C~~~~ 236 (250)
+||-.||.+.
T Consensus 154 ~~Cp~CG~~~ 163 (177)
T COG1439 154 DFCPICGSPL 163 (177)
T ss_pred CcCCCCCCce
Confidence 5666666554
No 264
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.02 E-value=20 Score=30.11 Aligned_cols=21 Identities=33% Similarity=0.654 Sum_probs=15.0
Q ss_pred ccCCCCCcceecc--CCCcceEE
Q 025608 202 NRCPNCKFYVEKK--DGCSYIRC 222 (250)
Q Consensus 202 ~~CP~C~~~i~k~--~GCnhm~C 222 (250)
++||.|+..|++. +|=.-..|
T Consensus 236 ~pC~~Cg~~I~~~~~~gR~ty~C 258 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGGRGTHFC 258 (269)
T ss_pred CCCCcCCCeeEEEEECCCCcEEC
Confidence 7999999999876 55333444
No 265
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=39.94 E-value=25 Score=25.42 Aligned_cols=36 Identities=25% Similarity=0.464 Sum_probs=26.8
Q ss_pred CCccCCCCCcceeccCCCcceEE-eccccccccccccc
Q 025608 200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQL 236 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~ 236 (250)
..+.|..|+.+.-...+.. ..| .|++.+|-.|+..-
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~~ 89 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVYS 89 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEET
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCcC
Confidence 5589999998765555554 889 99999999998773
No 266
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=39.46 E-value=15 Score=19.48 Aligned_cols=21 Identities=24% Similarity=0.681 Sum_probs=15.7
Q ss_pred ccccccccccCCCCCcCCCCCC
Q 025608 228 FCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 228 FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
.|-+|+++.++.. +|.|..|+
T Consensus 2 ~C~~C~~~~~~~~-~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE-eEEeCCCC
Confidence 5778888887655 88887764
No 267
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=39.20 E-value=20 Score=28.25 Aligned_cols=25 Identities=28% Similarity=0.782 Sum_probs=20.5
Q ss_pred ccCCCCCcceeccCCCcceEE-ecccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~ 227 (250)
-.||.|+.++.+.+. |.|.| .|++.
T Consensus 150 a~~~~~g~~~~~~~~-~~~~c~~~~~~ 175 (189)
T PRK09521 150 AMCSRCRTPLVKKGE-NELKCPNCGNI 175 (189)
T ss_pred EEccccCCceEECCC-CEEECCCCCCE
Confidence 469999998887544 99999 99864
No 268
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.04 E-value=25 Score=28.93 Aligned_cols=42 Identities=10% Similarity=0.257 Sum_probs=31.4
Q ss_pred CCCCce-ecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhc
Q 025608 37 ETSRSF-VCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQE 81 (250)
Q Consensus 37 ~~~~~~-~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 81 (250)
.+.+.| -|++|+.+...+.+. +=||.|+++|+..||..+-++
T Consensus 38 DsiK~FdcCsLtLqPc~dPvit---~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 38 DSIKPFDCCSLTLQPCRDPVIT---PDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred cccCCcceeeeecccccCCccC---CCCeeeeHHHHHHHHHHHHHH
Confidence 334444 589999888766543 559999999999999877554
No 269
>PLN03086 PRLI-interacting factor K; Provisional
Probab=38.99 E-value=17 Score=33.89 Aligned_cols=30 Identities=27% Similarity=0.803 Sum_probs=25.9
Q ss_pred CCCccCCC--CCcceeccCCCcceEE-eccccc
Q 025608 199 QKWNRCPN--CKFYVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 199 ~~~~~CP~--C~~~i~k~~GCnhm~C-~C~~~F 228 (250)
.....||+ |+..+.+.+.=+|.+| .|+..|
T Consensus 431 r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 431 RHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred CcceeCCcccccceeeccccccCccCCCCCCcc
Confidence 34578995 9999999999999999 998876
No 270
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=38.81 E-value=15 Score=23.13 Aligned_cols=13 Identities=23% Similarity=0.636 Sum_probs=11.1
Q ss_pred ccCCCCCcceecc
Q 025608 202 NRCPNCKFYVEKK 214 (250)
Q Consensus 202 ~~CP~C~~~i~k~ 214 (250)
+.||.||.+|.-+
T Consensus 4 kHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 4 KHCPVCGKPIPPD 16 (59)
T ss_pred CcCCcCCCcCCcc
Confidence 7899999999853
No 271
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=38.25 E-value=11 Score=21.86 Aligned_cols=25 Identities=20% Similarity=0.732 Sum_probs=15.0
Q ss_pred cccCCcccchhccccCcccCCCCCchh
Q 025608 150 ESECPNCHRLFCAQCKVAWHAGIECAD 176 (250)
Q Consensus 150 ~~~C~~C~~~~C~~C~~~~H~~~~C~~ 176 (250)
.+.|+.|+..||...+.+ ..+.|..
T Consensus 13 ~~~C~~C~~~FC~~Hr~~--e~H~C~~ 37 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKHRLP--EDHNCSK 37 (43)
T ss_dssp HEE-TTTS-EE-TTTHST--TTCT-SS
T ss_pred CeECCCCCcccCccccCc--cccCCcc
Confidence 478999999999999874 2334543
No 272
>PLN00209 ribosomal protein S27; Provisional
Probab=38.17 E-value=31 Score=23.44 Aligned_cols=30 Identities=17% Similarity=0.487 Sum_probs=20.1
Q ss_pred ecCCCCCCCCceecCccCccCcccCCcccchhc
Q 025608 129 FYCPFKDCSALLIDDAGEAIRESECPNCHRLFC 161 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C 161 (250)
+.|| +|...-..-.. ....+.|..|+...+
T Consensus 37 VkCp--~C~n~q~VFSh-A~t~V~C~~Cg~~L~ 66 (86)
T PLN00209 37 VKCQ--GCFNITTVFSH-SQTVVVCGSCQTVLC 66 (86)
T ss_pred EECC--CCCCeeEEEec-CceEEEccccCCEee
Confidence 5899 99875443321 135588999988876
No 273
>PRK10445 endonuclease VIII; Provisional
Probab=38.13 E-value=22 Score=29.74 Aligned_cols=13 Identities=31% Similarity=0.669 Sum_probs=10.6
Q ss_pred ccCCCCCcceecc
Q 025608 202 NRCPNCKFYVEKK 214 (250)
Q Consensus 202 ~~CP~C~~~i~k~ 214 (250)
++||.|+..|++.
T Consensus 236 ~~Cp~Cg~~I~~~ 248 (263)
T PRK10445 236 EACERCGGIIEKT 248 (263)
T ss_pred CCCCCCCCEeEEE
Confidence 7899998888765
No 274
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=38.10 E-value=12 Score=23.21 Aligned_cols=21 Identities=33% Similarity=0.708 Sum_probs=14.1
Q ss_pred CCccCCCCCcceeccCCCcceEE-ecc
Q 025608 200 KWNRCPNCKFYVEKKDGCSYIRC-RCG 225 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~ 225 (250)
.+..||+||.+... |..| .||
T Consensus 25 ~l~~c~~cg~~~~~-----H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKLP-----HRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEEST-----TSBCTTTB
T ss_pred ceeeeccCCCEecc-----cEeeCCCC
Confidence 55889999986552 4555 554
No 275
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=37.85 E-value=18 Score=29.75 Aligned_cols=14 Identities=29% Similarity=0.615 Sum_probs=8.3
Q ss_pred CCccCCCCCcceec
Q 025608 200 KWNRCPNCKFYVEK 213 (250)
Q Consensus 200 ~~~~CP~C~~~i~k 213 (250)
.+..||.|+.+..+
T Consensus 34 ~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 34 EVTICPKCGRYRIG 47 (236)
T ss_pred CceECCCCCCEECC
Confidence 44667777665443
No 276
>PHA02862 5L protein; Provisional
Probab=37.71 E-value=43 Score=25.26 Aligned_cols=46 Identities=15% Similarity=0.430 Sum_probs=32.5
Q ss_pred ecccCcccccCCCceecCCCC-----CcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCH
Q 025608 43 VCEICVETKLRNESFSIKGCS-----HMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEP 99 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~ 99 (250)
.|=||+++...+ . .+|. .....+||.+|+.. .....||. |+.....
T Consensus 4 iCWIC~~~~~e~--~--~PC~C~GS~K~VHq~CL~~WIn~-----S~k~~CeL--CkteY~I 54 (156)
T PHA02862 4 ICWICNDVCDER--N--NFCGCNEEYKVVHIKCMQLWINY-----SKKKECNL--CKTKYNI 54 (156)
T ss_pred EEEEecCcCCCC--c--ccccccCcchhHHHHHHHHHHhc-----CCCcCccC--CCCeEEE
Confidence 589999876433 1 3555 45899999999953 35678998 7766543
No 277
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.42 E-value=13 Score=31.39 Aligned_cols=30 Identities=27% Similarity=0.826 Sum_probs=20.7
Q ss_pred eecccCcccccCCCceecCCCCCc-chHHHHHHH
Q 025608 42 FVCEICVETKLRNESFSIKGCSHM-YCVDCTVKY 74 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~ 74 (250)
.-|.||++. +.+.+ +++|||. .|..|-+..
T Consensus 301 ~LC~ICmDa--P~DCv-fLeCGHmVtCt~CGkrm 331 (350)
T KOG4275|consen 301 RLCAICMDA--PRDCV-FLECGHMVTCTKCGKRM 331 (350)
T ss_pred HHHHHHhcC--CcceE-EeecCcEEeehhhcccc
Confidence 359999974 33434 4699998 588886543
No 278
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=37.36 E-value=73 Score=21.95 Aligned_cols=60 Identities=20% Similarity=0.374 Sum_probs=30.2
Q ss_pred CCCCHHHHhccCChH----HHHHHHHHHHhhccCCCCe-e----cCCCCCCCCceecCccCccCcccCCcccch
Q 025608 95 GSLEPEYCRDILPEE----AFDKWGKALCESLIPGAQK-F----YCPFKDCSALLIDDAGEAIRESECPNCHRL 159 (250)
Q Consensus 95 ~~l~~~~i~~~l~~~----~~~~~~~~~~~~~~~~~~~-~----~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 159 (250)
..++...|..+++.+ .++.+....... -+.+.. . .|- +|++.+..+.-. .-..||.|...
T Consensus 17 eplt~~ei~~~~~~~~~~~v~~~L~hiak~l-kr~g~~Llv~Pa~Ck--kCGfef~~~~ik--~pSRCP~CKSE 85 (97)
T COG3357 17 EPLTVAEIFELLNGEKEKEVYDHLEHIAKSL-KRKGKRLLVRPARCK--KCGFEFRDDKIK--KPSRCPKCKSE 85 (97)
T ss_pred CcchHHHHHHHHcCCchHHHHHHHHHHHHHH-HhCCceEEecChhhc--ccCccccccccC--CcccCCcchhh
Confidence 356667777666543 444443332211 112222 1 566 788877764321 23568777655
No 279
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=37.16 E-value=18 Score=31.81 Aligned_cols=46 Identities=24% Similarity=0.649 Sum_probs=33.5
Q ss_pred eecccCcccccCC-CceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCC
Q 025608 42 FVCEICVETKLRN-ESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCG 94 (250)
Q Consensus 42 ~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 94 (250)
..|..|.+.+... +-..-++|.|.|...|+..++.+. .+-.||. |.
T Consensus 366 L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n-----~~rsCP~--Cr 412 (518)
T KOG1941|consen 366 LYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENN-----GTRSCPN--CR 412 (518)
T ss_pred hhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhC-----CCCCCcc--HH
Confidence 4599999987432 223445999999999999999533 3457887 65
No 280
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=37.14 E-value=23 Score=29.76 Aligned_cols=13 Identities=31% Similarity=0.690 Sum_probs=11.3
Q ss_pred ccCCCCCcceecc
Q 025608 202 NRCPNCKFYVEKK 214 (250)
Q Consensus 202 ~~CP~C~~~i~k~ 214 (250)
++||.|+..|++.
T Consensus 245 ~pCprCG~~I~~~ 257 (272)
T PRK14810 245 EPCLNCKTPIRRV 257 (272)
T ss_pred CcCCCCCCeeEEE
Confidence 7999999998865
No 281
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=37.06 E-value=16 Score=25.20 Aligned_cols=27 Identities=30% Similarity=0.738 Sum_probs=23.3
Q ss_pred ccCCCCCcceeccCCCcceEE-eccccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~F 228 (250)
..||.|+..-.+..+----.| .|+..|
T Consensus 36 y~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred CcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 789999998888888778888 888776
No 282
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=36.65 E-value=25 Score=29.59 Aligned_cols=13 Identities=31% Similarity=0.611 Sum_probs=11.1
Q ss_pred ccCCCCCcceecc
Q 025608 202 NRCPNCKFYVEKK 214 (250)
Q Consensus 202 ~~CP~C~~~i~k~ 214 (250)
++||.|+..|++.
T Consensus 246 ~pC~~Cg~~I~~~ 258 (274)
T PRK01103 246 EPCRRCGTPIEKI 258 (274)
T ss_pred CCCCCCCCeeEEE
Confidence 6899999988866
No 283
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc-finger domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=36.37 E-value=5.5 Score=21.29 Aligned_cols=22 Identities=27% Similarity=0.572 Sum_probs=11.6
Q ss_pred cccCCCCCCCCCCCHHHHhccC
Q 025608 85 SIGCPVTDCGGSLEPEYCRDIL 106 (250)
Q Consensus 85 ~i~CP~~~C~~~l~~~~i~~~l 106 (250)
.|+||..+|...+.......++
T Consensus 2 ~vrCPvkdC~EEv~lgKY~~H~ 23 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSLGKYSHHL 23 (30)
T ss_dssp EEE--STT---EEEHHHHHHHH
T ss_pred ccccccccCcchhhhhhhcccc
Confidence 4789999999888776554443
No 284
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=36.13 E-value=28 Score=33.49 Aligned_cols=46 Identities=26% Similarity=0.694 Sum_probs=32.8
Q ss_pred CceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCC
Q 025608 40 RSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCG 94 (250)
Q Consensus 40 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 94 (250)
..+.|.+|.-.......+ ...|+|....+|.+.|+... + .||. +|+
T Consensus 1027 ~~~~C~~C~l~V~gss~~-Cg~C~Hv~H~sc~~eWf~~g--d-----~Cps-GCG 1072 (1081)
T KOG0309|consen 1027 FTFQCAICHLAVRGSSNF-CGTCGHVGHTSCMMEWFRTG--D-----VCPS-GCG 1072 (1081)
T ss_pred ceeeeeeEeeEeeccchh-hccccccccHHHHHHHHhcC--C-----cCCC-CCC
Confidence 345677777666655544 34899999999999999943 1 7886 444
No 285
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=36.06 E-value=36 Score=20.64 Aligned_cols=30 Identities=30% Similarity=0.501 Sum_probs=20.7
Q ss_pred ecccCcccccCCCceecCCCCCcchHHHHHHH
Q 025608 43 VCEICVETKLRNESFSIKGCSHMYCVDCTVKY 74 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 74 (250)
.|+||......-..+.+ .=+ .+|.+|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~-~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKI-KDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceec-cCc-cchHHHHHHh
Confidence 38999888754332333 445 7999999887
No 286
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PHA02825 LAP/PHD finger-like protein; Provisional
Probab=35.89 E-value=49 Score=25.36 Aligned_cols=49 Identities=16% Similarity=0.474 Sum_probs=33.4
Q ss_pred ceecccCcccccCCCceecCCCCC-----cchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHH
Q 025608 41 SFVCEICVETKLRNESFSIKGCSH-----MYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPE 100 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H-----~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~ 100 (250)
.-.|-||+++.... . .+|.. ....+|++.|+... ....|+. |+......
T Consensus 8 ~~~CRIC~~~~~~~--~--~PC~CkGs~k~VH~sCL~rWi~~s-----~~~~Cei--C~~~Y~i~ 61 (162)
T PHA02825 8 DKCCWICKDEYDVV--T--NYCNCKNENKIVHKECLEEWINTS-----KNKSCKI--CNGPYNIK 61 (162)
T ss_pred CCeeEecCCCCCCc--c--CCcccCCCchHHHHHHHHHHHhcC-----CCCcccc--cCCeEEEE
Confidence 34699999885422 1 25553 57999999999943 4568987 77655443
No 288
>PRK05978 hypothetical protein; Provisional
Probab=35.89 E-value=21 Score=27.11 Aligned_cols=10 Identities=40% Similarity=0.850 Sum_probs=8.2
Q ss_pred CCccCCCCCc
Q 025608 200 KWNRCPNCKF 209 (250)
Q Consensus 200 ~~~~CP~C~~ 209 (250)
-.-+||+|+.
T Consensus 32 l~grCP~CG~ 41 (148)
T PRK05978 32 FRGRCPACGE 41 (148)
T ss_pred HcCcCCCCCC
Confidence 3479999998
No 289
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.86 E-value=12 Score=34.01 Aligned_cols=43 Identities=30% Similarity=0.623 Sum_probs=25.3
Q ss_pred CccCCCCCcceeccCCCcceEEecccccccccccccc---CCCCCcCCCCC
Q 025608 201 WNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLS---TVSHGYYCPSC 248 (250)
Q Consensus 201 ~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~---~~~h~~~~~~~ 248 (250)
-..||=|-.+-. +--|| .||+-|||-|+..|- .-.-+-.||=|
T Consensus 186 ~~~CPICL~~~~----~p~~t-~CGHiFC~~CiLqy~~~s~~~~~~~CPiC 231 (513)
T KOG2164|consen 186 DMQCPICLEPPS----VPVRT-NCGHIFCGPCILQYWNYSAIKGPCSCPIC 231 (513)
T ss_pred CCcCCcccCCCC----ccccc-ccCceeeHHHHHHHHhhhcccCCccCCch
Confidence 378999877422 11111 488888888876662 12334467766
No 290
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=35.80 E-value=17 Score=21.61 Aligned_cols=33 Identities=15% Similarity=0.478 Sum_probs=23.9
Q ss_pred cccCcccccCCCceecCCCCCcchHHHHHHHHH
Q 025608 44 CEICVETKLRNESFSIKGCSHMYCVDCTVKYVD 76 (250)
Q Consensus 44 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 76 (250)
|.||........++....|+..|...|+.....
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~ 34 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEK 34 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHS
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccCCCChh
Confidence 778887666667677778887777777766555
No 291
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=35.66 E-value=18 Score=27.55 Aligned_cols=14 Identities=29% Similarity=0.729 Sum_probs=11.4
Q ss_pred CccCCCCCcceecc
Q 025608 201 WNRCPNCKFYVEKK 214 (250)
Q Consensus 201 ~~~CP~C~~~i~k~ 214 (250)
+..||+|+.+|.-.
T Consensus 39 I~~Cp~C~~~IrG~ 52 (158)
T PF10083_consen 39 ITSCPNCSTPIRGD 52 (158)
T ss_pred HHHCcCCCCCCCCc
Confidence 36899999998854
No 292
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=35.47 E-value=49 Score=27.77 Aligned_cols=33 Identities=27% Similarity=0.869 Sum_probs=19.4
Q ss_pred CCeecCCCCCCCCceecC--------ccCccCcccCCcccchh
Q 025608 126 AQKFYCPFKDCSALLIDD--------AGEAIRESECPNCHRLF 160 (250)
Q Consensus 126 ~~~~~Cp~~~C~~~~~~~--------~~~~~~~~~C~~C~~~~ 160 (250)
..-|.|| .|+..|... ...+.....|+.|+.+|
T Consensus 213 EKPF~C~--hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsF 253 (279)
T KOG2462|consen 213 EKPFSCP--HCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSF 253 (279)
T ss_pred CCCccCC--cccchhcchHHHHHHHHhhcCCccccCcchhhHH
Confidence 3456777 777666543 11234566777777665
No 293
>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=35.32 E-value=35 Score=20.39 Aligned_cols=28 Identities=18% Similarity=0.443 Sum_probs=16.6
Q ss_pred ecCCCCCCCCceecCcc-CccCcccCCcccc
Q 025608 129 FYCPFKDCSALLIDDAG-EAIRESECPNCHR 158 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~-~~~~~~~C~~C~~ 158 (250)
+.|+ +|+..+..... .......||.||.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCT--ACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeC--CCCCEeEEEEecCCCCCCCCCCCCC
Confidence 4787 88875544311 1124467888886
No 294
>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=35.06 E-value=22 Score=20.18 Aligned_cols=20 Identities=30% Similarity=0.953 Sum_probs=12.8
Q ss_pred ccCCCCCcc-eecc--CCCcceEE
Q 025608 202 NRCPNCKFY-VEKK--DGCSYIRC 222 (250)
Q Consensus 202 ~~CP~C~~~-i~k~--~GCnhm~C 222 (250)
+.||.|+.. ++|. .| ..+.|
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~C 24 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGC 24 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEEC
Confidence 689999984 4444 34 55555
No 295
>PLN02189 cellulose synthase
Probab=34.83 E-value=28 Score=34.83 Aligned_cols=61 Identities=18% Similarity=0.400 Sum_probs=38.1
Q ss_pred ecCCCCCCCCceecCccCccCcccCCcccchhccccCcccCCCCCchhHhhhccCCCchHHHHHHHHHhcCCCccCCCCC
Q 025608 129 FYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCK 208 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~C~ 208 (250)
..|. -|+.-+-.+. .....+.|..|+...|..|..- . .+...+.||.|+
T Consensus 35 ~~C~--iCgd~vg~~~-~g~~fvaC~~C~fpvCr~Cyey----------e------------------r~eg~q~CpqCk 83 (1040)
T PLN02189 35 QVCE--ICGDEIGLTV-DGDLFVACNECGFPVCRPCYEY----------E------------------RREGTQNCPQCK 83 (1040)
T ss_pred cccc--ccccccCcCC-CCCEEEeeccCCCccccchhhh----------h------------------hhcCCccCcccC
Confidence 3566 5665544432 2236689999999999888741 0 012236888888
Q ss_pred cceeccCCCcce
Q 025608 209 FYVEKKDGCSYI 220 (250)
Q Consensus 209 ~~i~k~~GCnhm 220 (250)
+...+--|+..+
T Consensus 84 t~Y~r~kgs~~v 95 (1040)
T PLN02189 84 TRYKRLKGSPRV 95 (1040)
T ss_pred CchhhccCCCCc
Confidence 877766665543
No 296
>PF11809 DUF3330: Domain of unknown function (DUF3330); InterPro: IPR021767 This family of proteins are functionally uncharacterised. This family is only found in bacteria.
Probab=34.68 E-value=18 Score=23.33 Aligned_cols=42 Identities=12% Similarity=0.501 Sum_probs=28.9
Q ss_pred CCCCceecccCcccccCCCceecCCC--CCcch-HHHHHHHHHHH
Q 025608 37 ETSRSFVCEICVETKLRNESFSIKGC--SHMYC-VDCTVKYVDSK 78 (250)
Q Consensus 37 ~~~~~~~C~iC~~~~~~~~~~~~~~C--~H~fC-~~Cl~~~~~~~ 78 (250)
.+.+...|.+|+.+++.+..+.-..= -+.|| .+|..+|....
T Consensus 7 ~~~~~~sC~vC~KEIPl~~a~t~E~~eYV~hFCGLeCY~~w~a~~ 51 (70)
T PF11809_consen 7 NDPKTTSCCVCCKEIPLDAAFTPEAAEYVEHFCGLECYQRWQARA 51 (70)
T ss_pred cccccchHHHHhhhCChhhccCcchHHHHHHHhhHHHHHHHHHHH
Confidence 34566789999999988766542111 15577 58999998655
No 297
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=34.21 E-value=29 Score=21.10 Aligned_cols=35 Identities=14% Similarity=0.491 Sum_probs=25.0
Q ss_pred ecccCcccccCC-CceecCCCCCcchHHHHHHHHHH
Q 025608 43 VCEICVETKLRN-ESFSIKGCSHMYCVDCTVKYVDS 77 (250)
Q Consensus 43 ~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~ 77 (250)
.|.+|...|..- .-.....||+.||.+|.......
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred cCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 588888777532 11335689999999999877553
No 298
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.78 E-value=18 Score=29.26 Aligned_cols=75 Identities=25% Similarity=0.572 Sum_probs=46.1
Q ss_pred cchhccccCcccCCCCCchhHhhhccCCCchHHHHHHHHHhcCCC-ccCCCCCcceeccCCCcceEEecccccccccccc
Q 025608 157 HRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKW-NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQ 235 (250)
Q Consensus 157 ~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~ 235 (250)
....|-.|....|+.---..|.+ ++...++ -.|--|++++...+ |-.+ +|-+-|=|.|+.+
T Consensus 20 RVNVCEhClV~nHpkCiVQSYLq---------------WL~DsDY~pNC~LC~t~La~gd-t~RL--vCyhlfHW~Clne 81 (299)
T KOG3970|consen 20 RVNVCEHCLVANHPKCIVQSYLQ---------------WLQDSDYNPNCRLCNTPLASGD-TTRL--VCYHLFHWKCLNE 81 (299)
T ss_pred hhhHHHHHHhccCchhhHHHHHH---------------HHhhcCCCCCCceeCCccccCc-ceee--hhhhhHHHHHhhH
Confidence 34556667777776533333333 3333322 45666777665322 2222 6888999999988
Q ss_pred c------cCCCCCcCCCCCC
Q 025608 236 L------STVSHGYYCPSCN 249 (250)
Q Consensus 236 ~------~~~~h~~~~~~~~ 249 (250)
+ .+..-+|-||-|+
T Consensus 82 raA~lPanTAPaGyqCP~Cs 101 (299)
T KOG3970|consen 82 RAANLPANTAPAGYQCPCCS 101 (299)
T ss_pred HHhhCCCcCCCCcccCCCCC
Confidence 7 4667788899997
No 299
>smart00336 BBOX B-Box-type zinc finger.
Probab=33.76 E-value=21 Score=19.97 Aligned_cols=24 Identities=38% Similarity=0.731 Sum_probs=19.5
Q ss_pred CcccCCcccchhccccCcccCCCC
Q 025608 149 RESECPNCHRLFCAQCKVAWHAGI 172 (250)
Q Consensus 149 ~~~~C~~C~~~~C~~C~~~~H~~~ 172 (250)
..+.|..|...+|..|....|.++
T Consensus 14 ~~~~C~~c~~~iC~~C~~~~H~~H 37 (42)
T smart00336 14 AEFFCEECGALLCRTCDEAEHRGH 37 (42)
T ss_pred eEEECCCCCcccccccChhhcCCC
Confidence 457899999999999997767654
No 300
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=33.26 E-value=32 Score=21.67 Aligned_cols=31 Identities=23% Similarity=0.475 Sum_probs=19.7
Q ss_pred eecCCCCCCCCceecCccCccCcccCCcccchhc
Q 025608 128 KFYCPFKDCSALLIDDAGEAIRESECPNCHRLFC 161 (250)
Q Consensus 128 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C 161 (250)
.+.|| +|.+....-... ...+.|..|+...+
T Consensus 11 ~VkCp--~C~n~q~vFsha-~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 11 KVKCP--DCGNEQVVFSHA-STVVRCLVCGKTLA 41 (59)
T ss_pred EEECC--CCCCeEEEEecC-CcEEECcccCCCcc
Confidence 35899 998754432211 24578888887764
No 301
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=33.24 E-value=23 Score=20.16 Aligned_cols=18 Identities=28% Similarity=0.888 Sum_probs=15.6
Q ss_pred cccCCcccchhccccCcc
Q 025608 150 ESECPNCHRLFCAQCKVA 167 (250)
Q Consensus 150 ~~~C~~C~~~~C~~C~~~ 167 (250)
.+.|..|+..||...+.+
T Consensus 12 ~f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLP 29 (39)
T ss_pred CeECCccCCccccccCCc
Confidence 478999999999999874
No 302
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=33.05 E-value=21 Score=35.77 Aligned_cols=43 Identities=21% Similarity=0.552 Sum_probs=29.7
Q ss_pred CcccCCcccchhccccCcccCCCCCchhHhhhccCCCchHHHHHHHHHhcCCCccCCCCCcceeccCCCcc
Q 025608 149 RESECPNCHRLFCAQCKVAWHAGIECADFQKLHKDEPESEDIILMKLAQNQKWNRCPNCKFYVEKKDGCSY 219 (250)
Q Consensus 149 ~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~C~~~i~k~~GCnh 219 (250)
..+.|..|+.-.|..|.. |. .+...+.||.|++...+.-|+..
T Consensus 35 ~FVAC~eC~FPVCrpCYE----------YE------------------r~eG~q~CPqCktrYkr~kgspr 77 (1079)
T PLN02638 35 PFVACDVCAFPVCRPCYE----------YE------------------RKDGNQSCPQCKTKYKRHKGSPA 77 (1079)
T ss_pred EEEEeccCCCccccchhh----------hh------------------hhcCCccCCccCCchhhhcCCCC
Confidence 668999999999988874 11 11223788888887776666554
No 303
>PRK11032 hypothetical protein; Provisional
Probab=32.96 E-value=35 Score=26.24 Aligned_cols=28 Identities=29% Similarity=0.745 Sum_probs=21.1
Q ss_pred CCcceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608 216 GCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 216 GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
|=-.|.| +||++..+ .+..+--+||+|+
T Consensus 121 g~G~LvC~~Cg~~~~~------~~p~~i~pCp~C~ 149 (160)
T PRK11032 121 GLGNLVCEKCHHHLAF------YTPEVLPLCPKCG 149 (160)
T ss_pred ecceEEecCCCCEEEe------cCCCcCCCCCCCC
Confidence 4457899 99998754 4567777899997
No 304
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.90 E-value=29 Score=29.13 Aligned_cols=13 Identities=31% Similarity=0.611 Sum_probs=11.6
Q ss_pred ccCCCCCcceecc
Q 025608 202 NRCPNCKFYVEKK 214 (250)
Q Consensus 202 ~~CP~C~~~i~k~ 214 (250)
++||.|+..|++.
T Consensus 246 ~pC~~Cg~~I~~~ 258 (272)
T TIGR00577 246 EPCRRCGTPIEKI 258 (272)
T ss_pred CCCCCCCCeeEEE
Confidence 6999999999876
No 305
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=32.53 E-value=30 Score=29.22 Aligned_cols=13 Identities=23% Similarity=0.608 Sum_probs=11.0
Q ss_pred ccCCCCCcceecc
Q 025608 202 NRCPNCKFYVEKK 214 (250)
Q Consensus 202 ~~CP~C~~~i~k~ 214 (250)
++||.|+..|.+.
T Consensus 255 ~pC~~Cg~~I~~~ 267 (282)
T PRK13945 255 KPCRKCGTPIERI 267 (282)
T ss_pred CCCCcCCCeeEEE
Confidence 7999999988865
No 306
>PF12675 DUF3795: Protein of unknown function (DUF3795); InterPro: IPR024227 This family of proteins is functionally uncharacterised and is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. These proteins are likely to be zinc binding given the conserved cysteines.
Probab=32.13 E-value=79 Score=20.91 Aligned_cols=36 Identities=28% Similarity=0.571 Sum_probs=25.8
Q ss_pred CCCccCCCCCcce--eccCCCcceEE--eccccccccccc
Q 025608 199 QKWNRCPNCKFYV--EKKDGCSYIRC--RCGHAFCYHCGV 234 (250)
Q Consensus 199 ~~~~~CP~C~~~i--~k~~GCnhm~C--~C~~~FC~~C~~ 234 (250)
..-..||.|+..- .....|.--.| .=|..|||.|..
T Consensus 32 ~~~~~C~GCr~~~~~~~~~~C~i~~C~~ekgv~~C~eC~e 71 (78)
T PF12675_consen 32 PEKIRCPGCRSGGGKCCCKSCKIRQCAKEKGVDFCGECPE 71 (78)
T ss_pred CCCCcCcCCcCCCCCcCCCCCCcCcHHhhCCCCeeecCCC
Confidence 3447899999865 35567887788 338888888853
No 307
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=31.51 E-value=50 Score=22.41 Aligned_cols=30 Identities=27% Similarity=0.576 Sum_probs=20.2
Q ss_pred ecCCCCCCCCceecCccCccCcccCCcccchhc
Q 025608 129 FYCPFKDCSALLIDDAGEAIRESECPNCHRLFC 161 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C 161 (250)
+.|| +|...-..-.. ....+.|..|+...|
T Consensus 36 VkCp--~C~n~q~VFSh-A~t~V~C~~Cg~~L~ 65 (85)
T PTZ00083 36 VKCP--GCSQITTVFSH-AQTVVLCGGCSSQLC 65 (85)
T ss_pred EECC--CCCCeeEEEec-CceEEEccccCCEee
Confidence 4899 99875443221 135588999998876
No 308
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=31.34 E-value=45 Score=23.56 Aligned_cols=23 Identities=22% Similarity=0.821 Sum_probs=19.7
Q ss_pred CCCCcchHHHHHHHHHHHhhcCcccccCCC
Q 025608 61 GCSHMYCVDCTVKYVDSKLQENVTSIGCPV 90 (250)
Q Consensus 61 ~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 90 (250)
.|.|.|..-|+.+|+++. -+||.
T Consensus 80 ~CNHaFH~hCisrWlktr-------~vCPL 102 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTR-------NVCPL 102 (114)
T ss_pred ecchHHHHHHHHHHHhhc-------CcCCC
Confidence 789999999999999944 46886
No 309
>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=31.27 E-value=39 Score=18.26 Aligned_cols=20 Identities=25% Similarity=0.639 Sum_probs=9.8
Q ss_pred ccccccccCCCCCcCCCCCC
Q 025608 230 YHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 230 ~~C~~~~~~~~h~~~~~~~~ 249 (250)
-.||-.+.+......||.|+
T Consensus 5 ~~CGy~y~~~~~~~~CP~Cg 24 (33)
T cd00350 5 PVCGYIYDGEEAPWVCPVCG 24 (33)
T ss_pred CCCCCEECCCcCCCcCcCCC
Confidence 34444443333444577775
No 310
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.11 E-value=15 Score=34.42 Aligned_cols=35 Identities=20% Similarity=0.524 Sum_probs=26.4
Q ss_pred eecccCcccccCCCc-eecCCCCCcchHHHHHHHHH
Q 025608 42 FVCEICVETKLRNES-FSIKGCSHMYCVDCTVKYVD 76 (250)
Q Consensus 42 ~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~ 76 (250)
..|+||+..|....+ ...+.|+|.+|.-|+.....
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 459999877754332 34669999999999988665
No 311
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=30.95 E-value=53 Score=22.65 Aligned_cols=31 Identities=23% Similarity=0.478 Sum_probs=24.7
Q ss_pred CCCccCCCCCcceeccCCCcceEE-ecccccc
Q 025608 199 QKWNRCPNCKFYVEKKDGCSYIRC-RCGHAFC 229 (250)
Q Consensus 199 ~~~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC 229 (250)
.....||.|+..-.+..+-.--.| .|+..|=
T Consensus 34 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 34 HAKYFCPFCGKHAVKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred hCCccCCCCCCCceeeeeeEEEEcCCCCCEEe
Confidence 344799999998888888788888 8888763
No 312
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=30.88 E-value=45 Score=23.04 Aligned_cols=30 Identities=27% Similarity=0.601 Sum_probs=24.5
Q ss_pred CCccCCCCCcceeccCCCcceEE-ecccccc
Q 025608 200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHAFC 229 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC 229 (250)
.-..||.|+..-.+..+----.| .|+..|=
T Consensus 34 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred cCccCCCCCCCceEEEeeEEEEcCCCCCEEe
Confidence 34799999998888888888888 8888763
No 313
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=30.75 E-value=24 Score=29.93 Aligned_cols=27 Identities=30% Similarity=0.842 Sum_probs=12.2
Q ss_pred ccCCCCCcc-----eeccC--CCcceEE-eccccc
Q 025608 202 NRCPNCKFY-----VEKKD--GCSYIRC-RCGHAF 228 (250)
Q Consensus 202 ~~CP~C~~~-----i~k~~--GCnhm~C-~C~~~F 228 (250)
..||-||.. |...+ |=-+++| .|+++|
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W 207 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEW 207 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EE
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCee
Confidence 799999983 33333 6677777 777665
No 314
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=30.65 E-value=45 Score=21.38 Aligned_cols=10 Identities=30% Similarity=0.600 Sum_probs=4.9
Q ss_pred ccCCCCCcce
Q 025608 202 NRCPNCKFYV 211 (250)
Q Consensus 202 ~~CP~C~~~i 211 (250)
-.||+|+...
T Consensus 54 L~Cp~c~r~Y 63 (68)
T PF03966_consen 54 LICPECGREY 63 (68)
T ss_dssp EEETTTTEEE
T ss_pred EEcCCCCCEE
Confidence 4555555443
No 315
>PRK12495 hypothetical protein; Provisional
Probab=30.63 E-value=47 Score=26.93 Aligned_cols=28 Identities=25% Similarity=0.577 Sum_probs=20.1
Q ss_pred CCccCCCCCcceeccCCCcceEEeccccccccccccc
Q 025608 200 KWNRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQL 236 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~ 236 (250)
..+.||.||.+|.+..|+ .||-.|...+
T Consensus 41 sa~hC~~CG~PIpa~pG~---------~~Cp~CQ~~~ 68 (226)
T PRK12495 41 TNAHCDECGDPIFRHDGQ---------EFCPTCQQPV 68 (226)
T ss_pred chhhcccccCcccCCCCe---------eECCCCCCcc
Confidence 448999999999977775 4555555444
No 316
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=30.63 E-value=13 Score=32.03 Aligned_cols=46 Identities=28% Similarity=0.789 Sum_probs=32.7
Q ss_pred cCCCCCcceeccCCCcceEEeccccccccccccccCCCCCcCCCCCCC
Q 025608 203 RCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLSTVSHGYYCPSCNK 250 (250)
Q Consensus 203 ~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~~~~h~~~~~~~~~ 250 (250)
.||-|--+|--.+ =|..-|.||+..|-.|...++..-.+ -||-|-|
T Consensus 16 ~cplcie~mditd-knf~pc~cgy~ic~fc~~~irq~lng-rcpacrr 61 (480)
T COG5175 16 YCPLCIEPMDITD-KNFFPCPCGYQICQFCYNNIRQNLNG-RCPACRR 61 (480)
T ss_pred cCccccccccccc-CCcccCCcccHHHHHHHHHHHhhccC-CChHhhh
Confidence 5998877665433 35677899999999998888644333 4888754
No 317
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.47 E-value=50 Score=22.69 Aligned_cols=17 Identities=12% Similarity=0.516 Sum_probs=14.3
Q ss_pred cchHHHHHHHHHHHhhc
Q 025608 65 MYCVDCTVKYVDSKLQE 81 (250)
Q Consensus 65 ~fC~~Cl~~~~~~~i~~ 81 (250)
-||+.||.+|.......
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 48999999999977654
No 318
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=30.19 E-value=23 Score=24.78 Aligned_cols=33 Identities=21% Similarity=0.510 Sum_probs=23.7
Q ss_pred CCCCceecccCcccccCCCceecCCCCCcchHHH
Q 025608 37 ETSRSFVCEICVETKLRNESFSIKGCSHMYCVDC 70 (250)
Q Consensus 37 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~C 70 (250)
...-.|+|..||-....+.+-. ..=++.+|++|
T Consensus 66 ~q~DEFTCssCFLV~HRSqLa~-~~~g~~iC~DC 98 (99)
T PF13834_consen 66 KQADEFTCSSCFLVHHRSQLAR-EKDGQPICRDC 98 (99)
T ss_pred CCCCceeeeeeeeEechhhhcc-ccCCCEecccc
Confidence 4455688999998877666543 34478889888
No 319
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=29.91 E-value=12 Score=35.55 Aligned_cols=56 Identities=27% Similarity=0.561 Sum_probs=40.1
Q ss_pred CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhcCcccccCCCCCCCCCCCHHHHh
Q 025608 39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQENVTSIGCPVTDCGGSLEPEYCR 103 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~ 103 (250)
....+|+||+..+..+ .++.|.|.||..|+..-+...-. ...||. |...+.....+
T Consensus 19 ~k~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~----~~~~~l--c~~~~eK~s~~ 74 (684)
T KOG4362|consen 19 QKILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKG----PKQCAL--CKSDIEKRSLR 74 (684)
T ss_pred hhhccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCc----cccchh--hhhhhhhhhcc
Confidence 4556899999987654 45699999999999988774422 566776 66555554444
No 320
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=29.19 E-value=46 Score=20.07 Aligned_cols=34 Identities=24% Similarity=0.507 Sum_probs=25.1
Q ss_pred CCceecccCcccccCCCceecCCCCCcchHHHHHHH
Q 025608 39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKY 74 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 74 (250)
..-|.|..|...+.....+. .=+..+|.+|..+.
T Consensus 24 ~~Cf~C~~C~~~l~~~~~~~--~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 24 PECFKCSKCGKPLNDGDFYE--KDGKPYCKDCYQKR 57 (58)
T ss_dssp TTTSBETTTTCBTTTSSEEE--ETTEEEEHHHHHHH
T ss_pred ccccccCCCCCccCCCeeEe--ECCEEECHHHHhhh
Confidence 45678999999888766443 33588999998764
No 321
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.12 E-value=33 Score=31.65 Aligned_cols=37 Identities=30% Similarity=0.841 Sum_probs=23.8
Q ss_pred CccCCCCCcceeccCCCcceEE-eccc----------cccccccccccCCCCCcCCCCCC
Q 025608 201 WNRCPNCKFYVEKKDGCSYIRC-RCGH----------AFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 201 ~~~CP~C~~~i~k~~GCnhm~C-~C~~----------~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
...|+.||.. +.| .|+. -.|-.||... +.... ||+|+
T Consensus 213 ~~~C~~Cg~~---------~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~-~~~~~--Cp~C~ 260 (505)
T TIGR00595 213 NLLCRSCGYI---------LCCPNCDVSLTYHKKEGKLRCHYCGYQE-PIPKT--CPQCG 260 (505)
T ss_pred eeEhhhCcCc---------cCCCCCCCceEEecCCCeEEcCCCcCcC-CCCCC--CCCCC
Confidence 3577777776 456 6763 3477787666 23344 89886
No 322
>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=28.82 E-value=45 Score=18.60 Aligned_cols=27 Identities=26% Similarity=0.609 Sum_probs=14.6
Q ss_pred cCCCCCCCCceecCccCccCcccCCcccc
Q 025608 130 YCPFKDCSALLIDDAGEAIRESECPNCHR 158 (250)
Q Consensus 130 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 158 (250)
.|| .|+.++.....+......|..||.
T Consensus 3 ~C~--~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 3 ICP--KCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EET--TTTEEEETTTB--SSTTBCTTTTE
T ss_pred CcC--CCCCccccccCCCCCCCccCCCCC
Confidence 466 777776655332234455666664
No 323
>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=28.40 E-value=19 Score=19.73 Aligned_cols=9 Identities=33% Similarity=0.992 Sum_probs=5.7
Q ss_pred CcCCCCCCC
Q 025608 242 GYYCPSCNK 250 (250)
Q Consensus 242 ~~~~~~~~~ 250 (250)
++.||+|+|
T Consensus 4 ~~~C~nC~R 12 (33)
T PF08209_consen 4 YVECPNCGR 12 (33)
T ss_dssp EEE-TTTSS
T ss_pred eEECCCCcC
Confidence 456888876
No 324
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=28.33 E-value=15 Score=22.74 Aligned_cols=14 Identities=29% Similarity=1.020 Sum_probs=10.9
Q ss_pred cccccccccccccc
Q 025608 224 CGHAFCYHCGVQLS 237 (250)
Q Consensus 224 C~~~FC~~C~~~~~ 237 (250)
=.+.||+.||-.+.
T Consensus 25 ~~~~YC~~Cg~~Y~ 38 (55)
T PF13821_consen 25 EEHNYCFWCGTKYD 38 (55)
T ss_pred hhCceeeeeCCccC
Confidence 34688999998885
No 325
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=28.25 E-value=1.2e+02 Score=21.61 Aligned_cols=50 Identities=20% Similarity=0.388 Sum_probs=29.3
Q ss_pred CChHHHHHHHHHHHhhccC-CCCeecCCCCCCCCceecCccCccCcccCCcccchhccccCcc
Q 025608 106 LPEEAFDKWGKALCESLIP-GAQKFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVA 167 (250)
Q Consensus 106 l~~~~~~~~~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~ 167 (250)
+++...+.+.+++.=.... ......|+ +|+....... .|+..+|..|+..
T Consensus 19 l~~~~~k~~~~il~Crt~~~G~~~~~C~--~Cg~~~~~~~----------SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 19 LSPYQRKAVEAILACRTEALGFHRYRCE--DCGHEKIVYN----------SCKNRHCPSCQAK 69 (111)
T ss_pred CCHHHHHHHHHHHhcCCccCCcceeecC--CCCceEEecC----------cccCcCCCCCCCh
Confidence 4555555555555422222 34456898 7876654433 6778888888763
No 326
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=28.07 E-value=27 Score=27.35 Aligned_cols=25 Identities=16% Similarity=0.341 Sum_probs=19.1
Q ss_pred HHHHHHHhcCCCccCCCCCcceecc
Q 025608 190 IILMKLAQNQKWNRCPNCKFYVEKK 214 (250)
Q Consensus 190 ~~~~~~~~~~~~~~CP~C~~~i~k~ 214 (250)
..+.++..+...++|++||.+....
T Consensus 146 ~~~~~f~~~~e~rtC~~CG~v~~~~ 170 (177)
T PRK13264 146 PVFAAFYASEELRTCDNCGTVHPGK 170 (177)
T ss_pred HHHHHHhcCHhhccCCcCCcccCcc
Confidence 4566777778889999999976543
No 327
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=28.02 E-value=43 Score=26.03 Aligned_cols=12 Identities=25% Similarity=0.523 Sum_probs=7.6
Q ss_pred CCccCCCCCcce
Q 025608 200 KWNRCPNCKFYV 211 (250)
Q Consensus 200 ~~~~CP~C~~~i 211 (250)
+-..||.|+.+|
T Consensus 155 GRP~CPlCg~Pl 166 (177)
T TIGR03847 155 GRPPCPLCGRPI 166 (177)
T ss_pred CCCCCCCCCCCC
Confidence 346777766665
No 328
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=27.87 E-value=53 Score=22.63 Aligned_cols=30 Identities=30% Similarity=0.653 Sum_probs=24.6
Q ss_pred CCccCCCCCcceeccCCCcceEE-ecccccc
Q 025608 200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHAFC 229 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~FC 229 (250)
.--.||.|+..-.+..+----.| .|+..|=
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred cCccCCCCCCCceEEEEEEEEEcCCCCCEEe
Confidence 34799999998888888888888 8888763
No 329
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=27.86 E-value=29 Score=26.67 Aligned_cols=21 Identities=19% Similarity=0.444 Sum_probs=16.1
Q ss_pred HHHHHHHHhcCCCccCCCCCc
Q 025608 189 DIILMKLAQNQKWNRCPNCKF 209 (250)
Q Consensus 189 ~~~~~~~~~~~~~~~CP~C~~ 209 (250)
...+.++..+...++|++||.
T Consensus 139 ~~~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 139 PPVFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred HHHHHHHhCChhhccCCccCC
Confidence 345667777788899999984
No 330
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=27.83 E-value=41 Score=27.99 Aligned_cols=28 Identities=14% Similarity=0.325 Sum_probs=21.6
Q ss_pred CCccCCCCCcceeccCCCcceEE-ecccc
Q 025608 200 KWNRCPNCKFYVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 200 ~~~~CP~C~~~i~k~~GCnhm~C-~C~~~ 227 (250)
..+-||.||..+....|=..+.| .|+..
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCCE
Confidence 45899999998776655567889 88854
No 331
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=27.56 E-value=37 Score=25.98 Aligned_cols=26 Identities=27% Similarity=0.816 Sum_probs=18.2
Q ss_pred CccCCCCCcceeccCCCcceEE-ecccc
Q 025608 201 WNRCPNCKFYVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 201 ~~~CP~C~~~i~k~~GCnhm~C-~C~~~ 227 (250)
+..||.|+..+...+. +...| +|+..
T Consensus 34 Y~aC~~C~kkv~~~~~-~~~~C~~C~~~ 60 (166)
T cd04476 34 YPACPGCNKKVVEEGN-GTYRCEKCNKS 60 (166)
T ss_pred EccccccCcccEeCCC-CcEECCCCCCc
Confidence 4789999998776654 55666 66654
No 332
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=27.38 E-value=55 Score=24.05 Aligned_cols=27 Identities=26% Similarity=0.787 Sum_probs=22.0
Q ss_pred CccCCCCCc---ceeccCCCcceEE-ecccc
Q 025608 201 WNRCPNCKF---YVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 201 ~~~CP~C~~---~i~k~~GCnhm~C-~C~~~ 227 (250)
...||.|+. .+.+.++=-.+.| .||..
T Consensus 93 yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 93 YVLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp HSSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred EEEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 489999998 4666788888999 89864
No 333
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=26.77 E-value=36 Score=17.15 Aligned_cols=18 Identities=28% Similarity=0.916 Sum_probs=13.8
Q ss_pred ccCCCCCCCCCCCHHHHhcc
Q 025608 86 IGCPVTDCGGSLEPEYCRDI 105 (250)
Q Consensus 86 i~CP~~~C~~~l~~~~i~~~ 105 (250)
+.||. |+..+..+.+..+
T Consensus 3 ~~C~~--CgR~F~~~~l~~H 20 (25)
T PF13913_consen 3 VPCPI--CGRKFNPDRLEKH 20 (25)
T ss_pred CcCCC--CCCEECHHHHHHH
Confidence 57887 9988888877654
No 334
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=26.62 E-value=41 Score=20.85 Aligned_cols=32 Identities=19% Similarity=0.436 Sum_probs=17.4
Q ss_pred eecCCCCCCCCceecCccCccCcccCCcccchhcc
Q 025608 128 KFYCPFKDCSALLIDDAGEAIRESECPNCHRLFCA 162 (250)
Q Consensus 128 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~ 162 (250)
.+.|| +|.+.-..-. .....+.|..|+...|.
T Consensus 7 ~VkCp--~C~~~q~vFS-ha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 7 DVKCP--GCYNIQTVFS-HAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EEE-T--TT-SEEEEET-T-SS-EE-SSSTSEEEE
T ss_pred EEECC--CCCCeeEEEe-cCCeEEEcccCCCEecC
Confidence 45899 9987544322 12355889999888763
No 335
>PLN02400 cellulose synthase
Probab=26.59 E-value=39 Score=33.98 Aligned_cols=18 Identities=22% Similarity=0.521 Sum_probs=15.6
Q ss_pred CcccCCcccchhccccCc
Q 025608 149 RESECPNCHRLFCAQCKV 166 (250)
Q Consensus 149 ~~~~C~~C~~~~C~~C~~ 166 (250)
..+.|..|+...|..|..
T Consensus 54 ~FVAC~eCaFPVCRpCYE 71 (1085)
T PLN02400 54 VFVACNECAFPVCRPCYE 71 (1085)
T ss_pred EEEEEccCCCccccchhh
Confidence 668999999999988875
No 336
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.52 E-value=38 Score=24.81 Aligned_cols=23 Identities=30% Similarity=0.780 Sum_probs=13.4
Q ss_pred ccccccccccccC----CCC---CcCCCCCC
Q 025608 226 HAFCYHCGVQLST----VSH---GYYCPSCN 249 (250)
Q Consensus 226 ~~FC~~C~~~~~~----~~h---~~~~~~~~ 249 (250)
..+| .|+..|.. ..| ++.||+|+
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cg 99 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCG 99 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCC
Confidence 3567 77766531 111 25699997
No 337
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=26.43 E-value=23 Score=22.32 Aligned_cols=26 Identities=27% Similarity=0.919 Sum_probs=15.2
Q ss_pred cCCCCCcc----eeccCCCcceEE-eccccc
Q 025608 203 RCPNCKFY----VEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 203 ~CP~C~~~----i~k~~GCnhm~C-~C~~~F 228 (250)
.||.|... .=+..|=.++.| .||++.
T Consensus 12 ~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 12 VCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred CCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 56666651 123455667777 777764
No 338
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=26.39 E-value=42 Score=24.76 Aligned_cols=15 Identities=20% Similarity=0.465 Sum_probs=10.7
Q ss_pred ccCCCCCcceeccCC
Q 025608 202 NRCPNCKFYVEKKDG 216 (250)
Q Consensus 202 ~~CP~C~~~i~k~~G 216 (250)
|.||+|+.-|--.++
T Consensus 111 K~C~~C~tGiYS~e~ 125 (128)
T PF11682_consen 111 KYCPKCGTGIYSIEV 125 (128)
T ss_pred EecCCCCCcccceec
Confidence 789999986654443
No 339
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.39 E-value=24 Score=30.05 Aligned_cols=43 Identities=30% Similarity=0.613 Sum_probs=31.4
Q ss_pred ccCCCCCcceeccCCCcceEE-ecccccccccccccc-CCCCCcCCCCCC
Q 025608 202 NRCPNCKFYVEKKDGCSYIRC-RCGHAFCYHCGVQLS-TVSHGYYCPSCN 249 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C-~C~~~FC~~C~~~~~-~~~h~~~~~~~~ 249 (250)
..|-=|..-+.|.+- +.= .|++.|=-.|..+|- +++|. ||.|+
T Consensus 324 veCaICms~fiK~d~---~~vlPC~H~FH~~Cv~kW~~~y~~~--CPvCr 368 (374)
T COG5540 324 VECAICMSNFIKNDR---LRVLPCDHRFHVGCVDKWLLGYSNK--CPVCR 368 (374)
T ss_pred ceEEEEhhhhcccce---EEEeccCceechhHHHHHHhhhccc--CCccC
Confidence 555555555445544 333 799999999999994 57888 99997
No 340
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=26.37 E-value=39 Score=21.15 Aligned_cols=13 Identities=38% Similarity=0.935 Sum_probs=10.5
Q ss_pred CccCCCCCcceec
Q 025608 201 WNRCPNCKFYVEK 213 (250)
Q Consensus 201 ~~~CP~C~~~i~k 213 (250)
++.||+|+.+..+
T Consensus 5 ~rkC~~cg~YTLk 17 (59)
T COG2260 5 IRKCPKCGRYTLK 17 (59)
T ss_pred hhcCcCCCceeec
Confidence 4789999998765
No 341
>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=26.01 E-value=39 Score=24.18 Aligned_cols=14 Identities=43% Similarity=1.307 Sum_probs=11.5
Q ss_pred cceEEecccccccc
Q 025608 218 SYIRCRCGHAFCYH 231 (250)
Q Consensus 218 nhm~C~C~~~FC~~ 231 (250)
.-+.|.||+.||-.
T Consensus 23 k~vkc~CGh~f~d~ 36 (112)
T PF08882_consen 23 KVVKCDCGHEFCDA 36 (112)
T ss_pred ceeeccCCCeecCh
Confidence 47888999999964
No 342
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=25.78 E-value=58 Score=18.66 Aligned_cols=23 Identities=22% Similarity=0.534 Sum_probs=12.6
Q ss_pred cccccccccccCCCCCcCCCCCC
Q 025608 227 AFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 227 ~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
.||..|.+.+....-++.|..|+
T Consensus 12 ~~C~~C~~~i~~~~~~~~C~~C~ 34 (49)
T smart00109 12 TKCCVCRKSIWGSFQGLRCSWCK 34 (49)
T ss_pred CCccccccccCcCCCCcCCCCCC
Confidence 45666666663222355666664
No 343
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=25.74 E-value=36 Score=18.24 Aligned_cols=10 Identities=40% Similarity=0.959 Sum_probs=6.2
Q ss_pred ccCCCCCcce
Q 025608 202 NRCPNCKFYV 211 (250)
Q Consensus 202 ~~CP~C~~~i 211 (250)
..||+|++-+
T Consensus 2 hlcpkcgvgv 11 (36)
T PF09151_consen 2 HLCPKCGVGV 11 (36)
T ss_dssp -B-TTTSSSB
T ss_pred ccCCccCceE
Confidence 4699999843
No 344
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.22 E-value=47 Score=21.18 Aligned_cols=21 Identities=24% Similarity=0.670 Sum_probs=15.4
Q ss_pred HHHhcCCCccCCCCCcceecc
Q 025608 194 KLAQNQKWNRCPNCKFYVEKK 214 (250)
Q Consensus 194 ~~~~~~~~~~CP~C~~~i~k~ 214 (250)
.+..+..+.+||.|..+|...
T Consensus 37 dL~~ge~Va~CpsCSL~I~Vi 57 (67)
T KOG2923|consen 37 DLENGEDVARCPSCSLIIRVI 57 (67)
T ss_pred HHhCCCeeecCCCceEEEEEE
Confidence 344556779999999887643
No 345
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=25.08 E-value=35 Score=24.49 Aligned_cols=11 Identities=27% Similarity=0.540 Sum_probs=6.5
Q ss_pred hhccccCcccC
Q 025608 159 LFCAQCKVAWH 169 (250)
Q Consensus 159 ~~C~~C~~~~H 169 (250)
..|..|+.+-+
T Consensus 86 D~CM~C~~pLT 96 (114)
T PF11023_consen 86 DACMHCKEPLT 96 (114)
T ss_pred hccCcCCCcCc
Confidence 44677776543
No 346
>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=25.04 E-value=55 Score=17.91 Aligned_cols=6 Identities=50% Similarity=1.503 Sum_probs=3.1
Q ss_pred CCCCCC
Q 025608 244 YCPSCN 249 (250)
Q Consensus 244 ~~~~~~ 249 (250)
.||.|+
T Consensus 20 ~CP~Cg 25 (34)
T cd00729 20 KCPICG 25 (34)
T ss_pred cCcCCC
Confidence 455554
No 347
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=24.95 E-value=81 Score=18.73 Aligned_cols=33 Identities=15% Similarity=0.497 Sum_probs=22.2
Q ss_pred ecccCcccccCCCceecCCCCCc-chHHHHHHHH
Q 025608 43 VCEICVETKLRNESFSIKGCSHM-YCVDCTVKYV 75 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~ 75 (250)
.|..|..+......+..+.|... .|.+|+..-.
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~ 35 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGA 35 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcC
Confidence 48888876655444556677544 7999988553
No 348
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=24.91 E-value=25 Score=31.01 Aligned_cols=40 Identities=23% Similarity=0.443 Sum_probs=29.0
Q ss_pred ccCCCCceecccCcccccCCCceecCCCCCcchHHHHHHHH
Q 025608 35 RSETSRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYV 75 (250)
Q Consensus 35 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 75 (250)
...+..+.+|+|||-.++... -...-|...+|.+||..+-
T Consensus 68 ls~~rr~~ecpicflyyps~~-n~~rcC~~~Ic~ecf~~~~ 107 (482)
T KOG2789|consen 68 LSTSRRKTECPICFLYYPSAK-NLVRCCSETICGECFAPFG 107 (482)
T ss_pred hhhccccccCceeeeeccccc-chhhhhccchhhhheeccc
Confidence 344456689999998876532 2234799999999998753
No 349
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=24.59 E-value=66 Score=19.87 Aligned_cols=10 Identities=30% Similarity=0.870 Sum_probs=6.5
Q ss_pred CeecCCCCCCCC
Q 025608 127 QKFYCPFKDCSA 138 (250)
Q Consensus 127 ~~~~Cp~~~C~~ 138 (250)
..+.|| -|++
T Consensus 3 ~Wi~CP--~Cgn 12 (55)
T PF14205_consen 3 EWILCP--ICGN 12 (55)
T ss_pred eEEECC--CCCC
Confidence 346788 6774
No 350
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=24.38 E-value=79 Score=26.70 Aligned_cols=30 Identities=23% Similarity=0.547 Sum_probs=25.0
Q ss_pred CCCccCCCCCcceeccCCCcceEE-eccccc
Q 025608 199 QKWNRCPNCKFYVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 199 ~~~~~CP~C~~~i~k~~GCnhm~C-~C~~~F 228 (250)
...+-||+||...+-..|=-.+.| .||+.+
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 355899999999888888888888 888764
No 351
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=24.37 E-value=56 Score=18.22 Aligned_cols=24 Identities=42% Similarity=0.999 Sum_probs=14.3
Q ss_pred ccCCCCCcce-eccCCCcceEE-ecccc
Q 025608 202 NRCPNCKFYV-EKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 202 ~~CP~C~~~i-~k~~GCnhm~C-~C~~~ 227 (250)
.+||.|+... ..++| ...| .||+.
T Consensus 9 ~~C~~C~~~~~~~~dG--~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDG--FYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCC--EEEhhhCceE
Confidence 4688888852 22244 5666 66654
No 352
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=24.18 E-value=70 Score=18.66 Aligned_cols=32 Identities=19% Similarity=0.524 Sum_probs=22.0
Q ss_pred ecccCcccccCCCceecCCCCCc-chHHHHHHHH
Q 025608 43 VCEICVETKLRNESFSIKGCSHM-YCVDCTVKYV 75 (250)
Q Consensus 43 ~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~ 75 (250)
.|.+|..++.. ..+....|... .|.+|+....
T Consensus 2 ~C~~C~~~i~g-~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIVG-VRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCCCCcC-CEEECCCCCCCcCHHHHHCcCc
Confidence 58888886654 44556677743 8999987543
No 353
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=23.97 E-value=42 Score=21.36 Aligned_cols=13 Identities=38% Similarity=0.593 Sum_probs=10.3
Q ss_pred CCccCCCCCccee
Q 025608 200 KWNRCPNCKFYVE 212 (250)
Q Consensus 200 ~~~~CP~C~~~i~ 212 (250)
...+||.|+..++
T Consensus 5 ~~v~CP~C~k~~~ 17 (62)
T PRK00418 5 ITVNCPTCGKPVE 17 (62)
T ss_pred ccccCCCCCCccc
Confidence 3478999999765
No 354
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=23.72 E-value=25 Score=18.78 Aligned_cols=18 Identities=39% Similarity=1.067 Sum_probs=9.1
Q ss_pred cccccccccccCCCCCcCCCCCC
Q 025608 227 AFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 227 ~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
.+|-+|+. + ..|-||.|+
T Consensus 3 ~~C~vC~~-~----~kY~Cp~C~ 20 (30)
T PF04438_consen 3 KLCSVCGN-P----AKYRCPRCG 20 (30)
T ss_dssp EEETSSSS-E----ESEE-TTT-
T ss_pred CCCccCcC-C----CEEECCCcC
Confidence 45666666 2 235577775
No 355
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=23.45 E-value=42 Score=33.67 Aligned_cols=18 Identities=22% Similarity=0.473 Sum_probs=15.4
Q ss_pred CcccCCcccchhccccCc
Q 025608 149 RESECPNCHRLFCAQCKV 166 (250)
Q Consensus 149 ~~~~C~~C~~~~C~~C~~ 166 (250)
..+.|..|+...|..|..
T Consensus 33 ~FVAC~eC~fpvCr~cye 50 (1044)
T PLN02915 33 PFVACHVCGFPVCKPCYE 50 (1044)
T ss_pred EEEEeccCCCccccchhh
Confidence 668999999999988874
No 356
>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=23.44 E-value=92 Score=23.39 Aligned_cols=52 Identities=17% Similarity=0.331 Sum_probs=28.5
Q ss_pred ChHHHHHHHHHHHhhccCC--CC-eecCCCCCCCCceecCccCc-------------cCcccCCcccchh
Q 025608 107 PEEAFDKWGKALCESLIPG--AQ-KFYCPFKDCSALLIDDAGEA-------------IRESECPNCHRLF 160 (250)
Q Consensus 107 ~~~~~~~~~~~~~~~~~~~--~~-~~~Cp~~~C~~~~~~~~~~~-------------~~~~~C~~C~~~~ 160 (250)
+.+..+++.+.+....+.- .+ ...|+ .|++.+...+.+. .....|+.||+.|
T Consensus 67 ~~~~~~QL~ev~~~~~l~~~~~~~~sRC~--~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 67 SDDPEEQLREVLERFGLKLRLDPIFSRCP--KCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCCHHHHHHHHHHHcCCccccCCCCCccC--CCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 3445556666655443332 33 34899 8888665432211 1356777777665
No 357
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.25 E-value=76 Score=22.01 Aligned_cols=41 Identities=15% Similarity=0.330 Sum_probs=31.1
Q ss_pred CCceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhh
Q 025608 39 SRSFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQ 80 (250)
Q Consensus 39 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~ 80 (250)
...+.|.||-.+.-..+.|++.+ .-++.-+|+..-....+.
T Consensus 4 lkewkC~VCg~~iieGqkFTF~~-kGsVH~eCl~~s~~~k~~ 44 (103)
T COG4847 4 LKEWKCYVCGGTIIEGQKFTFTK-KGSVHYECLAESKRKKPG 44 (103)
T ss_pred cceeeEeeeCCEeeeccEEEEee-CCcchHHHHHHHHhcCcC
Confidence 45689999999987667677666 667788999877665544
No 358
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=23.21 E-value=45 Score=20.96 Aligned_cols=37 Identities=22% Similarity=0.549 Sum_probs=25.8
Q ss_pred cCCCCCCCCceecCccCccCcccCCcccchhccccCccc
Q 025608 130 YCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKVAW 168 (250)
Q Consensus 130 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~ 168 (250)
.|| -|....-....+..+.-.|..|+...|..|+-..
T Consensus 4 ~CP--lCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFNP 40 (61)
T PF05715_consen 4 LCP--LCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFNP 40 (61)
T ss_pred cCC--cccchhhcCCCCCCCccHHHHHhhhhhcccCCCC
Confidence 466 6665554443344566789999999999998743
No 359
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=23.20 E-value=1.1e+02 Score=26.82 Aligned_cols=36 Identities=22% Similarity=0.565 Sum_probs=24.5
Q ss_pred CcchHHHHHHHHHHHhhcC------cccccCCCCCCCCCCCHHH
Q 025608 64 HMYCVDCTVKYVDSKLQEN------VTSIGCPVTDCGGSLEPEY 101 (250)
Q Consensus 64 H~fC~~Cl~~~~~~~i~~~------~~~i~CP~~~C~~~l~~~~ 101 (250)
-.-|.+|+.+|+.+.-++. .....||. |...+-..+
T Consensus 313 PmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPt--CRa~FCilD 354 (358)
T PF10272_consen 313 PMWCLECMGKWFASRQDQQHPETWLSGKCPCPT--CRAKFCILD 354 (358)
T ss_pred chHHHHHHHHHhhhcCCCCChhhhhcCCCCCCC--Ccccceeee
Confidence 3359999999999775442 13557776 887765443
No 360
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=23.01 E-value=72 Score=20.08 Aligned_cols=29 Identities=28% Similarity=0.620 Sum_probs=19.8
Q ss_pred cCCCCCCCCceecCccCccCcccCCcccch
Q 025608 130 YCPFKDCSALLIDDAGEAIRESECPNCHRL 159 (250)
Q Consensus 130 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 159 (250)
.|...+|.++++.+-... ..-.||.|+..
T Consensus 20 ~Ct~e~C~gWmR~nFs~~-~~p~CPlC~s~ 48 (59)
T PF14169_consen 20 ECTSEDCNGWMRDNFSFE-EEPVCPLCKSP 48 (59)
T ss_pred EeCCCCCCcccccccccC-CCccCCCcCCc
Confidence 799999999999873221 22457776643
No 361
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=22.46 E-value=1.8e+02 Score=20.53 Aligned_cols=28 Identities=18% Similarity=0.456 Sum_probs=21.7
Q ss_pred CCcchHHHHHHHHHHHhhc--CcccccCCC
Q 025608 63 SHMYCVDCTVKYVDSKLQE--NVTSIGCPV 90 (250)
Q Consensus 63 ~H~fC~~Cl~~~~~~~i~~--~~~~i~CP~ 90 (250)
.-.||.+||.......+.+ ....-.||.
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~ 66 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPK 66 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCC
Confidence 6779999999988876655 245678997
No 362
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=22.40 E-value=78 Score=24.45 Aligned_cols=14 Identities=29% Similarity=0.546 Sum_probs=10.6
Q ss_pred eecCCCCCCCCceecC
Q 025608 128 KFYCPFKDCSALLIDD 143 (250)
Q Consensus 128 ~~~Cp~~~C~~~~~~~ 143 (250)
...|| .|++.+...
T Consensus 97 ~~RCp--~CN~~L~~v 110 (165)
T COG1656 97 FSRCP--ECNGELEKV 110 (165)
T ss_pred cccCc--ccCCEeccC
Confidence 45899 999877754
No 363
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=22.37 E-value=17 Score=29.60 Aligned_cols=25 Identities=28% Similarity=0.672 Sum_probs=18.2
Q ss_pred ccCCCCCcceeccCCCcceEEecccccccccccccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLS 237 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~ 237 (250)
..|+.|+..+.+.++ +|+.|+.+..
T Consensus 25 ~~C~~C~~~~~~~~~-----------~C~~C~~~l~ 49 (225)
T COG1040 25 GLCSGCQADLPLIGN-----------LCPLCGLPLS 49 (225)
T ss_pred CcChhhhhchhHHHh-----------hhHhhhChhc
Confidence 578888888877665 6777777764
No 364
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=22.30 E-value=51 Score=24.51 Aligned_cols=28 Identities=29% Similarity=0.725 Sum_probs=20.7
Q ss_pred CCccCCCCCc---ceeccCCCcceEE-ecccc
Q 025608 200 KWNRCPNCKF---YVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 200 ~~~~CP~C~~---~i~k~~GCnhm~C-~C~~~ 227 (250)
....||.|+. .+.|.+.=..+.| .||+.
T Consensus 96 ~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 96 KYVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred heEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 3589999998 4556655556789 89875
No 365
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=22.25 E-value=56 Score=24.47 Aligned_cols=28 Identities=25% Similarity=0.679 Sum_probs=21.1
Q ss_pred CCccCCCCCc---ceeccCCCcceEE-ecccc
Q 025608 200 KWNRCPNCKF---YVEKKDGCSYIRC-RCGHA 227 (250)
Q Consensus 200 ~~~~CP~C~~---~i~k~~GCnhm~C-~C~~~ 227 (250)
....||.|+. .+.|.+.=-.+.| .||..
T Consensus 101 ~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 101 EYVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred hcEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 3589999998 4666666556889 89875
No 366
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=22.24 E-value=19 Score=30.61 Aligned_cols=46 Identities=26% Similarity=0.617 Sum_probs=33.7
Q ss_pred ccCCCCCcceeccC--------CCcceEE-eccccccccccccccCCCCCcCCCCCC
Q 025608 202 NRCPNCKFYVEKKD--------GCSYIRC-RCGHAFCYHCGVQLSTVSHGYYCPSCN 249 (250)
Q Consensus 202 ~~CP~C~~~i~k~~--------GCnhm~C-~C~~~FC~~C~~~~~~~~h~~~~~~~~ 249 (250)
-.|-.|.-+..|.. .=....| .|+.+||-.|-.=++..-|+ ||.|.
T Consensus 363 ~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~--C~gCe 417 (421)
T COG5151 363 THCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLHF--CIGCE 417 (421)
T ss_pred ccceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHHHhh--CCCCc
Confidence 44777777444331 2345789 99999999999888777888 88884
No 367
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=22.22 E-value=1.1e+02 Score=21.62 Aligned_cols=40 Identities=18% Similarity=0.297 Sum_probs=30.6
Q ss_pred ceecccCcccccCCCceecCCCCCcchHHHHHHHHHHHhhc
Q 025608 41 SFVCEICVETKLRNESFSIKGCSHMYCVDCTVKYVDSKLQE 81 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 81 (250)
.+.|.||-+++-..+.|++.+= -.+..+||..-+...+..
T Consensus 2 kWkC~iCg~~I~~gqlFTF~~k-G~VH~~C~~~~~~~k~~~ 41 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQLFTFTKK-GPVHYECFREKASKKLYG 41 (101)
T ss_pred ceEEEecCCeeeecceEEEecC-CcEeHHHHHHHHhhhccc
Confidence 4789999999877777776443 667789999988866554
No 368
>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=22.17 E-value=82 Score=19.77 Aligned_cols=31 Identities=19% Similarity=0.427 Sum_probs=19.7
Q ss_pred cccCcccccCCCceecCCCCCcchHH----HHHHHHH
Q 025608 44 CEICVETKLRNESFSIKGCSHMYCVD----CTVKYVD 76 (250)
Q Consensus 44 C~iC~~~~~~~~~~~~~~C~H~fC~~----Cl~~~~~ 76 (250)
|..|... .+.+...+.|++.+|.+ -...+++
T Consensus 1 C~~C~~~--~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~ 35 (63)
T PF02148_consen 1 CSVCGST--NSNLWLCLTCGYVGCGRYSNGHALKHYK 35 (63)
T ss_dssp -SSSHTC--SSSEEEETTTS-EEETTTSTSHHHHHHH
T ss_pred CCCCCCc--CCceEEeCCCCcccccCCcCcHHHHhhc
Confidence 5666644 34556677899999886 6666666
No 369
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=21.92 E-value=58 Score=14.99 Aligned_cols=16 Identities=25% Similarity=0.609 Sum_probs=10.3
Q ss_pred hccccCcccCCCCCch
Q 025608 160 FCAQCKVAWHAGIECA 175 (250)
Q Consensus 160 ~C~~C~~~~H~~~~C~ 175 (250)
.|+.|++.-|....|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 4677777777665553
No 370
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=21.85 E-value=1.1e+02 Score=17.86 Aligned_cols=33 Identities=21% Similarity=0.583 Sum_probs=20.4
Q ss_pred ceecccCcccccCCCceecCCCCCc-chHHHHHH
Q 025608 41 SFVCEICVETKLRNESFSIKGCSHM-YCVDCTVK 73 (250)
Q Consensus 41 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~ 73 (250)
.+.|..|..+......+..+.|... +|.+|+..
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 3578899874323344666678755 89999987
No 371
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=21.84 E-value=55 Score=18.92 Aligned_cols=13 Identities=31% Similarity=0.743 Sum_probs=9.1
Q ss_pred ccCCCCCcceecc
Q 025608 202 NRCPNCKFYVEKK 214 (250)
Q Consensus 202 ~~CP~C~~~i~k~ 214 (250)
..||.||....+.
T Consensus 3 ~~Cp~Cg~~~~~~ 15 (47)
T PF14690_consen 3 PRCPHCGSPSVHR 15 (47)
T ss_pred ccCCCcCCCceEC
Confidence 4799999865443
No 372
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=21.46 E-value=60 Score=23.26 Aligned_cols=27 Identities=26% Similarity=0.802 Sum_probs=20.3
Q ss_pred CCccCCCCCc---ceeccCCCcceEE-eccc
Q 025608 200 KWNRCPNCKF---YVEKKDGCSYIRC-RCGH 226 (250)
Q Consensus 200 ~~~~CP~C~~---~i~k~~GCnhm~C-~C~~ 226 (250)
....||.|+. .+.|.++=-.+.| .||.
T Consensus 79 ~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 79 EYVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred hcEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 3589999998 4666666666788 8886
No 373
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=21.37 E-value=39 Score=28.61 Aligned_cols=10 Identities=20% Similarity=0.717 Sum_probs=5.6
Q ss_pred CCccCCCCCc
Q 025608 200 KWNRCPNCKF 209 (250)
Q Consensus 200 ~~~~CP~C~~ 209 (250)
.+..|.-|+.
T Consensus 196 R~L~Cs~C~t 205 (290)
T PF04216_consen 196 RYLHCSLCGT 205 (290)
T ss_dssp EEEEETTT--
T ss_pred EEEEcCCCCC
Confidence 4567777777
No 374
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=21.25 E-value=67 Score=22.85 Aligned_cols=28 Identities=25% Similarity=0.676 Sum_probs=16.0
Q ss_pred ecCCCCCCCCceecCcc--CccCcccCCcccc
Q 025608 129 FYCPFKDCSALLIDDAG--EAIRESECPNCHR 158 (250)
Q Consensus 129 ~~Cp~~~C~~~~~~~~~--~~~~~~~C~~C~~ 158 (250)
.+|+ .|++.+.+..+ +......|..|..
T Consensus 5 rfC~--eCNNmLYPkEDked~~L~laCrnCd~ 34 (113)
T KOG2691|consen 5 RFCR--ECNNMLYPKEDKEDRILLLACRNCDY 34 (113)
T ss_pred chhh--hhhccccccccccccEEEEEecCCcc
Confidence 3676 78877776533 3334455555543
No 375
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=21.23 E-value=83 Score=26.98 Aligned_cols=28 Identities=25% Similarity=0.440 Sum_probs=20.4
Q ss_pred CccCCCCCc-ceeccCCCcceEE-eccccc
Q 025608 201 WNRCPNCKF-YVEKKDGCSYIRC-RCGHAF 228 (250)
Q Consensus 201 ~~~CP~C~~-~i~k~~GCnhm~C-~C~~~F 228 (250)
...||.|+. .+..+..=..+.| .||...
T Consensus 11 ~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 11 KLVCPECGSDKLIYDYERGEIVCADCGLVI 40 (310)
T ss_pred CCcCcCCCCCCeeEECCCCeEeecccCCcc
Confidence 368999997 4544555567999 999844
No 376
>PLN02436 cellulose synthase A
Probab=21.19 E-value=70 Score=32.28 Aligned_cols=34 Identities=18% Similarity=0.396 Sum_probs=21.9
Q ss_pred cCCCCCCCCceecCccCccCcccCCcccchhccccCc
Q 025608 130 YCPFKDCSALLIDDAGEAIRESECPNCHRLFCAQCKV 166 (250)
Q Consensus 130 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 166 (250)
-|. =|+--+-.+. .....+.|..|+...|..|..
T Consensus 38 iCq--ICGD~Vg~t~-dGe~FVACn~C~fpvCr~Cye 71 (1094)
T PLN02436 38 TCQ--ICGDEIELTV-DGEPFVACNECAFPVCRPCYE 71 (1094)
T ss_pred ccc--ccccccCcCC-CCCEEEeeccCCCccccchhh
Confidence 455 4554433332 223669999999999988874
No 377
>PRK12496 hypothetical protein; Provisional
Probab=20.79 E-value=66 Score=24.81 Aligned_cols=27 Identities=22% Similarity=0.503 Sum_probs=15.9
Q ss_pred ccCCCCCcceeccCCCcceEEecccccccccccccc
Q 025608 202 NRCPNCKFYVEKKDGCSYIRCRCGHAFCYHCGVQLS 237 (250)
Q Consensus 202 ~~CP~C~~~i~k~~GCnhm~C~C~~~FC~~C~~~~~ 237 (250)
..||.|+.....+. ...||-.||.+++
T Consensus 128 ~~C~gC~~~~~~~~---------~~~~C~~CG~~~~ 154 (164)
T PRK12496 128 KVCKGCKKKYPEDY---------PDDVCEICGSPVK 154 (164)
T ss_pred EECCCCCccccCCC---------CCCcCCCCCChhh
Confidence 45888776553210 1256888887763
Done!