Query psy12127
Match_columns 263
No_of_seqs 237 out of 1237
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 19:23:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12127.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12127hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3002|consensus 100.0 3.7E-36 8.1E-41 274.9 12.4 222 15-245 43-285 (299)
2 PF03145 Sina: Seven in absent 99.9 7.3E-28 1.6E-32 209.0 2.3 155 67-227 1-167 (198)
3 cd03829 Sina Seven in absentia 99.5 7E-16 1.5E-20 122.8 -0.9 93 137-235 1-101 (127)
4 KOG0297|consensus 99.4 8.2E-13 1.8E-17 125.9 6.6 118 15-136 16-139 (391)
5 PF14835 zf-RING_6: zf-RING of 98.8 2.1E-09 4.6E-14 76.7 1.8 61 15-76 2-65 (65)
6 PF15227 zf-C3HC4_4: zinc fing 98.5 4.6E-08 1E-12 64.6 1.0 34 23-58 1-42 (42)
7 smart00504 Ubox Modified RING 98.4 1.4E-07 3E-12 66.6 2.7 57 20-78 1-62 (63)
8 TIGR00599 rad18 DNA repair pro 98.4 9.9E-08 2.2E-12 91.0 1.9 64 14-79 20-88 (397)
9 KOG0320|consensus 98.3 1.2E-07 2.6E-12 80.4 0.6 51 13-63 124-178 (187)
10 PF13923 zf-C3HC4_2: Zinc fing 98.3 1.9E-07 4.1E-12 60.3 1.0 35 23-58 1-39 (39)
11 PLN03208 E3 ubiquitin-protein 98.3 2.2E-07 4.8E-12 80.3 1.3 45 17-63 15-79 (193)
12 KOG0287|consensus 98.2 1.3E-07 2.9E-12 87.2 -2.0 62 16-79 19-85 (442)
13 PF13920 zf-C3HC4_3: Zinc fing 98.2 5.9E-07 1.3E-11 61.1 0.9 42 20-63 2-48 (50)
14 KOG0823|consensus 98.1 7.4E-07 1.6E-11 78.6 1.0 45 17-63 44-95 (230)
15 PF02176 zf-TRAF: TRAF-type zi 98.1 1.2E-06 2.7E-11 61.3 2.0 52 77-130 6-60 (60)
16 PF14634 zf-RING_5: zinc-RING 98.0 1.2E-06 2.7E-11 58.1 0.6 38 22-60 1-44 (44)
17 PF04564 U-box: U-box domain; 97.9 5.1E-06 1.1E-10 61.1 2.3 60 18-79 2-67 (73)
18 PF13639 zf-RING_2: Ring finge 97.9 2.4E-06 5.2E-11 56.4 0.5 37 22-59 2-44 (44)
19 PF00097 zf-C3HC4: Zinc finger 97.9 4.2E-06 9.1E-11 54.2 1.2 35 23-58 1-41 (41)
20 cd00162 RING RING-finger (Real 97.8 6.8E-06 1.5E-10 52.9 0.8 40 22-62 1-45 (45)
21 PHA02929 N1R/p28-like protein; 97.8 9.3E-06 2E-10 72.7 1.3 46 18-63 172-227 (238)
22 KOG0317|consensus 97.7 7.4E-06 1.6E-10 74.4 0.5 45 18-64 237-285 (293)
23 KOG2177|consensus 97.6 2.2E-05 4.7E-10 69.1 0.6 68 14-84 7-78 (386)
24 COG5432 RAD18 RING-finger-cont 97.5 1.8E-05 4E-10 72.0 -0.3 46 16-63 21-70 (391)
25 PHA02926 zinc finger-like prot 97.5 2.2E-05 4.7E-10 69.2 -0.2 45 17-63 167-230 (242)
26 TIGR00570 cdk7 CDK-activating 97.5 7E-05 1.5E-09 69.2 2.6 56 20-76 3-72 (309)
27 KOG2164|consensus 97.4 3.9E-05 8.4E-10 74.5 0.6 42 20-63 186-236 (513)
28 KOG0311|consensus 97.3 1.1E-05 2.5E-10 75.0 -3.9 68 11-79 34-108 (381)
29 KOG0978|consensus 97.3 5.7E-05 1.2E-09 76.3 -0.4 47 17-65 640-691 (698)
30 COG5574 PEX10 RING-finger-cont 97.2 8.9E-05 1.9E-09 66.7 0.3 44 18-63 213-262 (271)
31 PF13445 zf-RING_UBOX: RING-ty 97.1 0.0001 2.2E-09 48.9 0.0 27 23-52 1-31 (43)
32 smart00184 RING Ring finger. E 97.1 0.00015 3.2E-09 44.8 0.4 34 23-58 1-39 (39)
33 PLN03086 PRLI-interacting fact 96.7 0.0017 3.6E-08 64.8 4.6 31 90-122 483-514 (567)
34 COG5152 Uncharacterized conser 96.7 0.00044 9.6E-09 60.0 0.4 57 20-78 196-256 (259)
35 PF02176 zf-TRAF: TRAF-type zi 96.5 0.0016 3.5E-08 45.3 1.9 47 102-148 1-53 (60)
36 PF12678 zf-rbx1: RING-H2 zinc 96.4 0.0016 3.5E-08 47.8 1.5 38 22-59 21-73 (73)
37 KOG4159|consensus 96.3 0.0011 2.4E-08 63.5 0.0 48 14-63 78-129 (398)
38 KOG2660|consensus 96.2 0.0012 2.5E-08 61.3 -0.3 64 15-79 10-82 (331)
39 KOG1813|consensus 96.1 0.0033 7.2E-08 57.6 2.4 41 21-63 242-286 (313)
40 COG5222 Uncharacterized conser 96.0 0.0023 5E-08 58.8 0.9 57 21-78 275-338 (427)
41 PLN03086 PRLI-interacting fact 95.6 0.0044 9.6E-08 61.9 0.8 51 77-131 404-454 (567)
42 KOG2879|consensus 95.5 0.0083 1.8E-07 54.5 2.4 49 14-63 233-287 (298)
43 PF11789 zf-Nse: Zinc-finger o 95.1 0.0056 1.2E-07 43.0 0.0 34 18-52 9-42 (57)
44 PF07800 DUF1644: Protein of u 94.7 0.039 8.5E-07 46.4 3.9 28 109-136 106-133 (162)
45 KOG0824|consensus 94.6 0.017 3.7E-07 53.1 1.6 42 21-64 8-54 (324)
46 PF07975 C1_4: TFIIH C1-like d 94.3 0.025 5.4E-07 38.9 1.5 37 23-59 2-50 (51)
47 KOG4172|consensus 94.2 0.0059 1.3E-07 42.5 -1.7 41 21-63 8-54 (62)
48 PF14570 zf-RING_4: RING/Ubox 93.8 0.022 4.7E-07 38.7 0.5 39 23-62 1-47 (48)
49 KOG0802|consensus 93.1 0.023 5E-07 56.7 -0.4 44 17-62 288-340 (543)
50 PF14447 Prok-RING_4: Prokaryo 92.8 0.099 2.2E-06 36.4 2.5 43 19-63 6-50 (55)
51 PF11793 FANCL_C: FANCL C-term 92.8 0.032 6.9E-07 40.6 0.0 44 20-63 2-66 (70)
52 KOG4739|consensus 92.7 0.06 1.3E-06 48.1 1.6 44 19-63 2-48 (233)
53 KOG4275|consensus 92.4 0.021 4.5E-07 52.5 -1.6 42 20-63 300-342 (350)
54 KOG1002|consensus 92.2 0.048 1E-06 53.8 0.5 48 14-63 530-586 (791)
55 PF07191 zinc-ribbons_6: zinc- 92.0 0.065 1.4E-06 39.2 0.9 38 20-63 1-41 (70)
56 PF10571 UPF0547: Uncharacteri 91.9 0.076 1.7E-06 31.4 1.0 23 22-44 2-24 (26)
57 PF12861 zf-Apc11: Anaphase-pr 91.6 0.085 1.8E-06 40.0 1.1 53 8-63 22-82 (85)
58 PF05290 Baculo_IE-1: Baculovi 88.3 0.19 4E-06 41.2 0.6 46 19-64 79-133 (140)
59 COG5219 Uncharacterized conser 88.0 0.11 2.3E-06 54.6 -1.1 51 13-63 1462-1523(1525)
60 KOG4265|consensus 87.7 0.19 4E-06 47.4 0.3 44 18-63 288-336 (349)
61 PF04641 Rtf2: Rtf2 RING-finge 87.4 0.41 8.8E-06 43.4 2.4 49 15-64 108-162 (260)
62 COG5175 MOT2 Transcriptional r 87.2 0.19 4.1E-06 47.3 0.1 40 23-63 17-64 (480)
63 KOG4367|consensus 86.8 0.18 3.9E-06 48.8 -0.3 33 17-51 1-33 (699)
64 COG5236 Uncharacterized conser 86.2 0.21 4.5E-06 47.1 -0.2 48 14-63 55-108 (493)
65 PF05605 zf-Di19: Drought indu 86.1 0.62 1.3E-05 31.9 2.2 49 81-136 3-54 (54)
66 PRK04023 DNA polymerase II lar 85.9 0.61 1.3E-05 49.5 3.0 44 19-64 625-675 (1121)
67 KOG1039|consensus 85.9 0.31 6.8E-06 46.1 0.9 46 18-63 159-221 (344)
68 KOG1571|consensus 85.9 0.31 6.8E-06 46.0 0.8 48 14-63 299-347 (355)
69 TIGR00622 ssl1 transcription f 85.6 0.59 1.3E-05 37.3 2.1 38 22-59 57-110 (112)
70 KOG1785|consensus 85.2 0.22 4.8E-06 47.7 -0.5 40 22-63 371-416 (563)
71 PF14319 Zn_Tnp_IS91: Transpos 84.0 0.9 1.9E-05 36.0 2.6 60 17-86 27-88 (111)
72 COG5540 RING-finger-containing 84.0 0.43 9.3E-06 44.3 0.8 44 20-63 323-372 (374)
73 KOG4185|consensus 83.6 0.71 1.5E-05 42.2 2.1 58 20-79 3-77 (296)
74 PF14446 Prok-RING_1: Prokaryo 83.4 0.55 1.2E-05 32.6 0.9 42 21-62 6-51 (54)
75 KOG1645|consensus 82.9 0.4 8.6E-06 46.1 0.1 44 20-63 4-56 (463)
76 KOG3039|consensus 82.5 0.67 1.5E-05 41.9 1.4 44 19-63 220-270 (303)
77 PF01363 FYVE: FYVE zinc finge 81.2 0.9 1.9E-05 32.3 1.4 33 19-51 8-42 (69)
78 KOG0804|consensus 80.6 0.58 1.3E-05 45.5 0.3 49 14-62 169-221 (493)
79 KOG0825|consensus 80.0 0.32 6.8E-06 50.3 -1.7 43 21-63 124-171 (1134)
80 PF13913 zf-C2HC_2: zinc-finge 79.0 0.99 2.1E-05 26.2 0.9 23 81-107 3-25 (25)
81 KOG2462|consensus 78.8 3.1 6.6E-05 38.2 4.3 24 109-134 214-238 (279)
82 PF13909 zf-H2C2_5: C2H2-type 78.0 1.4 3.1E-05 24.7 1.3 24 111-136 1-24 (24)
83 cd00065 FYVE FYVE domain; Zinc 77.8 1.1 2.5E-05 30.4 1.0 30 22-51 4-35 (57)
84 KOG1812|consensus 77.3 0.72 1.6E-05 44.3 -0.1 33 20-52 146-180 (384)
85 smart00064 FYVE Protein presen 76.7 1.3 2.9E-05 31.3 1.2 32 20-51 10-43 (68)
86 PRK14714 DNA polymerase II lar 76.5 2.3 4.9E-05 46.4 3.2 43 20-64 667-721 (1337)
87 PRK14890 putative Zn-ribbon RN 76.0 2.2 4.9E-05 30.1 2.1 38 22-59 9-55 (59)
88 KOG3800|consensus 75.3 1 2.2E-05 41.5 0.3 42 22-63 2-51 (300)
89 smart00647 IBR In Between Ring 74.4 2 4.3E-05 29.5 1.6 20 33-52 39-58 (64)
90 PF03604 DNA_RNApol_7kD: DNA d 72.2 3.3 7.2E-05 25.6 2.0 22 22-44 2-27 (32)
91 KOG2807|consensus 71.7 2 4.3E-05 40.3 1.3 37 23-59 333-374 (378)
92 KOG4692|consensus 70.2 1.3 2.7E-05 42.1 -0.4 43 19-63 421-467 (489)
93 PF13717 zinc_ribbon_4: zinc-r 70.0 3.3 7.1E-05 26.1 1.6 11 21-31 3-13 (36)
94 PF13240 zinc_ribbon_2: zinc-r 69.5 2.2 4.9E-05 24.3 0.7 20 23-42 2-21 (23)
95 PF02891 zf-MIZ: MIZ/SP-RING z 69.1 1.5 3.3E-05 29.7 -0.1 41 20-61 2-50 (50)
96 KOG3161|consensus 68.4 1.1 2.4E-05 45.4 -1.2 59 17-77 8-77 (861)
97 KOG1001|consensus 67.9 1.3 2.9E-05 45.5 -0.7 40 21-63 455-500 (674)
98 PF13719 zinc_ribbon_5: zinc-r 67.7 3.6 7.7E-05 26.0 1.5 13 21-33 3-15 (37)
99 COG2888 Predicted Zn-ribbon RN 67.3 5.3 0.00011 28.3 2.3 13 109-123 49-61 (61)
100 PF14445 Prok-RING_2: Prokaryo 66.4 0.49 1.1E-05 32.4 -2.8 45 19-63 6-52 (57)
101 KOG2231|consensus 66.4 3.3 7.1E-05 42.5 1.7 40 22-63 2-52 (669)
102 PF01485 IBR: IBR domain; Int 66.1 4.3 9.4E-05 27.7 1.8 32 21-52 19-58 (64)
103 PF14569 zf-UDP: Zinc-binding 64.3 2.8 6.1E-05 31.3 0.5 43 21-63 10-62 (80)
104 PF02318 FYVE_2: FYVE-type zin 64.0 4.5 9.8E-05 32.2 1.7 42 19-60 53-102 (118)
105 TIGR02098 MJ0042_CXXC MJ0042 f 63.0 5.2 0.00011 25.0 1.6 13 21-33 3-15 (38)
106 PF05605 zf-Di19: Drought indu 62.9 6.8 0.00015 26.6 2.2 25 111-137 3-27 (54)
107 PF04606 Ogr_Delta: Ogr/Delta- 62.3 5.2 0.00011 26.6 1.5 39 54-96 1-39 (47)
108 KOG2462|consensus 62.2 4.3 9.3E-05 37.2 1.5 101 18-136 159-268 (279)
109 PF01428 zf-AN1: AN1-like Zinc 62.0 4.8 0.0001 26.2 1.3 28 23-51 1-30 (43)
110 smart00661 RPOL9 RNA polymeras 61.2 5.2 0.00011 26.6 1.4 11 23-33 3-13 (52)
111 KOG2817|consensus 61.0 3.2 6.9E-05 39.8 0.4 43 17-61 331-383 (394)
112 KOG2932|consensus 60.4 3.1 6.8E-05 38.8 0.2 75 20-103 90-167 (389)
113 PF10235 Cript: Microtubule-as 60.4 4.8 0.0001 30.9 1.2 35 22-63 46-80 (90)
114 PF06906 DUF1272: Protein of u 60.3 5.3 0.00011 28.0 1.3 41 22-63 7-52 (57)
115 PF07295 DUF1451: Protein of u 59.9 6.9 0.00015 32.6 2.2 34 29-62 107-140 (146)
116 KOG4628|consensus 59.4 6.4 0.00014 37.4 2.1 42 21-63 230-278 (348)
117 PF10367 Vps39_2: Vacuolar sor 59.1 5.8 0.00013 30.0 1.5 35 17-51 75-109 (109)
118 COG5194 APC11 Component of SCF 58.8 3 6.6E-05 31.3 -0.1 52 9-63 22-81 (88)
119 smart00154 ZnF_AN1 AN1-like Zi 57.9 6.1 0.00013 25.4 1.2 24 23-47 1-25 (39)
120 PRK11088 rrmA 23S rRNA methylt 57.6 4.8 0.0001 36.2 0.9 24 20-44 2-27 (272)
121 COG5243 HRD1 HRD ubiquitin lig 57.4 4 8.6E-05 39.1 0.4 60 3-62 268-344 (491)
122 KOG1814|consensus 57.1 3.7 8.1E-05 39.6 0.2 106 15-123 179-322 (445)
123 PRK14892 putative transcriptio 56.5 7.7 0.00017 30.2 1.8 34 15-50 16-50 (99)
124 PF03966 Trm112p: Trm112p-like 56.2 8 0.00017 27.6 1.7 15 16-30 3-17 (68)
125 KOG0826|consensus 56.1 3.5 7.7E-05 38.7 -0.2 44 18-62 298-345 (357)
126 smart00659 RPOLCX RNA polymera 55.5 9 0.00019 25.3 1.8 9 54-62 21-29 (44)
127 KOG4362|consensus 54.8 2.4 5.2E-05 43.5 -1.6 52 10-63 11-69 (684)
128 KOG3039|consensus 54.3 6.2 0.00013 35.8 1.1 35 15-51 38-72 (303)
129 PRK14559 putative protein seri 54.3 8.3 0.00018 39.6 2.1 49 9-63 3-52 (645)
130 COG5220 TFB3 Cdk activating ki 53.9 1.8 3.9E-05 39.0 -2.3 56 21-76 11-82 (314)
131 PF09723 Zn-ribbon_8: Zinc rib 52.7 11 0.00023 24.5 1.8 26 35-60 6-34 (42)
132 PF05253 zf-U11-48K: U11-48K-l 52.4 6.7 0.00014 23.1 0.7 24 81-107 3-26 (27)
133 PRK14714 DNA polymerase II lar 52.3 8.8 0.00019 42.1 2.0 43 8-52 668-719 (1337)
134 COG3357 Predicted transcriptio 51.8 8.4 0.00018 29.7 1.3 31 30-62 56-86 (97)
135 KOG3002|consensus 51.5 5.7 0.00012 37.0 0.4 77 53-133 49-131 (299)
136 PF06221 zf-C2HC5: Putative zi 51.3 8.8 0.00019 26.9 1.3 28 34-63 18-46 (57)
137 PHA00626 hypothetical protein 51.1 10 0.00022 26.6 1.5 7 54-60 25-31 (59)
138 PF08209 Sgf11: Sgf11 (transcr 50.5 7.8 0.00017 24.2 0.8 25 79-107 3-27 (33)
139 COG3813 Uncharacterized protei 50.2 7.5 0.00016 28.7 0.8 28 35-63 23-52 (84)
140 COG3809 Uncharacterized protei 50.1 12 0.00027 28.0 1.9 45 21-81 2-46 (88)
141 PRK00398 rpoP DNA-directed RNA 50.1 4.8 0.0001 26.5 -0.2 10 54-63 23-32 (46)
142 PF03833 PolC_DP2: DNA polymer 49.3 5.6 0.00012 41.8 0.0 44 19-64 654-704 (900)
143 PF13248 zf-ribbon_3: zinc-rib 48.4 8 0.00017 22.4 0.6 7 22-28 4-10 (26)
144 PF10217 DUF2039: Uncharacteri 46.8 6.7 0.00015 30.2 0.1 26 36-61 57-90 (92)
145 PF10083 DUF2321: Uncharacteri 46.6 5.9 0.00013 33.4 -0.3 21 43-63 29-50 (158)
146 cd00729 rubredoxin_SM Rubredox 46.4 15 0.00032 22.8 1.6 9 53-61 19-27 (34)
147 PRK11032 hypothetical protein; 45.8 15 0.00033 31.1 2.1 30 32-61 122-151 (160)
148 PF10426 zf-RAG1: Recombinatio 45.5 13 0.00028 22.7 1.2 23 111-133 3-25 (30)
149 smart00301 DM Doublesex DNA-bi 45.3 12 0.00027 25.9 1.2 40 90-131 8-47 (54)
150 PF13894 zf-C2H2_4: C2H2-type 44.9 19 0.00041 19.1 1.8 22 112-135 2-24 (24)
151 PF09845 DUF2072: Zn-ribbon co 44.4 11 0.00025 30.8 1.1 28 35-62 2-29 (131)
152 COG3364 Zn-ribbon containing p 44.4 8.9 0.00019 30.1 0.5 26 35-61 3-29 (112)
153 KOG3608|consensus 43.9 17 0.00037 34.7 2.3 114 18-136 205-346 (467)
154 PF13453 zf-TFIIB: Transcripti 43.0 15 0.00032 23.5 1.3 20 54-77 21-40 (41)
155 PF07191 zinc-ribbons_6: zinc- 42.9 11 0.00023 27.6 0.7 39 8-50 18-58 (70)
156 PRK14559 putative protein seri 42.1 16 0.00035 37.6 2.0 21 42-62 15-37 (645)
157 PF03107 C1_2: C1 domain; Int 41.0 20 0.00044 21.4 1.6 28 21-48 1-29 (30)
158 PF14353 CpXC: CpXC protein 40.4 14 0.00031 29.4 1.1 10 54-63 40-49 (128)
159 KOG1100|consensus 40.3 16 0.00034 32.2 1.4 39 23-63 161-200 (207)
160 PRK11827 hypothetical protein; 40.1 14 0.0003 26.2 0.9 33 14-50 2-34 (60)
161 PRK09678 DNA-binding transcrip 40.0 13 0.00028 27.3 0.7 45 54-102 3-47 (72)
162 PTZ00303 phosphatidylinositol 39.9 15 0.00033 38.5 1.4 31 21-51 461-498 (1374)
163 PRK00420 hypothetical protein; 39.4 17 0.00037 29.0 1.4 25 21-50 24-48 (112)
164 PF06677 Auto_anti-p27: Sjogre 39.2 19 0.00041 23.5 1.3 22 22-48 19-40 (41)
165 PF05458 Siva: Cd27 binding pr 39.1 16 0.00034 31.4 1.2 31 19-49 123-154 (175)
166 PF02148 zf-UBP: Zn-finger in 39.0 17 0.00038 25.4 1.2 24 23-47 1-24 (63)
167 PF07649 C1_3: C1-like domain; 37.8 12 0.00026 22.2 0.2 27 22-48 2-29 (30)
168 PF13901 DUF4206: Domain of un 37.4 22 0.00048 30.9 1.9 41 19-60 151-197 (202)
169 PLN02189 cellulose synthase 37.1 19 0.0004 38.9 1.6 42 22-63 36-87 (1040)
170 PF12773 DZR: Double zinc ribb 36.6 24 0.00053 23.2 1.6 12 20-31 12-23 (50)
171 COG1198 PriA Primosomal protei 36.4 23 0.00049 37.0 2.1 36 22-61 446-484 (730)
172 COG4306 Uncharacterized protei 36.3 14 0.00031 30.2 0.5 20 44-63 30-50 (160)
173 PF04438 zf-HIT: HIT zinc fing 36.2 27 0.00059 21.1 1.6 22 22-46 4-25 (30)
174 PLN02436 cellulose synthase A 35.8 20 0.00044 38.8 1.6 42 22-63 38-89 (1094)
175 TIGR01562 FdhE formate dehydro 35.7 26 0.00056 32.7 2.2 41 19-60 183-232 (305)
176 PF04216 FdhE: Protein involve 35.6 18 0.00039 33.1 1.1 42 20-62 172-221 (290)
177 COG1645 Uncharacterized Zn-fin 35.5 18 0.0004 29.6 1.0 23 21-49 29-51 (131)
178 PF00412 LIM: LIM domain; Int 35.1 18 0.0004 24.1 0.8 32 18-50 24-55 (58)
179 PF09538 FYDLN_acid: Protein o 35.1 22 0.00047 28.1 1.3 21 43-63 10-37 (108)
180 cd00350 rubredoxin_like Rubred 35.1 27 0.00058 21.3 1.5 8 54-61 19-26 (33)
181 PF09297 zf-NADH-PPase: NADH p 34.9 22 0.00048 21.4 1.1 10 42-51 3-12 (32)
182 PF12172 DUF35_N: Rubredoxin-l 34.6 20 0.00042 22.3 0.8 22 20-41 11-32 (37)
183 KOG1428|consensus 34.1 16 0.00034 41.1 0.5 42 21-63 3487-3544(3738)
184 KOG0828|consensus 34.0 11 0.00024 37.4 -0.6 48 16-63 567-634 (636)
185 TIGR00595 priA primosomal prot 33.8 36 0.00077 33.8 2.9 21 41-61 239-262 (505)
186 COG5151 SSL1 RNA polymerase II 33.2 16 0.00034 34.4 0.3 39 22-60 364-418 (421)
187 KOG4218|consensus 32.7 21 0.00046 34.0 1.0 6 54-59 69-74 (475)
188 PRK05580 primosome assembly pr 32.0 32 0.00069 35.5 2.3 37 21-61 391-430 (679)
189 TIGR00416 sms DNA repair prote 31.7 22 0.00047 34.9 1.0 24 32-60 5-29 (454)
190 cd02249 ZZ Zinc finger, ZZ typ 31.6 23 0.00049 23.2 0.8 31 21-51 1-32 (46)
191 PRK11823 DNA repair protein Ra 31.4 24 0.00052 34.5 1.3 25 32-60 5-29 (446)
192 cd02340 ZZ_NBR1_like Zinc fing 30.9 26 0.00056 22.9 1.0 30 22-51 2-32 (43)
193 TIGR00595 priA primosomal prot 30.9 36 0.00077 33.8 2.4 34 8-42 223-261 (505)
194 KOG3362|consensus 30.6 18 0.00039 30.1 0.2 40 9-52 108-148 (156)
195 KOG3268|consensus 30.3 17 0.00036 31.5 -0.0 44 20-63 165-228 (234)
196 PLN02638 cellulose synthase A 30.2 29 0.00064 37.6 1.7 41 22-62 19-69 (1079)
197 KOG1734|consensus 30.0 12 0.00026 34.5 -1.0 43 20-63 224-281 (328)
198 PLN02400 cellulose synthase 29.9 31 0.00067 37.5 1.8 42 22-63 38-89 (1085)
199 smart00734 ZnF_Rad18 Rad18-lik 29.4 23 0.0005 20.6 0.5 14 118-131 7-20 (26)
200 KOG2272|consensus 29.3 35 0.00076 31.2 1.8 43 19-63 162-206 (332)
201 PF12756 zf-C2H2_2: C2H2 type 29.0 42 0.0009 24.5 2.0 26 109-136 49-76 (100)
202 PF03145 Sina: Seven in absent 29.0 43 0.00094 28.6 2.3 46 58-105 24-69 (198)
203 PF01783 Ribosomal_L32p: Ribos 28.6 43 0.00094 23.1 1.8 22 19-41 25-46 (56)
204 COG1198 PriA Primosomal protei 28.5 38 0.00083 35.4 2.2 36 7-43 444-484 (730)
205 TIGR01206 lysW lysine biosynth 28.0 37 0.0008 23.5 1.4 13 21-33 3-15 (54)
206 KOG2114|consensus 27.9 27 0.00059 36.9 1.0 45 16-61 836-881 (933)
207 PF15616 TerY-C: TerY-C metal 27.8 37 0.0008 27.8 1.6 45 15-63 72-116 (131)
208 PRK12286 rpmF 50S ribosomal pr 27.8 44 0.00095 23.3 1.7 23 18-41 25-47 (57)
209 PRK04023 DNA polymerase II lar 27.8 35 0.00075 36.9 1.7 42 9-52 628-673 (1121)
210 PF11781 RRN7: RNA polymerase 27.1 30 0.00066 21.8 0.7 25 21-50 9-33 (36)
211 COG1326 Uncharacterized archae 26.9 30 0.00065 30.3 0.9 8 20-27 6-13 (201)
212 PF05502 Dynactin_p62: Dynacti 26.7 44 0.00095 33.2 2.2 49 8-63 14-63 (483)
213 PLN02195 cellulose synthase A 26.3 37 0.0008 36.6 1.6 42 22-63 8-59 (977)
214 PF09862 DUF2089: Protein of u 26.2 37 0.00081 27.1 1.3 20 23-42 1-20 (113)
215 TIGR01031 rpmF_bact ribosomal 25.5 50 0.0011 22.8 1.7 25 17-42 23-47 (55)
216 COG4357 Zinc finger domain con 25.4 38 0.00083 26.4 1.2 21 43-63 63-91 (105)
217 PF07282 OrfB_Zn_ribbon: Putat 25.3 43 0.00092 23.5 1.3 9 54-62 48-56 (69)
218 PF08271 TF_Zn_Ribbon: TFIIB z 25.2 42 0.00091 21.6 1.2 22 22-48 2-25 (43)
219 KOG0297|consensus 25.1 42 0.00091 32.3 1.7 49 79-132 113-162 (391)
220 cd01121 Sms Sms (bacterial rad 25.0 32 0.00069 32.9 0.8 22 35-60 1-22 (372)
221 PRK14873 primosome assembly pr 24.8 60 0.0013 33.6 2.8 38 20-61 392-431 (665)
222 COG5109 Uncharacterized conser 24.7 29 0.00063 32.7 0.5 35 16-52 332-369 (396)
223 KOG1729|consensus 24.1 25 0.00055 32.5 -0.0 33 19-51 167-202 (288)
224 PRK11595 DNA utilization prote 24.0 29 0.00062 30.6 0.3 22 9-30 7-30 (227)
225 PRK06266 transcription initiat 24.0 32 0.0007 29.4 0.6 26 54-79 138-165 (178)
226 smart00834 CxxC_CXXC_SSSS Puta 23.6 57 0.0012 20.2 1.6 10 53-62 27-36 (41)
227 PHA03376 BARF1; Provisional 23.5 5.2E+02 0.011 22.9 8.8 55 188-244 87-155 (221)
228 smart00290 ZnF_UBP Ubiquitin C 23.2 47 0.001 21.7 1.1 23 23-47 2-24 (50)
229 PLN02915 cellulose synthase A 23.2 44 0.00095 36.2 1.5 45 19-63 14-68 (1044)
230 COG1996 RPC10 DNA-directed RNA 22.6 56 0.0012 22.2 1.4 9 54-62 26-34 (49)
231 KOG0298|consensus 22.6 16 0.00035 40.1 -1.8 45 16-63 1149-1199(1394)
232 TIGR02300 FYDLN_acid conserved 22.6 51 0.0011 26.9 1.4 10 54-63 28-37 (129)
233 PF03854 zf-P11: P-11 zinc fin 22.2 21 0.00046 24.2 -0.7 40 22-64 4-47 (50)
234 PF14803 Nudix_N_2: Nudix N-te 21.6 47 0.001 20.7 0.8 10 23-32 3-12 (34)
235 COG1997 RPL43A Ribosomal prote 21.5 47 0.001 25.4 1.0 18 14-31 29-46 (89)
236 TIGR01384 TFS_arch transcripti 21.4 48 0.001 25.3 1.1 22 22-49 2-23 (104)
237 PHA00616 hypothetical protein 21.2 45 0.00097 22.2 0.7 25 110-136 1-26 (44)
238 COG0675 Transposase and inacti 20.6 53 0.0011 29.5 1.3 22 36-63 311-333 (364)
239 PF12660 zf-TFIIIC: Putative z 20.3 45 0.00097 25.8 0.7 39 22-62 16-65 (99)
240 COG1592 Rubrerythrin [Energy p 20.3 63 0.0014 27.5 1.6 25 34-61 134-158 (166)
241 PF00301 Rubredoxin: Rubredoxi 20.2 50 0.0011 22.1 0.8 16 14-29 28-43 (47)
242 PRK05580 primosome assembly pr 20.2 72 0.0016 33.0 2.3 37 6-43 389-430 (679)
243 PF12013 DUF3505: Protein of u 20.0 85 0.0018 24.2 2.2 27 108-136 9-35 (109)
No 1
>KOG3002|consensus
Probab=100.00 E-value=3.7e-36 Score=274.89 Aligned_cols=222 Identities=23% Similarity=0.456 Sum_probs=186.4
Q ss_pred hcCCceeeeccccCccccccccccCCCceecccccccc-CCCCCCccCCcccccccHHHHHhhhcceecCCCCCCCceee
Q psy12127 15 ELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL-LKCPFCRITIDYSWQRNVALERIFTKLELPCRNFRFGCKVY 93 (263)
Q Consensus 15 ~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l-~~CP~Cr~~~~~~~~rn~~le~~v~~l~v~C~~~~~GC~~~ 93 (263)
..+.++|+||||.+++.+||+||.+ ||+.|++|..++ ++||.||.+++ .+|+++||++++++.++|+|+..||++.
T Consensus 43 ~~~~~lleCPvC~~~l~~Pi~QC~n-GHlaCssC~~~~~~~CP~Cr~~~g--~~R~~amEkV~e~~~vpC~~~~~GC~~~ 119 (299)
T KOG3002|consen 43 LLDLDLLDCPVCFNPLSPPIFQCDN-GHLACSSCRTKVSNKCPTCRLPIG--NIRCRAMEKVAEAVLVPCKNAKLGCTKS 119 (299)
T ss_pred ccchhhccCchhhccCcccceecCC-CcEehhhhhhhhcccCCccccccc--cHHHHHHHHHHHhceecccccccCCcee
Confidence 3467899999999999999999999 999999999765 69999999999 8999999999999999999999999999
Q ss_pred eccchhhhhhcccCCceecCCCC--CCCCccChhhHHHHHhcccCc--ceeeCCeEEEeecccccccccCcccceeEEEE
Q psy12127 94 LPKAKRDKHEDKCKFRQLKCPMH--ACPWTNSVLHLSEHLNQVHHL--HLLKGNGVNIEISNFKTKVSESETKVHKYVIL 169 (263)
Q Consensus 94 ~~~~~~~~He~~C~~~~~~CP~~--~C~~~g~~~~L~~Hl~~~H~~--~~~~g~~~~~~i~nf~~~~n~~~~~~~~~~~l 169 (263)
++|.+..+||+.|.|+|+.||.+ .|+|.|..++|..|+...|+. ....+..+.+. +++.+ +.+..+|++.
T Consensus 120 ~~Y~~~~~HE~~C~f~~~~CP~p~~~C~~~G~~~~l~~H~~~~hk~~~~~~~~~~~~~~----~~~~~--~~~~~~~~~~ 193 (299)
T KOG3002|consen 120 FPYGEKSKHEKVCEFRPCSCPVPGAECKYTGSYKDLYAHLNDTHKSDIITLTGFDFVFV----ATDEN--LLGAATWTLK 193 (299)
T ss_pred eccccccccccccccCCcCCCCCcccCCccCcHHHHHHHHHhhChhhhhhccccceecc----cCCcc--ccccchhhee
Confidence 99999999999999999999997 999999999999999999994 44555555555 56666 6778899766
Q ss_pred Ee-ecCceEEEEEecc---C-CeEEEEEEeeeC----CCCceEEEEEEeeccccccCCceeeeeecceee-------eec
Q psy12127 170 MN-CYSQYFICKLCLY---K-KVLTMSFVQISN----SSPFHFGVFVNIASNFKSMKGIVPIHYACPELH-------ISC 233 (263)
Q Consensus 170 ~~-~~g~~F~l~~~~~---~-~~~~v~~v~~~~----~~~~~y~~~l~~~~~~~~~~g~~~~~~q~~~~~-------v~~ 233 (263)
+. ++|+.|++.++.+ + +.++|++.++++ +.+|.|++++....+..+|.|.+|+.-|+.... +-.
T Consensus 194 ~~~~~~~~~~~~~~~q~~~~~~~~y~tv~~i~~~~~e~~~fsy~L~~~~~~~klt~~s~~~s~~~kvs~~~p~~dfm~ip 273 (299)
T KOG3002|consen 194 TSVCFGREFGLLFEVQCFREPHGVYVTVNRIAPSAPEAGEFSYSLALGGSGRKLTWQSPPRSIIQKVSKVRPEDDFMLIP 273 (299)
T ss_pred eeecCcEEEeeeeeehhhcCCCceEEEeehhccCCCcccccceeeecCCCCceEeecCCcceeecccceeccCCCceecc
Confidence 66 8999999988653 2 369999999755 346889999876666678999988888877733 334
Q ss_pred ccCCCCCCCCCc
Q psy12127 234 DALVTPWKSQDN 245 (263)
Q Consensus 234 ~~l~~~~~~~~~ 245 (263)
.+|+.+++..+-
T Consensus 274 ~~~~~~~~~~~~ 285 (299)
T KOG3002|consen 274 RSLLCLFSLLKM 285 (299)
T ss_pred HHHhhcccccCC
Confidence 445666666554
No 2
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=99.94 E-value=7.3e-28 Score=208.98 Aligned_cols=155 Identities=21% Similarity=0.503 Sum_probs=101.5
Q ss_pred cccHHHHHhhhcceecCCCCCCCceeeeccchhhhhhcccCCceecCCC--CCCCCccChhhHHHHHhcccCcceeeCCe
Q psy12127 67 QRNVALERIFTKLELPCRNFRFGCKVYLPKAKRDKHEDKCKFRQLKCPM--HACPWTNSVLHLSEHLNQVHHLHLLKGNG 144 (263)
Q Consensus 67 ~rn~~le~~v~~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~~~~CP~--~~C~~~g~~~~L~~Hl~~~H~~~~~~g~~ 144 (263)
.||++||++++++++||+|+.+||++.+++.++.+||++|+|+|+.||. .+|+|.|+.++|..|+.+.|+..+..+..
T Consensus 1 iR~~alE~v~~~~~~pC~~~~~GC~~~~~~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~~~~~~ 80 (198)
T PF03145_consen 1 IRNRALEKVAESIKFPCKNAKYGCTETFPYSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNVTDNGT 80 (198)
T ss_dssp --------------EE-CCGGGT---EE-GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHHHTTTSEEEESS
T ss_pred CCcHHHHHHHhhceecCCCCCCCCcccccccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHHHCCCccccCcc
Confidence 4899999999999999999999999999999999999999999999999 89999999999999999999965555444
Q ss_pred --EEEeecccccccccCcccceeEEEEE-eecCceEEEEEecc---CCeEEEEEEee----eCCCCceEEEEEEeecccc
Q psy12127 145 --VNIEISNFKTKVSESETKVHKYVILM-NCYSQYFICKLCLY---KKVLTMSFVQI----SNSSPFHFGVFVNIASNFK 214 (263)
Q Consensus 145 --~~~~i~nf~~~~n~~~~~~~~~~~l~-~~~g~~F~l~~~~~---~~~~~v~~v~~----~~~~~~~y~~~l~~~~~~~ 214 (263)
+.+. ..+.+ ..+..+|++++ +++|++|+|++... +..+++++||+ +.++.|+|++++.+..+..
T Consensus 81 ~~~~f~----~~~~~--~~~~~~~~~~~~~~~~~~F~l~~~~~~~~~~~v~~~~v~~~G~~~~a~~f~Yel~~~~~~rkl 154 (198)
T PF03145_consen 81 FSISFL----HSDIN--SVESPDWVLVQFSCFGKLFLLYVQKFELEGNAVYFAVVCYIGPAEEASNFSYELEVRSNGRKL 154 (198)
T ss_dssp -EEEEE----ECTTT---SSSEEEEEEE-EETTEEEEEEEEEEEEETEEEEEEEEEESS-HHHHTTEEEEEEEEETTEEE
T ss_pred ceEEEe----eeccc--ccCCceEEEeecccCCccEEEEEEEEccCCceEEEEEEEEccCchhhhceEEEEEEecCCcEE
Confidence 3444 22233 34567899998 99999999997653 56788888885 3568999999998755555
Q ss_pred ccCCceeeeeecc
Q psy12127 215 SMKGIVPIHYACP 227 (263)
Q Consensus 215 ~~~g~~~~~~q~~ 227 (263)
.|++.++|..+..
T Consensus 155 ~~~~~p~si~~~~ 167 (198)
T PF03145_consen 155 TWQSFPRSIREDI 167 (198)
T ss_dssp EEEE--EETTT-S
T ss_pred EEEEcCcchhhhH
Confidence 6777665544443
No 3
>cd03829 Sina Seven in absentia (Sina) protein family, C-terminal substrate binding domain; composed of the Drosophila Sina protein, the mammalian Sina homolog (Siah), the plant protein SINAT5, and similar proteins. Sina, Siah and SINAT5 are RING-containing proteins that function as E3 ubiquitin ligases, acting either as single proteins or as a part of multiprotein complexes. Sina is expressed in many cells in the developing eye but is essential specifically for R7 photoreceptor cell development. Sina cooperates with Phyllopod (Phyl), Ebi and the E2 ubiquitin-conjugating enzyme Ubcd1 to catalyze the ubiquitination and subsequent degradation of Tramtrack (Ttk88); Ttk88 is a transcriptional repressor that blocks photoreceptor differentiation. Similarly, the mammalian homologue Siah1 cooperates with SIP (Siah-interacting protein), Ebi and the adaptor protein Skp1, to target beta-catenin for ubiquitination and degradation via a p53-dependent mechanism. SINAT5 targets NAC1 for ubiquitin-medi
Probab=99.53 E-value=7e-16 Score=122.75 Aligned_cols=93 Identities=14% Similarity=0.197 Sum_probs=78.0
Q ss_pred cceeeCCeEEEeecccccccccCcccceeEEEEEeecCceEEEEEeccCC----eEEEEEEee----eCCCCceEEEEEE
Q psy12127 137 LHLLKGNGVNIEISNFKTKVSESETKVHKYVILMNCYSQYFICKLCLYKK----VLTMSFVQI----SNSSPFHFGVFVN 208 (263)
Q Consensus 137 ~~~~~g~~~~~~i~nf~~~~n~~~~~~~~~~~l~~~~g~~F~l~~~~~~~----~~~v~~v~~----~~~~~~~y~~~l~ 208 (263)
+++.+|+.++|+ ++++| ++++++|+|||+|+|++|+|++|+++. ..++++++. ..|.+|.|++||.
T Consensus 1 v~~~~G~di~fl----~t~~~--~~~a~~w~mv~sCfG~~F~L~~Ek~~l~~~~~~y~A~~~~iG~~~eA~nf~Y~Lel~ 74 (127)
T cd03829 1 VTTLQGEDIVFL----ATDIN--LPGATDWVMMQSCFGHHFMLVLEKQELYEGHQQFFAFVQLIGTEKQAENFTYRLELN 74 (127)
T ss_pred CccccCccEEEE----ecCCC--CccceeeeehhhhcCceEEEEEehhhhcCCcHHHHHHHHHHcCHhHHhcceEEEEEc
Confidence 467899999998 88888 899999999999999999999998653 456666663 5689999999999
Q ss_pred eeccccccCCceeeeeecceeeeeccc
Q psy12127 209 IASNFKSMKGIVPIHYACPELHISCDA 235 (263)
Q Consensus 209 ~~~~~~~~~g~~~~~~q~~~~~v~~~~ 235 (263)
+++|...|+|.|||+.++-...+.+.|
T Consensus 75 ~n~RkL~we~~PRSIrds~~~~~~~~D 101 (127)
T cd03829 75 GNRRRLTWEATPRSIREGHASVIDNSD 101 (127)
T ss_pred CCCcEEEeecCCccHHHhhHHHhhcCc
Confidence 999999999999999887776654443
No 4
>KOG0297|consensus
Probab=99.36 E-value=8.2e-13 Score=125.90 Aligned_cols=118 Identities=27% Similarity=0.514 Sum_probs=104.1
Q ss_pred hcCCceeeeccccCccccccccccCCCceecccccccc----CCCCCCccCCccc--ccccHHHHHhhhcceecCCCCCC
Q psy12127 15 ELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITIDYS--WQRNVALERIFTKLELPCRNFRF 88 (263)
Q Consensus 15 ~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~~~--~~rn~~le~~v~~l~v~C~~~~~ 88 (263)
+.+++.+.||+|..++.+|+. -..|||.||..|+.++ ..||.|+..+..+ .....++.+++.++.+.|.++..
T Consensus 16 ~~~~~~l~C~~C~~vl~~p~~-~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~~~~~~~~~~~~l~i~c~~~~~ 94 (391)
T KOG0297|consen 16 RPLDENLLCPICMSVLRDPVQ-TTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELPVPRALRRELLKLPIRCIFASR 94 (391)
T ss_pred CCCcccccCccccccccCCCC-CCCCCCcccccccchhhccCcCCcccccccchhhccCchHHHHHHHHhcccccccCCC
Confidence 447888999999999999974 2468999999999985 3899999887653 22357889999999999999999
Q ss_pred CceeeeccchhhhhhcccCCceecCCCCCCCCccChhhHHHHHhcccC
Q psy12127 89 GCKVYLPKAKRDKHEDKCKFRQLKCPMHACPWTNSVLHLSEHLNQVHH 136 (263)
Q Consensus 89 GC~~~~~~~~~~~He~~C~~~~~~CP~~~C~~~g~~~~L~~Hl~~~H~ 136 (263)
||+|.+.+..+..|+..| .+.+||. +|+..+.++++.+|++..+.
T Consensus 95 GC~~~~~l~~~~~Hl~~c--~~~~C~~-~C~~~~~~~d~~~hl~~~C~ 139 (391)
T KOG0297|consen 95 GCRADLELEALQGHLSTC--DPLKCPH-RCGVQVPRDDLEDHLEAECP 139 (391)
T ss_pred CccccccHHHHHhHhccC--CcccCcc-ccccccchHHHHHHHhcccc
Confidence 999999999999999999 9999997 49999999999999988776
No 5
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.79 E-value=2.1e-09 Score=76.68 Aligned_cols=61 Identities=23% Similarity=0.588 Sum_probs=32.3
Q ss_pred hcCCceeeeccccCccccccccccCCCceecccccccc--CCCCCCccCCccc-ccccHHHHHhh
Q psy12127 15 ELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL--LKCPFCRITIDYS-WQRNVALERIF 76 (263)
Q Consensus 15 ~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l--~~CP~Cr~~~~~~-~~rn~~le~~v 76 (263)
+.|++.+.|++|.++|+.||.. ..|+|+||+.|+..- +.||+|..|.... ...|+.++.++
T Consensus 2 ~~le~lLrCs~C~~~l~~pv~l-~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~~~NrqLd~~i 65 (65)
T PF14835_consen 2 ERLEELLRCSICFDILKEPVCL-GGCEHIFCSSCIRDCIGSECPVCHTPAWIQDIQINRQLDSMI 65 (65)
T ss_dssp HHHHHTTS-SSS-S--SS-B----SSS--B-TTTGGGGTTTB-SSS--B-S-SS----HHHHHHH
T ss_pred hHHHHhcCCcHHHHHhcCCcee-ccCccHHHHHHhHHhcCCCCCCcCChHHHHHHHhhhhhhccC
Confidence 3567889999999999999854 679999999999883 5899999986422 44466666543
No 6
>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=4.6e-08 Score=64.57 Aligned_cols=34 Identities=38% Similarity=1.044 Sum_probs=26.4
Q ss_pred eccccCccccccccccCCCceecccccccc------C--CCCCC
Q psy12127 23 CGVCLEPLDRGITSCQTCGNLVCTSCAARL------L--KCPFC 58 (263)
Q Consensus 23 CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l------~--~CP~C 58 (263)
||||+++|++|+.. .|||+||.+|+.++ . .||.|
T Consensus 1 CpiC~~~~~~Pv~l--~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSL--PCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE---SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCcccc--CCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 89999999999864 69999999999884 1 58776
No 7
>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=98.43 E-value=1.4e-07 Score=66.64 Aligned_cols=57 Identities=14% Similarity=0.145 Sum_probs=47.0
Q ss_pred eeeeccccCccccccccccCCCceecccccccc----CCCCCCccCCccc-ccccHHHHHhhhc
Q psy12127 20 ISECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITIDYS-WQRNVALERIFTK 78 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~~~-~~rn~~le~~v~~ 78 (263)
.|.||||.++|.+|+.. .|||+||..|+.++ ..||.|+.+++.. ...+..+++.+++
T Consensus 1 ~~~Cpi~~~~~~~Pv~~--~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~~l~~~i~~ 62 (63)
T smart00504 1 EFLCPISLEVMKDPVIL--PSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKSAIQE 62 (63)
T ss_pred CcCCcCCCCcCCCCEEC--CCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCHHHHHHHHh
Confidence 37899999999999753 57999999999985 4899999998643 6678888887763
No 8
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.40 E-value=9.9e-08 Score=90.96 Aligned_cols=64 Identities=23% Similarity=0.524 Sum_probs=52.5
Q ss_pred hhcCCceeeeccccCccccccccccCCCceecccccccc----CCCCCCccCCccc-ccccHHHHHhhhcc
Q psy12127 14 KELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITIDYS-WQRNVALERIFTKL 79 (263)
Q Consensus 14 ~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~~~-~~rn~~le~~v~~l 79 (263)
-+.|.+.+.|+||.+++..|+. ..|||.||..|+..+ ..||.|+..+... ..+|..|+++++.+
T Consensus 20 l~~Le~~l~C~IC~d~~~~Pvi--tpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~ 88 (397)
T TIGR00599 20 LYPLDTSLRCHICKDFFDVPVL--TSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNWLVSEIVESF 88 (397)
T ss_pred ccccccccCCCcCchhhhCccC--CCCCCchhHHHHHHHHhCCCCCCCCCCccccccCccchHHHHHHHHH
Confidence 3678899999999999999985 479999999999874 3799999988643 55688888877653
No 9
>KOG0320|consensus
Probab=98.33 E-value=1.2e-07 Score=80.44 Aligned_cols=51 Identities=25% Similarity=0.669 Sum_probs=40.5
Q ss_pred chhcCCceeeeccccCccccccccccCCCceecccccccc----CCCCCCccCCc
Q psy12127 13 CKELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITID 63 (263)
Q Consensus 13 ~~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~ 63 (263)
....-.+.+.||||++....-+..-++|||+||+.|++.. .+||+|++.++
T Consensus 124 ~~~~~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 124 DPLRKEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred cccccccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 3344467799999999999654233679999999999884 48999999876
No 10
>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=98.31 E-value=1.9e-07 Score=60.32 Aligned_cols=35 Identities=34% Similarity=1.035 Sum_probs=27.9
Q ss_pred eccccCccccccccccCCCceecccccccc----CCCCCC
Q psy12127 23 CGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFC 58 (263)
Q Consensus 23 CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~C 58 (263)
||||++.+.+|+.. ..|||+||.+|+.++ .+||.|
T Consensus 1 C~iC~~~~~~~~~~-~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVV-TPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEE-CTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEE-CCCCCchhHHHHHHHHHCcCCCcCC
Confidence 89999999999544 569999999999885 378876
No 11
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.29 E-value=2.2e-07 Score=80.26 Aligned_cols=45 Identities=27% Similarity=0.810 Sum_probs=38.4
Q ss_pred CCceeeeccccCccccccccccCCCceecccccccc--------------------CCCCCCccCCc
Q psy12127 17 IASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL--------------------LKCPFCRITID 63 (263)
Q Consensus 17 l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l--------------------~~CP~Cr~~~~ 63 (263)
+.+.++||||++.+++|+. +.|||.||..|+.++ ..||.||.++.
T Consensus 15 ~~~~~~CpICld~~~dPVv--T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is 79 (193)
T PLN03208 15 SGGDFDCNICLDQVRDPVV--TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVS 79 (193)
T ss_pred CCCccCCccCCCcCCCcEE--cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCC
Confidence 4567999999999999975 479999999999753 26999999886
No 12
>KOG0287|consensus
Probab=98.21 E-value=1.3e-07 Score=87.23 Aligned_cols=62 Identities=26% Similarity=0.693 Sum_probs=50.6
Q ss_pred cCCceeeeccccCccccccccccCCCceecccccccc----CCCCCCccCCccc-ccccHHHHHhhhcc
Q psy12127 16 LIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITIDYS-WQRNVALERIFTKL 79 (263)
Q Consensus 16 ~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~~~-~~rn~~le~~v~~l 79 (263)
.|.+.|.|.||+++|+.|+. +.|||.||+-|+.+. ..||+|+.++... ...|+.++.+++++
T Consensus 19 ~lD~lLRC~IC~eyf~ip~i--tpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 19 TLDDLLRCGICFEYFNIPMI--TPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred hhHHHHHHhHHHHHhcCcee--ccccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHHHHH
Confidence 46789999999999999975 359999999999984 4899999988644 44467777777665
No 13
>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=98.16 E-value=5.9e-07 Score=61.06 Aligned_cols=42 Identities=43% Similarity=0.973 Sum_probs=35.1
Q ss_pred eeeeccccCccccccccccCCCce-ecccccccc----CCCCCCccCCc
Q psy12127 20 ISECGVCLEPLDRGITSCQTCGNL-VCTSCAARL----LKCPFCRITID 63 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC~~CGH~-~C~~C~~~l----~~CP~Cr~~~~ 63 (263)
...|+||++...++++. .|||. +|..|..++ ..||.||+++.
T Consensus 2 ~~~C~iC~~~~~~~~~~--pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDVVLL--PCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSEEEE--TTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCCceEEe--CCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 46899999999998764 69999 999999997 58999999875
No 14
>KOG0823|consensus
Probab=98.13 E-value=7.4e-07 Score=78.57 Aligned_cols=45 Identities=24% Similarity=0.781 Sum_probs=39.4
Q ss_pred CCceeeeccccCccccccccccCCCceecccccccc-------CCCCCCccCCc
Q psy12127 17 IASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL-------LKCPFCRITID 63 (263)
Q Consensus 17 l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l-------~~CP~Cr~~~~ 63 (263)
-...|+|.||++..++||.. .|||+||-.|+.+| ..||+|+..++
T Consensus 44 ~~~~FdCNICLd~akdPVvT--lCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs 95 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPVVT--LCGHLFCWPCLYQWLQTRPNSKECPVCKAEVS 95 (230)
T ss_pred CCCceeeeeeccccCCCEEe--ecccceehHHHHHHHhhcCCCeeCCccccccc
Confidence 45789999999999999874 59999999999996 26899999876
No 15
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=98.13 E-value=1.2e-06 Score=61.33 Aligned_cols=52 Identities=29% Similarity=0.574 Sum_probs=39.1
Q ss_pred hcceecCCCCCCCceeeeccchhhhhhc-ccCCceecCCC--CCCCCccChhhHHHH
Q psy12127 77 TKLELPCRNFRFGCKVYLPKAKRDKHED-KCKFRQLKCPM--HACPWTNSVLHLSEH 130 (263)
Q Consensus 77 ~~l~v~C~~~~~GC~~~~~~~~~~~He~-~C~~~~~~CP~--~~C~~~g~~~~L~~H 130 (263)
....++|+|. ||...+...++.+|.+ +|+++++.|++ .||++.+.+.+|.+|
T Consensus 6 ~~~~v~C~~~--cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 6 PFRPVPCPNG--CCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp TTSEEE-TT----S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred CCCEeeCCCC--CcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 4567899983 6778899999999998 99999999998 899999999999987
No 16
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.04 E-value=1.2e-06 Score=58.05 Aligned_cols=38 Identities=37% Similarity=1.056 Sum_probs=30.2
Q ss_pred eeccccCcc--ccccccccCCCceeccccccccC----CCCCCcc
Q psy12127 22 ECGVCLEPL--DRGITSCQTCGNLVCTSCAARLL----KCPFCRI 60 (263)
Q Consensus 22 ~CpIC~~~l--~~Pv~qC~~CGH~~C~~C~~~l~----~CP~Cr~ 60 (263)
+|+||++.+ ..+.+. .+|||+||..|+.++. .||.|++
T Consensus 1 ~C~~C~~~~~~~~~~~l-~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRL-TSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEE-cccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 599999999 223233 5799999999999975 8999984
No 17
>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=97.94 E-value=5.1e-06 Score=61.06 Aligned_cols=60 Identities=20% Similarity=0.166 Sum_probs=44.7
Q ss_pred CceeeeccccCccccccccccCCCceecccccccc-----CCCCCCccCCccc-ccccHHHHHhhhcc
Q psy12127 18 ASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL-----LKCPFCRITIDYS-WQRNVALERIFTKL 79 (263)
Q Consensus 18 ~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~~~-~~rn~~le~~v~~l 79 (263)
.+.|.|||++++|.+||.. + +||+|+++++.++ ..||.++.++... ...|.+|++.|++.
T Consensus 2 P~~f~CpIt~~lM~dPVi~-~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~~ 67 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVIL-P-SGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNRALKSAIEEW 67 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEE-T-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-HHHHHHHHHH
T ss_pred CcccCCcCcCcHhhCceeC-C-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECHHHHHHHHHH
Confidence 4789999999999999864 4 5999999999884 3699999998753 77899999888754
No 18
>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=97.94 E-value=2.4e-06 Score=56.44 Aligned_cols=37 Identities=35% Similarity=0.942 Sum_probs=29.3
Q ss_pred eeccccCcccc--ccccccCCCceecccccccc----CCCCCCc
Q psy12127 22 ECGVCLEPLDR--GITSCQTCGNLVCTSCAARL----LKCPFCR 59 (263)
Q Consensus 22 ~CpIC~~~l~~--Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr 59 (263)
+|+||++.+.+ .+... .|||.||.+|+.++ .+||.||
T Consensus 2 ~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKL-PCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEE-TTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEc-cCCCeeCHHHHHHHHHhCCcCCccC
Confidence 59999999963 44454 49999999999986 4899997
No 19
>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=97.91 E-value=4.2e-06 Score=54.22 Aligned_cols=35 Identities=37% Similarity=1.139 Sum_probs=29.4
Q ss_pred eccccCccccccccccCCCceecccccccc------CCCCCC
Q psy12127 23 CGVCLEPLDRGITSCQTCGNLVCTSCAARL------LKCPFC 58 (263)
Q Consensus 23 CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l------~~CP~C 58 (263)
|+||.+.+..|+.. ..|||.||..|+.++ ..||.|
T Consensus 1 C~iC~~~~~~~~~~-~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVIL-LPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEE-TTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEE-ecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 89999999999733 579999999999874 268876
No 20
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=97.79 E-value=6.8e-06 Score=52.92 Aligned_cols=40 Identities=38% Similarity=1.001 Sum_probs=32.2
Q ss_pred eeccccCccccccccccCCCceecccccccc-----CCCCCCccCC
Q psy12127 22 ECGVCLEPLDRGITSCQTCGNLVCTSCAARL-----LKCPFCRITI 62 (263)
Q Consensus 22 ~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~ 62 (263)
.|+||.+.+..|+.. ..|||.||..|+..+ ..||.|+..+
T Consensus 1 ~C~iC~~~~~~~~~~-~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFREPVVL-LPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhCceEe-cCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 499999999777643 559999999999864 3799998753
No 21
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.76 E-value=9.3e-06 Score=72.70 Aligned_cols=46 Identities=24% Similarity=0.633 Sum_probs=35.8
Q ss_pred CceeeeccccCcccccc------ccccCCCceecccccccc----CCCCCCccCCc
Q psy12127 18 ASISECGVCLEPLDRGI------TSCQTCGNLVCTSCAARL----LKCPFCRITID 63 (263)
Q Consensus 18 ~~~l~CpIC~~~l~~Pv------~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~ 63 (263)
.+..+||||++.+..+. ..-+.|||.||..|+.++ ..||.||.++.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 34679999999877541 112469999999999885 48999999875
No 22
>KOG0317|consensus
Probab=97.75 E-value=7.4e-06 Score=74.38 Aligned_cols=45 Identities=31% Similarity=0.802 Sum_probs=38.9
Q ss_pred CceeeeccccCccccccccccCCCceecccccccc----CCCCCCccCCcc
Q psy12127 18 ASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITIDY 64 (263)
Q Consensus 18 ~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~~ 64 (263)
....+|.+|++....| .|+.|||+||-+|+..+ ..||.||..+.+
T Consensus 237 ~a~~kC~LCLe~~~~p--SaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~p 285 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNP--SATPCGHIFCWSCILEWCSEKAECPLCREKFQP 285 (293)
T ss_pred CCCCceEEEecCCCCC--CcCcCcchHHHHHHHHHHccccCCCcccccCCC
Confidence 3558999999999999 46889999999999986 379999998763
No 23
>KOG2177|consensus
Probab=97.55 E-value=2.2e-05 Score=69.09 Aligned_cols=68 Identities=28% Similarity=0.584 Sum_probs=52.5
Q ss_pred hhcCCceeeeccccCccccccccccCCCceecccccccc----CCCCCCccCCcccccccHHHHHhhhcceecCC
Q psy12127 14 KELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITIDYSWQRNVALERIFTKLELPCR 84 (263)
Q Consensus 14 ~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~~~~~rn~~le~~v~~l~v~C~ 84 (263)
.+.+.+.+.||||++.+..|.. ..|||.||..|+..+ ..||.||. ......+|..+.++++.+.....
T Consensus 7 ~~~~~~~~~C~iC~~~~~~p~~--l~C~H~~c~~C~~~~~~~~~~Cp~cr~-~~~~~~~n~~l~~~~~~~~~~~~ 78 (386)
T KOG2177|consen 7 LEVLQEELTCPICLEYFREPVL--LPCGHNFCRACLTRSWEGPLSCPVCRP-PSRNLRPNVLLANLVERLRQLRL 78 (386)
T ss_pred hhhccccccChhhHHHhhcCcc--ccccchHhHHHHHHhcCCCcCCcccCC-chhccCccHHHHHHHHHHHhcCC
Confidence 4567899999999999999932 468999999999884 38999996 32235567788887777655543
No 24
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=97.52 E-value=1.8e-05 Score=72.00 Aligned_cols=46 Identities=28% Similarity=0.595 Sum_probs=39.5
Q ss_pred cCCceeeeccccCccccccccccCCCceecccccccc----CCCCCCccCCc
Q psy12127 16 LIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITID 63 (263)
Q Consensus 16 ~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~ 63 (263)
.|...+.|-||.+.+..|+. +.|||.||+-|+.++ ..||.||.+..
T Consensus 21 ~LDs~lrC~IC~~~i~ip~~--TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 21 GLDSMLRCRICDCRISIPCE--TTCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred cchhHHHhhhhhheeeccee--cccccchhHHHHHHHhcCCCCCccccccHH
Confidence 46788999999999999975 579999999999984 37999998753
No 25
>PHA02926 zinc finger-like protein; Provisional
Probab=97.49 E-value=2.2e-05 Score=69.18 Aligned_cols=45 Identities=27% Similarity=0.831 Sum_probs=35.4
Q ss_pred CCceeeeccccCccccc---------cccccCCCceeccccccccC----------CCCCCccCCc
Q psy12127 17 IASISECGVCLEPLDRG---------ITSCQTCGNLVCTSCAARLL----------KCPFCRITID 63 (263)
Q Consensus 17 l~~~l~CpIC~~~l~~P---------v~qC~~CGH~~C~~C~~~l~----------~CP~Cr~~~~ 63 (263)
..++.+|+||++....+ +. .+|+|.||..|+.++. .||.||..+.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL--~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLL--DSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred ccCCCCCccCcccccccccccccccccc--CCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 35578999999987532 22 4799999999999862 3999999876
No 26
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.45 E-value=7e-05 Score=69.24 Aligned_cols=56 Identities=21% Similarity=0.501 Sum_probs=38.8
Q ss_pred eeeeccccC--cccccc--ccccCCCceecccccccc-----CCCCCCccCCccc-----ccccHHHHHhh
Q psy12127 20 ISECGVCLE--PLDRGI--TSCQTCGNLVCTSCAARL-----LKCPFCRITIDYS-----WQRNVALERIF 76 (263)
Q Consensus 20 ~l~CpIC~~--~l~~Pv--~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~~~-----~~rn~~le~~v 76 (263)
...||+|.. ++.+-. +. ..|||.||.+|+..+ ..||.|+.++... .+.+.++++.+
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i-~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr~q~F~D~~vekEV 72 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMV-NVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRVQLFEDPTVEKEV 72 (309)
T ss_pred CCCCCcCCCCCccCccccccc-CCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhccccccccHHHHHHH
Confidence 357999999 454432 22 259999999999984 3799999987532 34455555544
No 27
>KOG2164|consensus
Probab=97.43 E-value=3.9e-05 Score=74.51 Aligned_cols=42 Identities=36% Similarity=0.934 Sum_probs=36.2
Q ss_pred eeeeccccCccccccccccCCCceecccccccc---------CCCCCCccCCc
Q psy12127 20 ISECGVCLEPLDRGITSCQTCGNLVCTSCAARL---------LKCPFCRITID 63 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l---------~~CP~Cr~~~~ 63 (263)
...||||+++..-|+. ++|||+||..|+-.. ..||.|+..+.
T Consensus 186 ~~~CPICL~~~~~p~~--t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~ 236 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVR--TNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTIT 236 (513)
T ss_pred CCcCCcccCCCCcccc--cccCceeeHHHHHHHHhhhcccCCccCCchhhhcc
Confidence 6789999999998876 479999999998762 37999999886
No 28
>KOG0311|consensus
Probab=97.35 E-value=1.1e-05 Score=74.99 Aligned_cols=68 Identities=19% Similarity=0.453 Sum_probs=50.7
Q ss_pred ccchhcCCceeeeccccCccccccccccCCCceecccccccc-----CCCCCCccCCccc--ccccHHHHHhhhcc
Q psy12127 11 ANCKELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL-----LKCPFCRITIDYS--WQRNVALERIFTKL 79 (263)
Q Consensus 11 ~~~~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~~~--~~rn~~le~~v~~l 79 (263)
...=..+...+.||||+++++.-+. -..|+|.||.+|+.+. +.||+||+.+... ...+.....++.++
T Consensus 34 ~~~l~~~~~~v~c~icl~llk~tmt-tkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLis~i 108 (381)
T KOG0311|consen 34 MVDLAMFDIQVICPICLSLLKKTMT-TKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRIDPNFDALISKI 108 (381)
T ss_pred eecHHHhhhhhccHHHHHHHHhhcc-cHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCCCccHHHHHHHH
Confidence 3344567788999999999998754 3679999999999873 4899999987642 44455566666554
No 29
>KOG0978|consensus
Probab=97.26 E-value=5.7e-05 Score=76.34 Aligned_cols=47 Identities=23% Similarity=0.684 Sum_probs=39.4
Q ss_pred CCceeeeccccCccccccccccCCCceecccccccc-----CCCCCCccCCccc
Q psy12127 17 IASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL-----LKCPFCRITIDYS 65 (263)
Q Consensus 17 l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~~~ 65 (263)
....|.||+|..-.++-|. +.|||.||..|+.+. .+||.|..+|+.+
T Consensus 640 yK~~LkCs~Cn~R~Kd~vI--~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan 691 (698)
T KOG0978|consen 640 YKELLKCSVCNTRWKDAVI--TKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN 691 (698)
T ss_pred HHhceeCCCccCchhhHHH--HhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence 4688999999977777654 579999999999883 5999999999854
No 30
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.21 E-value=8.9e-05 Score=66.73 Aligned_cols=44 Identities=34% Similarity=0.767 Sum_probs=37.3
Q ss_pred CceeeeccccCccccccccccCCCceeccccccc-c-----CCCCCCccCCc
Q psy12127 18 ASISECGVCLEPLDRGITSCQTCGNLVCTSCAAR-L-----LKCPFCRITID 63 (263)
Q Consensus 18 ~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~-l-----~~CP~Cr~~~~ 63 (263)
...++|+||++....|. |+.|||+||-.|+-. + ..||.||....
T Consensus 213 ~~d~kC~lC~e~~~~ps--~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 213 LADYKCFLCLEEPEVPS--CTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccccceeeeecccCCcc--cccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 45789999999999995 578999999999877 4 26999998764
No 31
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.15 E-value=0.0001 Score=48.88 Aligned_cols=27 Identities=30% Similarity=0.953 Sum_probs=17.4
Q ss_pred eccccCcccc----ccccccCCCceecccccccc
Q psy12127 23 CGVCLEPLDR----GITSCQTCGNLVCTSCAARL 52 (263)
Q Consensus 23 CpIC~~~l~~----Pv~qC~~CGH~~C~~C~~~l 52 (263)
||||.+ +.. |+.. .|||+||..|+.++
T Consensus 1 CpIc~e-~~~~~n~P~~L--~CGH~~c~~cl~~l 31 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVL--PCGHVFCKDCLQKL 31 (43)
T ss_dssp -TTT-----TTSS-EEE---SSS-EEEHHHHHHH
T ss_pred CCcccc-ccCCCCCCEEE--eCccHHHHHHHHHH
Confidence 899999 776 8754 49999999999986
No 32
>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=97.10 E-value=0.00015 Score=44.85 Aligned_cols=34 Identities=38% Similarity=1.055 Sum_probs=27.6
Q ss_pred eccccCccccccccccCCCceecccccccc-----CCCCCC
Q psy12127 23 CGVCLEPLDRGITSCQTCGNLVCTSCAARL-----LKCPFC 58 (263)
Q Consensus 23 CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l-----~~CP~C 58 (263)
|+||.+....++.. .|||.||..|+..+ ..||.|
T Consensus 1 C~iC~~~~~~~~~~--~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVL--PCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEe--cCCChHHHHHHHHHHHhCcCCCCCC
Confidence 78999998877653 68999999999864 368876
No 33
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.74 E-value=0.0017 Score=64.84 Aligned_cols=31 Identities=29% Similarity=0.627 Sum_probs=17.4
Q ss_pred ceeeeccchhhhhhc-ccCCceecCCCCCCCCcc
Q psy12127 90 CKVYLPKAKRDKHED-KCKFRQLKCPMHACPWTN 122 (263)
Q Consensus 90 C~~~~~~~~~~~He~-~C~~~~~~CP~~~C~~~g 122 (263)
|+..+...++..|.. .|+.+++.|++ |+...
T Consensus 483 Cg~~~~R~~L~~H~~thCp~Kpi~C~f--C~~~v 514 (567)
T PLN03086 483 CGVVLEKEQMVQHQASTCPLRLITCRF--CGDMV 514 (567)
T ss_pred CCCCcchhHHHhhhhccCCCCceeCCC--CCCcc
Confidence 555555556666643 56666666654 55544
No 34
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.72 E-value=0.00044 Score=60.00 Aligned_cols=57 Identities=23% Similarity=0.547 Sum_probs=43.9
Q ss_pred eeeeccccCccccccccccCCCceeccccccc-c---CCCCCCccCCcccccccHHHHHhhhc
Q psy12127 20 ISECGVCLEPLDRGITSCQTCGNLVCTSCAAR-L---LKCPFCRITIDYSWQRNVALERIFTK 78 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~-l---~~CP~Cr~~~~~~~~rn~~le~~v~~ 78 (263)
-|.|.||..-...||. ++|||.||+.|..+ . ..|-.|.............++++++.
T Consensus 196 PF~C~iCKkdy~spvv--t~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~V~~d~~kmL~~ 256 (259)
T COG5152 196 PFLCGICKKDYESPVV--TECGHSFCSLCAIRKYQKGDECGVCGKATYGRFWVVSDLQKMLNK 256 (259)
T ss_pred ceeehhchhhccchhh--hhcchhHHHHHHHHHhccCCcceecchhhccceeHHhhHHHHHhh
Confidence 4689999999999985 57999999999765 3 38999988764334445667777754
No 35
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=96.48 E-value=0.0016 Score=45.33 Aligned_cols=47 Identities=26% Similarity=0.446 Sum_probs=31.4
Q ss_pred hhcccCCceecCCCCCCCCccChhhHHHHHhcccCc---ce---eeCCeEEEe
Q psy12127 102 HEDKCKFRQLKCPMHACPWTNSVLHLSEHLNQVHHL---HL---LKGNGVNIE 148 (263)
Q Consensus 102 He~~C~~~~~~CP~~~C~~~g~~~~L~~Hl~~~H~~---~~---~~g~~~~~~ 148 (263)
|++.|+++++.||+..|.....+.+|..|+.+.++. .- .+|....+.
T Consensus 1 H~~~C~~~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 1 HEEECPFRPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp HHTTSTTSEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred CcccCCCCEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 888999999999986777778999999999988872 22 247776665
No 36
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=96.39 E-value=0.0016 Score=47.81 Aligned_cols=38 Identities=34% Similarity=1.022 Sum_probs=28.3
Q ss_pred eeccccCcccccccc-------c----cCCCceecccccccc----CCCCCCc
Q psy12127 22 ECGVCLEPLDRGITS-------C----QTCGNLVCTSCAARL----LKCPFCR 59 (263)
Q Consensus 22 ~CpIC~~~l~~Pv~q-------C----~~CGH~~C~~C~~~l----~~CP~Cr 59 (263)
.|+||++.+..|... | ..|||.|-..|+.++ ..||+||
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 399999999544211 1 459999999999985 4899997
No 37
>KOG4159|consensus
Probab=96.25 E-value=0.0011 Score=63.52 Aligned_cols=48 Identities=35% Similarity=0.721 Sum_probs=41.1
Q ss_pred hhcCCceeeeccccCccccccccccCCCceecccccccc----CCCCCCccCCc
Q psy12127 14 KELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITID 63 (263)
Q Consensus 14 ~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~ 63 (263)
.+.+.+.|.|-||...+.+||.. .|||.+|..|+.+. ..||.||.++.
T Consensus 78 ~~~~~sef~c~vc~~~l~~pv~t--pcghs~c~~Cl~r~ld~~~~cp~Cr~~l~ 129 (398)
T KOG4159|consen 78 PEEIRSEFECCVCSRALYPPVVT--PCGHSFCLECLDRSLDQETECPLCRDELV 129 (398)
T ss_pred CccccchhhhhhhHhhcCCCccc--cccccccHHHHHHHhccCCCCcccccccc
Confidence 34568999999999999999864 78999999997773 48999999875
No 38
>KOG2660|consensus
Probab=96.17 E-value=0.0012 Score=61.31 Aligned_cols=64 Identities=27% Similarity=0.485 Sum_probs=49.2
Q ss_pred hcCCceeeeccccCccccccccccCCCceecccccccc----CCCCCCccCCccc-----ccccHHHHHhhhcc
Q psy12127 15 ELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITIDYS-----WQRNVALERIFTKL 79 (263)
Q Consensus 15 ~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~~~-----~~rn~~le~~v~~l 79 (263)
.++.....|.+|..+|.++... ..|=|+||.+|+-+. ..||.|...+... ...+++|+.++.+|
T Consensus 10 ~~~n~~itC~LC~GYliDATTI-~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t~pl~ni~~DrtlqdiVyKL 82 (331)
T KOG2660|consen 10 TELNPHITCRLCGGYLIDATTI-TECLHTFCKSCIVKYLEESKYCPTCDIVIHKTHPLLNIRSDRTLQDIVYKL 82 (331)
T ss_pred hhcccceehhhccceeecchhH-HHHHHHHHHHHHHHHHHHhccCCccceeccCccccccCCcchHHHHHHHHH
Confidence 4577889999999999999654 568999999999884 5899999887632 33366666665543
No 39
>KOG1813|consensus
Probab=96.13 E-value=0.0033 Score=57.57 Aligned_cols=41 Identities=27% Similarity=0.664 Sum_probs=35.5
Q ss_pred eeeccccCccccccccccCCCceecccccccc----CCCCCCccCCc
Q psy12127 21 SECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITID 63 (263)
Q Consensus 21 l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~ 63 (263)
+.|-||..++..||. ++|||.||..|..+. ..|++|...+.
T Consensus 242 f~c~icr~~f~~pVv--t~c~h~fc~~ca~~~~qk~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 242 FKCFICRKYFYRPVV--TKCGHYFCEVCALKPYQKGEKCYVCSQQTH 286 (313)
T ss_pred ccccccccccccchh--hcCCceeehhhhccccccCCcceecccccc
Confidence 469999999999986 579999999997763 38999999875
No 40
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.03 E-value=0.0023 Score=58.79 Aligned_cols=57 Identities=21% Similarity=0.515 Sum_probs=42.3
Q ss_pred eeeccccCccccccccccCCCceecccccccc-----CCCCCCccC--CcccccccHHHHHhhhc
Q psy12127 21 SECGVCLEPLDRGITSCQTCGNLVCTSCAARL-----LKCPFCRIT--IDYSWQRNVALERIFTK 78 (263)
Q Consensus 21 l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~--~~~~~~rn~~le~~v~~ 78 (263)
|.||.|..+++.|+.. +.|||.||..|+... ..||.|... +-....++...++.++.
T Consensus 275 LkCplc~~Llrnp~kT-~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~l~pD~dk~~EvE~ 338 (427)
T COG5222 275 LKCPLCHCLLRNPMKT-PCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLTPDIDKKLEVEK 338 (427)
T ss_pred ccCcchhhhhhCcccC-ccccchHHHHHHhhhhhhccccCCCcccccchhhccCccHHHHHHHHH
Confidence 8999999999999865 679999999999972 389999872 11124455555555543
No 41
>PLN03086 PRLI-interacting factor K; Provisional
Probab=95.56 E-value=0.0044 Score=61.88 Aligned_cols=51 Identities=29% Similarity=0.591 Sum_probs=39.7
Q ss_pred hcceecCCCCCCCceeeeccchhhhhhcccCCceecCCCCCCCCccChhhHHHHH
Q psy12127 77 TKLELPCRNFRFGCKVYLPKAKRDKHEDKCKFRQLKCPMHACPWTNSVLHLSEHL 131 (263)
Q Consensus 77 ~~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~~~~CP~~~C~~~g~~~~L~~Hl 131 (263)
+.-.+.|+| |.|.++..++..|+..|.|..+.||..+|+....+.++..|+
T Consensus 404 ~~~~V~C~N----C~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~ 454 (567)
T PLN03086 404 DVDTVECRN----CKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHV 454 (567)
T ss_pred CCCeEECCC----CCCccchhHHHHHHhhCCCcceeCCcccccceeeccccccCc
Confidence 345778998 999999999999999999999999964555555444444444
No 42
>KOG2879|consensus
Probab=95.54 E-value=0.0083 Score=54.53 Aligned_cols=49 Identities=31% Similarity=0.650 Sum_probs=39.5
Q ss_pred hhcCCceeeeccccCccccccccccCCCceecccccccc------CCCCCCccCCc
Q psy12127 14 KELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL------LKCPFCRITID 63 (263)
Q Consensus 14 ~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l------~~CP~Cr~~~~ 63 (263)
+..-.+..+||+|.+.-..|. +-..|||++|-.|+.+- -.||.|+++..
T Consensus 233 ss~~t~~~~C~~Cg~~PtiP~-~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 233 SSTGTSDTECPVCGEPPTIPH-VIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cccccCCceeeccCCCCCCCe-eeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 444567889999999999994 33569999999999873 28999998764
No 43
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.15 E-value=0.0056 Score=42.98 Aligned_cols=34 Identities=18% Similarity=0.463 Sum_probs=22.7
Q ss_pred CceeeeccccCccccccccccCCCceecccccccc
Q psy12127 18 ASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL 52 (263)
Q Consensus 18 ~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l 52 (263)
.-.+.|||...++.+||.. ..|||+|-+..+..+
T Consensus 9 ~~~~~CPiT~~~~~~PV~s-~~C~H~fek~aI~~~ 42 (57)
T PF11789_consen 9 TISLKCPITLQPFEDPVKS-KKCGHTFEKEAILQY 42 (57)
T ss_dssp B--SB-TTTSSB-SSEEEE-SSS--EEEHHHHHHH
T ss_pred EeccCCCCcCChhhCCcCc-CCCCCeecHHHHHHH
Confidence 3458999999999999854 679999988777663
No 44
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=94.71 E-value=0.039 Score=46.43 Aligned_cols=28 Identities=18% Similarity=0.523 Sum_probs=25.0
Q ss_pred ceecCCCCCCCCccChhhHHHHHhcccC
Q psy12127 109 RQLKCPMHACPWTNSVLHLSEHLNQVHH 136 (263)
Q Consensus 109 ~~~~CP~~~C~~~g~~~~L~~Hl~~~H~ 136 (263)
++-.|+..+|.|.|++.+|.+|.+..|+
T Consensus 106 K~RsC~~e~C~F~GtY~eLrKHar~~HP 133 (162)
T PF07800_consen 106 KKRSCSQESCSFSGTYSELRKHARSEHP 133 (162)
T ss_pred CCccCcccccccccCHHHHHHHHHhhCC
Confidence 4556777999999999999999999998
No 45
>KOG0824|consensus
Probab=94.59 E-value=0.017 Score=53.14 Aligned_cols=42 Identities=26% Similarity=0.592 Sum_probs=36.0
Q ss_pred eeeccccCccccccccccCCCceecccccccc-----CCCCCCccCCcc
Q psy12127 21 SECGVCLEPLDRGITSCQTCGNLVCTSCAARL-----LKCPFCRITIDY 64 (263)
Q Consensus 21 l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~~ 64 (263)
-+|+||+.-..-|+.. .|+|.||.-|++-. ..|+.||.++..
T Consensus 8 ~eC~IC~nt~n~Pv~l--~C~HkFCyiCiKGsy~ndk~~CavCR~pids 54 (324)
T KOG0824|consen 8 KECLICYNTGNCPVNL--YCFHKFCYICIKGSYKNDKKTCAVCRFPIDS 54 (324)
T ss_pred CcceeeeccCCcCccc--cccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence 3799999999999764 69999999999873 369999999874
No 46
>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=94.26 E-value=0.025 Score=38.87 Aligned_cols=37 Identities=35% Similarity=0.898 Sum_probs=22.2
Q ss_pred eccccCccccc--------cccccCCCceeccccc----cccCCCCCCc
Q psy12127 23 CGVCLEPLDRG--------ITSCQTCGNLVCTSCA----ARLLKCPFCR 59 (263)
Q Consensus 23 CpIC~~~l~~P--------v~qC~~CGH~~C~~C~----~~l~~CP~Cr 59 (263)
|--|..++..+ .++|+.|++.||..|- +.|..||-|.
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence 55677777664 6899999999999993 4467899884
No 47
>KOG4172|consensus
Probab=94.21 E-value=0.0059 Score=42.46 Aligned_cols=41 Identities=39% Similarity=0.940 Sum_probs=32.3
Q ss_pred eeeccccCccccccccccCCCce-ecccccccc-----CCCCCCccCCc
Q psy12127 21 SECGVCLEPLDRGITSCQTCGNL-VCTSCAARL-----LKCPFCRITID 63 (263)
Q Consensus 21 l~CpIC~~~l~~Pv~qC~~CGH~-~C~~C~~~l-----~~CP~Cr~~~~ 63 (263)
-+|-||.+-..+-|.- .|||. .|-.|-.++ +.||.||.++.
T Consensus 8 dECTICye~pvdsVlY--tCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 8 DECTICYEHPVDSVLY--TCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred cceeeeccCcchHHHH--HcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 4799999987776542 48996 899997664 48999999874
No 48
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.81 E-value=0.022 Score=38.67 Aligned_cols=39 Identities=36% Similarity=0.899 Sum_probs=18.2
Q ss_pred eccccCcccc---ccccccCCCceecccccccc-----CCCCCCccCC
Q psy12127 23 CGVCLEPLDR---GITSCQTCGNLVCTSCAARL-----LKCPFCRITI 62 (263)
Q Consensus 23 CpIC~~~l~~---Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~ 62 (263)
||+|.+.|.. -++-|+ ||..+|..|+.++ +.||.||++.
T Consensus 1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 6777777731 134464 8999999998774 4899999863
No 49
>KOG0802|consensus
Probab=93.14 E-value=0.023 Score=56.73 Aligned_cols=44 Identities=32% Similarity=0.656 Sum_probs=36.2
Q ss_pred CCceeeeccccCcccc-----ccccccCCCceecccccccc----CCCCCCccCC
Q psy12127 17 IASISECGVCLEPLDR-----GITSCQTCGNLVCTSCAARL----LKCPFCRITI 62 (263)
Q Consensus 17 l~~~l~CpIC~~~l~~-----Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~ 62 (263)
....-.|+||.+.|.. |..+ .|||.|+..|+.++ +.||+||..+
T Consensus 288 ~~~~~~C~IC~e~l~~~~~~~~~rL--~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 288 ALSDELCIICLEELHSGHNITPKRL--PCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred hhcCCeeeeechhhcccccccccee--ecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 3456789999999998 5444 48999999999986 5899999944
No 50
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=92.80 E-value=0.099 Score=36.40 Aligned_cols=43 Identities=28% Similarity=0.720 Sum_probs=30.9
Q ss_pred ceeeeccccCccccccccccCCCceeccccccc--cCCCCCCccCCc
Q psy12127 19 SISECGVCLEPLDRGITSCQTCGNLVCTSCAAR--LLKCPFCRITID 63 (263)
Q Consensus 19 ~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~--l~~CP~Cr~~~~ 63 (263)
....|-.|...-...+. ..|||.+|..|+.- .+-||.|..++.
T Consensus 6 ~~~~~~~~~~~~~~~~~--~pCgH~I~~~~f~~~rYngCPfC~~~~~ 50 (55)
T PF14447_consen 6 PEQPCVFCGFVGTKGTV--LPCGHLICDNCFPGERYNGCPFCGTPFE 50 (55)
T ss_pred cceeEEEcccccccccc--ccccceeeccccChhhccCCCCCCCccc
Confidence 44456666666444333 35899999999876 478999999986
No 51
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=92.76 E-value=0.032 Score=40.65 Aligned_cols=44 Identities=27% Similarity=0.643 Sum_probs=19.8
Q ss_pred eeeeccccCccc----ccccccc--CCCceecccccccc---------------CCCCCCccCCc
Q psy12127 20 ISECGVCLEPLD----RGITSCQ--TCGNLVCTSCAARL---------------LKCPFCRITID 63 (263)
Q Consensus 20 ~l~CpIC~~~l~----~Pv~qC~--~CGH~~C~~C~~~l---------------~~CP~Cr~~~~ 63 (263)
.++|+||+..+. .|...|. .|+..|=..|+.++ +.||.|+.++.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 468999999865 3667786 68888878888764 15999988875
No 52
>KOG4739|consensus
Probab=92.65 E-value=0.06 Score=48.13 Aligned_cols=44 Identities=20% Similarity=0.620 Sum_probs=33.2
Q ss_pred ceeeeccccCccc-cccccccCCCceecccccccc-C-CCCCCccCCc
Q psy12127 19 SISECGVCLEPLD-RGITSCQTCGNLVCTSCAARL-L-KCPFCRITID 63 (263)
Q Consensus 19 ~~l~CpIC~~~l~-~Pv~qC~~CGH~~C~~C~~~l-~-~CP~Cr~~~~ 63 (263)
+-..|..|+.--. .|.+. +.|+|+||..|...- . .||.|+.++.
T Consensus 2 ~~VhCn~C~~~~~~~~f~L-TaC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 2 DFVHCNKCFRFPSQDPFFL-TACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred ceEEeccccccCCCCceee-eechhhhhhhhcccCCccccccccceee
Confidence 3467888876444 45565 679999999998874 3 8999999864
No 53
>KOG4275|consensus
Probab=92.43 E-value=0.021 Score=52.46 Aligned_cols=42 Identities=31% Similarity=0.856 Sum_probs=36.4
Q ss_pred eeeeccccCccccccccccCCCce-eccccccccCCCCCCccCCc
Q psy12127 20 ISECGVCLEPLDRGITSCQTCGNL-VCTSCAARLLKCPFCRITID 63 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC~~CGH~-~C~~C~~~l~~CP~Cr~~~~ 63 (263)
...|.||.+..++=++. .|||. .|-.|-++++.||+||+.+.
T Consensus 300 ~~LC~ICmDaP~DCvfL--eCGHmVtCt~CGkrm~eCPICRqyi~ 342 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFL--ECGHMVTCTKCGKRMNECPICRQYIV 342 (350)
T ss_pred HHHHHHHhcCCcceEEe--ecCcEEeehhhccccccCchHHHHHH
Confidence 66899999999988875 69995 79999999999999998653
No 54
>KOG1002|consensus
Probab=92.25 E-value=0.048 Score=53.82 Aligned_cols=48 Identities=27% Similarity=0.747 Sum_probs=39.6
Q ss_pred hhcCCceeeeccccCccccccccccCCCceecccccccc---------CCCCCCccCCc
Q psy12127 14 KELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL---------LKCPFCRITID 63 (263)
Q Consensus 14 ~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l---------~~CP~Cr~~~~ 63 (263)
..+-.+..+|.+|.++..++|- ++|.|.||+-|+... ..||+|..+++
T Consensus 530 ~~enk~~~~C~lc~d~aed~i~--s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDPAEDYIE--SSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred CccccCceeecccCChhhhhHh--hhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 3445677899999999999975 579999999999763 28999998775
No 55
>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=92.03 E-value=0.065 Score=39.17 Aligned_cols=38 Identities=26% Similarity=0.678 Sum_probs=23.7
Q ss_pred eeeeccccCccccccccccCCCceecccccccc---CCCCCCccCCc
Q psy12127 20 ISECGVCLEPLDRGITSCQTCGNLVCTSCAARL---LKCPFCRITID 63 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l---~~CP~Cr~~~~ 63 (263)
++.||.|...|.+ .+ |+..|..|.... ..||.|..++.
T Consensus 1 e~~CP~C~~~L~~-----~~-~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 1 ENTCPKCQQELEW-----QG-GHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp --B-SSS-SBEEE-----ET-TEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred CCcCCCCCCccEE-----eC-CEEECccccccceecccCCCcccHHH
Confidence 3689999999776 24 899999998774 48999999875
No 56
>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=91.95 E-value=0.076 Score=31.36 Aligned_cols=23 Identities=22% Similarity=0.533 Sum_probs=15.8
Q ss_pred eeccccCccccccccccCCCcee
Q psy12127 22 ECGVCLEPLDRGITSCQTCGNLV 44 (263)
Q Consensus 22 ~CpIC~~~l~~Pv~qC~~CGH~~ 44 (263)
.||.|...+..-...|+.|||.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 47777777665556677777765
No 57
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=91.57 E-value=0.085 Score=40.04 Aligned_cols=53 Identities=23% Similarity=0.551 Sum_probs=34.7
Q ss_pred cccccchhcCCceeeeccccCcccc-ccccccCCCceecccccccc-------CCCCCCccCCc
Q psy12127 8 ECCANCKELIASISECGVCLEPLDR-GITSCQTCGNLVCTSCAARL-------LKCPFCRITID 63 (263)
Q Consensus 8 ~~~~~~~~~l~~~l~CpIC~~~l~~-Pv~qC~~CGH~~C~~C~~~l-------~~CP~Cr~~~~ 63 (263)
+.|.-+...++. .||.|..+-.+ |+.. ..|+|.|=..|+.++ ..||.||+++.
T Consensus 22 d~CgICr~~fdg--~Cp~Ck~Pgd~Cplv~-g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 22 DVCGICRMPFDG--CCPDCKFPGDDCPLVW-GKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CceeeEeccccc--CCCCccCCCCCCceee-ccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 334444433432 46666666553 4433 359999999999884 37999999875
No 58
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=88.27 E-value=0.19 Score=41.25 Aligned_cols=46 Identities=28% Similarity=0.712 Sum_probs=35.3
Q ss_pred ceeeeccccCccccccccc--cCCCceecccccccc-------CCCCCCccCCcc
Q psy12127 19 SISECGVCLEPLDRGITSC--QTCGNLVCTSCAARL-------LKCPFCRITIDY 64 (263)
Q Consensus 19 ~~l~CpIC~~~l~~Pv~qC--~~CGH~~C~~C~~~l-------~~CP~Cr~~~~~ 64 (263)
..++|.||.+.-.+.-+.= +.||-.+|..|-..| ..||.|++.+.+
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 6789999999876543321 239999999998774 489999998763
No 59
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.96 E-value=0.11 Score=54.61 Aligned_cols=51 Identities=33% Similarity=0.707 Sum_probs=42.3
Q ss_pred chhcCCceeeeccccCccc-----cccccccCCCceecccccccc------CCCCCCccCCc
Q psy12127 13 CKELIASISECGVCLEPLD-----RGITSCQTCGNLVCTSCAARL------LKCPFCRITID 63 (263)
Q Consensus 13 ~~~~l~~~l~CpIC~~~l~-----~Pv~qC~~CGH~~C~~C~~~l------~~CP~Cr~~~~ 63 (263)
.++.+...-+|+||+.++. -|-..|+.|-|-|=.+|+-+| +.||.||..++
T Consensus 1462 i~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1462 IDEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred hhhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 3556677778999999987 466789999999999999887 48999998775
No 60
>KOG4265|consensus
Probab=87.66 E-value=0.19 Score=47.39 Aligned_cols=44 Identities=36% Similarity=0.851 Sum_probs=36.3
Q ss_pred CceeeeccccCccccccccccCCCce-ecccccccc----CCCCCCccCCc
Q psy12127 18 ASISECGVCLEPLDRGITSCQTCGNL-VCTSCAARL----LKCPFCRITID 63 (263)
Q Consensus 18 ~~~l~CpIC~~~l~~Pv~qC~~CGH~-~C~~C~~~l----~~CP~Cr~~~~ 63 (263)
++--+|-||..-.++=+.. .|-|+ .|+.|.+.+ +.||.||.++.
T Consensus 288 ~~gkeCVIClse~rdt~vL--PCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSESRDTVVL--PCRHLCLCSGCAKSLRYQTNNCPICRQPIE 336 (349)
T ss_pred cCCCeeEEEecCCcceEEe--cchhhehhHhHHHHHHHhhcCCCccccchH
Confidence 4567999999988886543 48996 999999886 47999999986
No 61
>PF04641 Rtf2: Rtf2 RING-finger
Probab=87.37 E-value=0.41 Score=43.39 Aligned_cols=49 Identities=18% Similarity=0.348 Sum_probs=39.4
Q ss_pred hcCCceeeeccccCcccc--c-cccccCCCceeccccccccC---CCCCCccCCcc
Q psy12127 15 ELIASISECGVCLEPLDR--G-ITSCQTCGNLVCTSCAARLL---KCPFCRITIDY 64 (263)
Q Consensus 15 ~~l~~~l~CpIC~~~l~~--P-v~qC~~CGH~~C~~C~~~l~---~CP~Cr~~~~~ 64 (263)
..-...|.|||....|.. + ++. ..|||+|+..++..+. .||.|..++..
T Consensus 108 ~~~~~~~~CPvt~~~~~~~~~fv~l-~~cG~V~s~~alke~k~~~~Cp~c~~~f~~ 162 (260)
T PF04641_consen 108 DNSEGRFICPVTGKEFNGKHKFVYL-RPCGCVFSEKALKELKKSKKCPVCGKPFTE 162 (260)
T ss_pred ccCCceeECCCCCcccCCceeEEEE-cCCCCEeeHHHHHhhcccccccccCCcccc
Confidence 345789999999999964 2 233 4689999999999875 79999999863
No 62
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=87.18 E-value=0.19 Score=47.26 Aligned_cols=40 Identities=38% Similarity=1.042 Sum_probs=31.9
Q ss_pred eccccCcccc---ccccccCCCceecccccccc-----CCCCCCccCCc
Q psy12127 23 CGVCLEPLDR---GITSCQTCGNLVCTSCAARL-----LKCPFCRITID 63 (263)
Q Consensus 23 CpIC~~~l~~---Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~ 63 (263)
||.|-++|.. -.+-|+ ||-.+|+-|+..+ ++||.||....
T Consensus 17 cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y~ 64 (480)
T COG5175 17 CPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKYD 64 (480)
T ss_pred CcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhcc
Confidence 9999999872 245575 7999999998764 59999997654
No 63
>KOG4367|consensus
Probab=86.79 E-value=0.18 Score=48.81 Aligned_cols=33 Identities=24% Similarity=0.545 Sum_probs=28.6
Q ss_pred CCceeeeccccCccccccccccCCCceeccccccc
Q psy12127 17 IASISECGVCLEPLDRGITSCQTCGNLVCTSCAAR 51 (263)
Q Consensus 17 l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~ 51 (263)
++++|+||||...++.||.. .|||..|+.|...
T Consensus 1 meeelkc~vc~~f~~epiil--~c~h~lc~~ca~~ 33 (699)
T KOG4367|consen 1 MEEELKCPVCGSFYREPIIL--PCSHNLCQACARN 33 (699)
T ss_pred CcccccCceehhhccCceEe--ecccHHHHHHHHh
Confidence 36789999999999999875 5899999999754
No 64
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.15 E-value=0.21 Score=47.09 Aligned_cols=48 Identities=27% Similarity=0.726 Sum_probs=35.5
Q ss_pred hhcCCceeeeccccCccccccccccCCCceecccccccc------CCCCCCccCCc
Q psy12127 14 KELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL------LKCPFCRITID 63 (263)
Q Consensus 14 ~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l------~~CP~Cr~~~~ 63 (263)
|+.=++.-.|.||-.-+.---. ..|||..|.-|--++ ..||.||....
T Consensus 55 ddtDEen~~C~ICA~~~TYs~~--~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e 108 (493)
T COG5236 55 DDTDEENMNCQICAGSTTYSAR--YPCGHQICHACAVRLRALYMQKGCPLCRTETE 108 (493)
T ss_pred cccccccceeEEecCCceEEEe--ccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence 4445667789999998773211 248999999998775 37999998653
No 65
>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=86.09 E-value=0.62 Score=31.87 Aligned_cols=49 Identities=22% Similarity=0.482 Sum_probs=31.0
Q ss_pred ecCCCCCCCceeeeccchhhhhhcc--c-CCceecCCCCCCCCccChhhHHHHHhcccC
Q psy12127 81 LPCRNFRFGCKVYLPKAKRDKHEDK--C-KFRQLKCPMHACPWTNSVLHLSEHLNQVHH 136 (263)
Q Consensus 81 v~C~~~~~GC~~~~~~~~~~~He~~--C-~~~~~~CP~~~C~~~g~~~~L~~Hl~~~H~ 136 (263)
+.||| |...+....+..|..+ . .-+.+.||. |... ...+|..|+...|+
T Consensus 3 f~CP~----C~~~~~~~~L~~H~~~~H~~~~~~v~CPi--C~~~-~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPY----CGKGFSESSLVEHCEDEHRSESKNVVCPI--CSSR-VTDNLIRHLNSQHR 54 (54)
T ss_pred cCCCC----CCCccCHHHHHHHHHhHCcCCCCCccCCC--chhh-hhhHHHHHHHHhcC
Confidence 56776 6666666666666421 1 123578875 6654 33589999988874
No 66
>PRK04023 DNA polymerase II large subunit; Validated
Probab=85.95 E-value=0.61 Score=49.50 Aligned_cols=44 Identities=20% Similarity=0.499 Sum_probs=34.0
Q ss_pred ceeeeccccCccccccccccCCCc-----eecccccccc--CCCCCCccCCcc
Q psy12127 19 SISECGVCLEPLDRGITSCQTCGN-----LVCTSCAARL--LKCPFCRITIDY 64 (263)
Q Consensus 19 ~~l~CpIC~~~l~~Pv~qC~~CGH-----~~C~~C~~~l--~~CP~Cr~~~~~ 64 (263)
..-.||-|.... +.+.|++||. .+|..|.... ..||.|......
T Consensus 625 g~RfCpsCG~~t--~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 625 GRRKCPSCGKET--FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTP 675 (1121)
T ss_pred cCccCCCCCCcC--CcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCCc
Confidence 455788888875 4568888985 4999997775 379999988764
No 67
>KOG1039|consensus
Probab=85.94 E-value=0.31 Score=46.07 Aligned_cols=46 Identities=30% Similarity=0.873 Sum_probs=36.7
Q ss_pred CceeeeccccCcccccc-----cc-ccCCCceecccccccc-----------CCCCCCccCCc
Q psy12127 18 ASISECGVCLEPLDRGI-----TS-CQTCGNLVCTSCAARL-----------LKCPFCRITID 63 (263)
Q Consensus 18 ~~~l~CpIC~~~l~~Pv-----~q-C~~CGH~~C~~C~~~l-----------~~CP~Cr~~~~ 63 (263)
.....|.||.+....+. +. =++|-|.||..|+.++ ..||.||.+..
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 34779999999998765 31 1469999999999886 26999998764
No 68
>KOG1571|consensus
Probab=85.89 E-value=0.31 Score=45.97 Aligned_cols=48 Identities=31% Similarity=0.740 Sum_probs=35.8
Q ss_pred hhcCCceeeeccccCccccccccccCCCceec-cccccccCCCCCCccCCc
Q psy12127 14 KELIASISECGVCLEPLDRGITSCQTCGNLVC-TSCAARLLKCPFCRITID 63 (263)
Q Consensus 14 ~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C-~~C~~~l~~CP~Cr~~~~ 63 (263)
..++.....|-||.+-.++-++. .|||..| ..|...+.+||.||+.+.
T Consensus 299 ~~~~~~p~lcVVcl~e~~~~~fv--pcGh~ccct~cs~~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 299 FRELPQPDLCVVCLDEPKSAVFV--PCGHVCCCTLCSKHLPQCPVCRQRIR 347 (355)
T ss_pred ccccCCCCceEEecCCccceeee--cCCcEEEchHHHhhCCCCchhHHHHH
Confidence 44455566899999999987775 6899865 334445679999999774
No 69
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.56 E-value=0.59 Score=37.28 Aligned_cols=38 Identities=32% Similarity=0.725 Sum_probs=28.8
Q ss_pred eeccccCccccc------------cccccCCCceeccccccc----cCCCCCCc
Q psy12127 22 ECGVCLEPLDRG------------ITSCQTCGNLVCTSCAAR----LLKCPFCR 59 (263)
Q Consensus 22 ~CpIC~~~l~~P------------v~qC~~CGH~~C~~C~~~----l~~CP~Cr 59 (263)
.|-.|...+..+ .++|+.|++.||.+|-.- |..||.|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred cccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 488888877643 477999999999999433 46888885
No 70
>KOG1785|consensus
Probab=85.19 E-value=0.22 Score=47.71 Aligned_cols=40 Identities=43% Similarity=0.998 Sum_probs=32.0
Q ss_pred eeccccCccccccccccCCCceecccccccc------CCCCCCccCCc
Q psy12127 22 ECGVCLEPLDRGITSCQTCGNLVCTSCAARL------LKCPFCRITID 63 (263)
Q Consensus 22 ~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l------~~CP~Cr~~~~ 63 (263)
.|-||-+-=++ |.. +.|||+.|..|+..+ ..||.||..|.
T Consensus 371 LCKICaendKd-vkI-EPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 371 LCKICAENDKD-VKI-EPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHHhhccCCC-ccc-ccccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 58999887665 333 569999999999886 27999998775
No 71
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=84.02 E-value=0.9 Score=36.02 Aligned_cols=60 Identities=28% Similarity=0.548 Sum_probs=35.7
Q ss_pred CCceeeeccccCccccccccccCCCce--eccccccccCCCCCCccCCcccccccHHHHHhhhcceecCCCC
Q psy12127 17 IASISECGVCLEPLDRGITSCQTCGNL--VCTSCAARLLKCPFCRITIDYSWQRNVALERIFTKLELPCRNF 86 (263)
Q Consensus 17 l~~~l~CpIC~~~l~~Pv~qC~~CGH~--~C~~C~~~l~~CP~Cr~~~~~~~~rn~~le~~v~~l~v~C~~~ 86 (263)
+...+.|..=..- --++.|++|||. +..+|..+ .||.|+..-+ ..=+++..+.+ ++|+|.
T Consensus 27 ~~~il~Crt~~~G--~~~~~C~~Cg~~~~~~~SCk~R--~CP~C~~~~~-----~~W~~~~~~~l-l~~~y~ 88 (111)
T PF14319_consen 27 VEAILACRTEALG--FHRYRCEDCGHEKIVYNSCKNR--HCPSCQAKAT-----EQWIEKQREDL-LPVPYF 88 (111)
T ss_pred HHHHHhcCCccCC--cceeecCCCCceEEecCcccCc--CCCCCCChHH-----HHHHHHHHhhC-CCCCeE
Confidence 4445555542222 224678888884 78888776 8999987432 22344444444 667774
No 72
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.01 E-value=0.43 Score=44.29 Aligned_cols=44 Identities=25% Similarity=0.642 Sum_probs=34.2
Q ss_pred eeeeccccCccccc-cccccCCCceecccccccc-----CCCCCCccCCc
Q psy12127 20 ISECGVCLEPLDRG-ITSCQTCGNLVCTSCAARL-----LKCPFCRITID 63 (263)
Q Consensus 20 ~l~CpIC~~~l~~P-v~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~ 63 (263)
-.+|.||..-+.+- -+.-..|.|.|=..|++++ .+||+||.++.
T Consensus 323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 37899999887632 1122458999999999996 48999999875
No 73
>KOG4185|consensus
Probab=83.55 E-value=0.71 Score=42.17 Aligned_cols=58 Identities=36% Similarity=0.826 Sum_probs=39.0
Q ss_pred eeeeccccCcccc------ccccccCCCceecccccccc-----CCCCCCccCCcc------cccccHHHHHhhhcc
Q psy12127 20 ISECGVCLEPLDR------GITSCQTCGNLVCTSCAARL-----LKCPFCRITIDY------SWQRNVALERIFTKL 79 (263)
Q Consensus 20 ~l~CpIC~~~l~~------Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~~------~~~rn~~le~~v~~l 79 (263)
.+.|.||.+.+.. |-. ..|||.+|..|..++ ..||.||.+... ....|.++-..+...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~--l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~~~~~~~~~~l~kNf~ll~~~~~~ 77 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRV--LKCGHTICQNCASKLLGNSRILCPFCRETTEIPDGDVKSLQKNFALLQAIEHM 77 (296)
T ss_pred CCceeecCccccccCcccCCcc--cccCceehHhHHHHHhcCceeeccCCCCcccCCchhHhhhhhhHHHHHHHHHH
Confidence 4678888877652 311 248999999999996 268999998431 144466665555543
No 74
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=83.44 E-value=0.55 Score=32.64 Aligned_cols=42 Identities=24% Similarity=0.566 Sum_probs=34.3
Q ss_pred eeeccccCcc--ccccccccCCCceeccccccccCCCCC--CccCC
Q psy12127 21 SECGVCLEPL--DRGITSCQTCGNLVCTSCAARLLKCPF--CRITI 62 (263)
Q Consensus 21 l~CpIC~~~l--~~Pv~qC~~CGH~~C~~C~~~l~~CP~--Cr~~~ 62 (263)
-.|++|.+.+ .+.+.+|+.||-..=+.|+.+.+.|-. |.+++
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 4799999999 577889999998888888888887766 76654
No 75
>KOG1645|consensus
Probab=82.90 E-value=0.4 Score=46.09 Aligned_cols=44 Identities=23% Similarity=0.668 Sum_probs=34.6
Q ss_pred eeeeccccCccccccccc---cCCCceecccccccc------CCCCCCccCCc
Q psy12127 20 ISECGVCLEPLDRGITSC---QTCGNLVCTSCAARL------LKCPFCRITID 63 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC---~~CGH~~C~~C~~~l------~~CP~Cr~~~~ 63 (263)
--.||||++...-|.--| ..|||.|=++|++++ ..||.|...-.
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~kat 56 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKAT 56 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhH
Confidence 347999999998885322 348999999999985 37999987644
No 76
>KOG3039|consensus
Probab=82.55 E-value=0.67 Score=41.87 Aligned_cols=44 Identities=20% Similarity=0.455 Sum_probs=36.8
Q ss_pred ceeeeccccCccccccccc---cCCCceecccccccc----CCCCCCccCCc
Q psy12127 19 SISECGVCLEPLDRGITSC---QTCGNLVCTSCAARL----LKCPFCRITID 63 (263)
Q Consensus 19 ~~l~CpIC~~~l~~Pv~qC---~~CGH~~C~~C~~~l----~~CP~Cr~~~~ 63 (263)
..+.||||.+.|.+-+ -| ..|||+||..|.+++ ..||+|..++.
T Consensus 220 ~ryiCpvtrd~LtNt~-~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plk 270 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTT-PCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLK 270 (303)
T ss_pred cceecccchhhhcCcc-ceEEeccCCcEeeHHHHHHhccccccccCCCCcCc
Confidence 6799999999999753 23 457999999999997 37999999885
No 77
>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=81.22 E-value=0.9 Score=32.31 Aligned_cols=33 Identities=30% Similarity=0.860 Sum_probs=17.6
Q ss_pred ceeeeccccCcccc--ccccccCCCceeccccccc
Q psy12127 19 SISECGVCLEPLDR--GITSCQTCGNLVCTSCAAR 51 (263)
Q Consensus 19 ~~l~CpIC~~~l~~--Pv~qC~~CGH~~C~~C~~~ 51 (263)
+.-.|.+|...+.- --..|..||++||+.|...
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence 34468999888742 2367999999999999765
No 78
>KOG0804|consensus
Probab=80.58 E-value=0.58 Score=45.47 Aligned_cols=49 Identities=27% Similarity=0.594 Sum_probs=38.1
Q ss_pred hhcCCceeeeccccCcccccc--ccccCCCceecccccccc--CCCCCCccCC
Q psy12127 14 KELIASISECGVCLEPLDRGI--TSCQTCGNLVCTSCAARL--LKCPFCRITI 62 (263)
Q Consensus 14 ~~~l~~~l~CpIC~~~l~~Pv--~qC~~CGH~~C~~C~~~l--~~CP~Cr~~~ 62 (263)
.-.+.++-.||||++-|-+-+ ..-.-|.|.|=.+|..++ ..||+||--.
T Consensus 169 ~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~scpvcR~~q 221 (493)
T KOG0804|consen 169 PTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDSSCPVCRYCQ 221 (493)
T ss_pred CCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhcccCcChhhhhhc
Confidence 345678889999999998654 112348999999999997 5999999654
No 79
>KOG0825|consensus
Probab=79.99 E-value=0.32 Score=50.26 Aligned_cols=43 Identities=19% Similarity=0.549 Sum_probs=31.2
Q ss_pred eeeccccCccccccccc-cCCCceecccccccc----CCCCCCccCCc
Q psy12127 21 SECGVCLEPLDRGITSC-QTCGNLVCTSCAARL----LKCPFCRITID 63 (263)
Q Consensus 21 l~CpIC~~~l~~Pv~qC-~~CGH~~C~~C~~~l----~~CP~Cr~~~~ 63 (263)
-.||+|..-..+-...- ..|+|.||..|+..| ..||.||..+.
T Consensus 124 ~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 124 NQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFG 171 (1134)
T ss_pred hhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhh
Confidence 35888877666432111 248999999999987 48999998764
No 80
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=79.03 E-value=0.99 Score=26.17 Aligned_cols=23 Identities=35% Similarity=0.765 Sum_probs=16.9
Q ss_pred ecCCCCCCCceeeeccchhhhhhcccC
Q psy12127 81 LPCRNFRFGCKVYLPKAKRDKHEDKCK 107 (263)
Q Consensus 81 v~C~~~~~GC~~~~~~~~~~~He~~C~ 107 (263)
++|++ |+..+....+..|+..|.
T Consensus 3 ~~C~~----CgR~F~~~~l~~H~~~C~ 25 (25)
T PF13913_consen 3 VPCPI----CGRKFNPDRLEKHEKICK 25 (25)
T ss_pred CcCCC----CCCEECHHHHHHHHHhcC
Confidence 56764 777777778888887774
No 81
>KOG2462|consensus
Probab=78.76 E-value=3.1 Score=38.16 Aligned_cols=24 Identities=21% Similarity=0.497 Sum_probs=12.8
Q ss_pred ceecCCCCCCCCcc-ChhhHHHHHhcc
Q psy12127 109 RQLKCPMHACPWTN-SVLHLSEHLNQV 134 (263)
Q Consensus 109 ~~~~CP~~~C~~~g-~~~~L~~Hl~~~ 134 (263)
+|..|| .|+-.. .+..|..|+.++
T Consensus 214 KPF~C~--hC~kAFADRSNLRAHmQTH 238 (279)
T KOG2462|consen 214 KPFSCP--HCGKAFADRSNLRAHMQTH 238 (279)
T ss_pred CCccCC--cccchhcchHHHHHHHHhh
Confidence 455665 354442 455666666543
No 82
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=77.98 E-value=1.4 Score=24.70 Aligned_cols=24 Identities=38% Similarity=0.816 Sum_probs=17.6
Q ss_pred ecCCCCCCCCccChhhHHHHHhcccC
Q psy12127 111 LKCPMHACPWTNSVLHLSEHLNQVHH 136 (263)
Q Consensus 111 ~~CP~~~C~~~g~~~~L~~Hl~~~H~ 136 (263)
+.|+ .|+|..+..+|..|++..|+
T Consensus 1 y~C~--~C~y~t~~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCP--HCSYSTSKSNLKRHLKRHHP 24 (24)
T ss_dssp EE-S--SSS-EESHHHHHHHHHHHHS
T ss_pred CCCC--CCCCcCCHHHHHHHHHhhCc
Confidence 3565 58898888899999998774
No 83
>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=77.83 E-value=1.1 Score=30.42 Aligned_cols=30 Identities=27% Similarity=0.873 Sum_probs=22.4
Q ss_pred eeccccCcccc--ccccccCCCceeccccccc
Q psy12127 22 ECGVCLEPLDR--GITSCQTCGNLVCTSCAAR 51 (263)
Q Consensus 22 ~CpIC~~~l~~--Pv~qC~~CGH~~C~~C~~~ 51 (263)
.|.+|...+.. .-..|..||++||..|...
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~ 35 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSN 35 (57)
T ss_pred cCcccCccccCCccccccCcCcCCcChHHcCC
Confidence 57777665542 2367999999999999775
No 84
>KOG1812|consensus
Probab=77.34 E-value=0.72 Score=44.30 Aligned_cols=33 Identities=27% Similarity=0.704 Sum_probs=22.7
Q ss_pred eeeecccc-Ccccccccc-ccCCCceecccccccc
Q psy12127 20 ISECGVCL-EPLDRGITS-CQTCGNLVCTSCAARL 52 (263)
Q Consensus 20 ~l~CpIC~-~~l~~Pv~q-C~~CGH~~C~~C~~~l 52 (263)
..+|.||. +.....-.+ -..|||.||..|+.+.
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ 180 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQH 180 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHH
Confidence 56899999 443332222 2459999999998863
No 85
>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 PRK14714 DNA polymerase II large subunit; Provisional
Probab=76.47 E-value=2.3 Score=46.40 Aligned_cols=43 Identities=28% Similarity=0.796 Sum_probs=26.8
Q ss_pred eeeeccccCccccccccccCCCce-----ecccccccc-------CCCCCCccCCcc
Q psy12127 20 ISECGVCLEPLDRGITSCQTCGNL-----VCTSCAARL-------LKCPFCRITIDY 64 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC~~CGH~-----~C~~C~~~l-------~~CP~Cr~~~~~ 64 (263)
.+.||-|...... ..|+.||.. .|.+|-.++ ..||.|..++..
T Consensus 667 ~rkCPkCG~~t~~--~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~ 721 (1337)
T PRK14714 667 RRRCPSCGTETYE--NRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTP 721 (1337)
T ss_pred EEECCCCCCcccc--ccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCcccc
Confidence 4566666665433 256666654 366676553 279999988753
No 87
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=76.03 E-value=2.2 Score=30.11 Aligned_cols=38 Identities=26% Similarity=0.718 Sum_probs=20.8
Q ss_pred eeccccCcccc----ccccccCCCce---eccccccccC--CCCCCc
Q psy12127 22 ECGVCLEPLDR----GITSCQTCGNL---VCTSCAARLL--KCPFCR 59 (263)
Q Consensus 22 ~CpIC~~~l~~----Pv~qC~~CGH~---~C~~C~~~l~--~CP~Cr 59 (263)
.|..|...+.+ ..+.|++||.. -|..|++.-. .||.|.
T Consensus 9 ~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 9 KCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCG 55 (59)
T ss_pred cccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcCCceECCCCC
Confidence 46666655542 23556666654 3666655532 677664
No 88
>KOG3800|consensus
Probab=75.32 E-value=1 Score=41.50 Aligned_cols=42 Identities=26% Similarity=0.718 Sum_probs=29.0
Q ss_pred eeccccCcc-ccc-c-ccccCCCceecccccccc-----CCCCCCccCCc
Q psy12127 22 ECGVCLEPL-DRG-I-TSCQTCGNLVCTSCAARL-----LKCPFCRITID 63 (263)
Q Consensus 22 ~CpIC~~~l-~~P-v-~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~ 63 (263)
.||+|..-- ..| + ..-..|||..|.+|...+ ..||.|..++-
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR 51 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence 478886422 233 1 112359999999999986 38999998764
No 89
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=74.42 E-value=2 Score=29.52 Aligned_cols=20 Identities=25% Similarity=0.710 Sum_probs=16.1
Q ss_pred ccccccCCCceecccccccc
Q psy12127 33 GITSCQTCGNLVCTSCAARL 52 (263)
Q Consensus 33 Pv~qC~~CGH~~C~~C~~~l 52 (263)
+..+|+.||+.||..|...+
T Consensus 39 ~~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 39 NRVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred CeeECCCCCCeECCCCCCcC
Confidence 35679889999999998764
No 90
>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=72.16 E-value=3.3 Score=25.60 Aligned_cols=22 Identities=32% Similarity=0.877 Sum_probs=10.7
Q ss_pred eeccccCccc----cccccccCCCcee
Q psy12127 22 ECGVCLEPLD----RGITSCQTCGNLV 44 (263)
Q Consensus 22 ~CpIC~~~l~----~Pv~qC~~CGH~~ 44 (263)
.|.-|..... +|| +|+.|||.+
T Consensus 2 ~C~~Cg~~~~~~~~~~i-rC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPI-RCPECGHRI 27 (32)
T ss_dssp BESSSSSSE-BSTSSTS-SBSSSS-SE
T ss_pred CCCcCCCeeEcCCCCcE-ECCcCCCeE
Confidence 3555554443 333 677777753
No 91
>KOG2807|consensus
Probab=71.70 E-value=2 Score=40.32 Aligned_cols=37 Identities=38% Similarity=0.948 Sum_probs=28.0
Q ss_pred ecccc-CccccccccccCCCceecccccc----ccCCCCCCc
Q psy12127 23 CGVCL-EPLDRGITSCQTCGNLVCTSCAA----RLLKCPFCR 59 (263)
Q Consensus 23 CpIC~-~~l~~Pv~qC~~CGH~~C~~C~~----~l~~CP~Cr 59 (263)
|-.|. +.+..+.++|..|.+.||..|-. .|..||-|.
T Consensus 333 Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCe 374 (378)
T KOG2807|consen 333 CFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCE 374 (378)
T ss_pred eeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcC
Confidence 88884 44446788999999999999943 346888886
No 92
>KOG4692|consensus
Probab=70.18 E-value=1.3 Score=42.10 Aligned_cols=43 Identities=21% Similarity=0.587 Sum_probs=34.0
Q ss_pred ceeeeccccCccccccccccCCCceecccccccc----CCCCCCccCCc
Q psy12127 19 SISECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITID 63 (263)
Q Consensus 19 ~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~ 63 (263)
+.-.||||+---...+++ .|||.-|..|+.++ ..|-.|...+.
T Consensus 421 Ed~lCpICyA~pi~Avf~--PC~H~SC~~CI~qHlmN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 421 EDNLCPICYAGPINAVFA--PCSHRSCYGCITQHLMNCKRCFFCKTTVI 467 (489)
T ss_pred ccccCcceecccchhhcc--CCCCchHHHHHHHHHhcCCeeeEecceee
Confidence 445699999877777775 68999999999985 36888877553
No 93
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=69.97 E-value=3.3 Score=26.14 Aligned_cols=11 Identities=18% Similarity=0.540 Sum_probs=6.3
Q ss_pred eeeccccCccc
Q psy12127 21 SECGVCLEPLD 31 (263)
Q Consensus 21 l~CpIC~~~l~ 31 (263)
+.||-|...+.
T Consensus 3 i~Cp~C~~~y~ 13 (36)
T PF13717_consen 3 ITCPNCQAKYE 13 (36)
T ss_pred EECCCCCCEEe
Confidence 45666665554
No 94
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=69.46 E-value=2.2 Score=24.27 Aligned_cols=20 Identities=25% Similarity=0.775 Sum_probs=10.1
Q ss_pred eccccCccccccccccCCCc
Q psy12127 23 CGVCLEPLDRGITSCQTCGN 42 (263)
Q Consensus 23 CpIC~~~l~~Pv~qC~~CGH 42 (263)
||.|...+.+-...|++||+
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CcccCCCCCCcCcchhhhCC
Confidence 55566555544334444443
No 95
>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=69.08 E-value=1.5 Score=29.73 Aligned_cols=41 Identities=22% Similarity=0.570 Sum_probs=20.9
Q ss_pred eeeeccccCccccccccccCCCceecccccccc------C--CCCCCccC
Q psy12127 20 ISECGVCLEPLDRGITSCQTCGNLVCTSCAARL------L--KCPFCRIT 61 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l------~--~CP~Cr~~ 61 (263)
.|.||+-...+.-|++- ..|.|.-|-+=..-+ + +||.|.++
T Consensus 2 sL~CPls~~~i~~P~Rg-~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 2 SLRCPLSFQRIRIPVRG-KNCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp ESB-TTTSSB-SSEEEE-TT--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred eeeCCCCCCEEEeCccC-CcCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 37899999999999865 569998653311111 1 69999764
No 96
>KOG3161|consensus
Probab=68.40 E-value=1.1 Score=45.45 Aligned_cols=59 Identities=25% Similarity=0.427 Sum_probs=38.0
Q ss_pred CCceeeeccccCccc----cccccccCCCceecccccccc--CCCCC--CccCCc---ccccccHHHHHhhh
Q psy12127 17 IASISECGVCLEPLD----RGITSCQTCGNLVCTSCAARL--LKCPF--CRITID---YSWQRNVALERIFT 77 (263)
Q Consensus 17 l~~~l~CpIC~~~l~----~Pv~qC~~CGH~~C~~C~~~l--~~CP~--Cr~~~~---~~~~rn~~le~~v~ 77 (263)
..+.+.|+||...+. -|+.. .|||++|+.|.+++ ..||. ...... .+..+|.++-+++.
T Consensus 8 w~~~l~c~ic~n~f~~~~~~Pvsl--~cghtic~~c~~~lyn~scp~~~De~~~~~~~~e~p~n~alL~~~~ 77 (861)
T KOG3161|consen 8 WVLLLLCDICLNLFVVQRLEPVSL--QCGHTICGHCVQLLYNASCPTKRDEDSSLMQLKEEPRNYALLRREH 77 (861)
T ss_pred hHHHhhchHHHHHHHHHhcCcccc--cccchHHHHHHHhHhhccCCCCccccchhcChhhcchhHHHHHhhc
Confidence 457889999966554 45542 48999999999997 48882 222211 12556766655443
No 97
>KOG1001|consensus
Probab=67.92 E-value=1.3 Score=45.48 Aligned_cols=40 Identities=30% Similarity=0.821 Sum_probs=32.5
Q ss_pred eeeccccCccccccccccCCCceecccccccc------CCCCCCccCCc
Q psy12127 21 SECGVCLEPLDRGITSCQTCGNLVCTSCAARL------LKCPFCRITID 63 (263)
Q Consensus 21 l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l------~~CP~Cr~~~~ 63 (263)
+.|++|.+ ...++. +.|||.+|..|+.+. ..||.||..+.
T Consensus 455 ~~c~ic~~-~~~~~i--t~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~ 500 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFI--TRCGHDFCVECLKKSIQQSENAPCPLCRNVLK 500 (674)
T ss_pred cccccccc-ccccee--ecccchHHHHHHHhccccccCCCCcHHHHHHH
Confidence 79999999 666654 568999999999884 26999988664
No 98
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=67.66 E-value=3.6 Score=26.05 Aligned_cols=13 Identities=15% Similarity=0.330 Sum_probs=8.9
Q ss_pred eeeccccCccccc
Q psy12127 21 SECGVCLEPLDRG 33 (263)
Q Consensus 21 l~CpIC~~~l~~P 33 (263)
..||-|...+.-|
T Consensus 3 i~CP~C~~~f~v~ 15 (37)
T PF13719_consen 3 ITCPNCQTRFRVP 15 (37)
T ss_pred EECCCCCceEEcC
Confidence 5677777777654
No 99
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=67.26 E-value=5.3 Score=28.32 Aligned_cols=13 Identities=23% Similarity=0.915 Sum_probs=9.4
Q ss_pred ceecCCCCCCCCccC
Q psy12127 109 RQLKCPMHACPWTNS 123 (263)
Q Consensus 109 ~~~~CP~~~C~~~g~ 123 (263)
.+|.|| .|+|+|.
T Consensus 49 ~~Y~Cp--~CGF~GP 61 (61)
T COG2888 49 NPYRCP--KCGFEGP 61 (61)
T ss_pred CceECC--CcCccCC
Confidence 577886 5888874
No 100
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=66.44 E-value=0.49 Score=32.41 Aligned_cols=45 Identities=27% Similarity=0.623 Sum_probs=34.1
Q ss_pred ceeeeccccCcccc-ccccccCCCceecccccccc-CCCCCCccCCc
Q psy12127 19 SISECGVCLEPLDR-GITSCQTCGNLVCTSCAARL-LKCPFCRITID 63 (263)
Q Consensus 19 ~~l~CpIC~~~l~~-Pv~qC~~CGH~~C~~C~~~l-~~CP~Cr~~~~ 63 (263)
+.+.|..|...... -.+||.-||...|.+|++.- -.|-.|.+.+.
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~deYY~CksC~Gii~ 52 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDEYYTCKSCNGIIN 52 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhhHhHHHhhhchhh
Confidence 46778888876543 36899999999999999873 46777776553
No 101
>KOG2231|consensus
Probab=66.39 E-value=3.3 Score=42.49 Aligned_cols=40 Identities=35% Similarity=0.871 Sum_probs=31.6
Q ss_pred eeccccCccccccccccCCCc-eecccccccc----------CCCCCCccCCc
Q psy12127 22 ECGVCLEPLDRGITSCQTCGN-LVCTSCAARL----------LKCPFCRITID 63 (263)
Q Consensus 22 ~CpIC~~~l~~Pv~qC~~CGH-~~C~~C~~~l----------~~CP~Cr~~~~ 63 (263)
.|+||..-..-+.+ .+||| .+|..|..++ ..||.|+..+.
T Consensus 2 ~c~ic~~s~~~~~~--~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~ 52 (669)
T KOG2231|consen 2 SCAICAFSPDFVGR--GSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVE 52 (669)
T ss_pred CcceeecCcccccc--ccccccccchhhhhhhhhhcccccccccCccccccee
Confidence 48899888877765 57999 8999998774 14799998665
No 102
>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=66.06 E-value=4.3 Score=27.74 Aligned_cols=32 Identities=25% Similarity=0.718 Sum_probs=19.8
Q ss_pred eeecc--ccCccccc------cccccCCCceecccccccc
Q psy12127 21 SECGV--CLEPLDRG------ITSCQTCGNLVCTSCAARL 52 (263)
Q Consensus 21 l~CpI--C~~~l~~P------v~qC~~CGH~~C~~C~~~l 52 (263)
--||- |..++... ..+|+.||+.||..|...+
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 37877 88887732 1579889999999998764
No 103
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=64.30 E-value=2.8 Score=31.27 Aligned_cols=43 Identities=23% Similarity=0.672 Sum_probs=18.8
Q ss_pred eeeccccCccc-----cccccccCCCceecccccccc-----CCCCCCccCCc
Q psy12127 21 SECGVCLEPLD-----RGITSCQTCGNLVCTSCAARL-----LKCPFCRITID 63 (263)
Q Consensus 21 l~CpIC~~~l~-----~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~ 63 (263)
-.|.||.+-+- .+...|..|+--+|+.|.+-- ..||.|+.+..
T Consensus 10 qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 10 QICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp -B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred cccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 36999998765 455678899999999998652 47999997754
No 104
>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=64.04 E-value=4.5 Score=32.16 Aligned_cols=42 Identities=24% Similarity=0.634 Sum_probs=28.9
Q ss_pred ceeeeccccCccc---cccccccCCCceeccccccccC-----CCCCCcc
Q psy12127 19 SISECGVCLEPLD---RGITSCQTCGNLVCTSCAARLL-----KCPFCRI 60 (263)
Q Consensus 19 ~~l~CpIC~~~l~---~Pv~qC~~CGH~~C~~C~~~l~-----~CP~Cr~ 60 (263)
+.-.|.+|..++. .+-.+|..|+|.+|..|..... .|-+|..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQK 102 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSSSCCEEEHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCCCCCEEChhhHH
Confidence 4558999987643 3346899999999999977631 4666654
No 105
>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=62.98 E-value=5.2 Score=25.02 Aligned_cols=13 Identities=15% Similarity=0.353 Sum_probs=8.0
Q ss_pred eeeccccCccccc
Q psy12127 21 SECGVCLEPLDRG 33 (263)
Q Consensus 21 l~CpIC~~~l~~P 33 (263)
+.||-|...+.-+
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 5677777755533
No 106
>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=62.85 E-value=6.8 Score=26.62 Aligned_cols=25 Identities=32% Similarity=0.490 Sum_probs=21.2
Q ss_pred ecCCCCCCCCccChhhHHHHHhcccCc
Q psy12127 111 LKCPMHACPWTNSVLHLSEHLNQVHHL 137 (263)
Q Consensus 111 ~~CP~~~C~~~g~~~~L~~Hl~~~H~~ 137 (263)
+.||+ |+...+..+|..|+...|..
T Consensus 3 f~CP~--C~~~~~~~~L~~H~~~~H~~ 27 (54)
T PF05605_consen 3 FTCPY--CGKGFSESSLVEHCEDEHRS 27 (54)
T ss_pred cCCCC--CCCccCHHHHHHHHHhHCcC
Confidence 57886 88867889999999999983
No 107
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=62.27 E-value=5.2 Score=26.63 Aligned_cols=39 Identities=21% Similarity=0.429 Sum_probs=29.5
Q ss_pred CCCCCccCCcccccccHHHHHhhhcceecCCCCCCCceeeecc
Q psy12127 54 KCPFCRITIDYSWQRNVALERIFTKLELPCRNFRFGCKVYLPK 96 (263)
Q Consensus 54 ~CP~Cr~~~~~~~~rn~~le~~v~~l~v~C~~~~~GC~~~~~~ 96 (263)
.||.|+.... ......+.+.+.++-..|.|.+ |++.+..
T Consensus 1 ~CP~Cg~~a~--ir~S~~~s~~~~~~Y~qC~N~~--Cg~tfv~ 39 (47)
T PF04606_consen 1 RCPHCGSKAR--IRTSRQLSPLTRELYCQCTNPE--CGHTFVA 39 (47)
T ss_pred CcCCCCCeeE--EEEchhhCcceEEEEEEECCCc--CCCEEEE
Confidence 5999998775 4557778888899999999975 6555443
No 108
>KOG2462|consensus
Probab=62.17 E-value=4.3 Score=37.22 Aligned_cols=101 Identities=15% Similarity=0.305 Sum_probs=54.8
Q ss_pred CceeeeccccCcccc-ccccccCCCceeccccccccC-CCCCCccCCcccccccHHHHHhhhc----ceecCCCCCCCce
Q psy12127 18 ASISECGVCLEPLDR-GITSCQTCGNLVCTSCAARLL-KCPFCRITIDYSWQRNVALERIFTK----LELPCRNFRFGCK 91 (263)
Q Consensus 18 ~~~l~CpIC~~~l~~-Pv~qC~~CGH~~C~~C~~~l~-~CP~Cr~~~~~~~~rn~~le~~v~~----l~v~C~~~~~GC~ 91 (263)
...+.|++|...... |-.. .|+- -..+. .|++|++.+ .|...|+.=+.. -.+.|++ |.
T Consensus 159 ~ka~~C~~C~K~YvSmpALk----MHir----TH~l~c~C~iCGKaF----SRPWLLQGHiRTHTGEKPF~C~h----C~ 222 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALK----MHIR----THTLPCECGICGKAF----SRPWLLQGHIRTHTGEKPFSCPH----CG 222 (279)
T ss_pred cccccCCCCCceeeehHHHh----hHhh----ccCCCcccccccccc----cchHHhhcccccccCCCCccCCc----cc
Confidence 566788888876663 3221 3321 00011 677776654 344445444432 3455553 66
Q ss_pred eee-ccchhhhhhc-ccCCceecCCCCCCCCccChh-hHHHHHhcccC
Q psy12127 92 VYL-PKAKRDKHED-KCKFRQLKCPMHACPWTNSVL-HLSEHLNQVHH 136 (263)
Q Consensus 92 ~~~-~~~~~~~He~-~C~~~~~~CP~~~C~~~g~~~-~L~~Hl~~~H~ 136 (263)
..+ ...+|+.|+. -=..+++.|+ .|+-..++. -|.+|++..+.
T Consensus 223 kAFADRSNLRAHmQTHS~~K~~qC~--~C~KsFsl~SyLnKH~ES~C~ 268 (279)
T KOG2462|consen 223 KAFADRSNLRAHMQTHSDVKKHQCP--RCGKSFALKSYLNKHSESACL 268 (279)
T ss_pred chhcchHHHHHHHHhhcCCccccCc--chhhHHHHHHHHHHhhhhccc
Confidence 655 3456667764 2345567774 577666544 44577776654
No 109
>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=62.05 E-value=4.8 Score=26.22 Aligned_cols=28 Identities=21% Similarity=0.557 Sum_probs=16.7
Q ss_pred ecc--ccCccccccccccCCCceeccccccc
Q psy12127 23 CGV--CLEPLDRGITSCQTCGNLVCTSCAAR 51 (263)
Q Consensus 23 CpI--C~~~l~~Pv~qC~~CGH~~C~~C~~~ 51 (263)
|.+ |.....-|+ .|..||..||..=+..
T Consensus 1 C~~~~C~~~~~~~~-~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 1 CSFPGCKKKDFLPF-KCKHCGKSFCLKHRLP 30 (43)
T ss_dssp -SSTTT--BCTSHE-E-TTTS-EE-TTTHST
T ss_pred CccCcCcCccCCCe-ECCCCCcccCccccCc
Confidence 445 777777774 7999999999887655
No 110
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=61.17 E-value=5.2 Score=26.57 Aligned_cols=11 Identities=27% Similarity=0.365 Sum_probs=8.2
Q ss_pred eccccCccccc
Q psy12127 23 CGVCLEPLDRG 33 (263)
Q Consensus 23 CpIC~~~l~~P 33 (263)
||-|..+|.++
T Consensus 3 Cp~Cg~~l~~~ 13 (52)
T smart00661 3 CPKCGNMLIPK 13 (52)
T ss_pred CCCCCCccccc
Confidence 78888877665
No 111
>KOG2817|consensus
Probab=61.04 E-value=3.2 Score=39.85 Aligned_cols=43 Identities=28% Similarity=0.624 Sum_probs=30.8
Q ss_pred CCceeeeccccCccc---cccccccCCCceeccccccccC-------CCCCCccC
Q psy12127 17 IASISECGVCLEPLD---RGITSCQTCGNLVCTSCAARLL-------KCPFCRIT 61 (263)
Q Consensus 17 l~~~l~CpIC~~~l~---~Pv~qC~~CGH~~C~~C~~~l~-------~CP~Cr~~ 61 (263)
..+.|.|||=.+--. ||+.. .|||+++..=+.+++ +||-|...
T Consensus 331 fHSvF~CPVlKeqtsdeNPPm~L--~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 331 FHSVFICPVLKEQTSDENPPMML--ICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred ccceeecccchhhccCCCCCeee--eccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 468899999555443 67654 599999988888762 57777654
No 112
>KOG2932|consensus
Probab=60.39 E-value=3.1 Score=38.84 Aligned_cols=75 Identities=23% Similarity=0.445 Sum_probs=48.8
Q ss_pred eeeeccccCccccccccccCCCceecccccccc--CCCCCCccCCcccccccHHHHHhhhcceecCCCCCCCceee-ecc
Q psy12127 20 ISECGVCLEPLDRGITSCQTCGNLVCTSCAARL--LKCPFCRITIDYSWQRNVALERIFTKLELPCRNFRFGCKVY-LPK 96 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l--~~CP~Cr~~~~~~~~rn~~le~~v~~l~v~C~~~~~GC~~~-~~~ 96 (263)
+--|.-|..++.-==+. --|.|.||-.|.... +.||.|...+. -+|.....-.+-|. ...||..+ +.-
T Consensus 90 VHfCd~Cd~PI~IYGRm-IPCkHvFCl~CAr~~~dK~Cp~C~d~Vq-------rIeq~~~g~iFmC~-~~~GC~RTyLsq 160 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRM-IPCKHVFCLECARSDSDKICPLCDDRVQ-------RIEQIMMGGIFMCA-APHGCLRTYLSQ 160 (389)
T ss_pred eEeecccCCcceeeecc-cccchhhhhhhhhcCccccCcCcccHHH-------HHHHhcccceEEee-cchhHHHHHhhH
Confidence 45677888776631112 138999999997664 48999977653 45666656667776 56688764 344
Q ss_pred chhhhhh
Q psy12127 97 AKRDKHE 103 (263)
Q Consensus 97 ~~~~~He 103 (263)
.+++.|.
T Consensus 161 rDlqAHI 167 (389)
T KOG2932|consen 161 RDLQAHI 167 (389)
T ss_pred HHHHHHh
Confidence 5555554
No 113
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=60.36 E-value=4.8 Score=30.89 Aligned_cols=35 Identities=26% Similarity=0.660 Sum_probs=29.1
Q ss_pred eeccccCccccccccccCCCceeccccccccCCCCCCccCCc
Q psy12127 22 ECGVCLEPLDRGITSCQTCGNLVCTSCAARLLKCPFCRITID 63 (263)
Q Consensus 22 ~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l~~CP~Cr~~~~ 63 (263)
.|-||..-+..| ||.+|..|--+.+.|..|+..+.
T Consensus 46 ~C~~CK~~v~q~-------g~~YCq~CAYkkGiCamCGKki~ 80 (90)
T PF10235_consen 46 KCKICKTKVHQP-------GAKYCQTCAYKKGICAMCGKKIL 80 (90)
T ss_pred cccccccccccC-------CCccChhhhcccCcccccCCeec
Confidence 688887765543 89999999988899999999874
No 114
>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=60.29 E-value=5.3 Score=27.96 Aligned_cols=41 Identities=24% Similarity=0.554 Sum_probs=29.2
Q ss_pred eeccccCccccc---cccccCCCceecccccccc--CCCCCCccCCc
Q psy12127 22 ECGVCLEPLDRG---ITSCQTCGNLVCTSCAARL--LKCPFCRITID 63 (263)
Q Consensus 22 ~CpIC~~~l~~P---v~qC~~CGH~~C~~C~~~l--~~CP~Cr~~~~ 63 (263)
.|-.|..-|-+- .+.|+- .-+||..|.+.+ +.||.|++.+.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSf-ECTFC~~C~e~~l~~~CPNCgGelv 52 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSF-ECTFCADCAETMLNGVCPNCGGELV 52 (57)
T ss_pred CccccCCCCCCCCCcceEEeE-eCcccHHHHHHHhcCcCcCCCCccc
Confidence 355555555432 356666 668999999986 69999999875
No 115
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=59.91 E-value=6.9 Score=32.63 Aligned_cols=34 Identities=32% Similarity=0.612 Sum_probs=21.7
Q ss_pred ccccccccccCCCceeccccccccCCCCCCccCC
Q psy12127 29 PLDRGITSCQTCGNLVCTSCAARLLKCPFCRITI 62 (263)
Q Consensus 29 ~l~~Pv~qC~~CGH~~C~~C~~~l~~CP~Cr~~~ 62 (263)
+.-+-++.|.+|||...-.=-..+..||.|...-
T Consensus 107 ~~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 107 VVGPGTLVCENCGHEVELTHPERLPPCPKCGHTE 140 (146)
T ss_pred EecCceEecccCCCEEEecCCCcCCCCCCCCCCe
Confidence 3334466777788876554333356899998753
No 116
>KOG4628|consensus
Probab=59.40 E-value=6.4 Score=37.36 Aligned_cols=42 Identities=26% Similarity=0.752 Sum_probs=33.9
Q ss_pred eeeccccCccccc--cccccCCCceecccccccc-----CCCCCCccCCc
Q psy12127 21 SECGVCLEPLDRG--ITSCQTCGNLVCTSCAARL-----LKCPFCRITID 63 (263)
Q Consensus 21 l~CpIC~~~l~~P--v~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~ 63 (263)
..|.||++-+.+- +.. -.|+|.|=..|+++| ..||+|+..+.
T Consensus 230 ~~CaIClEdY~~GdklRi-LPC~H~FH~~CIDpWL~~~r~~CPvCK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRI-LPCSHKFHVNCIDPWLTQTRTFCPVCKRDIR 278 (348)
T ss_pred ceEEEeecccccCCeeeE-ecCCCchhhccchhhHhhcCccCCCCCCcCC
Confidence 6899999988853 333 468999999999996 25999999775
No 117
>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=59.12 E-value=5.8 Score=30.05 Aligned_cols=35 Identities=34% Similarity=0.739 Sum_probs=26.4
Q ss_pred CCceeeeccccCccccccccccCCCceeccccccc
Q psy12127 17 IASISECGVCLEPLDRGITSCQTCGNLVCTSCAAR 51 (263)
Q Consensus 17 l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~ 51 (263)
+.+.-.|++|...+....+.--.|||.+-.+|..+
T Consensus 75 i~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIKR 109 (109)
T ss_pred ECCCCCccCcCCcCCCceEEEeCCCeEEecccccC
Confidence 45566799999999976544344699999999753
No 118
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=58.79 E-value=3 Score=31.33 Aligned_cols=52 Identities=27% Similarity=0.538 Sum_probs=32.7
Q ss_pred ccccchhcCCceeeeccccCcccccccccc----CCCceecccccccc----CCCCCCccCCc
Q psy12127 9 CCANCKELIASISECGVCLEPLDRGITSCQ----TCGNLVCTSCAARL----LKCPFCRITID 63 (263)
Q Consensus 9 ~~~~~~~~l~~~l~CpIC~~~l~~Pv~qC~----~CGH~~C~~C~~~l----~~CP~Cr~~~~ 63 (263)
+|+-+...+.+ .||-|..-+. |--+|+ .|.|.|=..|+.++ +.||.+++++.
T Consensus 22 ~CaICRnhim~--~C~eCq~~~~-~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~ 81 (88)
T COG5194 22 VCAICRNHIMG--TCPECQFGMT-PGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWV 81 (88)
T ss_pred hhhhhhccccC--cCcccccCCC-CCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence 34444444433 4566655442 233442 48899989999885 48999999875
No 119
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=57.94 E-value=6.1 Score=25.37 Aligned_cols=24 Identities=38% Similarity=1.021 Sum_probs=16.7
Q ss_pred eccccCcccc-ccccccCCCceeccc
Q psy12127 23 CGVCLEPLDR-GITSCQTCGNLVCTS 47 (263)
Q Consensus 23 CpIC~~~l~~-Pv~qC~~CGH~~C~~ 47 (263)
|.+|.....- | +.|..||..||..
T Consensus 1 C~~C~~~~~l~~-f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTG-FKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCcccccC-eECCccCCccccc
Confidence 4556654444 6 5798899999876
No 120
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=57.58 E-value=4.8 Score=36.24 Aligned_cols=24 Identities=21% Similarity=0.524 Sum_probs=18.6
Q ss_pred eeeeccccCccc--cccccccCCCcee
Q psy12127 20 ISECGVCLEPLD--RGITSCQTCGNLV 44 (263)
Q Consensus 20 ~l~CpIC~~~l~--~Pv~qC~~CGH~~ 44 (263)
.|.||+|..+|. .....|.+ ||.|
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~-~h~f 27 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQ-NHQF 27 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCC-CCCC
Confidence 378999999996 34467877 8876
No 121
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=57.41 E-value=4 Score=39.11 Aligned_cols=60 Identities=20% Similarity=0.500 Sum_probs=39.9
Q ss_pred CCCCccccccc-hhcC-CceeeeccccCcccccccc-c----------cCCCceecccccccc----CCCCCCccCC
Q psy12127 3 CKKEPECCANC-KELI-ASISECGVCLEPLDRGITS-C----------QTCGNLVCTSCAARL----LKCPFCRITI 62 (263)
Q Consensus 3 ~~~~~~~~~~~-~~~l-~~~l~CpIC~~~l~~Pv~q-C----------~~CGH~~C~~C~~~l----~~CP~Cr~~~ 62 (263)
||.-+..++.. +|.| .+.-.|-||.+-|..|-.| - -.|||.+=-+|++.+ ..||.||.++
T Consensus 268 ~kdl~~~~~t~t~eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ 344 (491)
T COG5243 268 TKDLNAMYPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPV 344 (491)
T ss_pred hhHHHhhcchhhhhhhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcc
Confidence 34444555543 4444 3566899999985533211 0 148999999998876 4899999995
No 122
>KOG1814|consensus
Probab=57.14 E-value=3.7 Score=39.64 Aligned_cols=106 Identities=21% Similarity=0.505 Sum_probs=62.2
Q ss_pred hcCCceeeeccccCcccccc-ccccCCCceecccccccc------------CCCCCCccCC--ccc----------ccc-
Q psy12127 15 ELIASISECGVCLEPLDRGI-TSCQTCGNLVCTSCAARL------------LKCPFCRITI--DYS----------WQR- 68 (263)
Q Consensus 15 ~~l~~~l~CpIC~~~l~~Pv-~qC~~CGH~~C~~C~~~l------------~~CP~Cr~~~--~~~----------~~r- 68 (263)
.-+...+.|.||++-..-.+ ++=..|+|.||.+|.... -+||.+.-+- ... ..|
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 44578999999999776532 122469999999998763 1688644322 110 111
Q ss_pred -cHHHHHhhhcce--ecCCCCCCCceeeeccchhhhhhc---ccCCceec-CCC-----CCCCCccC
Q psy12127 69 -NVALERIFTKLE--LPCRNFRFGCKVYLPKAKRDKHED---KCKFRQLK-CPM-----HACPWTNS 123 (263)
Q Consensus 69 -n~~le~~v~~l~--v~C~~~~~GC~~~~~~~~~~~He~---~C~~~~~~-CP~-----~~C~~~g~ 123 (263)
-..+++-++.+. +.||++ -|.... ..+...-.. .|.|+-+. |.. ..|++++.
T Consensus 259 e~l~lqk~l~~msdv~yCPr~--~Cq~p~-~~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~ 322 (445)
T KOG1814|consen 259 EKLMLQKTLELMSDVVYCPRA--CCQLPV-KQDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAE 322 (445)
T ss_pred HHHHHHHHHHhhcccccCChh--hccCcc-ccCchhhhhhhccCccHHHHHHHHhhcCCCcccCchH
Confidence 223444445454 899986 466554 444444443 45555442 432 67888864
No 123
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=56.47 E-value=7.7 Score=30.25 Aligned_cols=34 Identities=21% Similarity=0.388 Sum_probs=18.7
Q ss_pred hcCCceeeeccccCcccc-ccccccCCCceecccccc
Q psy12127 15 ELIASISECGVCLEPLDR-GITSCQTCGNLVCTSCAA 50 (263)
Q Consensus 15 ~~l~~~l~CpIC~~~l~~-Pv~qC~~CGH~~C~~C~~ 50 (263)
..+...+.||-|.....+ |+-. .. +|+.|..|-.
T Consensus 16 ~klpt~f~CP~Cge~~v~v~~~k-~~-~h~~C~~CG~ 50 (99)
T PRK14892 16 PKLPKIFECPRCGKVSISVKIKK-NI-AIITCGNCGL 50 (99)
T ss_pred cCCCcEeECCCCCCeEeeeecCC-Cc-ceEECCCCCC
Confidence 345678888888854332 3322 23 5555555533
No 124
>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=56.25 E-value=8 Score=27.63 Aligned_cols=15 Identities=47% Similarity=0.930 Sum_probs=11.6
Q ss_pred cCCceeeeccccCcc
Q psy12127 16 LIASISECGVCLEPL 30 (263)
Q Consensus 16 ~l~~~l~CpIC~~~l 30 (263)
.+.+.|.||+|..+|
T Consensus 3 ~llniL~Cp~ck~pL 17 (68)
T PF03966_consen 3 LLLNILACPVCKGPL 17 (68)
T ss_dssp GGCGTBB-TTTSSBE
T ss_pred hHHhhhcCCCCCCcc
Confidence 456889999999977
No 125
>KOG0826|consensus
Probab=56.07 E-value=3.5 Score=38.70 Aligned_cols=44 Identities=20% Similarity=0.422 Sum_probs=33.3
Q ss_pred CceeeeccccCccccccccccCCCceecccccccc----CCCCCCccCC
Q psy12127 18 ASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITI 62 (263)
Q Consensus 18 ~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~ 62 (263)
.+.-.||+|..--.+|...-.+ |-+||-.|+-+. +.||+=..|.
T Consensus 298 ~~~~~CpvClk~r~Nptvl~vS-GyVfCY~Ci~~Yv~~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQNPTVLEVS-GYVFCYPCIFSYVVNYGHCPVTGYPA 345 (357)
T ss_pred CccccChhHHhccCCCceEEec-ceEEeHHHHHHHHHhcCCCCccCCcc
Confidence 3556899999999999543345 999999998773 6899654443
No 126
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=55.48 E-value=9 Score=25.33 Aligned_cols=9 Identities=33% Similarity=0.851 Sum_probs=4.6
Q ss_pred CCCCCccCC
Q psy12127 54 KCPFCRITI 62 (263)
Q Consensus 54 ~CP~Cr~~~ 62 (263)
.||.|+..+
T Consensus 21 rC~~CG~rI 29 (44)
T smart00659 21 RCRECGYRI 29 (44)
T ss_pred ECCCCCceE
Confidence 455555444
No 127
>KOG4362|consensus
Probab=54.83 E-value=2.4 Score=43.49 Aligned_cols=52 Identities=25% Similarity=0.620 Sum_probs=41.8
Q ss_pred cccchhcCCceeeeccccCccccccccccCCCceecccccccc-------CCCCCCccCCc
Q psy12127 10 CANCKELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARL-------LKCPFCRITID 63 (263)
Q Consensus 10 ~~~~~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l-------~~CP~Cr~~~~ 63 (263)
+++-...+...++||||......|+. ..|.|.||..|+..+ ..||.|+..+.
T Consensus 11 ~~~vi~~~~k~lEc~ic~~~~~~p~~--~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 11 VAQVINAMQKILECPICLEHVKEPSL--LKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred HHhHHHHHhhhccCCceeEEeeccch--hhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence 44445566788999999999999965 468999999999874 27999997654
No 128
>KOG3039|consensus
Probab=54.31 E-value=6.2 Score=35.82 Aligned_cols=35 Identities=17% Similarity=0.302 Sum_probs=29.4
Q ss_pred hcCCceeeeccccCccccccccccCCCceeccccccc
Q psy12127 15 ELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAAR 51 (263)
Q Consensus 15 ~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~ 51 (263)
+.+.+.--|..|+.+..+|| .|+. ||+||+.|+..
T Consensus 38 DsiK~FdcCsLtLqPc~dPv-it~~-GylfdrEaILe 72 (303)
T KOG3039|consen 38 DSIKPFDCCSLTLQPCRDPV-ITPD-GYLFDREAILE 72 (303)
T ss_pred cccCCcceeeeecccccCCc-cCCC-CeeeeHHHHHH
Confidence 44566667999999999997 5788 99999999875
No 129
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=54.30 E-value=8.3 Score=39.62 Aligned_cols=49 Identities=24% Similarity=0.564 Sum_probs=22.9
Q ss_pred ccccchhcCCc-eeeeccccCccccccccccCCCceeccccccccCCCCCCccCCc
Q psy12127 9 CCANCKELIAS-ISECGVCLEPLDRGITSCQTCGNLVCTSCAARLLKCPFCRITID 63 (263)
Q Consensus 9 ~~~~~~~~l~~-~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l~~CP~Cr~~~~ 63 (263)
.||.|..++.+ .--|+-|...+.. ..|+.||+.. -.....||.|+.+++
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l~~--~~Cp~CG~~~----~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSLTH--KPCPQCGTEV----PVDEAHCPNCGAETG 52 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCCCC--CcCCCCCCCC----CcccccccccCCccc
Confidence 45555444322 2236666665542 1355555430 000135777776654
No 130
>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=53.92 E-value=1.8 Score=39.02 Aligned_cols=56 Identities=25% Similarity=0.554 Sum_probs=35.4
Q ss_pred eeeccccC--ccccc--cccccCCCceecccccccc-----CCCC--CCccCCcc-----cccccHHHHHhh
Q psy12127 21 SECGVCLE--PLDRG--ITSCQTCGNLVCTSCAARL-----LKCP--FCRITIDY-----SWQRNVALERIF 76 (263)
Q Consensus 21 l~CpIC~~--~l~~P--v~qC~~CGH~~C~~C~~~l-----~~CP--~Cr~~~~~-----~~~rn~~le~~v 76 (263)
-.||+|.. +|.|- ++.-+.|=|.+|.+|..++ .+|| .|.+.+.. ..+.+..+|+.+
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~kf~~qtFeD~~vEkEv 82 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIKFIKQTFEDITVEKEV 82 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHhcccccccchhhhhhhh
Confidence 37999974 33333 2333458999999999985 3899 68875432 133445555544
No 131
>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=52.73 E-value=11 Score=24.48 Aligned_cols=26 Identities=23% Similarity=0.552 Sum_probs=16.6
Q ss_pred ccccCCCceeccccccc---cCCCCCCcc
Q psy12127 35 TSCQTCGNLVCTSCAAR---LLKCPFCRI 60 (263)
Q Consensus 35 ~qC~~CGH~~C~~C~~~---l~~CP~Cr~ 60 (263)
|.|..|||.|=..-.-. ...||.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 56888888764433211 137999987
No 132
>PF05253 zf-U11-48K: U11-48K-like CHHC zinc finger; InterPro: IPR022776 This zinc binding domain [] has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function []. ; PDB: 2VY5_A 2VY4_A.
Probab=52.38 E-value=6.7 Score=23.08 Aligned_cols=24 Identities=25% Similarity=0.436 Sum_probs=15.7
Q ss_pred ecCCCCCCCceeeeccchhhhhhcccC
Q psy12127 81 LPCRNFRFGCKVYLPKAKRDKHEDKCK 107 (263)
Q Consensus 81 v~C~~~~~GC~~~~~~~~~~~He~~C~ 107 (263)
+.|||. =.-.++-.+++.|...|+
T Consensus 3 v~CPyn---~~H~v~~~~l~~Hi~~C~ 26 (27)
T PF05253_consen 3 VRCPYN---PSHRVPASELQKHIKKCP 26 (27)
T ss_dssp EE-TTT---SS-EEEGGGHHHHHHHHH
T ss_pred eeCCCC---CCcCcCHHHHHHHHHHcC
Confidence 567773 456777788888887774
No 133
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=52.34 E-value=8.8 Score=42.10 Aligned_cols=43 Identities=23% Similarity=0.638 Sum_probs=34.3
Q ss_pred cccccchhcCCceeeeccccCccccccccccCCCce---------ecccccccc
Q psy12127 8 ECCANCKELIASISECGVCLEPLDRGITSCQTCGNL---------VCTSCAARL 52 (263)
Q Consensus 8 ~~~~~~~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~---------~C~~C~~~l 52 (263)
-.||.|...... ..||.|...+.+ ++.|++||.. +|..|-.++
T Consensus 668 rkCPkCG~~t~~-~fCP~CGs~te~-vy~CPsCGaev~~des~a~~CP~CGtpl 719 (1337)
T PRK14714 668 RRCPSCGTETYE-NRCPDCGTHTEP-VYVCPDCGAEVPPDESGRVECPRCDVEL 719 (1337)
T ss_pred EECCCCCCcccc-ccCcccCCcCCC-ceeCccCCCccCCCccccccCCCCCCcc
Confidence 368998776655 489999999875 4689999995 799998664
No 134
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=51.79 E-value=8.4 Score=29.66 Aligned_cols=31 Identities=19% Similarity=0.516 Sum_probs=20.7
Q ss_pred cccccccccCCCceeccccccccCCCCCCccCC
Q psy12127 30 LDRGITSCQTCGNLVCTSCAARLLKCPFCRITI 62 (263)
Q Consensus 30 l~~Pv~qC~~CGH~~C~~C~~~l~~CP~Cr~~~ 62 (263)
+.|| +|.+||-.|=..=+++-+.||.|....
T Consensus 56 v~Pa--~CkkCGfef~~~~ik~pSRCP~CKSE~ 86 (97)
T COG3357 56 VRPA--RCKKCGFEFRDDKIKKPSRCPKCKSEW 86 (97)
T ss_pred ecCh--hhcccCccccccccCCcccCCcchhhc
Confidence 4454 799999988442222236899998753
No 135
>KOG3002|consensus
Probab=51.46 E-value=5.7 Score=36.96 Aligned_cols=77 Identities=19% Similarity=0.325 Sum_probs=53.6
Q ss_pred CCCCCCccCCccc-cccc---HHHHHhhhcceecCCCCCCCceeeeccchhhhhhcccCCceecCCC--CCCCCccChhh
Q psy12127 53 LKCPFCRITIDYS-WQRN---VALERIFTKLELPCRNFRFGCKVYLPKAKRDKHEDKCKFRQLKCPM--HACPWTNSVLH 126 (263)
Q Consensus 53 ~~CP~Cr~~~~~~-~~rn---~~le~~v~~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~~~~CP~--~~C~~~g~~~~ 126 (263)
..||+|...+... .+.+ ++-..=-.++...||. |...++...-..=|+.++-..+.||+ .||.+..+.-+
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~----Cr~~~g~~R~~amEkV~e~~~vpC~~~~~GC~~~~~Y~~ 124 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPT----CRLPIGNIRCRAMEKVAEAVLVPCKNAKLGCTKSFPYGE 124 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhhhcccCCc----cccccccHHHHHHHHHHHhceecccccccCCceeecccc
Confidence 3799999988754 2222 4444444578888985 88888743333345688899999998 99999987666
Q ss_pred HHHHHhc
Q psy12127 127 LSEHLNQ 133 (263)
Q Consensus 127 L~~Hl~~ 133 (263)
-..|.+.
T Consensus 125 ~~~HE~~ 131 (299)
T KOG3002|consen 125 KSKHEKV 131 (299)
T ss_pred ccccccc
Confidence 5666543
No 136
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=51.34 E-value=8.8 Score=26.93 Aligned_cols=28 Identities=32% Similarity=0.950 Sum_probs=22.0
Q ss_pred cccccCCCceeccccccc-cCCCCCCccCCc
Q psy12127 34 ITSCQTCGNLVCTSCAAR-LLKCPFCRITID 63 (263)
Q Consensus 34 v~qC~~CGH~~C~~C~~~-l~~CP~Cr~~~~ 63 (263)
+-.|.+||.++|.. +. ++.||.|..++.
T Consensus 18 ~~NCl~CGkIiC~~--Eg~~~pC~fCg~~l~ 46 (57)
T PF06221_consen 18 APNCLNCGKIICEQ--EGPLGPCPFCGTPLL 46 (57)
T ss_pred cccccccChhhccc--ccCcCcCCCCCCccc
Confidence 55789999999875 33 479999998875
No 137
>PHA00626 hypothetical protein
Probab=51.06 E-value=10 Score=26.61 Aligned_cols=7 Identities=29% Similarity=0.572 Sum_probs=3.5
Q ss_pred CCCCCcc
Q psy12127 54 KCPFCRI 60 (263)
Q Consensus 54 ~CP~Cr~ 60 (263)
.||.|.-
T Consensus 25 kCkdCGY 31 (59)
T PHA00626 25 VCCDCGY 31 (59)
T ss_pred EcCCCCC
Confidence 4555543
No 138
>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=50.55 E-value=7.8 Score=24.15 Aligned_cols=25 Identities=24% Similarity=0.489 Sum_probs=16.2
Q ss_pred ceecCCCCCCCceeeeccchhhhhhcccC
Q psy12127 79 LELPCRNFRFGCKVYLPKAKRDKHEDKCK 107 (263)
Q Consensus 79 l~v~C~~~~~GC~~~~~~~~~~~He~~C~ 107 (263)
..+.|+| |...+.-..+..|.+.|.
T Consensus 3 ~~~~C~n----C~R~v~a~RfA~HLekCm 27 (33)
T PF08209_consen 3 PYVECPN----CGRPVAASRFAPHLEKCM 27 (33)
T ss_dssp -EEE-TT----TSSEEEGGGHHHHHHHHT
T ss_pred CeEECCC----CcCCcchhhhHHHHHHHH
Confidence 4566775 777777777777777664
No 139
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.20 E-value=7.5 Score=28.70 Aligned_cols=28 Identities=29% Similarity=0.591 Sum_probs=23.3
Q ss_pred ccccCCCceeccccccc-c-CCCCCCccCCc
Q psy12127 35 TSCQTCGNLVCTSCAAR-L-LKCPFCRITID 63 (263)
Q Consensus 35 ~qC~~CGH~~C~~C~~~-l-~~CP~Cr~~~~ 63 (263)
..|+- .++||..|.+. + +.||.|++.+.
T Consensus 23 ~ICtf-EcTFCadCae~~l~g~CPnCGGelv 52 (84)
T COG3813 23 RICTF-ECTFCADCAENRLHGLCPNCGGELV 52 (84)
T ss_pred eEEEE-eeehhHhHHHHhhcCcCCCCCchhh
Confidence 46777 88999999885 4 69999999875
No 140
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.14 E-value=12 Score=28.02 Aligned_cols=45 Identities=22% Similarity=0.361 Sum_probs=28.3
Q ss_pred eeeccccCccccccccccCCCceeccccccccCCCCCCccCCcccccccHHHHHhhhccee
Q psy12127 21 SECGVCLEPLDRGITSCQTCGNLVCTSCAARLLKCPFCRITIDYSWQRNVALERIFTKLEL 81 (263)
Q Consensus 21 l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l~~CP~Cr~~~~~~~~rn~~le~~v~~l~v 81 (263)
+.||||.--|..-+.+ |-- ...||.||+..- --..|+++++.-.+
T Consensus 2 llCP~C~v~l~~~~rs----~vE--------iD~CPrCrGVWL----DrGELdKli~r~r~ 46 (88)
T COG3809 2 LLCPICGVELVMSVRS----GVE--------IDYCPRCRGVWL----DRGELDKLIERSRY 46 (88)
T ss_pred cccCcCCceeeeeeec----Cce--------eeeCCccccEee----cchhHHHHHHHhcC
Confidence 5688888777764432 211 247999998753 22357777776553
No 141
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=50.13 E-value=4.8 Score=26.50 Aligned_cols=10 Identities=40% Similarity=1.215 Sum_probs=6.9
Q ss_pred CCCCCccCCc
Q psy12127 54 KCPFCRITID 63 (263)
Q Consensus 54 ~CP~Cr~~~~ 63 (263)
.||.|+.++.
T Consensus 23 ~Cp~CG~~~~ 32 (46)
T PRK00398 23 RCPYCGYRIL 32 (46)
T ss_pred ECCCCCCeEE
Confidence 6777777654
No 142
>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=49.31 E-value=5.6 Score=41.83 Aligned_cols=44 Identities=25% Similarity=0.626 Sum_probs=0.0
Q ss_pred ceeeeccccCccccccccccCCCce-----ecccccccc--CCCCCCccCCcc
Q psy12127 19 SISECGVCLEPLDRGITSCQTCGNL-----VCTSCAARL--LKCPFCRITIDY 64 (263)
Q Consensus 19 ~~l~CpIC~~~l~~Pv~qC~~CGH~-----~C~~C~~~l--~~CP~Cr~~~~~ 64 (263)
....||-|...-.. ..|+.||-. +|..|.... ..||.|......
T Consensus 654 ~~r~Cp~Cg~~t~~--~~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~~C~~~~~~ 704 (900)
T PF03833_consen 654 GRRRCPKCGKETFY--NRCPECGSHTEPVYVCPDCGIEVEEDECPKCGRETTS 704 (900)
T ss_dssp -----------------------------------------------------
T ss_pred ecccCcccCCcchh--hcCcccCCccccceeccccccccCccccccccccCcc
Confidence 44567777776444 356667755 788887775 489999987653
No 143
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=48.43 E-value=8 Score=22.42 Aligned_cols=7 Identities=29% Similarity=0.520 Sum_probs=3.5
Q ss_pred eeccccC
Q psy12127 22 ECGVCLE 28 (263)
Q Consensus 22 ~CpIC~~ 28 (263)
.||-|..
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 3555555
No 144
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=46.80 E-value=6.7 Score=30.22 Aligned_cols=26 Identities=31% Similarity=0.922 Sum_probs=21.4
Q ss_pred cccCCC--------ceeccccccccCCCCCCccC
Q psy12127 36 SCQTCG--------NLVCTSCAARLLKCPFCRIT 61 (263)
Q Consensus 36 qC~~CG--------H~~C~~C~~~l~~CP~Cr~~ 61 (263)
-|..|+ |++|..|-..+..|+.|..+
T Consensus 57 kC~~C~qktVk~AYh~iC~~Ca~~~~vCaKC~k~ 90 (92)
T PF10217_consen 57 KCNKCQQKTVKHAYHVICDPCAKELKVCAKCGKP 90 (92)
T ss_pred cccccccchHHHHHHHHHHHHHHhhccCcccCCC
Confidence 466666 88999999999999999875
No 145
>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=46.56 E-value=5.9 Score=33.37 Aligned_cols=21 Identities=33% Similarity=0.892 Sum_probs=17.5
Q ss_pred eecccccccc-CCCCCCccCCc
Q psy12127 43 LVCTSCAARL-LKCPFCRITID 63 (263)
Q Consensus 43 ~~C~~C~~~l-~~CP~Cr~~~~ 63 (263)
-||..|-.+. .+||.|..+|.
T Consensus 29 ~fC~kCG~~tI~~Cp~C~~~Ir 50 (158)
T PF10083_consen 29 KFCSKCGAKTITSCPNCSTPIR 50 (158)
T ss_pred HHHHHhhHHHHHHCcCCCCCCC
Confidence 4899998774 79999999885
No 146
>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=46.36 E-value=15 Score=22.79 Aligned_cols=9 Identities=44% Similarity=1.121 Sum_probs=6.2
Q ss_pred CCCCCCccC
Q psy12127 53 LKCPFCRIT 61 (263)
Q Consensus 53 ~~CP~Cr~~ 61 (263)
..||.|..+
T Consensus 19 ~~CP~Cg~~ 27 (34)
T cd00729 19 EKCPICGAP 27 (34)
T ss_pred CcCcCCCCc
Confidence 378888764
No 147
>PRK11032 hypothetical protein; Provisional
Probab=45.76 E-value=15 Score=31.07 Aligned_cols=30 Identities=23% Similarity=0.464 Sum_probs=17.5
Q ss_pred cccccccCCCceeccccccccCCCCCCccC
Q psy12127 32 RGITSCQTCGNLVCTSCAARLLKCPFCRIT 61 (263)
Q Consensus 32 ~Pv~qC~~CGH~~C~~C~~~l~~CP~Cr~~ 61 (263)
+-++.|.+|||...-.=-..+..||.|...
T Consensus 122 ~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 122 LGNLVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred cceEEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 334556666666533222234689999875
No 148
>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=45.49 E-value=13 Score=22.72 Aligned_cols=23 Identities=30% Similarity=0.632 Sum_probs=10.7
Q ss_pred ecCCCCCCCCccChhhHHHHHhc
Q psy12127 111 LKCPMHACPWTNSVLHLSEHLNQ 133 (263)
Q Consensus 111 ~~CP~~~C~~~g~~~~L~~Hl~~ 133 (263)
++||..+|+..........|+.+
T Consensus 3 vrCPvkdC~EEv~lgKY~~H~ss 25 (30)
T PF10426_consen 3 VRCPVKDCDEEVSLGKYSHHLSS 25 (30)
T ss_dssp EE--STT---EEEHHHHHHHHHT
T ss_pred cccccccCcchhhhhhhcccccc
Confidence 45666666666666666666543
No 149
>smart00301 DM Doublesex DNA-binding motif.
Probab=45.35 E-value=12 Score=25.93 Aligned_cols=40 Identities=23% Similarity=0.421 Sum_probs=30.6
Q ss_pred ceeeeccchhhhhhcccCCceecCCCCCCCCccChhhHHHHH
Q psy12127 90 CKVYLPKAKRDKHEDKCKFRQLKCPMHACPWTNSVLHLSEHL 131 (263)
Q Consensus 90 C~~~~~~~~~~~He~~C~~~~~~CP~~~C~~~g~~~~L~~Hl 131 (263)
|..-+....+..|-..|+|+.+.| +.|.....+..++...
T Consensus 8 CrnHg~~~~lKGHKr~C~~r~C~C--~kC~Li~~Rq~vma~q 47 (54)
T smart00301 8 CENHGVKVPLKGHKPECPFRDCEC--EKCTLVEKRRALMALQ 47 (54)
T ss_pred HhcCCCeeccCCcCCCCCCCCCcC--CCCcChHHHHHHHHHH
Confidence 333455667889999999999999 4798888777776654
No 150
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=44.85 E-value=19 Score=19.11 Aligned_cols=22 Identities=32% Similarity=0.637 Sum_probs=14.5
Q ss_pred cCCCCCCCCcc-ChhhHHHHHhccc
Q psy12127 112 KCPMHACPWTN-SVLHLSEHLNQVH 135 (263)
Q Consensus 112 ~CP~~~C~~~g-~~~~L~~Hl~~~H 135 (263)
.|+ .|+... +..+|..|+...|
T Consensus 2 ~C~--~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 2 QCP--ICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp E-S--STS-EESSHHHHHHHHHHHS
T ss_pred CCc--CCCCcCCcHHHHHHHHHhhC
Confidence 454 377664 6788999988776
No 151
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=44.44 E-value=11 Score=30.78 Aligned_cols=28 Identities=25% Similarity=0.559 Sum_probs=18.9
Q ss_pred ccccCCCceeccccccccCCCCCCccCC
Q psy12127 35 TSCQTCGNLVCTSCAARLLKCPFCRITI 62 (263)
Q Consensus 35 ~qC~~CGH~~C~~C~~~l~~CP~Cr~~~ 62 (263)
.||++||+.|=..=..-++-||.|+...
T Consensus 2 H~Ct~Cg~~f~dgs~eil~GCP~CGg~k 29 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKEILSGCPECGGNK 29 (131)
T ss_pred cccCcCCCCcCCCcHHHHccCcccCCcc
Confidence 5899999988433222245799998754
No 152
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=44.42 E-value=8.9 Score=30.13 Aligned_cols=26 Identities=27% Similarity=0.735 Sum_probs=18.0
Q ss_pred ccccCCCceeccccccc-cCCCCCCccC
Q psy12127 35 TSCQTCGNLVCTSCAAR-LLKCPFCRIT 61 (263)
Q Consensus 35 ~qC~~CGH~~C~~C~~~-l~~CP~Cr~~ 61 (263)
.||++|||+|=.. ... ++-||.|+..
T Consensus 3 H~CtrCG~vf~~g-~~~il~GCp~CG~n 29 (112)
T COG3364 3 HQCTRCGEVFDDG-SEEILSGCPKCGCN 29 (112)
T ss_pred ceecccccccccc-cHHHHccCccccch
Confidence 5899999998554 122 3578888764
No 153
>KOG3608|consensus
Probab=43.92 E-value=17 Score=34.74 Aligned_cols=114 Identities=19% Similarity=0.416 Sum_probs=74.5
Q ss_pred CceeeeccccCcccccc-------ccc--cCCCceecccccccc----------------CCCCCCccCCccc-ccccHH
Q psy12127 18 ASISECGVCLEPLDRGI-------TSC--QTCGNLVCTSCAARL----------------LKCPFCRITIDYS-WQRNVA 71 (263)
Q Consensus 18 ~~~l~CpIC~~~l~~Pv-------~qC--~~CGH~~C~~C~~~l----------------~~CP~Cr~~~~~~-~~rn~~ 71 (263)
+.++-||-|.+.+..-. +|- .. .|.-|+.|.++. -+||.|....+.. ..++..
T Consensus 205 eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~-n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~ 283 (467)
T KOG3608|consen 205 EKVVACPHCGELFRTKTKLFDHLRRQTELNT-NSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHI 283 (467)
T ss_pred CeEEecchHHHHhccccHHHHHHHhhhhhcC-CchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHH
Confidence 45778999998776321 110 12 577888887652 1799999876532 233444
Q ss_pred HHHhhhcceecCCCCCCCceee-eccchhhhhhcccCCceecCCCCCCCCcc-ChhhHHHHHhcccC
Q psy12127 72 LERIFTKLELPCRNFRFGCKVY-LPKAKRDKHEDKCKFRQLKCPMHACPWTN-SVLHLSEHLNQVHH 136 (263)
Q Consensus 72 le~~v~~l~v~C~~~~~GC~~~-~~~~~~~~He~~C~~~~~~CP~~~C~~~g-~~~~L~~Hl~~~H~ 136 (263)
+-+-.++-.++|. -|... +...++.+|...=.--.+.|-.+.|.+.. +..+|..|+...|.
T Consensus 284 r~rHs~dkpfKCd----~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhE 346 (467)
T KOG3608|consen 284 RYRHSKDKPFKCD----ECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHE 346 (467)
T ss_pred HhhhccCCCcccc----chhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhcc
Confidence 4455556677776 35553 45577888876433455678778888876 56788889888884
No 154
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=42.96 E-value=15 Score=23.52 Aligned_cols=20 Identities=25% Similarity=0.446 Sum_probs=11.2
Q ss_pred CCCCCccCCcccccccHHHHHhhh
Q psy12127 54 KCPFCRITIDYSWQRNVALERIFT 77 (263)
Q Consensus 54 ~CP~Cr~~~~~~~~rn~~le~~v~ 77 (263)
.||.|.+.. .....++++++
T Consensus 21 ~C~~C~G~W----~d~~el~~~~e 40 (41)
T PF13453_consen 21 VCPSCGGIW----FDAGELEKLLE 40 (41)
T ss_pred ECCCCCeEE----ccHHHHHHHHh
Confidence 677777654 33445555543
No 155
>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=42.86 E-value=11 Score=27.62 Aligned_cols=39 Identities=26% Similarity=0.699 Sum_probs=20.5
Q ss_pred cccccchhcCCceeeeccccCccccccccccCCC--ceecccccc
Q psy12127 8 ECCANCKELIASISECGVCLEPLDRGITSCQTCG--NLVCTSCAA 50 (263)
Q Consensus 8 ~~~~~~~~~l~~~l~CpIC~~~l~~Pv~qC~~CG--H~~C~~C~~ 50 (263)
.-|++++.++..+-.||-|..+|.. .+ .|| -.||..|..
T Consensus 18 ~~C~~C~~~~~~~a~CPdC~~~Le~--Lk--ACGAvdYFC~~c~g 58 (70)
T PF07191_consen 18 YHCEACQKDYKKEAFCPDCGQPLEV--LK--ACGAVDYFCNHCHG 58 (70)
T ss_dssp EEETTT--EEEEEEE-TTT-SB-EE--EE--ETTEEEEE-TTTT-
T ss_pred EECccccccceecccCCCcccHHHH--HH--HhcccceeeccCCc
Confidence 3466677777777777777777764 22 356 457777754
No 156
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=42.15 E-value=16 Score=37.60 Aligned_cols=21 Identities=33% Similarity=0.895 Sum_probs=9.1
Q ss_pred ceecccccccc--CCCCCCccCC
Q psy12127 42 NLVCTSCAARL--LKCPFCRITI 62 (263)
Q Consensus 42 H~~C~~C~~~l--~~CP~Cr~~~ 62 (263)
+.||..|-.++ ..||.|+..+
T Consensus 15 akFC~~CG~~l~~~~Cp~CG~~~ 37 (645)
T PRK14559 15 NRFCQKCGTSLTHKPCPQCGTEV 37 (645)
T ss_pred CccccccCCCCCCCcCCCCCCCC
Confidence 33444444433 2455554443
No 157
>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=40.95 E-value=20 Score=21.38 Aligned_cols=28 Identities=25% Similarity=0.545 Sum_probs=19.8
Q ss_pred eeeccccCccccc-cccccCCCceecccc
Q psy12127 21 SECGVCLEPLDRG-ITSCQTCGNLVCTSC 48 (263)
Q Consensus 21 l~CpIC~~~l~~P-v~qC~~CGH~~C~~C 48 (263)
+.|.+|.+.+... .+.|..|+-.+-..|
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~c~f~lh~~C 29 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFYHCSECCFTLHVRC 29 (30)
T ss_pred CCCCCCCCCcCCCEeEEeCCCCCeEcCcc
Confidence 3688888888877 788877765554444
No 158
>PF14353 CpXC: CpXC protein
Probab=40.43 E-value=14 Score=29.42 Aligned_cols=10 Identities=30% Similarity=0.850 Sum_probs=7.8
Q ss_pred CCCCCccCCc
Q psy12127 54 KCPFCRITID 63 (263)
Q Consensus 54 ~CP~Cr~~~~ 63 (263)
.||.|+..+.
T Consensus 40 ~CP~Cg~~~~ 49 (128)
T PF14353_consen 40 TCPSCGHKFR 49 (128)
T ss_pred ECCCCCCcee
Confidence 6999988654
No 159
>KOG1100|consensus
Probab=40.25 E-value=16 Score=32.16 Aligned_cols=39 Identities=28% Similarity=0.661 Sum_probs=27.5
Q ss_pred eccccCccccccccccCCCc-eeccccccccCCCCCCccCCc
Q psy12127 23 CGVCLEPLDRGITSCQTCGN-LVCTSCAARLLKCPFCRITID 63 (263)
Q Consensus 23 CpIC~~~l~~Pv~qC~~CGH-~~C~~C~~~l~~CP~Cr~~~~ 63 (263)
|-.|.+-=.. |.. -.|.| .+|..|-..+..||.|+.+..
T Consensus 161 Cr~C~~~~~~-Vll-lPCrHl~lC~~C~~~~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGEREAT-VLL-LPCRHLCLCGICDESLRICPICRSPKT 200 (207)
T ss_pred ceecCcCCce-EEe-ecccceEecccccccCccCCCCcChhh
Confidence 8888764333 221 23677 599999887789999998764
No 160
>PRK11827 hypothetical protein; Provisional
Probab=40.10 E-value=14 Score=26.19 Aligned_cols=33 Identities=21% Similarity=0.348 Sum_probs=21.7
Q ss_pred hhcCCceeeeccccCccccccccccCCCceecccccc
Q psy12127 14 KELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAA 50 (263)
Q Consensus 14 ~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~ 50 (263)
+..|.+.+-||+|...|.-- . .. ...+|..|..
T Consensus 2 d~~LLeILaCP~ckg~L~~~--~-~~-~~Lic~~~~l 34 (60)
T PRK11827 2 DHRLLEIIACPVCNGKLWYN--Q-EK-QELICKLDNL 34 (60)
T ss_pred ChHHHhheECCCCCCcCeEc--C-CC-CeEECCccCe
Confidence 45678899999999988741 1 22 3466666543
No 161
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=40.04 E-value=13 Score=27.32 Aligned_cols=45 Identities=13% Similarity=0.339 Sum_probs=30.7
Q ss_pred CCCCCccCCcccccccHHHHHhhhcceecCCCCCCCceeeeccchhhhh
Q psy12127 54 KCPFCRITIDYSWQRNVALERIFTKLELPCRNFRFGCKVYLPKAKRDKH 102 (263)
Q Consensus 54 ~CP~Cr~~~~~~~~rn~~le~~v~~l~v~C~~~~~GC~~~~~~~~~~~H 102 (263)
.||.|+.... ....+.+...+..+...|.|- .|+..+...+-..|
T Consensus 3 ~CP~Cg~~a~--irtSr~~s~~~~~~Y~qC~N~--eCg~tF~t~es~s~ 47 (72)
T PRK09678 3 HCPLCQHAAH--ARTSRYITDTTKERYHQCQNV--NCSATFITYESVQR 47 (72)
T ss_pred cCCCCCCccE--EEEChhcChhhheeeeecCCC--CCCCEEEEEEEEEE
Confidence 6999988764 444566666688888999986 46666655554444
No 162
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=39.90 E-value=15 Score=38.54 Aligned_cols=31 Identities=23% Similarity=0.682 Sum_probs=24.4
Q ss_pred eeeccccCccccc-----ccc--ccCCCceeccccccc
Q psy12127 21 SECGVCLEPLDRG-----ITS--CQTCGNLVCTSCAAR 51 (263)
Q Consensus 21 l~CpIC~~~l~~P-----v~q--C~~CGH~~C~~C~~~ 51 (263)
-.|..|...+..= +++ |.+||.+||..|-.+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSn 498 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITK 498 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCC
Confidence 3699999998531 234 999999999999765
No 163
>PRK00420 hypothetical protein; Validated
Probab=39.40 E-value=17 Score=28.98 Aligned_cols=25 Identities=32% Similarity=0.598 Sum_probs=16.3
Q ss_pred eeeccccCccccccccccCCCceecccccc
Q psy12127 21 SECGVCLEPLDRGITSCQTCGNLVCTSCAA 50 (263)
Q Consensus 21 l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~ 50 (263)
-.||+|..+|..- .+ |..+|..|-.
T Consensus 24 ~~CP~Cg~pLf~l----k~-g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFEL----KD-GEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceec----CC-CceECCCCCC
Confidence 4799999888763 23 6666555533
No 164
>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=39.20 E-value=19 Score=23.51 Aligned_cols=22 Identities=41% Similarity=0.963 Sum_probs=16.1
Q ss_pred eeccccCccccccccccCCCceecccc
Q psy12127 22 ECGVCLEPLDRGITSCQTCGNLVCTSC 48 (263)
Q Consensus 22 ~CpIC~~~l~~Pv~qC~~CGH~~C~~C 48 (263)
.||.|..+|... .+ |..+|-.|
T Consensus 19 ~Cp~C~~PL~~~----k~-g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMRD----KD-GKIYCVSC 40 (41)
T ss_pred ccCCCCCeeEEe----cC-CCEECCCC
Confidence 699998777763 24 77888776
No 165
>PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 [].
Probab=39.12 E-value=16 Score=31.40 Aligned_cols=31 Identities=32% Similarity=0.795 Sum_probs=15.4
Q ss_pred ceeeeccccCccccc-cccccCCCceeccccc
Q psy12127 19 SISECGVCLEPLDRG-ITSCQTCGNLVCTSCA 49 (263)
Q Consensus 19 ~~l~CpIC~~~l~~P-v~qC~~CGH~~C~~C~ 49 (263)
..-.|.-|...+=.. +++|..|+..||+.|.
T Consensus 123 ~~~~C~~Cdr~lC~~C~~~C~~C~~~~Cs~Cs 154 (175)
T PF05458_consen 123 IKSVCSQCDRALCESCIRSCSSCSEVFCSLCS 154 (175)
T ss_pred CCccccccCcHHHHHHHhhhhchhhhhhcCcc
Confidence 333455554444433 3455555555555554
No 166
>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=39.04 E-value=17 Score=25.39 Aligned_cols=24 Identities=33% Similarity=0.834 Sum_probs=16.0
Q ss_pred eccccCccccccccccCCCceeccc
Q psy12127 23 CGVCLEPLDRGITSCQTCGNLVCTS 47 (263)
Q Consensus 23 CpIC~~~l~~Pv~qC~~CGH~~C~~ 47 (263)
|.+|... ...+..|-.||+++|..
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEETT
T ss_pred CCCCCCc-CCceEEeCCCCcccccC
Confidence 5667755 45567888899998874
No 167
>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=37.76 E-value=12 Score=22.24 Aligned_cols=27 Identities=26% Similarity=0.711 Sum_probs=9.4
Q ss_pred eeccccCcccc-ccccccCCCceecccc
Q psy12127 22 ECGVCLEPLDR-GITSCQTCGNLVCTSC 48 (263)
Q Consensus 22 ~CpIC~~~l~~-Pv~qC~~CGH~~C~~C 48 (263)
.|.+|.+.... +.+.|..|.-.+-..|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 57777777776 6677777665554444
No 168
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=37.43 E-value=22 Score=30.93 Aligned_cols=41 Identities=22% Similarity=0.527 Sum_probs=28.8
Q ss_pred ceeeeccccC--cccc----ccccccCCCceeccccccccCCCCCCcc
Q psy12127 19 SISECGVCLE--PLDR----GITSCQTCGNLVCTSCAARLLKCPFCRI 60 (263)
Q Consensus 19 ~~l~CpIC~~--~l~~----Pv~qC~~CGH~~C~~C~~~l~~CP~Cr~ 60 (263)
.-+.|.+|.+ ++.| -+.+|+.|+..|=..|+.+ ..||.|..
T Consensus 151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~-~~CpkC~R 197 (202)
T PF13901_consen 151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK-KSCPKCAR 197 (202)
T ss_pred CCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC-CCCCCcHh
Confidence 3578999984 2221 2456888888877788776 78999964
No 169
>PLN02189 cellulose synthase
Probab=37.08 E-value=19 Score=38.93 Aligned_cols=42 Identities=26% Similarity=0.754 Sum_probs=33.8
Q ss_pred eeccccCccc-----cccccccCCCceecccccccc-----CCCCCCccCCc
Q psy12127 22 ECGVCLEPLD-----RGITSCQTCGNLVCTSCAARL-----LKCPFCRITID 63 (263)
Q Consensus 22 ~CpIC~~~l~-----~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~ 63 (263)
.|.||.+-+- .|...|..||--+|..|.+.- +.||.|++...
T Consensus 36 ~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 36 VCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 8999999765 355679889999999998653 38999998653
No 170
>PF12773 DZR: Double zinc ribbon
Probab=36.59 E-value=24 Score=23.15 Aligned_cols=12 Identities=33% Similarity=0.589 Sum_probs=6.3
Q ss_pred eeeeccccCccc
Q psy12127 20 ISECGVCLEPLD 31 (263)
Q Consensus 20 ~l~CpIC~~~l~ 31 (263)
..-|+.|...|.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 344555555555
No 171
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=36.45 E-value=23 Score=37.03 Aligned_cols=36 Identities=36% Similarity=0.730 Sum_probs=22.9
Q ss_pred eeccccCccccccccccCCCceecccccccc---CCCCCCccC
Q psy12127 22 ECGVCLEPLDRGITSCQTCGNLVCTSCAARL---LKCPFCRIT 61 (263)
Q Consensus 22 ~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l---~~CP~Cr~~ 61 (263)
.||-|..+|.-. | .. |...|..|-..- ..||.|...
T Consensus 446 ~Cp~Cd~~lt~H--~-~~-~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 446 ECPNCDSPLTLH--K-AT-GQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cCCCCCcceEEe--c-CC-CeeEeCCCCCCCCCCCCCCCCCCC
Confidence 444444444432 2 23 678899997663 489999987
No 172
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.34 E-value=14 Score=30.17 Aligned_cols=20 Identities=30% Similarity=1.055 Sum_probs=16.0
Q ss_pred eccccccc-cCCCCCCccCCc
Q psy12127 44 VCTSCAAR-LLKCPFCRITID 63 (263)
Q Consensus 44 ~C~~C~~~-l~~CP~Cr~~~~ 63 (263)
||+.|-.. +.+||.|..++.
T Consensus 30 fcskcgeati~qcp~csasir 50 (160)
T COG4306 30 FCSKCGEATITQCPICSASIR 50 (160)
T ss_pred HHhhhchHHHhcCCccCCccc
Confidence 78888765 469999998764
No 173
>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=36.15 E-value=27 Score=21.08 Aligned_cols=22 Identities=32% Similarity=0.825 Sum_probs=12.5
Q ss_pred eeccccCccccccccccCCCceecc
Q psy12127 22 ECGVCLEPLDRGITSCQTCGNLVCT 46 (263)
Q Consensus 22 ~CpIC~~~l~~Pv~qC~~CGH~~C~ 46 (263)
.|.||.. +.-+.|+.||-.+|+
T Consensus 4 ~C~vC~~---~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 4 LCSVCGN---PAKYRCPRCGARYCS 25 (30)
T ss_dssp EETSSSS---EESEE-TTT--EESS
T ss_pred CCccCcC---CCEEECCCcCCceeC
Confidence 5777777 333677777777765
No 174
>PLN02436 cellulose synthase A
Probab=35.84 E-value=20 Score=38.80 Aligned_cols=42 Identities=24% Similarity=0.757 Sum_probs=33.8
Q ss_pred eeccccCccc-----cccccccCCCceecccccccc-----CCCCCCccCCc
Q psy12127 22 ECGVCLEPLD-----RGITSCQTCGNLVCTSCAARL-----LKCPFCRITID 63 (263)
Q Consensus 22 ~CpIC~~~l~-----~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~ 63 (263)
.|.||.+-+- .|...|..||--+|..|.+.- +.||.|++...
T Consensus 38 iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 38 TCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 8999999764 355679889999999998653 38999998653
No 175
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=35.71 E-value=26 Score=32.73 Aligned_cols=41 Identities=32% Similarity=0.662 Sum_probs=26.9
Q ss_pred ceeeeccccCccccccccc---cCCC--ceecccccccc----CCCCCCcc
Q psy12127 19 SISECGVCLEPLDRGITSC---QTCG--NLVCTSCAARL----LKCPFCRI 60 (263)
Q Consensus 19 ~~l~CpIC~~~l~~Pv~qC---~~CG--H~~C~~C~~~l----~~CP~Cr~ 60 (263)
..-.||||...-.--+..= .. | +..|+-|-..+ .+||.|..
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~-G~RyL~CslC~teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKET-GLRYLSCSLCATEWHYVRVKCSHCEE 232 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCC-CceEEEcCCCCCcccccCccCCCCCC
Confidence 3558999998754322211 12 4 56899998876 37998875
No 176
>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=35.63 E-value=18 Score=33.10 Aligned_cols=42 Identities=29% Similarity=0.577 Sum_probs=19.4
Q ss_pred eeeeccccCccccccccccC----CCceecccccccc----CCCCCCccCC
Q psy12127 20 ISECGVCLEPLDRGITSCQT----CGNLVCTSCAARL----LKCPFCRITI 62 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC~~----CGH~~C~~C~~~l----~~CP~Cr~~~ 62 (263)
.-.||||...-.--+.. .. =-+.+|+-|-..+ ..||.|...-
T Consensus 172 ~g~CPvCGs~P~~s~l~-~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~ 221 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLR-GGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTD 221 (290)
T ss_dssp -SS-TTT---EEEEEEE-------EEEEEETTT--EEE--TTS-TTT---S
T ss_pred CCcCCCCCCcCceEEEe-cCCCCccEEEEcCCCCCeeeecCCCCcCCCCCC
Confidence 45899999875533222 11 0357999998886 3899998753
No 177
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=35.46 E-value=18 Score=29.61 Aligned_cols=23 Identities=35% Similarity=0.883 Sum_probs=17.4
Q ss_pred eeeccccCccccccccccCCCceeccccc
Q psy12127 21 SECGVCLEPLDRGITSCQTCGNLVCTSCA 49 (263)
Q Consensus 21 l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~ 49 (263)
.+||.|..||.. .. |-+||..|-
T Consensus 29 ~hCp~Cg~PLF~-----Kd-G~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFR-----KD-GEVFCPVCG 51 (131)
T ss_pred hhCcccCCccee-----eC-CeEECCCCC
Confidence 379999998876 34 888876665
No 178
>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=35.14 E-value=18 Score=24.12 Aligned_cols=32 Identities=25% Similarity=0.544 Sum_probs=20.1
Q ss_pred CceeeeccccCccccccccccCCCceecccccc
Q psy12127 18 ASISECGVCLEPLDRGITSCQTCGNLVCTSCAA 50 (263)
Q Consensus 18 ~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~ 50 (263)
.+=|.|..|...|.+..+.-.+ |..+|..|..
T Consensus 24 ~~Cf~C~~C~~~l~~~~~~~~~-~~~~C~~c~~ 55 (58)
T PF00412_consen 24 PECFKCSKCGKPLNDGDFYEKD-GKPYCKDCYQ 55 (58)
T ss_dssp TTTSBETTTTCBTTTSSEEEET-TEEEEHHHHH
T ss_pred ccccccCCCCCccCCCeeEeEC-CEEECHHHHh
Confidence 3456777777777765333345 7777777754
No 179
>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=35.08 E-value=22 Score=28.13 Aligned_cols=21 Identities=38% Similarity=0.855 Sum_probs=12.6
Q ss_pred eeccccccc---cC----CCCCCccCCc
Q psy12127 43 LVCTSCAAR---LL----KCPFCRITID 63 (263)
Q Consensus 43 ~~C~~C~~~---l~----~CP~Cr~~~~ 63 (263)
++|.+|-.+ |+ .||.|+..+.
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~~~ 37 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTEFP 37 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCccC
Confidence 455555444 32 5888887664
No 180
>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=35.06 E-value=27 Score=21.33 Aligned_cols=8 Identities=38% Similarity=1.136 Sum_probs=5.9
Q ss_pred CCCCCccC
Q psy12127 54 KCPFCRIT 61 (263)
Q Consensus 54 ~CP~Cr~~ 61 (263)
.||.|+.+
T Consensus 19 ~CP~Cg~~ 26 (33)
T cd00350 19 VCPVCGAP 26 (33)
T ss_pred cCcCCCCc
Confidence 78888764
No 181
>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=34.86 E-value=22 Score=21.43 Aligned_cols=10 Identities=30% Similarity=0.760 Sum_probs=3.2
Q ss_pred ceeccccccc
Q psy12127 42 NLVCTSCAAR 51 (263)
Q Consensus 42 H~~C~~C~~~ 51 (263)
|.||+.|-..
T Consensus 3 ~rfC~~CG~~ 12 (32)
T PF09297_consen 3 HRFCGRCGAP 12 (32)
T ss_dssp TSB-TTT--B
T ss_pred CcccCcCCcc
Confidence 4445555433
No 182
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=34.59 E-value=20 Score=22.33 Aligned_cols=22 Identities=23% Similarity=0.404 Sum_probs=10.9
Q ss_pred eeeeccccCccccccccccCCC
Q psy12127 20 ISECGVCLEPLDRGITSCQTCG 41 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC~~CG 41 (263)
.-.|.-|..+..+|-..|+.||
T Consensus 11 ~~rC~~Cg~~~~pPr~~Cp~C~ 32 (37)
T PF12172_consen 11 GQRCRDCGRVQFPPRPVCPHCG 32 (37)
T ss_dssp EEE-TTT--EEES--SEETTTT
T ss_pred EEEcCCCCCEecCCCcCCCCcC
Confidence 3467777777777765565554
No 183
>KOG1428|consensus
Probab=34.05 E-value=16 Score=41.14 Aligned_cols=42 Identities=21% Similarity=0.671 Sum_probs=30.9
Q ss_pred eeeccccCccc--cccccccCCCceecccccccc--------------CCCCCCccCCc
Q psy12127 21 SECGVCLEPLD--RGITSCQTCGNLVCTSCAARL--------------LKCPFCRITID 63 (263)
Q Consensus 21 l~CpIC~~~l~--~Pv~qC~~CGH~~C~~C~~~l--------------~~CP~Cr~~~~ 63 (263)
-.|-||+.--. .|-.| -.|||+|=-.|..++ -+||.|..++.
T Consensus 3487 DmCmICFTE~L~AAP~Iq-L~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3487 DMCMICFTEALSAAPAIQ-LDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred ceEEEEehhhhCCCccee-cCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 37999986554 34344 469999998887652 17999998875
No 184
>KOG0828|consensus
Probab=34.01 E-value=11 Score=37.39 Aligned_cols=48 Identities=21% Similarity=0.656 Sum_probs=34.6
Q ss_pred cCCceeeeccccCcccc-----c----c------ccccCCCceecccccccc----C-CCCCCccCCc
Q psy12127 16 LIASISECGVCLEPLDR-----G----I------TSCQTCGNLVCTSCAARL----L-KCPFCRITID 63 (263)
Q Consensus 16 ~l~~~l~CpIC~~~l~~-----P----v------~qC~~CGH~~C~~C~~~l----~-~CP~Cr~~~~ 63 (263)
.+...-.|+||.....- | + +.=+.|.|+|=.+|+.++ + .||+||.++.
T Consensus 567 ~~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 567 FVRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred hhhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 35677789999876431 1 0 112368999999999886 2 7999999875
No 185
>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=33.82 E-value=36 Score=33.85 Aligned_cols=21 Identities=33% Similarity=0.798 Sum_probs=15.1
Q ss_pred Cceecccccccc---CCCCCCccC
Q psy12127 41 GNLVCTSCAARL---LKCPFCRIT 61 (263)
Q Consensus 41 GH~~C~~C~~~l---~~CP~Cr~~ 61 (263)
+...|..|-.+. ..||.|...
T Consensus 239 ~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 239 GKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CeEEcCCCcCcCCCCCCCCCCCCC
Confidence 456788886663 489999875
No 186
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=33.24 E-value=16 Score=34.35 Aligned_cols=39 Identities=28% Similarity=0.759 Sum_probs=23.8
Q ss_pred eeccccCccccc------------cccccCCCceeccccc----cccCCCCCCcc
Q psy12127 22 ECGVCLEPLDRG------------ITSCQTCGNLVCTSCA----ARLLKCPFCRI 60 (263)
Q Consensus 22 ~CpIC~~~l~~P------------v~qC~~CGH~~C~~C~----~~l~~CP~Cr~ 60 (263)
.|-+|..++-.| -|||+.|-..||..|- +.|..|+-|..
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~C~gCe~ 418 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLHFCIGCEL 418 (421)
T ss_pred cceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHHHhhCCCCcC
Confidence 477777755433 2567777777777773 22456776654
No 187
>KOG4218|consensus
Probab=32.69 E-value=21 Score=34.02 Aligned_cols=6 Identities=67% Similarity=1.951 Sum_probs=5.0
Q ss_pred CCCCCc
Q psy12127 54 KCPFCR 59 (263)
Q Consensus 54 ~CP~Cr 59 (263)
+||.||
T Consensus 69 RCP~CR 74 (475)
T KOG4218|consen 69 RCPSCR 74 (475)
T ss_pred cCCchh
Confidence 688887
No 188
>PRK05580 primosome assembly protein PriA; Validated
Probab=31.97 E-value=32 Score=35.48 Aligned_cols=37 Identities=30% Similarity=0.547 Sum_probs=22.6
Q ss_pred eeeccccCccccccccccCCCceecccccccc---CCCCCCccC
Q psy12127 21 SECGVCLEPLDRGITSCQTCGNLVCTSCAARL---LKCPFCRIT 61 (263)
Q Consensus 21 l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l---~~CP~Cr~~ 61 (263)
..||.|..+|.-.- .. +...|..|-.+. ..||.|...
T Consensus 391 ~~C~~C~~~l~~h~---~~-~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHR---FQ-RRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEEC---CC-CeEECCCCcCCCCCCCCCCCCcCC
Confidence 35666666555321 12 456788886653 489999775
No 189
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=31.67 E-value=22 Score=34.94 Aligned_cols=24 Identities=33% Similarity=0.733 Sum_probs=16.3
Q ss_pred cccccccCCCceeccccccc-cCCCCCCcc
Q psy12127 32 RGITSCQTCGNLVCTSCAAR-LLKCPFCRI 60 (263)
Q Consensus 32 ~Pv~qC~~CGH~~C~~C~~~-l~~CP~Cr~ 60 (263)
.+.|+|++||+.. .+ +.+||.|+.
T Consensus 5 ~~~y~C~~Cg~~~-----~~~~g~Cp~C~~ 29 (454)
T TIGR00416 5 KSKFVCQHCGADS-----PKWQGKCPACHA 29 (454)
T ss_pred CCeEECCcCCCCC-----ccccEECcCCCC
Confidence 4568888888753 22 358888875
No 190
>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=31.61 E-value=23 Score=23.21 Aligned_cols=31 Identities=32% Similarity=0.719 Sum_probs=21.5
Q ss_pred eeeccccCccccccccccCCC-ceeccccccc
Q psy12127 21 SECGVCLEPLDRGITSCQTCG-NLVCTSCAAR 51 (263)
Q Consensus 21 l~CpIC~~~l~~Pv~qC~~CG-H~~C~~C~~~ 51 (263)
+.|.+|..++....+.|..|. -..|..|...
T Consensus 1 ~~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~ 32 (46)
T cd02249 1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAK 32 (46)
T ss_pred CCCcCCCCCCcCCEEECCCCCCCcCHHHHHCc
Confidence 358888887777667777766 3577777654
No 191
>PRK11823 DNA repair protein RadA; Provisional
Probab=31.43 E-value=24 Score=34.47 Aligned_cols=25 Identities=32% Similarity=0.687 Sum_probs=16.1
Q ss_pred cccccccCCCceeccccccccCCCCCCcc
Q psy12127 32 RGITSCQTCGNLVCTSCAARLLKCPFCRI 60 (263)
Q Consensus 32 ~Pv~qC~~CGH~~C~~C~~~l~~CP~Cr~ 60 (263)
.+.|+|++||+.. .+.+.+||.|+.
T Consensus 5 ~~~y~C~~Cg~~~----~~~~g~Cp~C~~ 29 (446)
T PRK11823 5 KTAYVCQECGAES----PKWLGRCPECGA 29 (446)
T ss_pred CCeEECCcCCCCC----cccCeeCcCCCC
Confidence 4567888888753 111358888875
No 192
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=30.94 E-value=26 Score=22.86 Aligned_cols=30 Identities=30% Similarity=0.687 Sum_probs=20.0
Q ss_pred eeccccCccccccccccCC-Cceeccccccc
Q psy12127 22 ECGVCLEPLDRGITSCQTC-GNLVCTSCAAR 51 (263)
Q Consensus 22 ~CpIC~~~l~~Pv~qC~~C-GH~~C~~C~~~ 51 (263)
.|..|..++...-++|..| .--+|..|...
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~ 32 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAK 32 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCc
Confidence 5777887666666777776 34567777553
No 193
>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=30.87 E-value=36 Score=33.85 Aligned_cols=34 Identities=26% Similarity=0.680 Sum_probs=15.7
Q ss_pred cccccchhcC-----CceeeeccccCccccccccccCCCc
Q psy12127 8 ECCANCKELI-----ASISECGVCLEPLDRGITSCQTCGN 42 (263)
Q Consensus 8 ~~~~~~~~~l-----~~~l~CpIC~~~l~~Pv~qC~~CGH 42 (263)
..||+|+..| ...+.|.-|......| ..|++||.
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~-~~Cp~C~s 261 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIP-KTCPQCGS 261 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcCcCCCC-CCCCCCCC
Confidence 3455554443 2445555555444444 24444443
No 194
>KOG3362|consensus
Probab=30.65 E-value=18 Score=30.15 Aligned_cols=40 Identities=25% Similarity=0.397 Sum_probs=24.7
Q ss_pred ccccchhcCCceeeeccccCccccccccccCCCceecc-cccccc
Q psy12127 9 CCANCKELIASISECGVCLEPLDRGITSCQTCGNLVCT-SCAARL 52 (263)
Q Consensus 9 ~~~~~~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~-~C~~~l 52 (263)
+||.....- ..--|.||. + +-++.|.+||..+|+ .|...+
T Consensus 108 ~~a~p~~KP-~r~fCaVCG-~--~S~ysC~~CG~kyCsv~C~~~H 148 (156)
T KOG3362|consen 108 AYAKPSFKP-LRKFCAVCG-Y--DSKYSCVNCGTKYCSVRCLKTH 148 (156)
T ss_pred cccCCCCCC-cchhhhhcC-C--CchhHHHhcCCceeechhhhhc
Confidence 344444442 334599999 2 224789999998886 455443
No 195
>KOG3268|consensus
Probab=30.26 E-value=17 Score=31.54 Aligned_cols=44 Identities=25% Similarity=0.695 Sum_probs=26.8
Q ss_pred eeeeccccCcccc---ccccccC--CCceecccccccc---------------CCCCCCccCCc
Q psy12127 20 ISECGVCLEPLDR---GITSCQT--CGNLVCTSCAARL---------------LKCPFCRITID 63 (263)
Q Consensus 20 ~l~CpIC~~~l~~---Pv~qC~~--CGH~~C~~C~~~l---------------~~CP~Cr~~~~ 63 (263)
.-.|.||+.+-.+ |-+.|.+ ||..|=+-|+..+ +.||-|..|+.
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 3456666665543 3344544 6766666676543 26888888875
No 196
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=30.16 E-value=29 Score=37.65 Aligned_cols=41 Identities=24% Similarity=0.733 Sum_probs=33.0
Q ss_pred eeccccCccc-----cccccccCCCceecccccccc-----CCCCCCccCC
Q psy12127 22 ECGVCLEPLD-----RGITSCQTCGNLVCTSCAARL-----LKCPFCRITI 62 (263)
Q Consensus 22 ~CpIC~~~l~-----~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~ 62 (263)
.|.||.+-+- .|...|..||--+|+.|-+-- ..||.|++..
T Consensus 19 iCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrY 69 (1079)
T PLN02638 19 VCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKY 69 (1079)
T ss_pred eeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCch
Confidence 7999999754 355679999999999998652 3799999865
No 197
>KOG1734|consensus
Probab=30.03 E-value=12 Score=34.46 Aligned_cols=43 Identities=26% Similarity=0.661 Sum_probs=31.4
Q ss_pred eeeeccccCccccc---------cccccCCCceecccccccc------CCCCCCccCCc
Q psy12127 20 ISECGVCLEPLDRG---------ITSCQTCGNLVCTSCAARL------LKCPFCRITID 63 (263)
Q Consensus 20 ~l~CpIC~~~l~~P---------v~qC~~CGH~~C~~C~~~l------~~CP~Cr~~~~ 63 (263)
.-.|.||..-+..- +++ -+|+|+|=+.|+.-+ ..||-|++.+.
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~-LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYK-LSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred cchhHhhcchheeecchhhhhhhhee-eecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 34577777766543 244 469999999998874 48999998775
No 198
>PLN02400 cellulose synthase
Probab=29.94 E-value=31 Score=37.51 Aligned_cols=42 Identities=24% Similarity=0.662 Sum_probs=33.6
Q ss_pred eeccccCccc-----cccccccCCCceecccccccc-----CCCCCCccCCc
Q psy12127 22 ECGVCLEPLD-----RGITSCQTCGNLVCTSCAARL-----LKCPFCRITID 63 (263)
Q Consensus 22 ~CpIC~~~l~-----~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~ 63 (263)
.|.||.+-+- .|...|..||--+|+.|-+-- ..||.|++...
T Consensus 38 iCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 38 ICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred eeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 8999999755 355679999999999998652 37999998653
No 199
>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=29.36 E-value=23 Score=20.60 Aligned_cols=14 Identities=21% Similarity=0.271 Sum_probs=5.3
Q ss_pred CCCccChhhHHHHH
Q psy12127 118 CPWTNSVLHLSEHL 131 (263)
Q Consensus 118 C~~~g~~~~L~~Hl 131 (263)
|++..+...+-+|+
T Consensus 7 C~~~v~~~~in~HL 20 (26)
T smart00734 7 CFREVPENLINSHL 20 (26)
T ss_pred CcCcccHHHHHHHH
Confidence 33333333333333
No 200
>KOG2272|consensus
Probab=29.29 E-value=35 Score=31.21 Aligned_cols=43 Identities=26% Similarity=0.560 Sum_probs=29.1
Q ss_pred ceeeeccccCccccccccccCCCceeccccccccC--CCCCCccCCc
Q psy12127 19 SISECGVCLEPLDRGITSCQTCGNLVCTSCAARLL--KCPFCRITID 63 (263)
Q Consensus 19 ~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l~--~CP~Cr~~~~ 63 (263)
..+.|..|...|..-.+. -+ |-++|-.|.++.+ .|-.|+.+|.
T Consensus 162 yHFkCt~C~keL~sdaRe-vk-~eLyClrChD~mgipiCgaC~rpIe 206 (332)
T KOG2272|consen 162 YHFKCTTCGKELTSDARE-VK-GELYCLRCHDKMGIPICGACRRPIE 206 (332)
T ss_pred cceecccccccccchhhh-hc-cceeccccccccCCcccccccCchH
Confidence 456777777777755433 34 7788888888763 6667777775
No 201
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=29.05 E-value=42 Score=24.48 Aligned_cols=26 Identities=35% Similarity=0.607 Sum_probs=18.8
Q ss_pred ceecCCCCCCCCcc-ChhhHHHHHhcc-cC
Q psy12127 109 RQLKCPMHACPWTN-SVLHLSEHLNQV-HH 136 (263)
Q Consensus 109 ~~~~CP~~~C~~~g-~~~~L~~Hl~~~-H~ 136 (263)
....|+ .|+... +...|..|+... |.
T Consensus 49 ~~~~C~--~C~~~f~s~~~l~~Hm~~~~H~ 76 (100)
T PF12756_consen 49 ESFRCP--YCNKTFRSREALQEHMRSKHHK 76 (100)
T ss_dssp SSEEBS--SSS-EESSHHHHHHHHHHTTTT
T ss_pred CCCCCC--ccCCCCcCHHHHHHHHcCccCC
Confidence 367785 477764 789999999976 54
No 202
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=29.00 E-value=43 Score=28.65 Aligned_cols=46 Identities=15% Similarity=0.097 Sum_probs=26.9
Q ss_pred CccCCcccccccHHHHHhhhcceecCCCCCCCceeeeccchhhhhhcc
Q psy12127 58 CRITIDYSWQRNVALERIFTKLELPCRNFRFGCKVYLPKAKRDKHEDK 105 (263)
Q Consensus 58 Cr~~~~~~~~rn~~le~~v~~l~v~C~~~~~GC~~~~~~~~~~~He~~ 105 (263)
|...+. ...-..=|+.-.-....||....||+|.+.+.++..|...
T Consensus 24 C~~~~~--~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~ 69 (198)
T PF03145_consen 24 CTETFP--YSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRD 69 (198)
T ss_dssp ---EE---GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHH
T ss_pred Cccccc--ccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHH
Confidence 555444 2333334666777889999877899999999999999764
No 203
>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=28.56 E-value=43 Score=23.07 Aligned_cols=22 Identities=32% Similarity=0.753 Sum_probs=12.1
Q ss_pred ceeeeccccCccccccccccCCC
Q psy12127 19 SISECGVCLEPLDRGITSCQTCG 41 (263)
Q Consensus 19 ~~l~CpIC~~~l~~Pv~qC~~CG 41 (263)
+...||.|.++-. |-..|.+||
T Consensus 25 ~l~~c~~cg~~~~-~H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKL-PHRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEES-TTSBCTTTB
T ss_pred ceeeeccCCCEec-ccEeeCCCC
Confidence 5567777776333 334454444
No 204
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=28.46 E-value=38 Score=35.41 Aligned_cols=36 Identities=25% Similarity=0.514 Sum_probs=24.3
Q ss_pred ccccccchhcC-----CceeeeccccCccccccccccCCCce
Q psy12127 7 PECCANCKELI-----ASISECGVCLEPLDRGITSCQTCGNL 43 (263)
Q Consensus 7 ~~~~~~~~~~l-----~~~l~CpIC~~~l~~Pv~qC~~CGH~ 43 (263)
-..||+||..+ ...+.|.-|...-..| .+|++||..
T Consensus 444 v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p-~~Cp~Cgs~ 484 (730)
T COG1198 444 IAECPNCDSPLTLHKATGQLRCHYCGYQEPIP-QSCPECGSE 484 (730)
T ss_pred cccCCCCCcceEEecCCCeeEeCCCCCCCCCC-CCCCCCCCC
Confidence 34577777665 4677888887774444 567777764
No 205
>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=28.00 E-value=37 Score=23.50 Aligned_cols=13 Identities=23% Similarity=0.434 Sum_probs=9.6
Q ss_pred eeeccccCccccc
Q psy12127 21 SECGVCLEPLDRG 33 (263)
Q Consensus 21 l~CpIC~~~l~~P 33 (263)
++||.|...+.-|
T Consensus 3 ~~CP~CG~~iev~ 15 (54)
T TIGR01206 3 FECPDCGAEIELE 15 (54)
T ss_pred cCCCCCCCEEecC
Confidence 5788888877654
No 206
>KOG2114|consensus
Probab=27.87 E-value=27 Score=36.87 Aligned_cols=45 Identities=29% Similarity=0.534 Sum_probs=35.5
Q ss_pred cCCceeeeccccCccccccccccCCCceeccccccc-cCCCCCCccC
Q psy12127 16 LIASISECGVCLEPLDRGITSCQTCGNLVCTSCAAR-LLKCPFCRIT 61 (263)
Q Consensus 16 ~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~-l~~CP~Cr~~ 61 (263)
.+-.+-.|..|...|.-|+.- -.|||.+=..|... ...||.|+-.
T Consensus 836 ~i~q~skCs~C~~~LdlP~Vh-F~CgHsyHqhC~e~~~~~CP~C~~e 881 (933)
T KOG2114|consen 836 QIFQVSKCSACEGTLDLPFVH-FLCGHSYHQHCLEDKEDKCPKCLPE 881 (933)
T ss_pred ceeeeeeecccCCccccceee-eecccHHHHHhhccCcccCCccchh
Confidence 344556999999999999522 35899999999985 4699999874
No 207
>PF15616 TerY-C: TerY-C metal binding domain
Probab=27.83 E-value=37 Score=27.84 Aligned_cols=45 Identities=22% Similarity=0.575 Sum_probs=31.3
Q ss_pred hcCCceeeeccccCccccccccccCCCceeccccccccCCCCCCccCCc
Q psy12127 15 ELIASISECGVCLEPLDRGITSCQTCGNLVCTSCAARLLKCPFCRITID 63 (263)
Q Consensus 15 ~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l~~CP~Cr~~~~ 63 (263)
++|...--||-|....-- ..| .||+++|-+= .....||.|.....
T Consensus 72 seL~g~PgCP~CGn~~~f--a~C-~CGkl~Ci~g-~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 72 SELIGAPGCPHCGNQYAF--AVC-GCGKLFCIDG-EGEVTCPWCGNEGS 116 (131)
T ss_pred HHhcCCCCCCCCcChhcE--EEe-cCCCEEEeCC-CCCEECCCCCCeee
Confidence 445566789999987554 357 5899998442 22358999998654
No 208
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=27.80 E-value=44 Score=23.31 Aligned_cols=23 Identities=35% Similarity=0.762 Sum_probs=11.5
Q ss_pred CceeeeccccCccccccccccCCC
Q psy12127 18 ASISECGVCLEPLDRGITSCQTCG 41 (263)
Q Consensus 18 ~~~l~CpIC~~~l~~Pv~qC~~CG 41 (263)
.....||.|.++..+ -..|.+||
T Consensus 25 ~~l~~C~~CG~~~~~-H~vC~~CG 47 (57)
T PRK12286 25 PGLVECPNCGEPKLP-HRVCPSCG 47 (57)
T ss_pred CcceECCCCCCccCC-eEECCCCC
Confidence 445566666664443 33444444
No 209
>PRK04023 DNA polymerase II large subunit; Validated
Probab=27.78 E-value=35 Score=36.90 Aligned_cols=42 Identities=21% Similarity=0.581 Sum_probs=25.9
Q ss_pred ccccchhcCCceeeeccccCccccccccccCCCce----ecccccccc
Q psy12127 9 CCANCKELIASISECGVCLEPLDRGITSCQTCGNL----VCTSCAARL 52 (263)
Q Consensus 9 ~~~~~~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~----~C~~C~~~l 52 (263)
.|+.|.... ..+.||.|... ..|++.|+.||+. .|..|-.++
T Consensus 628 fCpsCG~~t-~~frCP~CG~~-Te~i~fCP~CG~~~~~y~CPKCG~El 673 (1121)
T PRK04023 628 KCPSCGKET-FYRRCPFCGTH-TEPVYRCPRCGIEVEEDECEKCGREP 673 (1121)
T ss_pred cCCCCCCcC-CcccCCCCCCC-CCcceeCccccCcCCCCcCCCCCCCC
Confidence 466665554 44677777776 4556667777763 366665553
No 210
>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=27.09 E-value=30 Score=21.79 Aligned_cols=25 Identities=24% Similarity=0.515 Sum_probs=16.1
Q ss_pred eeeccccCccccccccccCCCceecccccc
Q psy12127 21 SECGVCLEPLDRGITSCQTCGNLVCTSCAA 50 (263)
Q Consensus 21 l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~ 50 (263)
..|++|...+..+ .. |..+|.+|-.
T Consensus 9 ~~C~~C~~~~~~~----~d-G~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSRWFYS----DD-GFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCeEeEc----cC-CEEEhhhCce
Confidence 4599999985544 23 6666666643
No 211
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=26.93 E-value=30 Score=30.27 Aligned_cols=8 Identities=38% Similarity=0.712 Sum_probs=4.9
Q ss_pred eeeecccc
Q psy12127 20 ISECGVCL 27 (263)
Q Consensus 20 ~l~CpIC~ 27 (263)
-+.||.|.
T Consensus 6 y~~Cp~Cg 13 (201)
T COG1326 6 YIECPSCG 13 (201)
T ss_pred EEECCCCC
Confidence 35666666
No 212
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=26.67 E-value=44 Score=33.17 Aligned_cols=49 Identities=20% Similarity=0.508 Sum_probs=27.4
Q ss_pred cccccchhcCCceeeeccccCccccccccccCCCceecc-ccccccCCCCCCccCCc
Q psy12127 8 ECCANCKELIASISECGVCLEPLDRGITSCQTCGNLVCT-SCAARLLKCPFCRITID 63 (263)
Q Consensus 8 ~~~~~~~~~l~~~l~CpIC~~~l~~Pv~qC~~CGH~~C~-~C~~~l~~CP~Cr~~~~ 63 (263)
+.|+.|-..=.+-+-||.|+.-+-..-. .. ....|. +|+ .||.|..++.
T Consensus 14 irc~~c~~~Ei~~~yCp~CL~~~p~~e~--~~-~~nrC~r~Cf----~CP~C~~~L~ 63 (483)
T PF05502_consen 14 IRCPRCVSEEIDSYYCPNCLFEVPSSEA--RS-EKNRCSRNCF----DCPICFSPLS 63 (483)
T ss_pred cCChhhcccccceeECccccccCChhhh--ee-ccceeccccc----cCCCCCCcce
Confidence 4566654443445557777765554321 11 123444 553 6999998876
No 213
>PLN02195 cellulose synthase A
Probab=26.33 E-value=37 Score=36.55 Aligned_cols=42 Identities=24% Similarity=0.617 Sum_probs=33.3
Q ss_pred eeccccCccc-----cccccccCCCceecccccccc-----CCCCCCccCCc
Q psy12127 22 ECGVCLEPLD-----RGITSCQTCGNLVCTSCAARL-----LKCPFCRITID 63 (263)
Q Consensus 22 ~CpIC~~~l~-----~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~ 63 (263)
.|.||.+-+- .|...|..||--+|+.|.+-- ..||.|++...
T Consensus 8 ~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 8 ICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred cceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcCCccCCccCCccc
Confidence 6999998544 555679999999999998652 37999998764
No 214
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=26.20 E-value=37 Score=27.10 Aligned_cols=20 Identities=35% Similarity=0.748 Sum_probs=11.1
Q ss_pred eccccCccccccccccCCCc
Q psy12127 23 CGVCLEPLDRGITSCQTCGN 42 (263)
Q Consensus 23 CpIC~~~l~~Pv~qC~~CGH 42 (263)
||+|...|.---+.|++||-
T Consensus 1 CPvCg~~l~vt~l~C~~C~t 20 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGT 20 (113)
T ss_pred CCCCCCceEEEEEEcCCCCC
Confidence 77777777643333444333
No 215
>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=25.50 E-value=50 Score=22.80 Aligned_cols=25 Identities=24% Similarity=0.462 Sum_probs=14.6
Q ss_pred CCceeeeccccCccccccccccCCCc
Q psy12127 17 IASISECGVCLEPLDRGITSCQTCGN 42 (263)
Q Consensus 17 l~~~l~CpIC~~~l~~Pv~qC~~CGH 42 (263)
......||.|.++..+ -..|.+||.
T Consensus 23 ~p~l~~C~~cG~~~~~-H~vc~~cG~ 47 (55)
T TIGR01031 23 APTLVVCPNCGEFKLP-HRVCPSCGY 47 (55)
T ss_pred CCcceECCCCCCcccC-eeECCccCe
Confidence 3456678888874443 345555553
No 216
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=25.43 E-value=38 Score=26.38 Aligned_cols=21 Identities=29% Similarity=0.983 Sum_probs=15.9
Q ss_pred eecccccccc--------CCCCCCccCCc
Q psy12127 43 LVCTSCAARL--------LKCPFCRITID 63 (263)
Q Consensus 43 ~~C~~C~~~l--------~~CP~Cr~~~~ 63 (263)
++|+.|+..| ..||.|+.++.
T Consensus 63 iiCGvC~~~LT~~EY~~~~~Cp~C~spFN 91 (105)
T COG4357 63 IICGVCRKLLTRAEYGMCGSCPYCQSPFN 91 (105)
T ss_pred EEhhhhhhhhhHHHHhhcCCCCCcCCCCC
Confidence 5777777765 37999999886
No 217
>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=25.26 E-value=43 Score=23.50 Aligned_cols=9 Identities=33% Similarity=1.110 Sum_probs=5.3
Q ss_pred CCCCCccCC
Q psy12127 54 KCPFCRITI 62 (263)
Q Consensus 54 ~CP~Cr~~~ 62 (263)
.||.|+...
T Consensus 48 ~C~~Cg~~~ 56 (69)
T PF07282_consen 48 TCPNCGFEM 56 (69)
T ss_pred EcCCCCCEE
Confidence 577666543
No 218
>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=25.22 E-value=42 Score=21.57 Aligned_cols=22 Identities=32% Similarity=0.709 Sum_probs=11.1
Q ss_pred eeccccCcc--ccccccccCCCceecccc
Q psy12127 22 ECGVCLEPL--DRGITSCQTCGNLVCTSC 48 (263)
Q Consensus 22 ~CpIC~~~l--~~Pv~qC~~CGH~~C~~C 48 (263)
.||.|.... .++ .. |-.+|..|
T Consensus 2 ~Cp~Cg~~~~~~D~----~~-g~~vC~~C 25 (43)
T PF08271_consen 2 KCPNCGSKEIVFDP----ER-GELVCPNC 25 (43)
T ss_dssp SBTTTSSSEEEEET----TT-TEEEETTT
T ss_pred CCcCCcCCceEEcC----CC-CeEECCCC
Confidence 466666632 232 13 55565555
No 219
>KOG0297|consensus
Probab=25.12 E-value=42 Score=32.29 Aligned_cols=49 Identities=27% Similarity=0.556 Sum_probs=35.5
Q ss_pred ceecCCCCCCCceeeeccchhhhhh-cccCCceecCCCCCCCCccChhhHHHHHh
Q psy12127 79 LELPCRNFRFGCKVYLPKAKRDKHE-DKCKFRQLKCPMHACPWTNSVLHLSEHLN 132 (263)
Q Consensus 79 l~v~C~~~~~GC~~~~~~~~~~~He-~~C~~~~~~CP~~~C~~~g~~~~L~~Hl~ 132 (263)
-.++|++ +|...+...++.+|. ..|+++...|....+. ....++..|..
T Consensus 113 ~~~~C~~---~C~~~~~~~d~~~hl~~~C~~~~~~c~~~~~~--~~~~~~~~h~~ 162 (391)
T KOG0297|consen 113 DPLKCPH---RCGVQVPRDDLEDHLEAECPRRSLKCSLCQSD--SILILLEAHEE 162 (391)
T ss_pred CcccCcc---ccccccchHHHHHHHhcccccccccchhhcCc--cchhhhhhcCC
Confidence 4688988 599999999999997 6999999988763333 23334444443
No 220
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=25.03 E-value=32 Score=32.87 Aligned_cols=22 Identities=36% Similarity=0.762 Sum_probs=13.5
Q ss_pred ccccCCCceeccccccccCCCCCCcc
Q psy12127 35 TSCQTCGNLVCTSCAARLLKCPFCRI 60 (263)
Q Consensus 35 ~qC~~CGH~~C~~C~~~l~~CP~Cr~ 60 (263)
|.|++||+.. .+.+.+||.|+.
T Consensus 1 ~~c~~cg~~~----~~~~g~cp~c~~ 22 (372)
T cd01121 1 YVCSECGYVS----PKWLGKCPECGE 22 (372)
T ss_pred CCCCCCCCCC----CCccEECcCCCC
Confidence 4577777753 111358999975
No 221
>PRK14873 primosome assembly protein PriA; Provisional
Probab=24.76 E-value=60 Score=33.55 Aligned_cols=38 Identities=29% Similarity=0.637 Sum_probs=22.6
Q ss_pred eeeeccccCccccccccccCCCceecccccccc--CCCCCCccC
Q psy12127 20 ISECGVCLEPLDRGITSCQTCGNLVCTSCAARL--LKCPFCRIT 61 (263)
Q Consensus 20 ~l~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l--~~CP~Cr~~ 61 (263)
...||.|..+|.-. + .. +...|..|-... ..||.|+..
T Consensus 392 ~~~C~~C~~~L~~h--~-~~-~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 392 PARCRHCTGPLGLP--S-AG-GTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eeECCCCCCceeEe--c-CC-CeeECCCCcCCCcCccCCCCcCC
Confidence 34677777766632 1 12 345566664432 489999875
No 222
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=24.74 E-value=29 Score=32.70 Aligned_cols=35 Identities=20% Similarity=0.307 Sum_probs=23.1
Q ss_pred cCCceeeeccccCccc---cccccccCCCceecccccccc
Q psy12127 16 LIASISECGVCLEPLD---RGITSCQTCGNLVCTSCAARL 52 (263)
Q Consensus 16 ~l~~~l~CpIC~~~l~---~Pv~qC~~CGH~~C~~C~~~l 52 (263)
...+.|.||+=.+.-. ||+.. .|||++=..=..++
T Consensus 332 hfHs~FiCPVlKe~~t~ENpP~ml--~CgHVIskeal~~L 369 (396)
T COG5109 332 HFHSLFICPVLKELCTDENPPVML--ECGHVISKEALSVL 369 (396)
T ss_pred cccceeeccccHhhhcccCCCeee--eccceeeHHHHHHH
Confidence 3568899999666554 67654 68998754444443
No 223
>KOG1729|consensus
Probab=24.06 E-value=25 Score=32.54 Aligned_cols=33 Identities=30% Similarity=0.714 Sum_probs=25.1
Q ss_pred ceeeeccccCcccccc---ccccCCCceeccccccc
Q psy12127 19 SISECGVCLEPLDRGI---TSCQTCGNLVCTSCAAR 51 (263)
Q Consensus 19 ~~l~CpIC~~~l~~Pv---~qC~~CGH~~C~~C~~~ 51 (263)
+.-.|.+|...-...+ .-|.+||++||..|...
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n 202 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRN 202 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhhhhhcC
Confidence 5678999999533222 34999999999999776
No 224
>PRK11595 DNA utilization protein GntX; Provisional
Probab=24.00 E-value=29 Score=30.58 Aligned_cols=22 Identities=32% Similarity=0.661 Sum_probs=9.9
Q ss_pred ccccchhcCC--ceeeeccccCcc
Q psy12127 9 CCANCKELIA--SISECGVCLEPL 30 (263)
Q Consensus 9 ~~~~~~~~l~--~~l~CpIC~~~l 30 (263)
.|..|++.+. +...|+.|..-+
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l 30 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRAL 30 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhC
Confidence 4555544332 123466565544
No 225
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.96 E-value=32 Score=29.42 Aligned_cols=26 Identities=19% Similarity=0.373 Sum_probs=14.7
Q ss_pred CCCCCccCCccc--ccccHHHHHhhhcc
Q psy12127 54 KCPFCRITIDYS--WQRNVALERIFTKL 79 (263)
Q Consensus 54 ~CP~Cr~~~~~~--~~rn~~le~~v~~l 79 (263)
.||.|++++..- ...-.+|++.++.|
T Consensus 138 ~Cp~Cg~~L~~~dn~~~~~~l~~~I~~l 165 (178)
T PRK06266 138 RCPQCGEMLEEYDNSELIKELKEQIKEL 165 (178)
T ss_pred cCCCCCCCCeecccHHHHHHHHHHHHHH
Confidence 899999887631 11233455555443
No 226
>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=23.58 E-value=57 Score=20.18 Aligned_cols=10 Identities=30% Similarity=0.773 Sum_probs=7.4
Q ss_pred CCCCCCccCC
Q psy12127 53 LKCPFCRITI 62 (263)
Q Consensus 53 ~~CP~Cr~~~ 62 (263)
..||.|+..+
T Consensus 27 ~~CP~Cg~~~ 36 (41)
T smart00834 27 ATCPECGGDV 36 (41)
T ss_pred CCCCCCCCcc
Confidence 4799998744
No 227
>PHA03376 BARF1; Provisional
Probab=23.46 E-value=5.2e+02 Score=22.89 Aligned_cols=55 Identities=7% Similarity=0.104 Sum_probs=30.0
Q ss_pred EEEEEEeeeCCCCceEEEEEEeeccc-cccCCc------eeee-eecce------eeeecccCCCCCCCCC
Q psy12127 188 LTMSFVQISNSSPFHFGVFVNIASNF-KSMKGI------VPIH-YACPE------LHISCDALVTPWKSQD 244 (263)
Q Consensus 188 ~~v~~v~~~~~~~~~y~~~l~~~~~~-~~~~g~------~~~~-~q~~~------~~v~~~~l~~~~~~~~ 244 (263)
+++....+..+++.+|+|.+....+- ++.+-+ +=|. -+.|+ ..|.|+ |+|||.+.
T Consensus 87 vsLvI~~l~lSDdGtY~C~fQkge~~~~k~ehLt~V~~~~Lsv~a~~~dFp~~~~~~i~C~--sggfP~P~ 155 (221)
T PHA03376 87 FFLVVTAANISHDGNYLCRMKLGETEVTKQEHLSVVKPLTLSVHSERSQFPDFSVLTVTCT--VNAFPHPH 155 (221)
T ss_pred EEEEEEeeeecCCceEEEEEEcCCCceeeeeeeeeeecceEEEEeccccCCCCCeeEEEEe--cCCcCCch
Confidence 34443446777888999999744322 222211 1111 11122 236787 89999986
No 228
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=23.20 E-value=47 Score=21.67 Aligned_cols=23 Identities=35% Similarity=0.814 Sum_probs=14.0
Q ss_pred eccccCccccccccccCCCceeccc
Q psy12127 23 CGVCLEPLDRGITSCQTCGNLVCTS 47 (263)
Q Consensus 23 CpIC~~~l~~Pv~qC~~CGH~~C~~ 47 (263)
|..|..... ++.|-.||+.+|..
T Consensus 2 C~~C~~~~~--l~~CL~C~~~~c~~ 24 (50)
T smart00290 2 CSVCGTIEN--LWLCLTCGQVGCGR 24 (50)
T ss_pred cccCCCcCC--eEEecCCCCcccCC
Confidence 556664332 56677777777654
No 229
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=23.18 E-value=44 Score=36.24 Aligned_cols=45 Identities=27% Similarity=0.705 Sum_probs=34.7
Q ss_pred ceeeeccccCccc-----cccccccCCCceecccccccc-----CCCCCCccCCc
Q psy12127 19 SISECGVCLEPLD-----RGITSCQTCGNLVCTSCAARL-----LKCPFCRITID 63 (263)
Q Consensus 19 ~~l~CpIC~~~l~-----~Pv~qC~~CGH~~C~~C~~~l-----~~CP~Cr~~~~ 63 (263)
+.-.|.||.+-+- .|...|..||--+|+.|.+-- ..||.|++...
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 3456999998754 355679999999999998642 37999998653
No 230
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=22.64 E-value=56 Score=22.22 Aligned_cols=9 Identities=44% Similarity=1.457 Sum_probs=5.2
Q ss_pred CCCCCccCC
Q psy12127 54 KCPFCRITI 62 (263)
Q Consensus 54 ~CP~Cr~~~ 62 (263)
.||-|+..+
T Consensus 26 rCp~Cg~rI 34 (49)
T COG1996 26 RCPYCGSRI 34 (49)
T ss_pred eCCCCCcEE
Confidence 566666543
No 231
>KOG0298|consensus
Probab=22.61 E-value=16 Score=40.13 Aligned_cols=45 Identities=27% Similarity=0.712 Sum_probs=35.4
Q ss_pred cCCceeeeccccCccccc--cccccCCCceecccccccc----CCCCCCccCCc
Q psy12127 16 LIASISECGVCLEPLDRG--ITSCQTCGNLVCTSCAARL----LKCPFCRITID 63 (263)
Q Consensus 16 ~l~~~l~CpIC~~~l~~P--v~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~ 63 (263)
.+.....|+||++++..- |++ |||.+|..|...+ ..||.|....+
T Consensus 1149 ~~~~~~~c~ic~dil~~~~~I~~---cgh~~c~~c~~~~l~~~s~~~~~ksi~~ 1199 (1394)
T KOG0298|consen 1149 NLSGHFVCEICLDILRNQGGIAG---CGHEPCCRCDELWLYASSRCPICKSIKG 1199 (1394)
T ss_pred HhhcccchHHHHHHHHhcCCeee---echhHhhhHHHHHHHHhccCcchhhhhh
Confidence 345677999999999943 444 7999999998774 58999987654
No 232
>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=22.56 E-value=51 Score=26.94 Aligned_cols=10 Identities=10% Similarity=0.242 Sum_probs=7.3
Q ss_pred CCCCCccCCc
Q psy12127 54 KCPFCRITID 63 (263)
Q Consensus 54 ~CP~Cr~~~~ 63 (263)
.||.|+..+.
T Consensus 28 vcP~cg~~~~ 37 (129)
T TIGR02300 28 VSPYTGEQFP 37 (129)
T ss_pred cCCCcCCccC
Confidence 6888887654
No 233
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=22.20 E-value=21 Score=24.23 Aligned_cols=40 Identities=20% Similarity=0.617 Sum_probs=21.1
Q ss_pred eeccccCccccccccccCCCceecccccccc----CCCCCCccCCcc
Q psy12127 22 ECGVCLEPLDRGITSCQTCGNLVCTSCAARL----LKCPFCRITIDY 64 (263)
Q Consensus 22 ~CpIC~~~l~~Pv~qC~~CGH~~C~~C~~~l----~~CP~Cr~~~~~ 64 (263)
.|--|--.-+.= ..|. .|..|-.|+..+ ..||.|..++.+
T Consensus 4 nCKsCWf~~k~L-i~C~--dHYLCl~CLt~ml~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 4 NCKSCWFANKGL-IKCS--DHYLCLNCLTLMLSRSDRCPICGKPLPT 47 (50)
T ss_dssp ---SS-S--SSE-EE-S--S-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred cChhhhhcCCCe-eeec--chhHHHHHHHHHhccccCCCcccCcCcc
Confidence 344444433332 3464 799999999885 379999998763
No 234
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=21.64 E-value=47 Score=20.73 Aligned_cols=10 Identities=50% Similarity=1.122 Sum_probs=4.0
Q ss_pred eccccCcccc
Q psy12127 23 CGVCLEPLDR 32 (263)
Q Consensus 23 CpIC~~~l~~ 32 (263)
||.|..+|..
T Consensus 3 C~~CG~~l~~ 12 (34)
T PF14803_consen 3 CPQCGGPLER 12 (34)
T ss_dssp -TTT--B-EE
T ss_pred cccccChhhh
Confidence 6777777664
No 235
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=21.52 E-value=47 Score=25.37 Aligned_cols=18 Identities=11% Similarity=0.139 Sum_probs=11.5
Q ss_pred hhcCCceeeeccccCccc
Q psy12127 14 KELIASISECGVCLEPLD 31 (263)
Q Consensus 14 ~~~l~~~l~CpIC~~~l~ 31 (263)
++...+...||.|...-.
T Consensus 29 e~~~~~~~~Cp~C~~~~V 46 (89)
T COG1997 29 EAQQRAKHVCPFCGRTTV 46 (89)
T ss_pred HHHHhcCCcCCCCCCcce
Confidence 344566777888877633
No 236
>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=21.44 E-value=48 Score=25.30 Aligned_cols=22 Identities=32% Similarity=0.670 Sum_probs=13.4
Q ss_pred eeccccCccccccccccCCCceeccccc
Q psy12127 22 ECGVCLEPLDRGITSCQTCGNLVCTSCA 49 (263)
Q Consensus 22 ~CpIC~~~l~~Pv~qC~~CGH~~C~~C~ 49 (263)
-||.|..+|.+. . +...|..|-
T Consensus 2 fC~~Cg~~l~~~-----~-~~~~C~~C~ 23 (104)
T TIGR01384 2 FCPKCGSLMTPK-----N-GVYVCPSCG 23 (104)
T ss_pred CCcccCcccccC-----C-CeEECcCCC
Confidence 488888888542 2 455555554
No 237
>PHA00616 hypothetical protein
Probab=21.20 E-value=45 Score=22.16 Aligned_cols=25 Identities=28% Similarity=0.385 Sum_probs=19.2
Q ss_pred eecCCCCCCCCcc-ChhhHHHHHhcccC
Q psy12127 110 QLKCPMHACPWTN-SVLHLSEHLNQVHH 136 (263)
Q Consensus 110 ~~~CP~~~C~~~g-~~~~L~~Hl~~~H~ 136 (263)
|+.|| .|+-.- ..++|..|+...|+
T Consensus 1 pYqC~--~CG~~F~~~s~l~~H~r~~hg 26 (44)
T PHA00616 1 MYQCL--RCGGIFRKKKEVIEHLLSVHK 26 (44)
T ss_pred CCccc--hhhHHHhhHHHHHHHHHHhcC
Confidence 45675 577664 67899999999997
No 238
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.58 E-value=53 Score=29.48 Aligned_cols=22 Identities=45% Similarity=1.140 Sum_probs=12.6
Q ss_pred cccCCCceecccccc-ccCCCCCCccCCc
Q psy12127 36 SCQTCGNLVCTSCAA-RLLKCPFCRITID 63 (263)
Q Consensus 36 qC~~CGH~~C~~C~~-~l~~CP~Cr~~~~ 63 (263)
.|+.||| +. +.-.||.|+....
T Consensus 311 ~C~~cg~------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 311 TCPCCGH------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred cccccCC------ccceeEECCCCCCeeh
Confidence 4666777 21 1236888876543
No 239
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=20.32 E-value=45 Score=25.75 Aligned_cols=39 Identities=26% Similarity=0.700 Sum_probs=14.7
Q ss_pred eeccccCccc--cc-cccccCCCceecccccccc--------CCCCCCccCC
Q psy12127 22 ECGVCLEPLD--RG-ITSCQTCGNLVCTSCAARL--------LKCPFCRITI 62 (263)
Q Consensus 22 ~CpIC~~~l~--~P-v~qC~~CGH~~C~~C~~~l--------~~CP~Cr~~~ 62 (263)
.|++|...+. ++ +.+|.+ ||.+ ..|...+ ..|+.|....
T Consensus 16 ~C~~C~~~i~~~~~~~~~C~~-GH~w-~RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 16 KCPICGAPIPFDDLDEAQCEN-GHVW-PRCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp -------------SSEEE-TT-S-EE-EB-SSS-SBS-SS-EEE-TTT--EE
T ss_pred cccccccccccCCcCEeECCC-CCEE-eeeeeeeeeeccCCeeEcCCCCCEE
Confidence 6999999775 33 478999 9985 6776552 2799998754
No 240
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=20.28 E-value=63 Score=27.54 Aligned_cols=25 Identities=24% Similarity=0.615 Sum_probs=14.5
Q ss_pred cccccCCCceeccccccccCCCCCCccC
Q psy12127 34 ITSCQTCGNLVCTSCAARLLKCPFCRIT 61 (263)
Q Consensus 34 v~qC~~CGH~~C~~C~~~l~~CP~Cr~~ 61 (263)
++.|..|||++ .. ..-..||.|..+
T Consensus 134 ~~vC~vCGy~~-~g--e~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTH-EG--EAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcc-cC--CCCCcCCCCCCh
Confidence 56677777753 11 112478888765
No 241
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=20.19 E-value=50 Score=22.11 Aligned_cols=16 Identities=31% Similarity=0.395 Sum_probs=10.4
Q ss_pred hhcCCceeeeccccCc
Q psy12127 14 KELIASISECGVCLEP 29 (263)
Q Consensus 14 ~~~l~~~l~CpIC~~~ 29 (263)
-++|.+.+.||+|...
T Consensus 28 F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 28 FEDLPDDWVCPVCGAP 43 (47)
T ss_dssp GGGS-TT-B-TTTSSB
T ss_pred HHHCCCCCcCcCCCCc
Confidence 4678999999999764
No 242
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.17 E-value=72 Score=32.95 Aligned_cols=37 Identities=19% Similarity=0.425 Sum_probs=23.2
Q ss_pred CccccccchhcC-----CceeeeccccCccccccccccCCCce
Q psy12127 6 EPECCANCKELI-----ASISECGVCLEPLDRGITSCQTCGNL 43 (263)
Q Consensus 6 ~~~~~~~~~~~l-----~~~l~CpIC~~~l~~Pv~qC~~CGH~ 43 (263)
+...||+|+..| .+.+.|.-|......| ..|+.||..
T Consensus 389 ~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~-~~Cp~Cg~~ 430 (679)
T PRK05580 389 WVAECPHCDASLTLHRFQRRLRCHHCGYQEPIP-KACPECGST 430 (679)
T ss_pred CccCCCCCCCceeEECCCCeEECCCCcCCCCCC-CCCCCCcCC
Confidence 345677776655 3567777777666555 357766654
No 243
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=20.05 E-value=85 Score=24.18 Aligned_cols=27 Identities=30% Similarity=0.699 Sum_probs=22.9
Q ss_pred CceecCCCCCCCCccChhhHHHHHhcccC
Q psy12127 108 FRQLKCPMHACPWTNSVLHLSEHLNQVHH 136 (263)
Q Consensus 108 ~~~~~CP~~~C~~~g~~~~L~~Hl~~~H~ 136 (263)
++.+.| ..|.+....+++..||++.|.
T Consensus 9 ~~vlIC--~~C~~av~~~~v~~HL~~~H~ 35 (109)
T PF12013_consen 9 YRVLIC--RQCQYAVQPSEVESHLRKRHH 35 (109)
T ss_pred CCEEEe--CCCCcccCchHHHHHHHHhcc
Confidence 566778 469999888999999998886
Done!