Query psy17995
Match_columns 120
No_of_seqs 145 out of 1065
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 19:36:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17995.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17995hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00570 cdk7 CDK-activating 100.0 8.8E-45 1.9E-49 282.2 10.2 120 1-120 1-120 (309)
2 COG5220 TFB3 Cdk activating ki 100.0 2.2E-37 4.8E-42 232.9 4.5 119 1-119 8-130 (314)
3 KOG3800|consensus 100.0 1.7E-36 3.7E-41 232.3 6.6 116 5-120 2-118 (300)
4 PF06391 MAT1: CDK-activating 99.9 1.6E-24 3.4E-29 160.5 0.2 68 53-120 1-68 (200)
5 PF15227 zf-C3HC4_4: zinc fing 99.4 3.4E-13 7.4E-18 77.0 2.5 39 6-49 1-42 (42)
6 smart00504 Ubox Modified RING 99.3 6.1E-12 1.3E-16 76.5 3.8 51 3-59 1-51 (63)
7 KOG0320|consensus 99.2 3.1E-12 6.8E-17 93.0 2.3 52 3-58 131-182 (187)
8 TIGR00599 rad18 DNA repair pro 99.2 1.4E-11 3.1E-16 99.6 5.4 75 3-83 26-100 (397)
9 PLN03208 E3 ubiquitin-protein 99.2 8.8E-12 1.9E-16 92.0 3.6 54 2-60 17-85 (193)
10 PF13923 zf-C3HC4_2: Zinc fing 99.2 1.3E-11 2.9E-16 69.0 2.0 39 6-49 1-39 (39)
11 PF14634 zf-RING_5: zinc-RING 99.1 3.1E-11 6.7E-16 69.3 3.0 44 5-51 1-44 (44)
12 PF00097 zf-C3HC4: Zinc finger 99.1 7E-11 1.5E-15 66.4 2.2 40 6-49 1-41 (41)
13 PF13920 zf-C3HC4_3: Zinc fing 99.1 7.1E-11 1.5E-15 69.3 2.3 47 2-54 1-48 (50)
14 cd00162 RING RING-finger (Real 99.0 4.2E-10 9.1E-15 62.9 3.4 44 5-52 1-44 (45)
15 PF13639 zf-RING_2: Ring finge 98.9 2.5E-10 5.4E-15 65.2 1.1 43 5-50 2-44 (44)
16 KOG2164|consensus 98.9 1.3E-09 2.9E-14 89.7 5.6 101 3-112 186-295 (513)
17 PF04564 U-box: U-box domain; 98.9 7.5E-10 1.6E-14 69.9 1.8 62 2-72 3-64 (73)
18 PF14835 zf-RING_6: zf-RING of 98.9 4.7E-10 1E-14 69.2 0.8 55 4-73 8-62 (65)
19 KOG0287|consensus 98.9 5.8E-10 1.3E-14 88.4 1.5 74 3-82 23-96 (442)
20 PHA02929 N1R/p28-like protein; 98.9 2.1E-09 4.6E-14 81.9 4.2 50 3-54 174-227 (238)
21 PF13445 zf-RING_UBOX: RING-ty 98.8 1.8E-09 4E-14 61.9 2.2 40 6-47 1-43 (43)
22 smart00184 RING Ring finger. E 98.8 3E-09 6.6E-14 57.3 2.9 39 6-49 1-39 (39)
23 KOG0978|consensus 98.8 1.3E-09 2.9E-14 93.0 1.8 52 4-60 644-695 (698)
24 KOG0823|consensus 98.7 5.6E-09 1.2E-13 78.8 2.6 51 3-58 47-99 (230)
25 KOG0317|consensus 98.7 7E-09 1.5E-13 80.4 2.7 49 3-57 239-287 (293)
26 KOG2177|consensus 98.7 5.7E-09 1.2E-13 77.4 1.8 44 2-51 12-55 (386)
27 PHA02926 zinc finger-like prot 98.6 2.9E-08 6.2E-13 74.9 3.7 52 3-54 170-230 (242)
28 COG5432 RAD18 RING-finger-cont 98.6 1.9E-08 4.1E-13 78.6 2.5 50 4-59 26-75 (391)
29 KOG0297|consensus 98.6 6.6E-08 1.4E-12 78.3 4.9 85 3-100 21-110 (391)
30 KOG0311|consensus 98.5 9.1E-09 2E-13 81.7 -1.2 53 3-59 43-96 (381)
31 COG5574 PEX10 RING-finger-cont 98.4 9E-08 2E-12 73.5 2.1 48 3-55 215-263 (271)
32 PF12678 zf-rbx1: RING-H2 zinc 98.3 6.4E-07 1.4E-11 56.6 3.2 46 3-50 19-73 (73)
33 KOG2879|consensus 98.2 8.8E-07 1.9E-11 68.5 3.1 49 2-54 238-287 (298)
34 COG5152 Uncharacterized conser 98.2 4E-07 8.6E-12 67.9 1.1 45 4-54 197-241 (259)
35 PF11789 zf-Nse: Zinc-finger o 98.2 8.1E-07 1.7E-11 53.8 1.7 42 3-49 11-54 (57)
36 KOG3039|consensus 98.1 1.5E-06 3.2E-11 66.6 2.9 54 3-59 221-275 (303)
37 KOG4159|consensus 98.1 1.1E-06 2.5E-11 71.3 2.3 48 2-55 83-130 (398)
38 COG5222 Uncharacterized conser 98.1 3.7E-06 8E-11 66.2 3.9 62 4-73 275-337 (427)
39 KOG4739|consensus 98.0 3.2E-06 7E-11 64.2 2.5 51 1-57 1-51 (233)
40 COG5540 RING-finger-containing 98.0 2.7E-06 6E-11 66.9 2.1 49 4-54 324-372 (374)
41 KOG2660|consensus 98.0 4.2E-06 9E-11 66.2 3.0 58 3-65 15-72 (331)
42 PF04641 Rtf2: Rtf2 RING-finge 98.0 4.6E-06 1E-10 64.2 3.1 53 3-59 113-166 (260)
43 KOG1813|consensus 97.9 3E-06 6.4E-11 66.2 1.2 45 4-54 242-286 (313)
44 KOG4628|consensus 97.8 1.5E-05 3.3E-10 63.7 2.9 50 5-56 231-280 (348)
45 PF14570 zf-RING_4: RING/Ubox 97.8 2.7E-05 5.8E-10 45.6 3.2 47 6-53 1-47 (48)
46 KOG4172|consensus 97.7 9.7E-06 2.1E-10 48.7 0.4 46 4-54 8-54 (62)
47 KOG0802|consensus 97.6 3.7E-05 8E-10 64.7 2.4 52 3-55 291-342 (543)
48 KOG0824|consensus 97.6 3.3E-05 7E-10 60.7 1.8 46 4-54 8-53 (324)
49 PF05290 Baculo_IE-1: Baculovi 97.5 9E-05 1.9E-09 52.0 2.8 51 4-57 81-135 (140)
50 COG5243 HRD1 HRD ubiquitin lig 97.4 0.00011 2.4E-09 59.5 3.2 51 2-53 286-344 (491)
51 PF12861 zf-Apc11: Anaphase-pr 97.4 0.00015 3.2E-09 47.2 3.3 34 21-54 47-82 (85)
52 KOG1002|consensus 97.4 0.00017 3.6E-09 60.7 4.0 48 3-55 536-587 (791)
53 COG5236 Uncharacterized conser 97.3 0.00027 5.9E-09 56.8 4.2 92 2-101 60-175 (493)
54 PF14447 Prok-RING_4: Prokaryo 97.3 0.00013 2.9E-09 43.7 1.3 31 23-56 22-52 (55)
55 KOG1039|consensus 97.1 0.00038 8.2E-09 55.8 2.8 55 3-57 161-224 (344)
56 COG5175 MOT2 Transcriptional r 97.0 0.00029 6.3E-09 56.5 1.6 54 4-59 15-69 (480)
57 KOG0827|consensus 96.9 0.00057 1.2E-08 55.5 2.3 66 4-72 5-74 (465)
58 KOG1001|consensus 96.9 0.00024 5.1E-09 61.4 -0.1 51 4-60 455-506 (674)
59 PF14569 zf-UDP: Zinc-binding 96.7 0.003 6.5E-08 40.4 4.1 54 3-56 9-64 (80)
60 KOG1645|consensus 96.7 0.0016 3.5E-08 53.2 3.4 55 4-58 5-60 (463)
61 KOG0804|consensus 96.7 0.00062 1.4E-08 56.1 1.0 45 4-53 176-221 (493)
62 KOG4692|consensus 96.7 0.001 2.2E-08 53.7 2.1 47 2-54 421-467 (489)
63 KOG4367|consensus 96.6 0.00084 1.8E-08 55.5 1.4 35 2-41 3-37 (699)
64 KOG1814|consensus 96.6 0.0011 2.3E-08 54.2 1.5 46 3-50 184-236 (445)
65 KOG4185|consensus 96.6 0.0022 4.8E-08 49.7 3.2 52 1-53 1-54 (296)
66 PF11793 FANCL_C: FANCL C-term 96.5 0.0008 1.7E-08 42.1 0.6 52 3-54 2-66 (70)
67 KOG1785|consensus 96.4 0.0013 2.8E-08 53.9 1.1 46 5-55 371-417 (563)
68 KOG0825|consensus 96.3 0.00066 1.4E-08 59.4 -0.9 48 4-56 124-173 (1134)
69 KOG4265|consensus 96.2 0.0024 5.2E-08 51.2 1.6 45 4-54 291-336 (349)
70 KOG0828|consensus 96.2 0.0024 5.1E-08 53.5 1.4 51 4-54 572-634 (636)
71 COG5194 APC11 Component of SCF 95.9 0.0093 2E-07 38.5 2.8 49 5-54 33-81 (88)
72 KOG1812|consensus 95.7 0.0084 1.8E-07 48.8 2.7 52 3-55 146-204 (384)
73 KOG3002|consensus 95.5 0.0091 2E-07 47.1 2.3 44 3-54 48-91 (299)
74 KOG1734|consensus 95.2 0.0056 1.2E-07 47.8 0.2 53 2-54 223-281 (328)
75 smart00744 RINGv The RING-vari 95.1 0.024 5.1E-07 33.0 2.6 43 5-50 1-49 (49)
76 PRK00420 hypothetical protein; 95.0 0.12 2.5E-06 35.4 6.0 22 87-108 89-110 (112)
77 PF07191 zinc-ribbons_6: zinc- 94.7 0.0034 7.5E-08 39.4 -1.7 41 3-54 1-41 (70)
78 COG5219 Uncharacterized conser 94.5 0.016 3.5E-07 52.1 1.1 48 4-54 1470-1523(1525)
79 KOG2817|consensus 94.4 0.035 7.6E-07 45.2 2.9 47 4-52 335-383 (394)
80 KOG1941|consensus 94.2 0.015 3.3E-07 47.6 0.4 47 4-51 366-413 (518)
81 PLN02436 cellulose synthase A 94.1 0.052 1.1E-06 49.2 3.6 53 4-56 37-91 (1094)
82 PLN02189 cellulose synthase 94.1 0.054 1.2E-06 49.0 3.6 53 4-56 35-89 (1040)
83 KOG0826|consensus 93.9 0.04 8.8E-07 44.0 2.3 47 2-53 299-345 (357)
84 KOG3113|consensus 93.9 0.043 9.3E-07 42.5 2.3 51 3-58 111-162 (293)
85 PLN02638 cellulose synthase A 93.9 0.047 1E-06 49.5 2.8 52 4-55 18-71 (1079)
86 PLN02915 cellulose synthase A 93.4 0.07 1.5E-06 48.3 3.1 53 3-55 15-69 (1044)
87 KOG1493|consensus 93.2 0.039 8.5E-07 35.3 0.9 35 20-54 45-81 (84)
88 PLN02195 cellulose synthase A 93.2 0.12 2.7E-06 46.5 4.2 52 4-55 7-60 (977)
89 KOG4362|consensus 93.1 0.03 6.4E-07 48.6 0.2 52 4-60 22-75 (684)
90 PLN02400 cellulose synthase 92.0 0.098 2.1E-06 47.6 2.1 52 4-55 37-90 (1085)
91 KOG1940|consensus 92.0 0.13 2.7E-06 40.3 2.4 47 3-51 158-204 (276)
92 PF03854 zf-P11: P-11 zinc fin 91.9 0.057 1.2E-06 31.5 0.4 46 3-55 2-47 (50)
93 KOG1571|consensus 91.6 0.072 1.6E-06 42.9 0.8 42 4-54 306-347 (355)
94 PF10571 UPF0547: Uncharacteri 91.6 0.12 2.6E-06 26.3 1.3 9 5-13 2-10 (26)
95 KOG3799|consensus 90.9 0.11 2.3E-06 36.9 1.0 27 2-37 64-90 (169)
96 PHA03096 p28-like protein; Pro 90.9 0.15 3.2E-06 40.1 1.8 50 4-53 179-236 (284)
97 PF08746 zf-RING-like: RING-li 90.5 0.31 6.6E-06 27.5 2.5 41 6-49 1-43 (43)
98 PF10235 Cript: Microtubule-as 90.2 0.18 3.9E-06 33.2 1.5 35 5-54 46-80 (90)
99 KOG2114|consensus 90.2 0.13 2.9E-06 45.6 1.2 43 4-54 841-883 (933)
100 KOG3161|consensus 89.9 0.093 2E-06 45.5 -0.0 37 4-41 12-48 (861)
101 KOG1428|consensus 89.8 0.29 6.3E-06 46.5 3.0 50 3-55 3486-3545(3738)
102 KOG4275|consensus 89.5 0.032 7E-07 44.1 -2.8 43 3-55 300-343 (350)
103 PRK14559 putative protein seri 88.4 0.27 5.9E-06 42.7 1.8 20 4-34 2-21 (645)
104 KOG0298|consensus 87.3 0.14 3.1E-06 47.2 -0.6 44 4-52 1154-1197(1394)
105 KOG2113|consensus 87.1 0.4 8.6E-06 38.5 1.8 44 1-52 341-385 (394)
106 KOG2068|consensus 86.8 0.53 1.1E-05 37.7 2.4 84 27-112 1-92 (327)
107 PF12773 DZR: Double zinc ribb 86.8 0.61 1.3E-05 26.6 2.1 29 27-55 11-41 (50)
108 KOG0006|consensus 86.4 0.91 2E-05 36.6 3.5 37 1-37 313-353 (446)
109 PF02891 zf-MIZ: MIZ/SP-RING z 86.3 0.58 1.3E-05 27.2 1.9 44 4-52 3-50 (50)
110 COG3813 Uncharacterized protei 85.6 0.64 1.4E-05 29.5 1.9 51 5-59 7-57 (84)
111 PF07800 DUF1644: Protein of u 85.4 2.3 4.9E-05 30.8 4.8 15 87-101 115-130 (162)
112 PF06906 DUF1272: Protein of u 85.1 1 2.2E-05 27.1 2.5 46 5-56 7-54 (57)
113 PF10272 Tmpp129: Putative tra 83.9 1.3 2.9E-05 35.9 3.5 25 31-55 316-352 (358)
114 KOG3039|consensus 83.7 0.73 1.6E-05 35.8 1.8 31 5-40 45-75 (303)
115 cd00350 rubredoxin_like Rubred 83.4 1.1 2.4E-05 23.6 2.0 11 42-52 16-26 (33)
116 KOG2930|consensus 82.6 1.1 2.3E-05 30.4 2.1 28 24-52 79-106 (114)
117 PF09723 Zn-ribbon_8: Zinc rib 82.1 0.23 5.1E-06 27.8 -1.1 28 25-54 10-38 (42)
118 PF05605 zf-Di19: Drought indu 81.6 0.71 1.5E-05 26.9 0.9 40 2-53 1-41 (54)
119 COG5109 Uncharacterized conser 81.1 1.3 2.8E-05 35.6 2.4 48 4-53 337-386 (396)
120 KOG1815|consensus 80.8 1 2.2E-05 37.2 1.8 49 3-55 70-127 (444)
121 PF07975 C1_4: TFIIH C1-like d 80.4 1.4 3E-05 26.0 1.8 25 25-50 26-50 (51)
122 smart00834 CxxC_CXXC_SSSS Puta 80.2 0.59 1.3E-05 25.3 0.2 13 43-55 26-38 (41)
123 PF13248 zf-ribbon_3: zinc-rib 79.7 0.42 9E-06 24.0 -0.5 6 5-10 4-9 (26)
124 cd00065 FYVE FYVE domain; Zinc 79.5 1.8 3.9E-05 25.0 2.1 36 4-40 3-38 (57)
125 KOG2932|consensus 78.7 0.82 1.8E-05 36.7 0.6 27 24-53 107-133 (389)
126 PF09889 DUF2116: Uncharacteri 78.6 2.5 5.5E-05 25.6 2.6 30 44-77 4-33 (59)
127 smart00064 FYVE Protein presen 77.2 2.4 5.2E-05 25.5 2.3 36 4-40 11-46 (68)
128 KOG2034|consensus 77.2 1.2 2.5E-05 40.0 1.1 35 3-40 817-851 (911)
129 KOG1952|consensus 77.2 1.6 3.4E-05 39.1 1.9 51 2-54 190-247 (950)
130 KOG2979|consensus 76.8 3.5 7.6E-05 32.1 3.5 45 3-52 176-222 (262)
131 PF10083 DUF2321: Uncharacteri 76.4 1.9 4.1E-05 31.1 1.8 27 27-57 27-53 (158)
132 KOG3842|consensus 75.7 2.7 5.8E-05 34.0 2.7 41 24-65 376-426 (429)
133 KOG2068|consensus 75.7 3.1 6.8E-05 33.4 3.1 51 4-56 250-300 (327)
134 PLN02248 cellulose synthase-li 75.5 2.2 4.9E-05 39.3 2.5 33 25-58 149-181 (1135)
135 KOG1100|consensus 75.3 1.5 3.2E-05 32.9 1.1 39 6-54 161-200 (207)
136 PF03604 DNA_RNApol_7kD: DNA d 74.5 2.6 5.7E-05 22.3 1.7 9 4-12 1-9 (32)
137 PF13240 zinc_ribbon_2: zinc-r 73.7 0.61 1.3E-05 22.9 -0.9 7 45-51 15-21 (23)
138 PF14319 Zn_Tnp_IS91: Transpos 73.6 1.3 2.9E-05 29.9 0.5 10 25-34 57-66 (111)
139 COG1645 Uncharacterized Zn-fin 73.4 0.92 2E-05 31.8 -0.4 9 43-51 44-52 (131)
140 smart00647 IBR In Between Ring 73.0 1.8 3.9E-05 25.3 0.9 33 5-37 20-57 (64)
141 PHA02862 5L protein; Provision 72.3 4 8.6E-05 29.3 2.6 47 1-54 1-53 (156)
142 PF02318 FYVE_2: FYVE-type zin 72.1 2 4.3E-05 29.1 1.0 48 2-51 53-102 (118)
143 PRK11595 DNA utilization prote 71.6 3.7 8.1E-05 30.7 2.5 39 5-54 7-45 (227)
144 PF09297 zf-NADH-PPase: NADH p 71.6 0.65 1.4E-05 24.3 -1.2 24 28-51 3-29 (32)
145 TIGR02605 CxxC_CxxC_SSSS putat 71.4 1.4 3E-05 25.3 0.1 9 43-51 26-34 (52)
146 PF05883 Baculo_RING: Baculovi 70.9 1.6 3.5E-05 30.7 0.4 33 4-38 27-65 (134)
147 PF01363 FYVE: FYVE zinc finge 70.5 1.4 3E-05 26.7 -0.0 35 4-39 10-44 (69)
148 PF10497 zf-4CXXC_R1: Zinc-fin 69.6 5.7 0.00012 26.6 2.8 25 27-51 37-69 (105)
149 PF10146 zf-C4H2: Zinc finger- 69.4 3.7 8E-05 31.3 2.1 28 29-57 195-222 (230)
150 PF06677 Auto_anti-p27: Sjogre 68.6 2 4.3E-05 24.1 0.4 11 1-11 15-25 (41)
151 PF09538 FYDLN_acid: Protein o 68.5 2.1 4.6E-05 28.9 0.6 27 30-56 11-39 (108)
152 PF13719 zinc_ribbon_5: zinc-r 68.2 2.1 4.5E-05 23.2 0.4 13 4-17 3-15 (37)
153 PHA02825 LAP/PHD finger-like p 67.2 7.8 0.00017 28.1 3.3 46 3-54 8-59 (162)
154 PRK13130 H/ACA RNA-protein com 67.0 11 0.00023 22.6 3.4 31 44-74 18-48 (56)
155 PF09237 GAGA: GAGA factor; I 66.5 3.5 7.6E-05 24.5 1.1 13 43-55 24-36 (54)
156 PF04423 Rad50_zn_hook: Rad50 66.4 2 4.3E-05 25.0 0.1 11 44-54 21-31 (54)
157 KOG1812|consensus 66.2 3.1 6.7E-05 34.0 1.2 42 5-48 308-350 (384)
158 KOG4185|consensus 66.1 1.8 4E-05 33.4 -0.1 27 26-52 239-265 (296)
159 PF01485 IBR: IBR domain; Int 64.8 3 6.5E-05 24.3 0.7 32 5-36 20-56 (64)
160 TIGR00622 ssl1 transcription f 64.8 8.1 0.00018 26.4 2.8 25 25-50 86-110 (112)
161 PF11781 RRN7: RNA polymerase 64.1 4.2 9.2E-05 22.0 1.1 8 5-12 10-17 (36)
162 PF06676 DUF1178: Protein of u 63.7 8.7 0.00019 27.4 2.9 24 25-53 9-42 (148)
163 KOG2169|consensus 63.4 3.5 7.6E-05 35.8 1.1 43 3-54 306-356 (636)
164 smart00154 ZnF_AN1 AN1-like Zi 61.4 5.6 0.00012 21.8 1.3 24 6-32 1-24 (39)
165 COG3364 Zn-ribbon containing p 60.8 5.4 0.00012 27.0 1.4 25 23-52 5-29 (112)
166 PF03119 DNA_ligase_ZBD: NAD-d 60.6 3 6.5E-05 21.3 0.1 11 45-55 1-11 (28)
167 PF07754 DUF1610: Domain of un 60.4 2.1 4.5E-05 21.4 -0.5 9 43-51 16-24 (24)
168 COG2093 DNA-directed RNA polym 59.0 3.7 8.1E-05 25.2 0.3 21 31-52 7-27 (64)
169 PF07503 zf-HYPF: HypF finger; 58.9 8.9 0.00019 20.7 1.8 24 30-53 1-31 (35)
170 PF13945 NST1: Salt tolerance 58.9 12 0.00026 27.8 3.1 16 93-108 160-175 (190)
171 PF04981 NMD3: NMD3 family ; 58.3 13 0.00029 28.0 3.3 43 6-58 1-50 (236)
172 PF04710 Pellino: Pellino; In 57.1 3.5 7.6E-05 34.0 0.0 42 24-66 363-414 (416)
173 COG2331 Uncharacterized protei 57.0 3.6 7.8E-05 26.3 0.0 30 24-55 16-45 (82)
174 PRK00398 rpoP DNA-directed RNA 56.9 7.4 0.00016 21.8 1.3 12 1-12 1-12 (46)
175 KOG4445|consensus 56.6 4 8.6E-05 32.7 0.2 49 4-54 116-186 (368)
176 KOG2462|consensus 56.6 6.6 0.00014 30.9 1.4 51 4-54 162-226 (279)
177 PF09943 DUF2175: Uncharacteri 56.0 10 0.00023 25.4 2.1 34 3-39 2-35 (101)
178 PF04216 FdhE: Protein involve 55.9 2 4.2E-05 33.4 -1.6 44 4-52 173-220 (290)
179 COG1592 Rubrerythrin [Energy p 55.8 3.2 7E-05 30.2 -0.4 20 25-52 139-158 (166)
180 PRK04023 DNA polymerase II lar 55.3 10 0.00022 34.9 2.6 45 3-56 626-676 (1121)
181 PRK12495 hypothetical protein; 55.2 5.3 0.00011 30.4 0.7 11 44-54 59-69 (226)
182 PHA00626 hypothetical protein 55.1 9 0.0002 23.1 1.5 14 43-56 23-36 (59)
183 KOG3268|consensus 55.1 14 0.0003 27.6 2.8 49 5-54 167-228 (234)
184 PF10013 DUF2256: Uncharacteri 55.0 7.4 0.00016 22.0 1.1 12 43-54 8-19 (42)
185 PRK11088 rrmA 23S rRNA methylt 54.6 7.6 0.00017 29.5 1.5 26 3-30 2-27 (272)
186 KOG4451|consensus 54.3 8.8 0.00019 29.6 1.7 28 29-57 250-277 (286)
187 PF10367 Vps39_2: Vacuolar sor 54.0 3 6.5E-05 26.9 -0.7 17 21-37 93-109 (109)
188 KOG3899|consensus 53.8 7.9 0.00017 31.0 1.5 30 27-56 326-367 (381)
189 PF13913 zf-C2HC_2: zinc-finge 53.6 6.2 0.00013 19.5 0.6 12 44-55 3-14 (25)
190 smart00659 RPOLCX RNA polymera 53.5 8.3 0.00018 21.8 1.2 12 42-53 18-29 (44)
191 COG5627 MMS21 DNA repair prote 53.0 20 0.00043 27.8 3.5 47 3-53 189-238 (275)
192 PF12906 RINGv: RING-variant d 52.7 11 0.00023 21.4 1.6 41 6-49 1-47 (47)
193 KOG0309|consensus 52.4 10 0.00022 34.1 2.0 43 4-50 1029-1072(1081)
194 PRK12496 hypothetical protein; 52.2 4.1 8.9E-05 29.3 -0.3 27 31-57 130-157 (164)
195 PRK11032 hypothetical protein; 51.7 7.7 0.00017 28.1 1.0 23 24-52 128-151 (160)
196 smart00734 ZnF_Rad18 Rad18-lik 51.2 7.7 0.00017 19.4 0.7 9 45-53 3-11 (26)
197 TIGR03826 YvyF flagellar opero 50.5 11 0.00023 26.6 1.6 27 1-37 1-27 (137)
198 PF08882 Acetone_carb_G: Aceto 50.4 6.5 0.00014 26.8 0.4 10 24-33 27-36 (112)
199 COG2816 NPY1 NTP pyrophosphohy 50.3 4.3 9.2E-05 31.9 -0.5 27 27-53 110-139 (279)
200 cd00729 rubredoxin_SM Rubredox 49.1 10 0.00023 20.1 1.1 10 43-52 18-27 (34)
201 KOG0825|consensus 49.0 12 0.00025 33.9 1.8 50 3-53 96-153 (1134)
202 KOG2231|consensus 48.9 14 0.00031 32.4 2.4 45 5-54 2-52 (669)
203 TIGR03830 CxxCG_CxxCG_HTH puta 48.9 5.8 0.00012 26.4 0.0 41 6-53 1-41 (127)
204 PF06869 DUF1258: Protein of u 48.6 37 0.0008 26.5 4.4 21 27-49 17-37 (258)
205 COG3024 Uncharacterized protei 47.4 9.4 0.0002 23.6 0.8 13 43-55 7-19 (65)
206 COG4647 AcxC Acetone carboxyla 47.2 8.5 0.00018 27.2 0.6 16 17-33 66-82 (165)
207 PRK01343 zinc-binding protein; 47.1 12 0.00026 22.5 1.2 12 43-54 9-20 (57)
208 KOG4080|consensus 46.7 16 0.00035 26.7 2.0 14 27-40 105-118 (176)
209 COG1773 Rubredoxin [Energy pro 46.4 7.7 0.00017 23.2 0.3 13 1-14 1-13 (55)
210 COG4357 Zinc finger domain con 46.3 10 0.00022 25.4 0.8 28 29-56 63-93 (105)
211 PF13717 zinc_ribbon_4: zinc-r 46.1 12 0.00027 20.1 1.0 12 4-16 3-14 (36)
212 TIGR01562 FdhE formate dehydro 46.0 8.5 0.00018 30.6 0.6 44 4-52 185-233 (305)
213 TIGR00627 tfb4 transcription f 45.5 6.1 0.00013 31.0 -0.3 24 29-53 256-279 (279)
214 KOG2807|consensus 44.6 13 0.00029 30.1 1.4 10 25-34 350-359 (378)
215 PF00096 zf-C2H2: Zinc finger, 43.0 7.1 0.00015 18.1 -0.2 11 45-55 2-12 (23)
216 COG1867 TRM1 N2,N2-dimethylgua 42.7 42 0.00091 27.6 4.1 42 27-68 238-283 (380)
217 PRK08351 DNA-directed RNA poly 42.4 13 0.00027 22.7 0.8 10 44-53 16-25 (61)
218 PF14471 DUF4428: Domain of un 42.4 25 0.00053 20.4 2.0 30 5-38 1-30 (51)
219 PF08271 TF_Zn_Ribbon: TFIIB z 42.1 13 0.00027 20.5 0.7 8 4-11 1-8 (43)
220 PRK00448 polC DNA polymerase I 41.8 24 0.00052 33.8 2.8 14 44-57 934-947 (1437)
221 PRK00418 DNA gyrase inhibitor; 41.0 19 0.00041 22.0 1.4 11 44-54 7-17 (62)
222 PF13894 zf-C2H2_4: C2H2-type 40.9 11 0.00023 17.1 0.3 10 45-54 2-11 (24)
223 PF15616 TerY-C: TerY-C metal 40.6 13 0.00028 26.0 0.8 39 4-54 78-116 (131)
224 PF10217 DUF2039: Uncharacteri 40.6 13 0.00028 24.5 0.7 21 27-52 70-90 (92)
225 PRK14714 DNA polymerase II lar 40.4 15 0.00032 34.6 1.3 48 4-56 668-722 (1337)
226 TIGR01405 polC_Gram_pos DNA po 39.7 28 0.0006 32.8 2.9 14 44-57 709-722 (1213)
227 COG4338 Uncharacterized protei 39.2 11 0.00023 22.2 0.1 11 44-54 13-23 (54)
228 PF07227 DUF1423: Protein of u 39.1 32 0.00069 28.9 2.9 108 4-115 129-255 (446)
229 PF01667 Ribosomal_S27e: Ribos 39.0 10 0.00022 22.7 -0.0 8 4-11 8-15 (55)
230 COG1885 Uncharacterized protei 39.0 17 0.00037 24.6 1.1 14 42-55 48-61 (115)
231 KOG4718|consensus 38.9 14 0.0003 28.2 0.7 43 5-52 183-225 (235)
232 KOG3579|consensus 38.1 14 0.0003 29.5 0.6 36 3-41 268-305 (352)
233 COG1499 NMD3 NMD protein affec 37.0 69 0.0015 26.1 4.5 49 2-60 5-60 (355)
234 KOG1829|consensus 36.9 16 0.00034 31.7 0.8 23 25-51 536-558 (580)
235 PHA00616 hypothetical protein 36.8 11 0.00023 21.5 -0.1 12 44-55 2-13 (44)
236 PF14353 CpXC: CpXC protein 36.6 14 0.00031 24.9 0.5 11 45-55 3-13 (128)
237 COG1997 RPL43A Ribosomal prote 36.5 25 0.00054 23.0 1.5 21 43-63 53-73 (89)
238 PF13453 zf-TFIIB: Transcripti 36.1 14 0.0003 20.2 0.3 12 45-56 1-12 (41)
239 KOG3476|consensus 36.1 3.7 8E-05 27.0 -2.4 35 5-54 56-90 (100)
240 COG2260 Predicted Zn-ribbon RN 35.9 75 0.0016 19.2 3.4 13 44-56 18-30 (59)
241 PRK11827 hypothetical protein; 35.8 22 0.00047 21.6 1.1 12 4-15 9-20 (60)
242 PRK03564 formate dehydrogenase 35.6 17 0.00036 29.0 0.8 45 3-52 187-235 (309)
243 COG5082 AIR1 Arginine methyltr 35.5 19 0.00041 26.8 1.0 43 2-51 59-105 (190)
244 PRK00415 rps27e 30S ribosomal 35.5 19 0.00042 21.8 0.8 11 44-54 31-41 (59)
245 PRK04179 rpl37e 50S ribosomal 35.2 10 0.00023 23.2 -0.4 25 27-51 16-40 (62)
246 COG1198 PriA Primosomal protei 35.1 15 0.00033 32.6 0.5 24 27-52 461-484 (730)
247 PF08792 A2L_zn_ribbon: A2L zi 35.1 19 0.00041 19.1 0.7 11 1-11 1-11 (33)
248 COG0068 HypF Hydrogenase matur 34.9 21 0.00046 31.7 1.3 50 4-54 102-184 (750)
249 PF14164 YqzH: YqzH-like prote 34.8 39 0.00085 20.8 2.1 16 97-112 49-64 (64)
250 KOG1729|consensus 34.8 11 0.00023 29.8 -0.4 52 3-54 168-225 (288)
251 COG4306 Uncharacterized protei 34.6 23 0.00051 24.9 1.3 27 29-59 29-55 (160)
252 PF13465 zf-H2C2_2: Zinc-finge 34.5 11 0.00024 18.5 -0.3 12 43-54 14-25 (26)
253 PRK06393 rpoE DNA-directed RNA 34.5 19 0.00042 22.1 0.7 16 43-58 17-32 (64)
254 PF14446 Prok-RING_1: Prokaryo 33.7 62 0.0013 19.2 2.8 43 4-53 6-51 (54)
255 PF09986 DUF2225: Uncharacteri 33.6 14 0.00031 27.6 0.1 15 43-57 5-19 (214)
256 PRK00564 hypA hydrogenase nick 33.5 22 0.00047 24.1 1.0 8 45-52 90-97 (117)
257 KOG3475|consensus 33.2 17 0.00037 23.7 0.4 28 27-54 15-42 (92)
258 PF06689 zf-C4_ClpX: ClpX C4-t 32.9 45 0.00097 18.3 2.0 35 4-40 2-36 (41)
259 TIGR02300 FYDLN_acid conserved 32.9 34 0.00073 24.0 1.8 27 30-56 11-39 (129)
260 KOG3507|consensus 32.8 19 0.00041 21.9 0.5 8 44-51 38-45 (62)
261 KOG3970|consensus 32.7 41 0.00088 26.1 2.4 45 5-53 52-104 (299)
262 PF14149 YhfH: YhfH-like prote 32.7 15 0.00032 20.2 0.0 16 38-53 7-23 (37)
263 COG1996 RPC10 DNA-directed RNA 32.5 15 0.00033 21.4 0.0 9 44-52 25-33 (49)
264 PF03884 DUF329: Domain of unk 32.3 14 0.0003 22.2 -0.2 12 44-55 3-14 (57)
265 PF11290 DUF3090: Protein of u 32.2 47 0.001 24.3 2.6 16 41-56 152-167 (171)
266 PF12760 Zn_Tnp_IS1595: Transp 32.2 53 0.0012 18.2 2.3 20 33-52 5-27 (46)
267 smart00132 LIM Zinc-binding do 32.1 38 0.00082 17.1 1.6 10 44-53 28-37 (39)
268 PF05715 zf-piccolo: Piccolo Z 31.9 34 0.00075 20.8 1.5 30 3-37 2-31 (61)
269 TIGR01206 lysW lysine biosynth 31.9 22 0.00047 21.1 0.6 11 44-54 3-13 (54)
270 PF07807 RED_C: RED-like prote 31.1 32 0.00069 23.7 1.4 21 85-105 37-57 (118)
271 PRK03681 hypA hydrogenase nick 31.0 24 0.00052 23.8 0.8 9 44-52 88-96 (114)
272 PF10122 Mu-like_Com: Mu-like 31.0 29 0.00063 20.4 1.1 10 44-53 25-34 (51)
273 PF01396 zf-C4_Topoisom: Topoi 30.6 20 0.00043 19.6 0.3 11 44-54 2-12 (39)
274 TIGR03847 conserved hypothetic 30.4 53 0.0011 24.2 2.6 16 41-56 154-169 (177)
275 PF04135 Nop10p: Nucleolar RNA 30.4 72 0.0016 18.8 2.7 29 45-73 19-47 (53)
276 PRK02224 chromosome segregatio 30.2 81 0.0018 28.0 4.2 15 43-57 451-465 (880)
277 PRK00241 nudC NADH pyrophospha 30.1 12 0.00027 28.7 -0.8 27 27-53 98-127 (256)
278 PF09845 DUF2072: Zn-ribbon co 30.1 30 0.00065 24.3 1.2 24 24-52 5-28 (131)
279 KOG3053|consensus 30.0 31 0.00068 27.1 1.4 53 2-55 19-83 (293)
280 PF06844 DUF1244: Protein of u 29.9 34 0.00073 21.3 1.3 13 29-41 11-23 (68)
281 PTZ00083 40S ribosomal protein 29.1 25 0.00055 22.8 0.7 10 44-53 55-64 (85)
282 COG1655 Uncharacterized protei 28.5 32 0.0007 26.6 1.2 21 38-58 14-34 (267)
283 PF14690 zf-ISL3: zinc-finger 28.4 27 0.00059 19.1 0.6 23 43-65 2-25 (47)
284 PF00412 LIM: LIM domain; Int 28.2 44 0.00095 18.8 1.6 40 6-57 1-40 (58)
285 COG2126 RPL37A Ribosomal prote 28.1 19 0.00041 21.9 -0.1 26 27-52 15-40 (61)
286 PF14768 RPA_interact_C: Repli 27.9 42 0.0009 21.2 1.5 8 5-12 1-8 (82)
287 PF14169 YdjO: Cold-inducible 27.9 34 0.00074 20.7 1.0 14 43-56 39-52 (59)
288 PRK10246 exonuclease subunit S 27.6 34 0.00073 31.5 1.4 11 43-53 503-513 (1047)
289 PF07295 DUF1451: Protein of u 27.5 11 0.00025 26.7 -1.3 24 24-52 116-139 (146)
290 PF05502 Dynactin_p62: Dynacti 27.4 35 0.00075 28.8 1.4 8 4-11 27-34 (483)
291 COG5216 Uncharacterized conser 27.2 25 0.00054 21.5 0.3 37 16-53 15-54 (67)
292 TIGR00375 conserved hypothetic 27.1 22 0.00047 29.1 0.1 29 26-55 241-270 (374)
293 PF04959 ARS2: Arsenite-resist 27.0 24 0.00051 26.7 0.3 15 44-58 78-92 (214)
294 PF01428 zf-AN1: AN1-like Zinc 26.9 24 0.00053 19.4 0.3 10 25-34 18-27 (43)
295 PF13824 zf-Mss51: Zinc-finger 26.6 24 0.00053 21.0 0.2 12 43-54 14-25 (55)
296 PLN00209 ribosomal protein S27 26.5 29 0.00062 22.6 0.6 10 44-53 56-65 (86)
297 PF13901 DUF4206: Domain of un 26.3 62 0.0013 23.9 2.4 42 4-51 153-197 (202)
298 PF14311 DUF4379: Domain of un 26.1 46 0.00099 19.1 1.4 23 25-49 33-55 (55)
299 PTZ00303 phosphatidylinositol 26.0 41 0.00088 30.8 1.6 34 5-38 462-499 (1374)
300 smart00249 PHD PHD zinc finger 26.0 33 0.00072 17.9 0.7 31 5-38 1-32 (47)
301 PRK14559 putative protein seri 25.9 51 0.0011 28.9 2.1 38 4-55 16-53 (645)
302 smart00661 RPOL9 RNA polymeras 25.6 51 0.0011 18.3 1.5 11 44-54 21-31 (52)
303 PF14803 Nudix_N_2: Nudix N-te 25.4 30 0.00064 18.5 0.4 10 45-54 2-11 (34)
304 PRK03922 hypothetical protein; 25.3 39 0.00086 23.0 1.1 15 42-56 48-62 (113)
305 COG1439 Predicted nucleic acid 25.2 18 0.00038 26.7 -0.7 24 31-55 142-165 (177)
306 PF10186 Atg14: UV radiation r 24.9 54 0.0012 24.7 1.9 22 5-39 1-22 (302)
307 smart00570 AWS associated with 24.8 1.1E+02 0.0024 17.8 2.8 24 24-52 16-40 (51)
308 KOG3726|consensus 24.7 51 0.0011 29.2 1.9 42 5-52 656-698 (717)
309 PRK10220 hypothetical protein; 24.6 55 0.0012 22.3 1.7 29 1-30 1-30 (111)
310 PF12660 zf-TFIIIC: Putative z 24.4 9.6 0.00021 25.2 -2.0 48 4-54 15-66 (99)
311 KOG1814|consensus 24.4 42 0.0009 28.0 1.3 35 4-39 369-405 (445)
312 KOG4021|consensus 24.3 41 0.00088 25.4 1.1 22 32-53 97-118 (239)
313 PF03811 Zn_Tnp_IS1: InsA N-te 24.3 40 0.00087 18.2 0.8 10 3-12 5-14 (36)
314 cd01412 SIRT5_Af1_CobB SIRT5_A 24.2 85 0.0018 23.1 2.8 14 43-56 130-143 (224)
315 PF08772 NOB1_Zn_bind: Nin one 23.9 15 0.00033 23.1 -1.0 22 31-52 12-33 (73)
316 PF09862 DUF2089: Protein of u 23.3 38 0.00082 23.1 0.7 8 46-53 1-8 (113)
317 TIGR00373 conserved hypothetic 23.2 87 0.0019 22.2 2.6 12 43-54 128-139 (158)
318 PF08274 PhnA_Zn_Ribbon: PhnA 23.1 30 0.00066 18.0 0.2 7 5-11 4-10 (30)
319 COG4068 Uncharacterized protei 22.8 92 0.002 19.0 2.2 12 44-55 9-20 (64)
320 cd01407 SIR2-fam SIR2 family o 22.7 95 0.0021 22.9 2.8 14 43-56 133-146 (218)
321 COG3677 Transposase and inacti 22.5 72 0.0016 22.0 2.0 13 43-55 53-65 (129)
322 PF00301 Rubredoxin: Rubredoxi 22.4 43 0.00094 19.1 0.7 8 3-10 34-41 (47)
323 COG2176 PolC DNA polymerase II 22.2 31 0.00068 32.6 0.2 31 27-57 913-953 (1444)
324 KOG1818|consensus 22.1 35 0.00076 29.9 0.4 51 2-53 164-221 (634)
325 cd00029 C1 Protein kinase C co 22.1 41 0.00088 18.3 0.6 26 28-53 11-38 (50)
326 TIGR02098 MJ0042_CXXC MJ0042 f 21.9 40 0.00086 17.7 0.5 11 44-54 26-36 (38)
327 TIGR00686 phnA alkylphosphonat 21.8 45 0.00097 22.7 0.8 25 4-29 3-28 (109)
328 PF01783 Ribosomal_L32p: Ribos 21.7 52 0.0011 19.3 1.0 6 45-50 41-46 (56)
329 PF11682 DUF3279: Protein of u 21.7 56 0.0012 22.8 1.3 12 42-53 109-120 (128)
330 cd00730 rubredoxin Rubredoxin; 21.5 50 0.0011 19.1 0.9 8 3-10 34-41 (50)
331 PF14165 YtzH: YtzH-like prote 21.3 81 0.0018 20.6 1.9 27 87-117 20-46 (87)
332 COG2995 PqiA Uncharacterized p 21.3 33 0.00071 28.5 0.1 31 25-55 217-247 (418)
333 PF14952 zf-tcix: Putative tre 21.3 47 0.001 18.9 0.7 11 42-52 10-20 (44)
334 smart00355 ZnF_C2H2 zinc finge 21.2 50 0.0011 14.7 0.7 10 45-54 2-11 (26)
335 COG1675 TFA1 Transcription ini 21.2 66 0.0014 23.6 1.7 19 36-55 126-144 (176)
336 PTZ00073 60S ribosomal protein 21.1 26 0.00057 23.0 -0.4 27 27-53 15-41 (91)
337 PF08069 Ribosomal_S13_N: Ribo 21.1 78 0.0017 19.2 1.7 13 99-111 30-42 (60)
338 PF14205 Cys_rich_KTR: Cystein 21.0 39 0.00084 20.2 0.3 9 45-53 6-14 (55)
339 PF04606 Ogr_Delta: Ogr/Delta- 20.9 38 0.00082 19.1 0.3 6 25-30 32-37 (47)
340 PF08273 Prim_Zn_Ribbon: Zinc- 20.6 42 0.00091 18.6 0.4 9 44-52 4-12 (40)
341 KOG3460|consensus 20.6 47 0.001 21.6 0.7 25 80-104 17-44 (91)
342 PF10588 NADH-G_4Fe-4S_3: NADH 20.5 74 0.0016 17.4 1.4 17 35-51 5-21 (41)
343 PF06750 DiS_P_DiS: Bacterial 20.3 69 0.0015 20.7 1.5 12 44-55 34-45 (92)
344 PF10170 C6_DPF: Cysteine-rich 20.3 95 0.0021 20.6 2.1 11 28-38 71-81 (97)
345 PF04475 DUF555: Protein of un 20.1 59 0.0013 21.8 1.1 15 42-56 46-60 (102)
346 PRK06266 transcription initiat 20.1 1.4E+02 0.0031 21.6 3.2 13 43-55 136-148 (178)
347 TIGR00595 priA primosomal prot 20.0 1E+02 0.0022 26.0 2.8 10 43-52 253-262 (505)
No 1
>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=100.00 E-value=8.8e-45 Score=282.17 Aligned_cols=120 Identities=73% Similarity=1.286 Sum_probs=117.0
Q ss_pred CCCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCccccccchhHHHHHHHHHHhhh
Q psy17995 1 MDDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRVQLFDDSSVEKEVEIRKKLLK 80 (120)
Q Consensus 1 ~d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~~~~f~d~~~~~e~~~rk~~~k 80 (120)
||+++||+|+++.|.+|.+++++++|||+||.+|++.+|..++.+||+|+.++++.+|++++|+|..+++|++|||||++
T Consensus 1 md~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr~q~F~D~~vekEV~iRkrv~~ 80 (309)
T TIGR00570 1 MDDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRVQLFEDPTVEKEVDIRKRVLK 80 (309)
T ss_pred CCCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhccccccccHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999998888999999999999999999999999999999999999
Q ss_pred hhhcccCCccCHHHHHHHHHHHHHHHHHHhcccchhhhcC
Q psy17995 81 DYNKVEEDFNSLAEYNDYLEEIEEIVFNLCNNIDILETNK 120 (120)
Q Consensus 81 ~~~~~~~~~~~l~~y~~yle~~E~~i~~L~~~~d~~~~~~ 120 (120)
|||++++||.||++||||||+||+|||||++|+|+++|++
T Consensus 81 i~Nk~e~dF~~l~~yNdYLE~vEdii~nL~~~~d~~~te~ 120 (309)
T TIGR00570 81 IYNKREEDFPSLREYNDYLEEVEDIVYNLTNNIDLENTKK 120 (309)
T ss_pred HHccchhccCCHHHHHHHHHHHHHHHHHhhcCCcHHHHHH
Confidence 9999999999999999999999999999999999999874
No 2
>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=100.00 E-value=2.2e-37 Score=232.89 Aligned_cols=119 Identities=49% Similarity=0.953 Sum_probs=114.9
Q ss_pred CCCccCcccCCCcccCCCCcccccc-cCCccchhHHHHHhhcCCCCCC--CCCccccCCCCccccccchhHHHHHHHHHH
Q psy17995 1 MDDQECPRCKTTKYRKPTLKLMVNI-CGHPLCEGCVDLLFLKGTGNCY--ECNQPLRRGNFRVQLFDDSSVEKEVEIRKK 77 (120)
Q Consensus 1 ~d~~~CpiC~~~~~~~p~~~~~~~~-CGH~fC~~Ci~~~~~~~~~~CP--~C~~~~~~~~~~~~~f~d~~~~~e~~~rk~ 77 (120)
|.+-+||+|+++.|+||+++++++| |.|++|.+|++++|+.|+.+|| .|++.+++..|+.++|+|..+++|+++||+
T Consensus 8 ~~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~kf~~qtFeD~~vEkEvdvRkr 87 (314)
T COG5220 8 MEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIKFIKQTFEDITVEKEVDVRKR 87 (314)
T ss_pred hhcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHhcccccccchhhhhhhhhHHHH
Confidence 4566999999999999999999995 9999999999999999999999 999999999999999999999999999999
Q ss_pred hhhhhhcccCCc-cCHHHHHHHHHHHHHHHHHHhcccchhhhc
Q psy17995 78 LLKDYNKVEEDF-NSLAEYNDYLEEIEEIVFNLCNNIDILETN 119 (120)
Q Consensus 78 ~~k~~~~~~~~~-~~l~~y~~yle~~E~~i~~L~~~~d~~~~~ 119 (120)
++.+||+...+| |+|.+||+|||+||+|+|+|++++|++.|+
T Consensus 88 ~~r~Fnk~~~eF~gdl~~YNdYLEevE~l~f~l~~~idv~~te 130 (314)
T COG5220 88 LLRAFNKEEEEFGGDLAKYNDYLEEVEELVFELLELIDVSLTE 130 (314)
T ss_pred HHHHhccchhhhCccHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Confidence 999999999999 799999999999999999999999999986
No 3
>KOG3800|consensus
Probab=100.00 E-value=1.7e-36 Score=232.35 Aligned_cols=116 Identities=61% Similarity=1.106 Sum_probs=113.4
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCccccccchhHHHHHHHHHHhhhhhhc
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRVQLFDDSSVEKEVEIRKKLLKDYNK 84 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~~~~f~d~~~~~e~~~rk~~~k~~~~ 84 (120)
.||+|+++.|+||++++++++|||++|.+|++++|..|+..||+|...+++.+|+.++|+|+.+++|+++||+++++||+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr~q~fED~~vekEv~iRrri~~~~nk 81 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFRVQTFEDPTVEKEVDIRRRILRIFNK 81 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcccchhhcchhHHHHHHHHHHHHHHHhcc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCc-cCHHHHHHHHHHHHHHHHHHhcccchhhhcC
Q psy17995 85 VEEDF-NSLAEYNDYLEEIEEIVFNLCNNIDILETNK 120 (120)
Q Consensus 85 ~~~~~-~~l~~y~~yle~~E~~i~~L~~~~d~~~~~~ 120 (120)
.+++| ++|.+||||||++||++|||++++|+.+|++
T Consensus 82 ~~eeF~~~LaeyndylEe~Ediv~nl~~~~dv~~t~~ 118 (300)
T KOG3800|consen 82 KEEEFTGSLAEYNDYLEEVEDIVFNLGNNIDVTETKE 118 (300)
T ss_pred chhhhhhhHHHHhcccHHHHHHHHHhhcccchhHHHH
Confidence 99999 6999999999999999999999999999874
No 4
>PF06391 MAT1: CDK-activating kinase assembly factor MAT1; InterPro: IPR015877 MAT1 (menage a trois 1) is a RING finger protein with a characteristic C3HC4 motif located in the N-terminal domain. This entry represents the central region of MAT1. MAT1 stabilises the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex which then goes on to activate many of the CDK enzymes intimately involved in the cell cycle []. CDK7 forms a stable complex with cyclin H and MAT1 in vivo only when phosphorylated on either one of two residues (Ser164 or Thr170) in its T-loop. The requirement for MAT1 for the activation of CAK can be by-passed by the phosphorylation of CDK7 on the T-loop. The two mechanisms for CDK7 complex stabilisation and activation (MAT1 addition and T-loop phosphorylation), which can operate independently in vitro, actually cooperate under physiological conditions to maintain complex integrity. With prolonged exposure to elevated temperature, dissociation to monomeric subunits occurs in vivo when CDK7 is dephosphorylated, even in the presence of MAT1 []. The Cyclin H-MAT1-CDK7 complex also forms part of TFIIH, a multiprotein complex required for both transcription and DNA repair.; GO: 0007049 cell cycle, 0005634 nucleus; PDB: 1G25_A.
Probab=99.89 E-value=1.6e-24 Score=160.48 Aligned_cols=68 Identities=65% Similarity=1.012 Sum_probs=4.5
Q ss_pred ccCCCCccccccchhHHHHHHHHHHhhhhhhcccCCccCHHHHHHHHHHHHHHHHHHhcccchhhhcC
Q psy17995 53 LRRGNFRVQLFDDSSVEKEVEIRKKLLKDYNKVEEDFNSLAEYNDYLEEIEEIVFNLCNNIDILETNK 120 (120)
Q Consensus 53 ~~~~~~~~~~f~d~~~~~e~~~rk~~~k~~~~~~~~~~~l~~y~~yle~~E~~i~~L~~~~d~~~~~~ 120 (120)
|++++|+.++|+|+.|+||++|||||+++||++++||+||++||||||+||+|||||++|+|+++|++
T Consensus 1 LRK~~Fr~Q~FeD~~VekEv~iRkrV~~ifNk~eeDF~~l~~YNdYLE~vE~iifnL~~~idv~~te~ 68 (200)
T PF06391_consen 1 LRKNNFRTQTFEDLGVEKEVDIRKRVLKIFNKREEDFESLREYNDYLEEVEDIIFNLVNGIDVEETEA 68 (200)
T ss_dssp -SS---EEE-----------------------------------------------------------
T ss_pred CccccchhhcccchhHHHHHHHHHHHHHHHccChhhcCCHHHHHHHHHHHHHHHHHHhcCCCHHHHHH
Confidence 57889999999999999999999999999999999999999999999999999999999999999974
No 5
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.36 E-value=3.4e-13 Score=77.04 Aligned_cols=39 Identities=33% Similarity=0.967 Sum_probs=29.7
Q ss_pred CcccCCCcccCCCCcccccccCCccchhHHHHHhhcCC---CCCCCC
Q psy17995 6 CPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGT---GNCYEC 49 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~---~~CP~C 49 (120)
||||+ +++.+| +..+|||+||.+||.++|.... ..||+|
T Consensus 1 CpiC~-~~~~~P----v~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICL-DLFKDP----VSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTT-SB-SSE----EE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccc-hhhCCc----cccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 89999 599999 3459999999999999998642 479987
No 6
>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=99.25 E-value=6.1e-12 Score=76.49 Aligned_cols=51 Identities=18% Similarity=0.316 Sum_probs=43.3
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFR 59 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~ 59 (120)
++.||||++ ++.+| ++++|||+||..||..++.. ...||.|+.++...++.
T Consensus 1 ~~~Cpi~~~-~~~~P----v~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~~~~l~ 51 (63)
T smart00504 1 EFLCPISLE-VMKDP----VILPSGQTYERRAIEKWLLS-HGTDPVTGQPLTHEDLI 51 (63)
T ss_pred CcCCcCCCC-cCCCC----EECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCChhhce
Confidence 468999995 88999 56799999999999999987 47899999998765543
No 7
>KOG0320|consensus
Probab=99.24 E-value=3.1e-12 Score=93.00 Aligned_cols=52 Identities=21% Similarity=0.628 Sum_probs=40.1
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNF 58 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~ 58 (120)
-|.||||+.+ +..- ..+.+.|||+||..||+.++..+ .+||+|++.+..+.|
T Consensus 131 ~~~CPiCl~~-~sek--~~vsTkCGHvFC~~Cik~alk~~-~~CP~C~kkIt~k~~ 182 (187)
T KOG0320|consen 131 TYKCPICLDS-VSEK--VPVSTKCGHVFCSQCIKDALKNT-NKCPTCRKKITHKQF 182 (187)
T ss_pred ccCCCceecc-hhhc--cccccccchhHHHHHHHHHHHhC-CCCCCcccccchhhh
Confidence 4799999964 3322 11347999999999999999864 799999998876654
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=99.22 E-value=1.4e-11 Score=99.57 Aligned_cols=75 Identities=21% Similarity=0.455 Sum_probs=62.5
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCccccccchhHHHHHHHHHHhhhhh
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRVQLFDDSSVEKEVEIRKKLLKDY 82 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~~~~f~d~~~~~e~~~rk~~~k~~ 82 (120)
.+.|+||++ ++.+| ++++|||.||..||..++... ..||+|+..+....++.+++-+..++.=...|..++...
T Consensus 26 ~l~C~IC~d-~~~~P----vitpCgH~FCs~CI~~~l~~~-~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~~~~R~~Lle~~ 99 (397)
T TIGR00599 26 SLRCHICKD-FFDVP----VLTSCSHTFCSLCIRRCLSNQ-PKCPLCRAEDQESKLRSNWLVSEIVESFKNLRPSLLEFL 99 (397)
T ss_pred ccCCCcCch-hhhCc----cCCCCCCchhHHHHHHHHhCC-CCCCCCCCccccccCccchHHHHHHHHHHHhhHHHHHHh
Confidence 579999995 88999 467999999999999988764 589999999988788888887888887777777777664
Q ss_pred h
Q psy17995 83 N 83 (120)
Q Consensus 83 ~ 83 (120)
.
T Consensus 100 ~ 100 (397)
T TIGR00599 100 R 100 (397)
T ss_pred c
Confidence 3
No 9
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.21 E-value=8.8e-12 Score=92.00 Aligned_cols=54 Identities=24% Similarity=0.624 Sum_probs=42.9
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc---------------CCCCCCCCCccccCCCCcc
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK---------------GTGNCYECNQPLRRGNFRV 60 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~---------------~~~~CP~C~~~~~~~~~~~ 60 (120)
+++.||||++ .+.+| ++++|||.||..||..++.. +...||+|+..+...++.+
T Consensus 17 ~~~~CpICld-~~~dP----VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvP 85 (193)
T PLN03208 17 GDFDCNICLD-QVRDP----VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVP 85 (193)
T ss_pred CccCCccCCC-cCCCc----EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEE
Confidence 3579999995 78888 56899999999999986531 2368999999997665543
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=99.16 E-value=1.3e-11 Score=69.04 Aligned_cols=39 Identities=36% Similarity=1.012 Sum_probs=31.6
Q ss_pred CcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCC
Q psy17995 6 CPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYEC 49 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C 49 (120)
||||++ .+.+| +++++|||.||.+|+.++++. ...||.|
T Consensus 1 C~iC~~-~~~~~---~~~~~CGH~fC~~C~~~~~~~-~~~CP~C 39 (39)
T PF13923_consen 1 CPICLD-ELRDP---VVVTPCGHSFCKECIEKYLEK-NPKCPVC 39 (39)
T ss_dssp ETTTTS-B-SSE---EEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred CCCCCC-cccCc---CEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence 899995 77777 235799999999999999988 5899987
No 11
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=99.15 E-value=3.1e-11 Score=69.29 Aligned_cols=44 Identities=30% Similarity=0.681 Sum_probs=35.5
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCc
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQ 51 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~ 51 (120)
.|++|.+ .| ++..+.++++|||.||..|+..+. .....||+|++
T Consensus 1 ~C~~C~~-~~-~~~~~~~l~~CgH~~C~~C~~~~~-~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFE-KY-SEERRPRLTSCGHIFCEKCLKKLK-GKSVKCPICRK 44 (44)
T ss_pred CCcCcCc-cc-cCCCCeEEcccCCHHHHHHHHhhc-CCCCCCcCCCC
Confidence 4999996 55 445556788999999999999987 44578999985
No 12
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=99.07 E-value=7e-11 Score=66.37 Aligned_cols=40 Identities=30% Similarity=0.903 Sum_probs=33.6
Q ss_pred CcccCCCcccCCCCcccccccCCccchhHHHHHhh-cCCCCCCCC
Q psy17995 6 CPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFL-KGTGNCYEC 49 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~-~~~~~CP~C 49 (120)
||||.+ .+.+|. .+++|||+||..|+..+++ .+...||.|
T Consensus 1 C~iC~~-~~~~~~---~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLE-PFEDPV---ILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSS-BCSSEE---EETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCc-cccCCC---EEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 899995 778772 2569999999999999999 556889987
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=99.07 E-value=7.1e-11 Score=69.35 Aligned_cols=47 Identities=36% Similarity=0.853 Sum_probs=36.0
Q ss_pred CCccCcccCCCcccCCCCcccccccCCc-cchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHP-LCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~-fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
++..|+||++ ...++ ++.+|||. ||..|+.+++. ....||+|++++.
T Consensus 1 ~~~~C~iC~~-~~~~~----~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 1 EDEECPICFE-NPRDV----VLLPCGHLCFCEECAERLLK-RKKKCPICRQPIE 48 (50)
T ss_dssp -HSB-TTTSS-SBSSE----EEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-S
T ss_pred CcCCCccCCc-cCCce----EEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhc
Confidence 3578999996 44443 45699999 99999999988 4589999999875
No 14
>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=99.00 E-value=4.2e-10 Score=62.85 Aligned_cols=44 Identities=36% Similarity=1.019 Sum_probs=34.7
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
.|+||++ .+.++ +.+.+|||.||..|+..++..+...||.|+..
T Consensus 1 ~C~iC~~-~~~~~---~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLE-EFREP---VVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCCcCch-hhhCc---eEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 4999996 44444 23457999999999999888766889999875
No 15
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.94 E-value=2.5e-10 Score=65.24 Aligned_cols=43 Identities=26% Similarity=0.695 Sum_probs=32.3
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCC
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECN 50 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~ 50 (120)
.||||++ .+.+. ..++..+|||.||.+||..+++.. ..||+||
T Consensus 2 ~C~IC~~-~~~~~-~~~~~l~C~H~fh~~Ci~~~~~~~-~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLE-EFEDG-EKVVKLPCGHVFHRSCIKEWLKRN-NSCPVCR 44 (44)
T ss_dssp CETTTTC-BHHTT-SCEEEETTSEEEEHHHHHHHHHHS-SB-TTTH
T ss_pred CCcCCCh-hhcCC-CeEEEccCCCeeCHHHHHHHHHhC-CcCCccC
Confidence 6999996 44432 223456899999999999988874 6999996
No 16
>KOG2164|consensus
Probab=98.94 E-value=1.3e-09 Score=89.73 Aligned_cols=101 Identities=20% Similarity=0.403 Sum_probs=70.0
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcC----CCCCCCCCccccCCCCccccccchhHHHHHHHHHHh
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKG----TGNCYECNQPLRRGNFRVQLFDDSSVEKEVEIRKKL 78 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~----~~~CP~C~~~~~~~~~~~~~f~d~~~~~e~~~rk~~ 78 (120)
++.||||++ ...-| +.+.|||.||-.||-.+|..+ ...||.|+..+..+++.+...++.....++..
T Consensus 186 ~~~CPICL~-~~~~p----~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~e~~qkke~l~~---- 256 (513)
T KOG2164|consen 186 DMQCPICLE-PPSVP----VRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVFIEDDQKKEELKL---- 256 (513)
T ss_pred CCcCCcccC-CCCcc----cccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeeeeccccccHHHHH----
Confidence 578999996 33333 245799999999999999864 46899999999999998888888755555432
Q ss_pred hhhhh---cccCCc-cCH-HHHHHHHHHHHHHHHHHhcc
Q psy17995 79 LKDYN---KVEEDF-NSL-AEYNDYLEEIEEIVFNLCNN 112 (120)
Q Consensus 79 ~k~~~---~~~~~~-~~l-~~y~~yle~~E~~i~~L~~~ 112 (120)
...-| .-.--| +.. +.+.+++.++...++-++.+
T Consensus 257 ~~~~ng~~~~~r~F~~d~~r~~p~fl~dl~~~a~~~i~~ 295 (513)
T KOG2164|consen 257 HQDPNGIPDYNRRFSGDPARFVPDFLMDLPTYARINIRN 295 (513)
T ss_pred HhcccCCCccccceecCcccccHHHHHhHHHHHHHHHHH
Confidence 21111 111235 443 77888888877766655543
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=98.88 E-value=7.5e-10 Score=69.95 Aligned_cols=62 Identities=18% Similarity=0.338 Sum_probs=44.8
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCccccccchhHHHHH
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRVQLFDDSSVEKEV 72 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~~~~f~d~~~~~e~ 72 (120)
+.+.|||+++ ++.+| +++++||+|++++|...+..+...||.++.++...++. .+..++..|
T Consensus 3 ~~f~CpIt~~-lM~dP----Vi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~----pn~~Lk~~I 64 (73)
T PF04564_consen 3 DEFLCPITGE-LMRDP----VILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLI----PNRALKSAI 64 (73)
T ss_dssp GGGB-TTTSS-B-SSE----EEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSE----E-HHHHHHH
T ss_pred cccCCcCcCc-HhhCc----eeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccce----ECHHHHHHH
Confidence 5689999995 99999 67799999999999999998678999999998765443 444444444
No 18
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.88 E-value=4.7e-10 Score=69.24 Aligned_cols=55 Identities=20% Similarity=0.603 Sum_probs=26.2
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCccccccchhHHHHHH
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRVQLFDDSSVEKEVE 73 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~~~~f~d~~~~~e~~ 73 (120)
+.|++|.+ ++..|. ..+.|.|.||..||...+. ..||+|+++-. ..|..+.|+++
T Consensus 8 LrCs~C~~-~l~~pv---~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw--------~qD~~~NrqLd 62 (65)
T PF14835_consen 8 LRCSICFD-ILKEPV---CLGGCEHIFCSSCIRDCIG---SECPVCHTPAW--------IQDIQINRQLD 62 (65)
T ss_dssp TS-SSS-S---SS-B------SSS--B-TTTGGGGTT---TB-SSS--B-S---------SS----HHHH
T ss_pred cCCcHHHH-HhcCCc---eeccCccHHHHHHhHHhcC---CCCCCcCChHH--------HHHHHhhhhhh
Confidence 68999995 889992 1469999999999987554 35999998754 45555555554
No 19
>KOG0287|consensus
Probab=98.88 E-value=5.8e-10 Score=88.37 Aligned_cols=74 Identities=22% Similarity=0.416 Sum_probs=61.4
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCccccccchhHHHHHHHHHHhhhhh
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRVQLFDDSSVEKEVEIRKKLLKDY 82 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~~~~f~d~~~~~e~~~rk~~~k~~ 82 (120)
-+.|.||++ .|.-| +++||||.||.-||..++... +.||.|..+++...++.+.+-|-.++-=-.+|--+++.+
T Consensus 23 lLRC~IC~e-yf~ip----~itpCsHtfCSlCIR~~L~~~-p~CP~C~~~~~Es~Lr~n~il~Eiv~S~~~~R~~Ll~fl 96 (442)
T KOG0287|consen 23 LLRCGICFE-YFNIP----MITPCSHTFCSLCIRKFLSYK-PQCPTCCVTVTESDLRNNRILDEIVKSLNFARNHLLQFL 96 (442)
T ss_pred HHHHhHHHH-HhcCc----eeccccchHHHHHHHHHhccC-CCCCceecccchhhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 358999995 77878 678999999999999998864 789999999999888888877777776666777766664
No 20
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.87 E-value=2.1e-09 Score=81.90 Aligned_cols=50 Identities=24% Similarity=0.674 Sum_probs=36.6
Q ss_pred CccCcccCCCcccCCCC---cc-cccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 3 DQECPRCKTTKYRKPTL---KL-MVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~---~~-~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
+..||||++. +.++.. .+ ++++|||.||..||..++.. ...||+||.++.
T Consensus 174 ~~eC~ICle~-~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-~~tCPlCR~~~~ 227 (238)
T PHA02929 174 DKECAICMEK-VYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-KNTCPVCRTPFI 227 (238)
T ss_pred CCCCccCCcc-cccCccccccceecCCCCCcccHHHHHHHHhc-CCCCCCCCCEee
Confidence 4689999974 444321 11 24589999999999986554 578999999774
No 21
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.83 E-value=1.8e-09 Score=61.91 Aligned_cols=40 Identities=35% Similarity=0.730 Sum_probs=21.9
Q ss_pred CcccCCCcccCCCCcccccccCCccchhHHHHHhhcC---CCCCC
Q psy17995 6 CPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKG---TGNCY 47 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~---~~~CP 47 (120)
||||++ +.++...-++.+|||+||+.|+.++++.+ ...||
T Consensus 1 CpIc~e--~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE--FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT------TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc--ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899995 56632222456799999999999999864 46676
No 22
>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=98.83 E-value=3e-09 Score=57.33 Aligned_cols=39 Identities=33% Similarity=0.962 Sum_probs=31.1
Q ss_pred CcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCC
Q psy17995 6 CPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYEC 49 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C 49 (120)
|+||++ ...++ ++.+|||.||..|+..++..+...||.|
T Consensus 1 C~iC~~-~~~~~----~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLE-ELKDP----VVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCcc-CCCCc----EEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 899996 43444 4569999999999999888556789987
No 23
>KOG0978|consensus
Probab=98.82 E-value=1.3e-09 Score=92.97 Aligned_cols=52 Identities=25% Similarity=0.747 Sum_probs=43.9
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCcc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRV 60 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~~ 60 (120)
+.||+|.+ ..++- +++.|||.||..|+...+......||.|+++|...+|.+
T Consensus 644 LkCs~Cn~-R~Kd~----vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 644 LKCSVCNT-RWKDA----VITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHR 695 (698)
T ss_pred eeCCCccC-chhhH----HHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccc
Confidence 68999994 44544 578999999999999998877789999999999887653
No 24
>KOG0823|consensus
Probab=98.74 E-value=5.6e-09 Score=78.75 Aligned_cols=51 Identities=22% Similarity=0.561 Sum_probs=42.1
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc--CCCCCCCCCccccCCCC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK--GTGNCYECNQPLRRGNF 58 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~--~~~~CP~C~~~~~~~~~ 58 (120)
.+.|.||++ .-.+| ++|.|||-||=.||.+++.. +...||+|+..+..+.+
T Consensus 47 ~FdCNICLd-~akdP----VvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~v 99 (230)
T KOG0823|consen 47 FFDCNICLD-LAKDP----VVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTV 99 (230)
T ss_pred ceeeeeecc-ccCCC----EEeecccceehHHHHHHHhhcCCCeeCCccccccccceE
Confidence 478999995 77999 78999999999999998774 34679999998765543
No 25
>KOG0317|consensus
Probab=98.72 E-value=7e-09 Score=80.40 Aligned_cols=49 Identities=20% Similarity=0.596 Sum_probs=40.1
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGN 57 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~ 57 (120)
..+|.+|++ .-.||. .+||||.||-+||..+.... ..||.||..+.+.+
T Consensus 239 ~~kC~LCLe-~~~~pS----aTpCGHiFCWsCI~~w~~ek-~eCPlCR~~~~psk 287 (293)
T KOG0317|consen 239 TRKCSLCLE-NRSNPS----ATPCGHIFCWSCILEWCSEK-AECPLCREKFQPSK 287 (293)
T ss_pred CCceEEEec-CCCCCC----cCcCcchHHHHHHHHHHccc-cCCCcccccCCCcc
Confidence 368999996 557883 57999999999999877654 56999999987654
No 26
>KOG2177|consensus
Probab=98.70 E-value=5.7e-09 Score=77.43 Aligned_cols=44 Identities=30% Similarity=0.853 Sum_probs=38.8
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCc
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQ 51 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~ 51 (120)
+.+.||||++ .|..| .+.+|||+||..|+..+|. ....||.|+.
T Consensus 12 ~~~~C~iC~~-~~~~p----~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLE-YFREP----VLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred ccccChhhHH-HhhcC----ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 5689999995 88999 3679999999999999998 6689999994
No 27
>PHA02926 zinc finger-like protein; Provisional
Probab=98.63 E-value=2.9e-08 Score=74.86 Aligned_cols=52 Identities=25% Similarity=0.624 Sum_probs=37.4
Q ss_pred CccCcccCCCcccCC--CC-ccc-ccccCCccchhHHHHHhhcC-----CCCCCCCCcccc
Q psy17995 3 DQECPRCKTTKYRKP--TL-KLM-VNICGHPLCEGCVDLLFLKG-----TGNCYECNQPLR 54 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p--~~-~~~-~~~CGH~fC~~Ci~~~~~~~-----~~~CP~C~~~~~ 54 (120)
+..|+||++.++..+ +- .+. ..+|||.||-+||....+.. ...||.||..+.
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred CCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 568999998655432 11 223 45999999999999876532 246999999875
No 28
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.62 E-value=1.9e-08 Score=78.58 Aligned_cols=50 Identities=22% Similarity=0.542 Sum_probs=41.1
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFR 59 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~ 59 (120)
+.|-||.. .+.-| +.|+|||.||.-||.+++... +.||+|+......-++
T Consensus 26 lrC~IC~~-~i~ip----~~TtCgHtFCslCIR~hL~~q-p~CP~Cr~~~~esrlr 75 (391)
T COG5432 26 LRCRICDC-RISIP----CETTCGHTFCSLCIRRHLGTQ-PFCPVCREDPCESRLR 75 (391)
T ss_pred HHhhhhhh-eeecc----eecccccchhHHHHHHHhcCC-CCCccccccHHhhhcc
Confidence 47999995 77878 578999999999999998864 7899999987654443
No 29
>KOG0297|consensus
Probab=98.58 E-value=6.6e-08 Score=78.34 Aligned_cols=85 Identities=24% Similarity=0.430 Sum_probs=64.8
Q ss_pred CccCcccCCCcccCCCCcccc-cccCCccchhHHHHHhhcCCCCCCCCCccccCCCCccccccchhHHHHHHHHHHhhhh
Q psy17995 3 DQECPRCKTTKYRKPTLKLMV-NICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRVQLFDDSSVEKEVEIRKKLLKD 81 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~-~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~~~~f~d~~~~~e~~~rk~~~k~ 81 (120)
++.||+|. .++.+| ++ +.|||.||..|+...... ...||+|+..+..+. ..+.+....+++.. +.+
T Consensus 21 ~l~C~~C~-~vl~~p----~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~~---~~~~~~~~~~~~~~----l~i 87 (391)
T KOG0297|consen 21 NLLCPICM-SVLRDP----VQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQAE---ELPVPRALRRELLK----LPI 87 (391)
T ss_pred cccCcccc-ccccCC----CCCCCCCCcccccccchhhcc-CcCCcccccccchhh---ccCchHHHHHHHHh----ccc
Confidence 58999999 488999 45 499999999999998777 689999988776543 33355666666653 566
Q ss_pred hhccc---CCc-cCHHHHHHHHH
Q psy17995 82 YNKVE---EDF-NSLAEYNDYLE 100 (120)
Q Consensus 82 ~~~~~---~~~-~~l~~y~~yle 100 (120)
++... +-| ..++.|++|+.
T Consensus 88 ~c~~~~~GC~~~~~l~~~~~Hl~ 110 (391)
T KOG0297|consen 88 RCIFASRGCRADLELEALQGHLS 110 (391)
T ss_pred ccccCCCCccccccHHHHHhHhc
Confidence 66432 667 89999999985
No 30
>KOG0311|consensus
Probab=98.53 E-value=9.1e-09 Score=81.73 Aligned_cols=53 Identities=25% Similarity=0.611 Sum_probs=42.0
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc-CCCCc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR-RGNFR 59 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~-~~~~~ 59 (120)
+++||||++ ++++. |.+..|+|+||..||...++.+...||.|++.+. +..++
T Consensus 43 ~v~c~icl~-llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr 96 (381)
T KOG0311|consen 43 QVICPICLS-LLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLR 96 (381)
T ss_pred hhccHHHHH-HHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCC
Confidence 579999995 66655 1233899999999999999988899999999875 33443
No 31
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.44 E-value=9e-08 Score=73.53 Aligned_cols=48 Identities=25% Similarity=0.536 Sum_probs=38.0
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcC-CCCCCCCCccccC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKG-TGNCYECNQPLRR 55 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~-~~~CP~C~~~~~~ 55 (120)
++.|++|.+ ...+| .-++|||.||-+||-..|... ...||.||+..-.
T Consensus 215 d~kC~lC~e-~~~~p----s~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~p 263 (271)
T COG5574 215 DYKCFLCLE-EPEVP----SCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYP 263 (271)
T ss_pred ccceeeeec-ccCCc----ccccccchhhHHHHHHHHHhhccccCchhhhhccc
Confidence 689999996 55777 347999999999999866654 4569999986643
No 32
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=98.30 E-value=6.4e-07 Score=56.60 Aligned_cols=46 Identities=22% Similarity=0.614 Sum_probs=32.6
Q ss_pred CccCcccCCCcccCCC---------CcccccccCCccchhHHHHHhhcCCCCCCCCC
Q psy17995 3 DQECPRCKTTKYRKPT---------LKLMVNICGHPLCEGCVDLLFLKGTGNCYECN 50 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~---------~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~ 50 (120)
+..|+||++ .+.+|. ..++..+|||.|...||.+.+..+ ..||.||
T Consensus 19 ~d~C~IC~~-~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICRE-PLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-NTCPLCR 73 (73)
T ss_dssp CSBETTTTS-BTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-SB-TTSS
T ss_pred CCcccccCh-hhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-CcCCCCC
Confidence 346999996 444432 223345899999999999988765 5999996
No 33
>KOG2879|consensus
Probab=98.22 E-value=8.8e-07 Score=68.54 Aligned_cols=49 Identities=31% Similarity=0.689 Sum_probs=39.3
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc-CCCCCCCCCcccc
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK-GTGNCYECNQPLR 54 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~-~~~~CP~C~~~~~ 54 (120)
++..||+|.+ .|.+++++.+|||++|-.|+...... .++.||.|+++..
T Consensus 238 ~~~~C~~Cg~----~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 238 SDTECPVCGE----PPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred CCceeeccCC----CCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 4568999996 45555666789999999999987664 4689999999775
No 34
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=98.22 E-value=4e-07 Score=67.87 Aligned_cols=45 Identities=33% Similarity=0.769 Sum_probs=38.0
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
+.|.||+. -|..| +++.|||.||..|..+-+..+ ..|-+|++...
T Consensus 197 F~C~iCKk-dy~sp----vvt~CGH~FC~~Cai~~y~kg-~~C~~Cgk~t~ 241 (259)
T COG5152 197 FLCGICKK-DYESP----VVTECGHSFCSLCAIRKYQKG-DECGVCGKATY 241 (259)
T ss_pred eeehhchh-hccch----hhhhcchhHHHHHHHHHhccC-Ccceecchhhc
Confidence 58999997 67889 678999999999988877765 78999998653
No 35
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.18 E-value=8.1e-07 Score=53.79 Aligned_cols=42 Identities=19% Similarity=0.508 Sum_probs=29.1
Q ss_pred CccCcccCCCcccCCCCccccc-ccCCccchhHHHHHhhc-CCCCCCCC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVN-ICGHPLCEGCVDLLFLK-GTGNCYEC 49 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~-~CGH~fC~~Ci~~~~~~-~~~~CP~C 49 (120)
.+.||+.+. .+.+| +.+ .|||.|.++.|..++.. +...||+-
T Consensus 11 ~~~CPiT~~-~~~~P----V~s~~C~H~fek~aI~~~i~~~~~~~CPv~ 54 (57)
T PF11789_consen 11 SLKCPITLQ-PFEDP----VKSKKCGHTFEKEAILQYIQRNGSKRCPVA 54 (57)
T ss_dssp -SB-TTTSS-B-SSE----EEESSS--EEEHHHHHHHCTTTS-EE-SCC
T ss_pred ccCCCCcCC-hhhCC----cCcCCCCCeecHHHHHHHHHhcCCCCCCCC
Confidence 478999995 89999 455 89999999999999954 45789983
No 36
>KOG3039|consensus
Probab=98.15 E-value=1.5e-06 Score=66.59 Aligned_cols=54 Identities=19% Similarity=0.298 Sum_probs=43.6
Q ss_pred CccCcccCCCcccCCCCccc-ccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCc
Q psy17995 3 DQECPRCKTTKYRKPTLKLM-VNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFR 59 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~-~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~ 59 (120)
.|+||+|+. .+.|. ++.. ..+|||+||..|+.+++... +.||+|+.+++..++.
T Consensus 221 ryiCpvtrd-~LtNt-~~ca~Lr~sg~Vv~~ecvEklir~D-~v~pv~d~plkdrdiI 275 (303)
T KOG3039|consen 221 RYICPVTRD-TLTNT-TPCAVLRPSGHVVTKECVEKLIRKD-MVDPVTDKPLKDRDII 275 (303)
T ss_pred ceecccchh-hhcCc-cceEEeccCCcEeeHHHHHHhcccc-ccccCCCCcCcccceE
Confidence 689999995 66765 3333 45999999999999998864 8999999999876643
No 37
>KOG4159|consensus
Probab=98.14 E-value=1.1e-06 Score=71.34 Aligned_cols=48 Identities=29% Similarity=0.675 Sum_probs=40.4
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccC
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~ 55 (120)
+++.|-||. ..+.+| ++++|||.||..||.+.+.. ...||.|+..+..
T Consensus 83 sef~c~vc~-~~l~~p----v~tpcghs~c~~Cl~r~ld~-~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 83 SEFECCVCS-RALYPP----VVTPCGHSFCLECLDRSLDQ-ETECPLCRDELVE 130 (398)
T ss_pred chhhhhhhH-hhcCCC----ccccccccccHHHHHHHhcc-CCCCccccccccc
Confidence 468999999 488888 45699999999999997664 4899999998864
No 38
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.08 E-value=3.7e-06 Score=66.21 Aligned_cols=62 Identities=31% Similarity=0.686 Sum_probs=45.5
Q ss_pred ccCcccCCCcccCCCCccccc-ccCCccchhHHHHHhhcCCCCCCCCCccccCCCCccccccchhHHHHHH
Q psy17995 4 QECPRCKTTKYRKPTLKLMVN-ICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRVQLFDDSSVEKEVE 73 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~-~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~~~~f~d~~~~~e~~ 73 (120)
+.||.|+. ++.+| +-+ .|||.||+.||...+-.....||.|.. +.-+...+.+|..-++|++
T Consensus 275 LkCplc~~-Llrnp----~kT~cC~~~fc~eci~~al~dsDf~CpnC~r---kdvlld~l~pD~dk~~EvE 337 (427)
T COG5222 275 LKCPLCHC-LLRNP----MKTPCCGHTFCDECIGTALLDSDFKCPNCSR---KDVLLDGLTPDIDKKLEVE 337 (427)
T ss_pred ccCcchhh-hhhCc----ccCccccchHHHHHHhhhhhhccccCCCccc---ccchhhccCccHHHHHHHH
Confidence 78999995 88999 335 799999999999988776799999975 1112233446666555554
No 39
>KOG4739|consensus
Probab=98.02 E-value=3.2e-06 Score=64.21 Aligned_cols=51 Identities=24% Similarity=0.566 Sum_probs=39.1
Q ss_pred CCCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCC
Q psy17995 1 MDDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGN 57 (120)
Q Consensus 1 ~d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~ 57 (120)
|+-..|-.|.- +.+ ..++++|.|+|+||..|..... +..||.|+++++-..
T Consensus 1 m~~VhCn~C~~--~~~-~~~f~LTaC~HvfC~~C~k~~~---~~~C~lCkk~ir~i~ 51 (233)
T KOG4739|consen 1 MDFVHCNKCFR--FPS-QDPFFLTACRHVFCEPCLKASS---PDVCPLCKKSIRIIQ 51 (233)
T ss_pred CceEEeccccc--cCC-CCceeeeechhhhhhhhcccCC---ccccccccceeeeee
Confidence 77889999983 344 5667899999999999986422 238999999976543
No 40
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.01 E-value=2.7e-06 Score=66.86 Aligned_cols=49 Identities=29% Similarity=0.600 Sum_probs=39.8
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
..|.||++++.++- +++++||.|+|-.+|+++++..-..+||+|++++.
T Consensus 324 veCaICms~fiK~d--~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 324 VECAICMSNFIKND--RLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred ceEEEEhhhhcccc--eEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 47999998665433 46688999999999999987755689999999874
No 41
>KOG2660|consensus
Probab=98.01 E-value=4.2e-06 Score=66.15 Aligned_cols=58 Identities=17% Similarity=0.447 Sum_probs=45.7
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCccccccc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFRVQLFDD 65 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~~~~f~d 65 (120)
..+|++|.. .+.|+.. ++.|-|.||++||-+++.. ...||.|+..+.+.....++-.|
T Consensus 15 ~itC~LC~G-YliDATT---I~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih~t~pl~ni~~D 72 (331)
T KOG2660|consen 15 HITCRLCGG-YLIDATT---ITECLHTFCKSCIVKYLEE-SKYCPTCDIVIHKTHPLLNIRSD 72 (331)
T ss_pred ceehhhccc-eeecchh---HHHHHHHHHHHHHHHHHHH-hccCCccceeccCccccccCCcc
Confidence 358999995 7888853 5699999999999999987 58999999988776544444333
No 42
>PF04641 Rtf2: Rtf2 RING-finger
Probab=98.00 E-value=4.6e-06 Score=64.15 Aligned_cols=53 Identities=19% Similarity=0.424 Sum_probs=42.2
Q ss_pred CccCcccCCCcccCCCCcccc-cccCCccchhHHHHHhhcCCCCCCCCCccccCCCCc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMV-NICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFR 59 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~-~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~ 59 (120)
.+.|||... .+ ++..+++. -+|||+|+..++..+- ....||+|+++|...++.
T Consensus 113 ~~~CPvt~~-~~-~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~~~DiI 166 (260)
T PF04641_consen 113 RFICPVTGK-EF-NGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFTEEDII 166 (260)
T ss_pred eeECCCCCc-cc-CCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccccCCEE
Confidence 579999995 44 66666654 4999999999999983 346799999999987654
No 43
>KOG1813|consensus
Probab=97.94 E-value=3e-06 Score=66.21 Aligned_cols=45 Identities=36% Similarity=0.859 Sum_probs=38.1
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
+.|-||+. .|.+| +++.|||.||..|....+..+ .+|++|+...-
T Consensus 242 f~c~icr~-~f~~p----Vvt~c~h~fc~~ca~~~~qk~-~~c~vC~~~t~ 286 (313)
T KOG1813|consen 242 FKCFICRK-YFYRP----VVTKCGHYFCEVCALKPYQKG-EKCYVCSQQTH 286 (313)
T ss_pred cccccccc-ccccc----hhhcCCceeehhhhccccccC-Ccceecccccc
Confidence 46999995 78999 679999999999988877764 78999998653
No 44
>KOG4628|consensus
Probab=97.79 E-value=1.5e-05 Score=63.71 Aligned_cols=50 Identities=26% Similarity=0.563 Sum_probs=40.3
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCC
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRG 56 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~ 56 (120)
.|.||+++ |.. .-++.+.||+|.|-..||+.++...-..||+|+..+++.
T Consensus 231 ~CaIClEd-Y~~-GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~ 280 (348)
T KOG4628|consen 231 TCAICLED-YEK-GDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD 280 (348)
T ss_pred eEEEeecc-ccc-CCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence 89999975 443 345567899999999999999887656799999977654
No 45
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=97.79 E-value=2.7e-05 Score=45.58 Aligned_cols=47 Identities=23% Similarity=0.653 Sum_probs=23.8
Q ss_pred CcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccc
Q psy17995 6 CPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPL 53 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~ 53 (120)
||+|-+.+ ..-...+.--+||+.+|..|...+.+.....||.|++++
T Consensus 1 cp~C~e~~-d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEEL-DETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B---CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCccccc-ccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 78888643 111222222389999999999999986678999999875
No 46
>KOG4172|consensus
Probab=97.70 E-value=9.7e-06 Score=48.69 Aligned_cols=46 Identities=28% Similarity=0.612 Sum_probs=36.0
Q ss_pred ccCcccCCCcccCCCCcccccccCCc-cchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHP-LCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~-fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
..|.||.+. -.|. ++..|||- +|-.|-.++|......||+|+.+++
T Consensus 8 dECTICye~-pvds----VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 8 DECTICYEH-PVDS----VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred cceeeeccC-cchH----HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 469999962 2222 34589998 8999999999876789999999875
No 47
>KOG0802|consensus
Probab=97.59 E-value=3.7e-05 Score=64.67 Aligned_cols=52 Identities=21% Similarity=0.429 Sum_probs=38.6
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~ 55 (120)
+..|+||.+.+..-+++.....+|||.|+..|+..+++. ...||.|+..+..
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~~~ 342 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVLYD 342 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHH-hCcCCcchhhhhc
Confidence 468999997554433321123499999999999999987 5789999995543
No 48
>KOG0824|consensus
Probab=97.58 E-value=3.3e-05 Score=60.66 Aligned_cols=46 Identities=24% Similarity=0.547 Sum_probs=36.7
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
-.|+||+. .---| +..+|+|.||--||+.....+...||+|+.++.
T Consensus 8 ~eC~IC~n-t~n~P----v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 8 KECLICYN-TGNCP----VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred Ccceeeec-cCCcC----ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 36999995 33444 234999999999999988877677999999885
No 49
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=97.48 E-value=9e-05 Score=51.95 Aligned_cols=51 Identities=25% Similarity=0.601 Sum_probs=38.1
Q ss_pred ccCcccCCCcccCCCCccc-cc-ccCCccchhHHHHHhhcCC--CCCCCCCccccCCC
Q psy17995 4 QECPRCKTTKYRKPTLKLM-VN-ICGHPLCEGCVDLLFLKGT--GNCYECNQPLRRGN 57 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~-~~-~CGH~fC~~Ci~~~~~~~~--~~CP~C~~~~~~~~ 57 (120)
|.|-||++. ..++. ++ -+ -||-++|..|--.+|.... +.||+|+++|+.++
T Consensus 81 YeCnIC~et-S~ee~--FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 81 YECNICKET-SAEER--FLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS 135 (140)
T ss_pred eeccCcccc-cchhh--cCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence 689999963 33321 11 12 5999999999999999643 78999999998653
No 50
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=97.45 E-value=0.00011 Score=59.45 Aligned_cols=51 Identities=22% Similarity=0.487 Sum_probs=38.5
Q ss_pred CCccCcccCCCcccCCCC--------cccccccCCccchhHHHHHhhcCCCCCCCCCccc
Q psy17995 2 DDQECPRCKTTKYRKPTL--------KLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPL 53 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~--------~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~ 53 (120)
++-.|.||++.++..|+. +-.-.||||.|--+|++.+.++ +..||+|+.++
T Consensus 286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER-qQTCPICr~p~ 344 (491)
T COG5243 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER-QQTCPICRRPV 344 (491)
T ss_pred CCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh-ccCCCcccCcc
Confidence 466899999766655422 1112389999999999988776 47999999985
No 51
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=97.45 E-value=0.00015 Score=47.24 Aligned_cols=34 Identities=26% Similarity=0.592 Sum_probs=27.9
Q ss_pred ccccccCCccchhHHHHHhhcC--CCCCCCCCcccc
Q psy17995 21 LMVNICGHPLCEGCVDLLFLKG--TGNCYECNQPLR 54 (120)
Q Consensus 21 ~~~~~CGH~fC~~Ci~~~~~~~--~~~CP~C~~~~~ 54 (120)
++...|||.|-..||.+.++.. ...||.||.++.
T Consensus 47 lv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 47 LVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred eeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 3445899999999999988853 478999998764
No 52
>KOG1002|consensus
Probab=97.41 E-value=0.00017 Score=60.75 Aligned_cols=48 Identities=21% Similarity=0.481 Sum_probs=38.1
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc----CCCCCCCCCccccC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK----GTGNCYECNQPLRR 55 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~----~~~~CP~C~~~~~~ 55 (120)
...|.+|.+ .-.++ +.+.|.|.||+-|+..+... ..-.||+|..++.-
T Consensus 536 ~~~C~lc~d-~aed~----i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Lsi 587 (791)
T KOG1002|consen 536 EVECGLCHD-PAEDY----IESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSI 587 (791)
T ss_pred ceeecccCC-hhhhh----HhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccc
Confidence 457999994 66777 56899999999999887653 23789999998853
No 53
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.33 E-value=0.00027 Score=56.82 Aligned_cols=92 Identities=20% Similarity=0.329 Sum_probs=59.3
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc-CCCCCCCCCccccC-----C---CCc------------c
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK-GTGNCYECNQPLRR-----G---NFR------------V 60 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~-~~~~CP~C~~~~~~-----~---~~~------------~ 60 (120)
+...|.||-..+.... ++||||.+|..|.-++-.- ....||.|++.-.. . ++. -
T Consensus 60 en~~C~ICA~~~TYs~-----~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e~V~fT~~~~~DI~D~~~~k~~~EK~G 134 (493)
T COG5236 60 ENMNCQICAGSTTYSA-----RYPCGHQICHACAVRLRALYMQKGCPLCRTETEAVVFTASSPADITDRRQWKGREEKVG 134 (493)
T ss_pred ccceeEEecCCceEEE-----eccCCchHHHHHHHHHHHHHhccCCCccccccceEEEecCCCCcchhHhhhccccccee
Confidence 3457999986554433 5799999999998776553 35789999873311 1 100 0
Q ss_pred ccccchhHHHHHHHHHHhhhhhhccc-CCc--cCHHHHHHHHHH
Q psy17995 61 QLFDDSSVEKEVEIRKKLLKDYNKVE-EDF--NSLAEYNDYLEE 101 (120)
Q Consensus 61 ~~f~d~~~~~e~~~rk~~~k~~~~~~-~~~--~~l~~y~~yle~ 101 (120)
-.|.+..+..|... +|+.+|... ++- +.+.+|+.|+..
T Consensus 135 I~y~~E~v~~E~~~---LL~F~CP~skc~~~C~~~k~lk~H~K~ 175 (493)
T COG5236 135 IFYEGEDVRDEMED---LLSFKCPKSKCHRRCGSLKELKKHYKA 175 (493)
T ss_pred eeecchHHHHHHHH---HHHhcCCchhhhhhhhhHHHHHHHHHh
Confidence 02556677777763 677777544 333 568889888764
No 54
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=97.26 E-value=0.00013 Score=43.70 Aligned_cols=31 Identities=29% Similarity=0.663 Sum_probs=24.3
Q ss_pred ccccCCccchhHHHHHhhcCCCCCCCCCccccCC
Q psy17995 23 VNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRG 56 (120)
Q Consensus 23 ~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~ 56 (120)
+.+|||.+|..|....-- .-||.|++++...
T Consensus 22 ~~pCgH~I~~~~f~~~rY---ngCPfC~~~~~~~ 52 (55)
T PF14447_consen 22 VLPCGHLICDNCFPGERY---NGCPFCGTPFEFD 52 (55)
T ss_pred cccccceeeccccChhhc---cCCCCCCCcccCC
Confidence 569999999999875322 4599999988654
No 55
>KOG1039|consensus
Probab=97.10 E-value=0.00038 Score=55.83 Aligned_cols=55 Identities=24% Similarity=0.472 Sum_probs=38.0
Q ss_pred CccCcccCCCcccCC--CCccccc-ccCCccchhHHHHHhhc-C-----CCCCCCCCccccCCC
Q psy17995 3 DQECPRCKTTKYRKP--TLKLMVN-ICGHPLCEGCVDLLFLK-G-----TGNCYECNQPLRRGN 57 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p--~~~~~~~-~CGH~fC~~Ci~~~~~~-~-----~~~CP~C~~~~~~~~ 57 (120)
+..|.||++.++..+ ..++.+. +|-|.||..||..+-.. . ...||.|+.+.+...
T Consensus 161 ~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~ 224 (344)
T KOG1039|consen 161 EKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVN 224 (344)
T ss_pred cccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccccc
Confidence 568999998665433 1123344 69999999999875422 1 368999999876543
No 56
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=97.03 E-value=0.00029 Score=56.52 Aligned_cols=54 Identities=22% Similarity=0.522 Sum_probs=39.5
Q ss_pred ccCcccCCCcc-cCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCc
Q psy17995 4 QECPRCKTTKY-RKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFR 59 (120)
Q Consensus 4 ~~CpiC~~~~~-~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~ 59 (120)
..||.|.+.+- .+- .++--+||-.+|+.|...+...-.+.||.||..+...+.+
T Consensus 15 d~cplcie~mditdk--nf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~ 69 (480)
T COG5175 15 DYCPLCIEPMDITDK--NFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVR 69 (480)
T ss_pred ccCcccccccccccC--CcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccccee
Confidence 35999997432 222 2233589999999999988776457999999988766544
No 57
>KOG0827|consensus
Probab=96.91 E-value=0.00057 Score=55.53 Aligned_cols=66 Identities=24% Similarity=0.440 Sum_probs=44.3
Q ss_pred ccCcccCCCcccCCCCccc--ccccCCccchhHHHHHhhcCC--CCCCCCCccccCCCCccccccchhHHHHH
Q psy17995 4 QECPRCKTTKYRKPTLKLM--VNICGHPLCEGCVDLLFLKGT--GNCYECNQPLRRGNFRVQLFDDSSVEKEV 72 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~--~~~CGH~fC~~Ci~~~~~~~~--~~CP~C~~~~~~~~~~~~~f~d~~~~~e~ 72 (120)
..|.||- +.+ |+..-+ +..|||.|-..|+..+|+-.| ..||+|+..+....+....|-|..++.+.
T Consensus 5 A~C~Ic~-d~~--p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~N~~~~d~vvEe~~ 74 (465)
T KOG0827|consen 5 AECHICI-DGR--PNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVANPSTVDHVVEESV 74 (465)
T ss_pred ceeeEec-cCC--ccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccceeeechhhhhhhhccch
Confidence 4799996 443 332222 347999999999999998654 47999996666555444455565554443
No 58
>KOG1001|consensus
Probab=96.87 E-value=0.00024 Score=61.42 Aligned_cols=51 Identities=20% Similarity=0.520 Sum_probs=39.6
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcC-CCCCCCCCccccCCCCcc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKG-TGNCYECNQPLRRGNFRV 60 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~-~~~CP~C~~~~~~~~~~~ 60 (120)
+.|++|.+ ...+ +++.|||.||.+|+...+... ..+||.|+..+....+..
T Consensus 455 ~~c~ic~~--~~~~----~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s 506 (674)
T KOG1001|consen 455 HWCHICCD--LDSF----FITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLS 506 (674)
T ss_pred cccccccc--cccc----eeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhh
Confidence 68999995 3444 578999999999999988753 368999998876554443
No 59
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=96.72 E-value=0.003 Score=40.43 Aligned_cols=54 Identities=22% Similarity=0.512 Sum_probs=26.7
Q ss_pred CccCcccCCCcccCCCCcccc--cccCCccchhHHHHHhhcCCCCCCCCCccccCC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMV--NICGHPLCEGCVDLLFLKGTGNCYECNQPLRRG 56 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~--~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~ 56 (120)
...|.||.+++-.+.+-.+++ ..||--.|+.|..--.+.+...||.|++.+++.
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKRH 64 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B----
T ss_pred CcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcccc
Confidence 357999998877777666565 389999999999988888889999999988754
No 60
>KOG1645|consensus
Probab=96.70 E-value=0.0016 Score=53.20 Aligned_cols=55 Identities=18% Similarity=0.437 Sum_probs=40.9
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcC-CCCCCCCCccccCCCC
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKG-TGNCYECNQPLRRGNF 58 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~-~~~CP~C~~~~~~~~~ 58 (120)
..||||++.....-+-.++...|||-|=.+||.+++.+. .+.||.|...-.++.+
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~i 60 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQI 60 (463)
T ss_pred ccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHHH
Confidence 489999975444444455556899999999999988643 3789999876655543
No 61
>KOG0804|consensus
Probab=96.69 E-value=0.00062 Score=56.07 Aligned_cols=45 Identities=18% Similarity=0.487 Sum_probs=32.8
Q ss_pred ccCcccCCCcccCCCCccccc-ccCCccchhHHHHHhhcCCCCCCCCCccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVN-ICGHPLCEGCVDLLFLKGTGNCYECNQPL 53 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~-~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~ 53 (120)
-+||||++.+ |+....+++ .|-|+|-.+|+..+|- ..||+||-..
T Consensus 176 PTCpVCLERM--D~s~~gi~t~~c~Hsfh~~cl~~w~~---~scpvcR~~q 221 (493)
T KOG0804|consen 176 PTCPVCLERM--DSSTTGILTILCNHSFHCSCLMKWWD---SSCPVCRYCQ 221 (493)
T ss_pred CCcchhHhhc--CccccceeeeecccccchHHHhhccc---CcChhhhhhc
Confidence 4899999853 555544444 8999999999988764 4577776533
No 62
>KOG4692|consensus
Probab=96.68 E-value=0.001 Score=53.69 Aligned_cols=47 Identities=23% Similarity=0.667 Sum_probs=36.4
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
++-.||||... -.+. +.+||||+-|..||.+.+.+. ..|--|++.+.
T Consensus 421 Ed~lCpICyA~-pi~A----vf~PC~H~SC~~CI~qHlmN~-k~CFfCktTv~ 467 (489)
T KOG4692|consen 421 EDNLCPICYAG-PINA----VFAPCSHRSCYGCITQHLMNC-KRCFFCKTTVI 467 (489)
T ss_pred ccccCcceecc-cchh----hccCCCCchHHHHHHHHHhcC-CeeeEecceee
Confidence 45689999952 2333 457999999999999998864 78999988764
No 63
>KOG4367|consensus
Probab=96.64 E-value=0.00084 Score=55.55 Aligned_cols=35 Identities=31% Similarity=0.981 Sum_probs=29.5
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK 41 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~ 41 (120)
++++||||. ..|.+| .+.+|||++|+.|......+
T Consensus 3 eelkc~vc~-~f~~ep----iil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 3 EELKCPVCG-SFYREP----IILPCSHNLCQACARNILVQ 37 (699)
T ss_pred ccccCceeh-hhccCc----eEeecccHHHHHHHHhhccc
Confidence 458999999 599999 46799999999998876654
No 64
>KOG1814|consensus
Probab=96.55 E-value=0.0011 Score=54.23 Aligned_cols=46 Identities=17% Similarity=0.354 Sum_probs=32.7
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc-------CCCCCCCCC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK-------GTGNCYECN 50 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~-------~~~~CP~C~ 50 (120)
.+.|.||.+. ...+.-++..||+|+||++|+..++.. +...||.++
T Consensus 184 lf~C~ICf~e--~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 184 LFDCCICFEE--QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred cccceeeehh--hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 4689999963 333333445699999999999999863 236788644
No 65
>KOG4185|consensus
Probab=96.55 E-value=0.0022 Score=49.66 Aligned_cols=52 Identities=27% Similarity=0.545 Sum_probs=39.4
Q ss_pred CCCccCcccCCCcccCCC--CcccccccCCccchhHHHHHhhcCCCCCCCCCccc
Q psy17995 1 MDDQECPRCKTTKYRKPT--LKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPL 53 (120)
Q Consensus 1 ~d~~~CpiC~~~~~~~p~--~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~ 53 (120)
|.-+.|-||.+ .|.+-. ..-.+..|||.||..|+..+...+...||-|+.+.
T Consensus 1 m~~~~c~~c~~-~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 1 MSFPECEICNE-DYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CCCCceeecCc-cccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 77889999996 454321 10013369999999999999998878899999974
No 66
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.55 E-value=0.0008 Score=42.09 Aligned_cols=52 Identities=25% Similarity=0.592 Sum_probs=23.5
Q ss_pred CccCcccCCCcccCCCCcccc-c--ccCCccchhHHHHHhhc--CC--------CCCCCCCcccc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMV-N--ICGHPLCEGCVDLLFLK--GT--------GNCYECNQPLR 54 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~-~--~CGH~fC~~Ci~~~~~~--~~--------~~CP~C~~~~~ 54 (120)
+..|+||......+.....++ . .||+.|-..||...|.. ++ +.||.|++++.
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 467999996443233232222 2 79999999999998873 11 46999999874
No 67
>KOG1785|consensus
Probab=96.39 E-value=0.0013 Score=53.86 Aligned_cols=46 Identities=22% Similarity=0.562 Sum_probs=34.5
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhhcC-CCCCCCCCccccC
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKG-TGNCYECNQPLRR 55 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~-~~~CP~C~~~~~~ 55 (120)
.|-||-+. +-+. .+-||||-+|.+|+..+..+. ...||-|+-.++-
T Consensus 371 LCKICaen---dKdv--kIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG 417 (563)
T KOG1785|consen 371 LCKICAEN---DKDV--KIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG 417 (563)
T ss_pred HHHHhhcc---CCCc--ccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence 68999862 3332 256999999999998765443 5789999988764
No 68
>KOG0825|consensus
Probab=96.34 E-value=0.00066 Score=59.39 Aligned_cols=48 Identities=21% Similarity=0.422 Sum_probs=34.3
Q ss_pred ccCcccCCCcccCCCCccccc--ccCCccchhHHHHHhhcCCCCCCCCCccccCC
Q psy17995 4 QECPRCKTTKYRKPTLKLMVN--ICGHPLCEGCVDLLFLKGTGNCYECNQPLRRG 56 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~--~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~ 56 (120)
-.||+|.. .+.+. +..+ +|||.||.+||..+ ......||+|+..|.+.
T Consensus 124 ~~CP~Ci~-s~~Dq---L~~~~k~c~H~FC~~Ci~sW-sR~aqTCPiDR~EF~~v 173 (1134)
T KOG0825|consen 124 NQCPNCLK-SCNDQ---LEESEKHTAHYFCEECVGSW-SRCAQTCPVDRGEFGEV 173 (1134)
T ss_pred hhhhHHHH-HHHHH---hhccccccccccHHHHhhhh-hhhcccCchhhhhhhee
Confidence 46888884 44443 2233 79999999999874 44457899999988654
No 69
>KOG4265|consensus
Probab=96.19 E-value=0.0024 Score=51.20 Aligned_cols=45 Identities=40% Similarity=0.833 Sum_probs=34.4
Q ss_pred ccCcccCCCcccCCCCcccccccCCc-cchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHP-LCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~-fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
..|.||++. .+|= ++.||-|- +|++|.+.+.-. ...||+||.++.
T Consensus 291 keCVIClse-~rdt----~vLPCRHLCLCs~Ca~~Lr~q-~n~CPICRqpi~ 336 (349)
T KOG4265|consen 291 KECVICLSE-SRDT----VVLPCRHLCLCSGCAKSLRYQ-TNNCPICRQPIE 336 (349)
T ss_pred CeeEEEecC-Ccce----EEecchhhehhHhHHHHHHHh-hcCCCccccchH
Confidence 579999963 2432 45699999 999999887532 467999999875
No 70
>KOG0828|consensus
Probab=96.16 E-value=0.0024 Score=53.47 Aligned_cols=51 Identities=22% Similarity=0.355 Sum_probs=36.4
Q ss_pred ccCcccCCCccc----CCCCc--------ccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYR----KPTLK--------LMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~----~p~~~--------~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
.-|+||.+++-. .+-+. .++|||-|.|-..|+.+....-...||+|+.++.
T Consensus 572 ~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 572 NDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred ccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 469999976431 12111 2356999999999999876644578999999874
No 71
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=95.86 E-value=0.0093 Score=38.50 Aligned_cols=49 Identities=18% Similarity=0.407 Sum_probs=33.8
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
.||-|+.....+-+-+++...|.|.|-..||.+.+.. ...||.+++++.
T Consensus 33 ~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w~ 81 (88)
T COG5194 33 TCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTWV 81 (88)
T ss_pred cCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCceeE
Confidence 4777764331222223334589999999999998886 478999988763
No 72
>KOG1812|consensus
Probab=95.68 E-value=0.0084 Score=48.78 Aligned_cols=52 Identities=25% Similarity=0.500 Sum_probs=34.7
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc-----CCCCCC--CCCccccC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK-----GTGNCY--ECNQPLRR 55 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~-----~~~~CP--~C~~~~~~ 55 (120)
...|+||.... ..+...+.+..|||.||..|+.+++.. ..+.|| .|...+..
T Consensus 146 ~~~C~iC~~e~-~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~ 204 (384)
T KOG1812|consen 146 KEECGICFVED-PEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTL 204 (384)
T ss_pred cccCccCcccc-ccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCH
Confidence 45799999322 333222234589999999999998873 347788 46665543
No 73
>KOG3002|consensus
Probab=95.54 E-value=0.0091 Score=47.14 Aligned_cols=44 Identities=25% Similarity=0.623 Sum_probs=32.5
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
-+.||||.. .+.-|- ++-+=||-.|.+|-.+. +..||.|+.++.
T Consensus 48 lleCPvC~~-~l~~Pi---~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 48 LLDCPVCFN-PLSPPI---FQCDNGHLACSSCRTKV----SNKCPTCRLPIG 91 (299)
T ss_pred hccCchhhc-cCcccc---eecCCCcEehhhhhhhh----cccCCccccccc
Confidence 468999996 556671 22234999999997542 468999999886
No 74
>KOG1734|consensus
Probab=95.22 E-value=0.0056 Score=47.83 Aligned_cols=53 Identities=19% Similarity=0.357 Sum_probs=35.7
Q ss_pred CCccCcccCCCcccCCCC-----cccccccCCccchhHHHHHhhcC-CCCCCCCCcccc
Q psy17995 2 DDQECPRCKTTKYRKPTL-----KLMVNICGHPLCEGCVDLLFLKG-TGNCYECNQPLR 54 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~-----~~~~~~CGH~fC~~Ci~~~~~~~-~~~CP~C~~~~~ 54 (120)
++-.|.||...+..+-+- +.....|+|+|-+.||....--| .+.||=|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 456799998654322100 11234899999999999876554 478999987553
No 75
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=95.11 E-value=0.024 Score=33.02 Aligned_cols=43 Identities=16% Similarity=0.413 Sum_probs=30.7
Q ss_pred cCcccCCCcccCCCCcccccccC-----CccchhHHHHHhhcC-CCCCCCCC
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICG-----HPLCEGCVDLLFLKG-TGNCYECN 50 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CG-----H~fC~~Ci~~~~~~~-~~~CP~C~ 50 (120)
.|-||++ ..++... +++||. |.+-.+|+.+.+... ...||+|+
T Consensus 1 ~CrIC~~--~~~~~~~-l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD--EGDEGDP-LVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCC--CCCCCCe-eEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4889995 2233222 467885 889999999988753 46899995
No 76
>PRK00420 hypothetical protein; Validated
Probab=94.95 E-value=0.12 Score=35.39 Aligned_cols=22 Identities=36% Similarity=0.446 Sum_probs=17.3
Q ss_pred CCccCHHHHHHHHHHHHHHHHH
Q psy17995 87 EDFNSLAEYNDYLEEIEEIVFN 108 (120)
Q Consensus 87 ~~~~~l~~y~~yle~~E~~i~~ 108 (120)
.+.+...++-.+|+.+|+|..-
T Consensus 89 ~~~~ri~Ei~~~l~~l~ki~~~ 110 (112)
T PRK00420 89 EDIERITEIIRYLEVLERIRKI 110 (112)
T ss_pred cchhHHHHHHHHHHHHHHHHHH
Confidence 3557788999999999988754
No 77
>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=94.74 E-value=0.0034 Score=39.43 Aligned_cols=41 Identities=32% Similarity=0.722 Sum_probs=22.5
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
+..||.|... ..+ +. ||-.|..|-..+... +.||.|+.++.
T Consensus 1 e~~CP~C~~~--L~~------~~-~~~~C~~C~~~~~~~--a~CPdC~~~Le 41 (70)
T PF07191_consen 1 ENTCPKCQQE--LEW------QG-GHYHCEACQKDYKKE--AFCPDCGQPLE 41 (70)
T ss_dssp --B-SSS-SB--EEE------ET-TEEEETTT--EEEEE--EE-TTT-SB-E
T ss_pred CCcCCCCCCc--cEE------eC-CEEECccccccceec--ccCCCcccHHH
Confidence 4689999953 233 22 899999998765433 68999999874
No 78
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.46 E-value=0.016 Score=52.09 Aligned_cols=48 Identities=21% Similarity=0.547 Sum_probs=35.3
Q ss_pred ccCcccCCCccc-----CCCCcccccccCCccchhHHHHHhhc-CCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYR-----KPTLKLMVNICGHPLCEGCVDLLFLK-GTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~-----~p~~~~~~~~CGH~fC~~Ci~~~~~~-~~~~CP~C~~~~~ 54 (120)
..|+||.. ++. -|+.+ -..|.|.|-.+|+.+++++ +...||.||..+.
T Consensus 1470 eECaICYs-vL~~vdr~lPskr--C~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1470 EECAICYS-VLDMVDRSLPSKR--CATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred chhhHHHH-HHHHHhccCCccc--cchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 47999984 543 23221 1269999999999999986 4589999997653
No 79
>KOG2817|consensus
Probab=94.43 E-value=0.035 Score=45.21 Aligned_cols=47 Identities=23% Similarity=0.444 Sum_probs=34.2
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCC--CCCCCCCcc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGT--GNCYECNQP 52 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~--~~CP~C~~~ 52 (120)
+.|||=++ -..+-|.+| ...|||++++.-+.++...|. .+||=|-..
T Consensus 335 F~CPVlKe-qtsdeNPPm-~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 335 FICPVLKE-QTSDENPPM-MLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred eecccchh-hccCCCCCe-eeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 57999875 333323232 348999999999999988876 789988653
No 80
>KOG1941|consensus
Probab=94.18 E-value=0.015 Score=47.56 Aligned_cols=47 Identities=23% Similarity=0.478 Sum_probs=35.9
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc-CCCCCCCCCc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK-GTGNCYECNQ 51 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~-~~~~CP~C~~ 51 (120)
+.|..|.+.+-..|. .+...||.|.|-..|+..++.+ ++..||.|++
T Consensus 366 L~Cg~CGe~~Glk~e-~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 366 LYCGLCGESIGLKNE-RLQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred hhhhhhhhhhcCCcc-cccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 569999875555542 2233599999999999999876 4688999995
No 81
>PLN02436 cellulose synthase A
Probab=94.13 E-value=0.052 Score=49.24 Aligned_cols=53 Identities=25% Similarity=0.514 Sum_probs=42.3
Q ss_pred ccCcccCCCcccCCCCcccc--cccCCccchhHHHHHhhcCCCCCCCCCccccCC
Q psy17995 4 QECPRCKTTKYRKPTLKLMV--NICGHPLCEGCVDLLFLKGTGNCYECNQPLRRG 56 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~--~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~ 56 (120)
..|.||.+++-.+.+-.+++ +.||--.|..|.+.-.+.+...||.|++.+++-
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r~ 91 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYKRI 91 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhc
Confidence 47999998876555554555 489999999999777777889999999988743
No 82
>PLN02189 cellulose synthase
Probab=94.09 E-value=0.054 Score=48.99 Aligned_cols=53 Identities=32% Similarity=0.605 Sum_probs=41.7
Q ss_pred ccCcccCCCcccCCCCcccc--cccCCccchhHHHHHhhcCCCCCCCCCccccCC
Q psy17995 4 QECPRCKTTKYRKPTLKLMV--NICGHPLCEGCVDLLFLKGTGNCYECNQPLRRG 56 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~--~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~ 56 (120)
..|.||.+++-.+.+-.+++ ..||--.|..|.+.-.+.+...||.|++.+++-
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~r~ 89 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYKRL 89 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhc
Confidence 47999998766555444444 489999999999777777889999999998743
No 83
>KOG0826|consensus
Probab=93.94 E-value=0.04 Score=44.02 Aligned_cols=47 Identities=28% Similarity=0.650 Sum_probs=36.1
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccc
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPL 53 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~ 53 (120)
++-.||+|+. .-.||. +...-|-+||-.|+-.+... -..||+-+.+.
T Consensus 299 ~~~~CpvClk-~r~Npt---vl~vSGyVfCY~Ci~~Yv~~-~~~CPVT~~p~ 345 (357)
T KOG0826|consen 299 DREVCPVCLK-KRQNPT---VLEVSGYVFCYPCIFSYVVN-YGHCPVTGYPA 345 (357)
T ss_pred ccccChhHHh-ccCCCc---eEEecceEEeHHHHHHHHHh-cCCCCccCCcc
Confidence 4568999996 446774 24456999999999998884 47899988765
No 84
>KOG3113|consensus
Probab=93.92 E-value=0.043 Score=42.54 Aligned_cols=51 Identities=14% Similarity=0.331 Sum_probs=36.5
Q ss_pred CccCcccCCCcccCCCCccccc-ccCCccchhHHHHHhhcCCCCCCCCCccccCCCC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVN-ICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNF 58 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~-~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~ 58 (120)
.+.|||-.- .+ |..-+++.. +|||+|=..-+..+- ...|++|+..+...+.
T Consensus 111 ~fiCPvtgl-eM-ng~~~F~~l~~CGcV~SerAlKeik---as~C~~C~a~y~~~dv 162 (293)
T KOG3113|consen 111 RFICPVTGL-EM-NGKYRFCALRCCGCVFSERALKEIK---ASVCHVCGAAYQEDDV 162 (293)
T ss_pred eeecccccc-ee-cceEEEEEEeccceeccHHHHHHhh---hccccccCCcccccCe
Confidence 468999873 33 333344444 999999998888764 4679999999876543
No 85
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=93.88 E-value=0.047 Score=49.49 Aligned_cols=52 Identities=23% Similarity=0.603 Sum_probs=42.2
Q ss_pred ccCcccCCCcccCCCCcccc--cccCCccchhHHHHHhhcCCCCCCCCCccccC
Q psy17995 4 QECPRCKTTKYRKPTLKLMV--NICGHPLCEGCVDLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~--~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~ 55 (120)
..|-||.+++-.+++-.++| +.||--.|+.|.+--.+.+...||.|++.+++
T Consensus 18 qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYkr 71 (1079)
T PLN02638 18 QVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYKR 71 (1079)
T ss_pred ceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchhh
Confidence 47999998877666555555 49999999999976666788999999998873
No 86
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=93.44 E-value=0.07 Score=48.30 Aligned_cols=53 Identities=26% Similarity=0.629 Sum_probs=42.8
Q ss_pred CccCcccCCCcccCCCCcccc--cccCCccchhHHHHHhhcCCCCCCCCCccccC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMV--NICGHPLCEGCVDLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~--~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~ 55 (120)
...|.||.+++-.+++-.+++ ..||--.|+.|.+--.+.+...||.|++.+++
T Consensus 15 ~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~~ 69 (1044)
T PLN02915 15 AKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYKR 69 (1044)
T ss_pred cchhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchhh
Confidence 357999998877776665555 48999999999976666678899999998874
No 87
>KOG1493|consensus
Probab=93.25 E-value=0.039 Score=35.34 Aligned_cols=35 Identities=23% Similarity=0.469 Sum_probs=27.4
Q ss_pred cccccccCCccchhHHHHHhhcC--CCCCCCCCcccc
Q psy17995 20 KLMVNICGHPLCEGCVDLLFLKG--TGNCYECNQPLR 54 (120)
Q Consensus 20 ~~~~~~CGH~fC~~Ci~~~~~~~--~~~CP~C~~~~~ 54 (120)
+++..-|-|.|-..||.+.+... ...||.||..+.
T Consensus 45 PLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 45 PLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred ccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 34456899999999999987743 478999998653
No 88
>PLN02195 cellulose synthase A
Probab=93.16 E-value=0.12 Score=46.51 Aligned_cols=52 Identities=23% Similarity=0.591 Sum_probs=41.7
Q ss_pred ccCcccCCCcccCCCCcccc--cccCCccchhHHHHHhhcCCCCCCCCCccccC
Q psy17995 4 QECPRCKTTKYRKPTLKLMV--NICGHPLCEGCVDLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~--~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~ 55 (120)
..|.||.+.+-.+++-.+++ ..||--.|+.|.+--.+.|...||.|++.++.
T Consensus 7 ~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk~ 60 (977)
T PLN02195 7 PICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEGRKVCLRCGGPYDA 60 (977)
T ss_pred ccceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcCCccCCccCCcccc
Confidence 37999998776666555555 48999999999976666678899999999883
No 89
>KOG4362|consensus
Probab=93.06 E-value=0.03 Score=48.58 Aligned_cols=52 Identities=27% Similarity=0.659 Sum_probs=41.6
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc--CCCCCCCCCccccCCCCcc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK--GTGNCYECNQPLRRGNFRV 60 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~--~~~~CP~C~~~~~~~~~~~ 60 (120)
+.||||.. .+..| ..+.|-|.||..|+...|.. +...||+|+..+.+...+.
T Consensus 22 lEc~ic~~-~~~~p----~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s~~E 75 (684)
T KOG4362|consen 22 LECPICLE-HVKEP----SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRSLRE 75 (684)
T ss_pred ccCCceeE-Eeecc----chhhhhHHHHhhhhhceeeccCccccchhhhhhhhhhhccc
Confidence 58999996 67777 23599999999999998774 3578999998887766554
No 90
>PLN02400 cellulose synthase
Probab=92.02 E-value=0.098 Score=47.56 Aligned_cols=52 Identities=31% Similarity=0.590 Sum_probs=41.8
Q ss_pred ccCcccCCCcccCCCCcccc--cccCCccchhHHHHHhhcCCCCCCCCCccccC
Q psy17995 4 QECPRCKTTKYRKPTLKLMV--NICGHPLCEGCVDLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~--~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~ 55 (120)
..|.||.+++-.+.+-.+++ ..||--.|+.|.+--.+.+...||.|++.+++
T Consensus 37 qiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYkR 90 (1085)
T PLN02400 37 QICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYRR 90 (1085)
T ss_pred ceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCcccc
Confidence 37999998877666655555 48999999999976556678899999998874
No 91
>KOG1940|consensus
Probab=91.97 E-value=0.13 Score=40.34 Aligned_cols=47 Identities=26% Similarity=0.555 Sum_probs=34.7
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQ 51 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~ 51 (120)
+..||+|.+.+|..- ....+.+|||..=..|+....-.+ .+||+|.+
T Consensus 158 ~~ncPic~e~l~~s~-~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSF-EDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred cCCCchhHHHhcccc-ccCCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence 456999997554321 111245999999999998877777 99999998
No 92
>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=91.90 E-value=0.057 Score=31.50 Aligned_cols=46 Identities=24% Similarity=0.652 Sum_probs=23.7
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~ 55 (120)
.+.|-.|.- .+-+ ++.-=.|-.|..|+...++. +..||+|+.++..
T Consensus 2 r~nCKsCWf---~~k~---Li~C~dHYLCl~CLt~ml~~-s~~C~iC~~~LPt 47 (50)
T PF03854_consen 2 RYNCKSCWF---ANKG---LIKCSDHYLCLNCLTLMLSR-SDRCPICGKPLPT 47 (50)
T ss_dssp -----SS-S-----SS---EEE-SS-EEEHHHHHHT-SS-SSEETTTTEE---
T ss_pred CccChhhhh---cCCC---eeeecchhHHHHHHHHHhcc-ccCCCcccCcCcc
Confidence 356777762 2222 13333599999999988876 4789999998753
No 93
>KOG1571|consensus
Probab=91.62 E-value=0.072 Score=42.94 Aligned_cols=42 Identities=29% Similarity=0.599 Sum_probs=27.3
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
..|.||.+. ..+. +--||||.-| |..- +..-+.||+|+..++
T Consensus 306 ~lcVVcl~e-~~~~----~fvpcGh~cc--ct~c--s~~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 306 DLCVVCLDE-PKSA----VFVPCGHVCC--CTLC--SKHLPQCPVCRQRIR 347 (355)
T ss_pred CceEEecCC-ccce----eeecCCcEEE--chHH--HhhCCCCchhHHHHH
Confidence 479999963 3333 2349999966 6443 333466999998664
No 94
>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=91.60 E-value=0.12 Score=26.31 Aligned_cols=9 Identities=33% Similarity=1.058 Sum_probs=5.8
Q ss_pred cCcccCCCc
Q psy17995 5 ECPRCKTTK 13 (120)
Q Consensus 5 ~CpiC~~~~ 13 (120)
.||.|...+
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 578887533
No 95
>KOG3799|consensus
Probab=90.91 E-value=0.11 Score=36.91 Aligned_cols=27 Identities=41% Similarity=0.930 Sum_probs=19.4
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHH
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDL 37 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~ 37 (120)
|+..|.||+.+.|- ..|||. |..|-.+
T Consensus 64 ddatC~IC~KTKFA--------DG~GH~-C~YCq~r 90 (169)
T KOG3799|consen 64 DDATCGICHKTKFA--------DGCGHN-CSYCQTR 90 (169)
T ss_pred cCcchhhhhhcccc--------cccCcc-cchhhhh
Confidence 57799999975433 469997 7888544
No 96
>PHA03096 p28-like protein; Provisional
Probab=90.86 E-value=0.15 Score=40.11 Aligned_cols=50 Identities=12% Similarity=0.150 Sum_probs=31.6
Q ss_pred ccCcccCCCcccCCCC--ccc-ccccCCccchhHHHHHhhcC--C---CCCCCCCccc
Q psy17995 4 QECPRCKTTKYRKPTL--KLM-VNICGHPLCEGCVDLLFLKG--T---GNCYECNQPL 53 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~--~~~-~~~CGH~fC~~Ci~~~~~~~--~---~~CP~C~~~~ 53 (120)
-.|.||++.++..|.. .+. .+.|-|.||..|+....... . +.||+|+..+
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~~~~~ 236 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRLNTVI 236 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccchhhHH
Confidence 4699999877655411 222 34899999999998654431 2 3455555443
No 97
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=90.52 E-value=0.31 Score=27.55 Aligned_cols=41 Identities=24% Similarity=0.552 Sum_probs=20.5
Q ss_pred CcccCCCcccCCCCccccc-ccCCccchhHHHHHhhcCC-CCCCCC
Q psy17995 6 CPRCKTTKYRKPTLKLMVN-ICGHPLCEGCVDLLFLKGT-GNCYEC 49 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~-~CGH~fC~~Ci~~~~~~~~-~~CP~C 49 (120)
|.+|++ +..-..+ =.+ .|+=++-..|+..+|+..+ ..||.|
T Consensus 1 C~~C~~-iv~~G~~--C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKE-IVTQGQR--CSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-S-B-SSSEE---SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred Ccccch-hHeeecc--CCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 667885 4332200 012 5888999999999999754 369987
No 98
>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=90.23 E-value=0.18 Score=33.18 Aligned_cols=35 Identities=34% Similarity=0.831 Sum_probs=25.5
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
.|-+|.. ....+ ||.||..|... ...|+.||+.+.
T Consensus 46 ~C~~CK~-~v~q~---------g~~YCq~CAYk-----kGiCamCGKki~ 80 (90)
T PF10235_consen 46 KCKICKT-KVHQP---------GAKYCQTCAYK-----KGICAMCGKKIL 80 (90)
T ss_pred ccccccc-ccccC---------CCccChhhhcc-----cCcccccCCeec
Confidence 6788884 22322 89999999643 368999999873
No 99
>KOG2114|consensus
Probab=90.23 E-value=0.13 Score=45.63 Aligned_cols=43 Identities=26% Similarity=0.750 Sum_probs=32.2
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
-+|..|.. .+--| +|---|||.|-+.|+. .+...||.|+..++
T Consensus 841 skCs~C~~-~LdlP---~VhF~CgHsyHqhC~e----~~~~~CP~C~~e~~ 883 (933)
T KOG2114|consen 841 SKCSACEG-TLDLP---FVHFLCGHSYHQHCLE----DKEDKCPKCLPELR 883 (933)
T ss_pred eeecccCC-ccccc---eeeeecccHHHHHhhc----cCcccCCccchhhh
Confidence 47999995 33445 3445999999999987 45689999987443
No 100
>KOG3161|consensus
Probab=89.86 E-value=0.093 Score=45.50 Aligned_cols=37 Identities=30% Similarity=0.660 Sum_probs=25.6
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK 41 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~ 41 (120)
+.|+||.. .|.+...--+...|||.+|..|+..+...
T Consensus 12 l~c~ic~n-~f~~~~~~Pvsl~cghtic~~c~~~lyn~ 48 (861)
T KOG3161|consen 12 LLCDICLN-LFVVQRLEPVSLQCGHTICGHCVQLLYNA 48 (861)
T ss_pred hhchHHHH-HHHHHhcCcccccccchHHHHHHHhHhhc
Confidence 57999974 55443221123389999999999987764
No 101
>KOG1428|consensus
Probab=89.77 E-value=0.29 Score=46.46 Aligned_cols=50 Identities=22% Similarity=0.457 Sum_probs=36.8
Q ss_pred CccCcccCCCccc-CCCCcccccccCCccchhHHHHHhhc---CC------CCCCCCCccccC
Q psy17995 3 DQECPRCKTTKYR-KPTLKLMVNICGHPLCEGCVDLLFLK---GT------GNCYECNQPLRR 55 (120)
Q Consensus 3 ~~~CpiC~~~~~~-~p~~~~~~~~CGH~fC~~Ci~~~~~~---~~------~~CP~C~~~~~~ 55 (120)
+.+|-||.+..+. .| ..+..|||.|--.|..+++++ |+ ..||+|..++..
T Consensus 3486 DDmCmICFTE~L~AAP---~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3486 DDMCMICFTEALSAAP---AIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred CceEEEEehhhhCCCc---ceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence 4589999865432 33 124599999999999999875 33 479999988753
No 102
>KOG4275|consensus
Probab=89.47 E-value=0.032 Score=44.08 Aligned_cols=43 Identities=28% Similarity=0.617 Sum_probs=28.8
Q ss_pred CccCcccCCCcccCCCCcccccccCCcc-chhHHHHHhhcCCCCCCCCCccccC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPL-CEGCVDLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~f-C~~Ci~~~~~~~~~~CP~C~~~~~~ 55 (120)
+..|.||.+ .-.+- +..+|||.. |-.|-.+. ..||+||+.+++
T Consensus 300 ~~LC~ICmD-aP~DC----vfLeCGHmVtCt~CGkrm-----~eCPICRqyi~r 343 (350)
T KOG4275|consen 300 RRLCAICMD-APRDC----VFLECGHMVTCTKCGKRM-----NECPICRQYIVR 343 (350)
T ss_pred HHHHHHHhc-CCcce----EEeecCcEEeehhhcccc-----ccCchHHHHHHH
Confidence 467999995 43443 345999974 66664432 479999886543
No 103
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=88.44 E-value=0.27 Score=42.66 Aligned_cols=20 Identities=30% Similarity=1.044 Sum_probs=13.2
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhH
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGC 34 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~C 34 (120)
..||-|.. .+|. |++||..|
T Consensus 2 ~~Cp~Cg~---~n~~--------~akFC~~C 21 (645)
T PRK14559 2 LICPQCQF---ENPN--------NNRFCQKC 21 (645)
T ss_pred CcCCCCCC---cCCC--------CCcccccc
Confidence 47999995 3442 56666666
No 104
>KOG0298|consensus
Probab=87.29 E-value=0.14 Score=47.25 Aligned_cols=44 Identities=25% Similarity=0.548 Sum_probs=34.6
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
..|++|++ +..+-.+ +..|||-+|..|....... ...||.|+..
T Consensus 1154 ~~c~ic~d-il~~~~~---I~~cgh~~c~~c~~~~l~~-~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1154 FVCEICLD-ILRNQGG---IAGCGHEPCCRCDELWLYA-SSRCPICKSI 1197 (1394)
T ss_pred cchHHHHH-HHHhcCC---eeeechhHhhhHHHHHHHH-hccCcchhhh
Confidence 47999995 7776543 7899999999998876654 4789999853
No 105
>KOG2113|consensus
Probab=87.10 E-value=0.4 Score=38.47 Aligned_cols=44 Identities=5% Similarity=-0.077 Sum_probs=31.4
Q ss_pred CCCccCcccCCCcccCCCCcccccccCCc-cchhHHHHHhhcCCCCCCCCCcc
Q psy17995 1 MDDQECPRCKTTKYRKPTLKLMVNICGHP-LCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 1 ~d~~~CpiC~~~~~~~p~~~~~~~~CGH~-fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
|..+.|-+|........ ..+|||+ ||.+|.. .+..+.||+|...
T Consensus 341 ~s~~~~~~~~~~~~st~-----~~~~~~n~~~~~~a~---~s~~~~~~~c~~~ 385 (394)
T KOG2113|consen 341 MSSLKGTSAGFGLLSTI-----WSGGNMNLSPGSLAS---ASASPTSSTCDHN 385 (394)
T ss_pred hhhcccccccCceeeeE-----eecCCcccChhhhhh---cccCCcccccccc
Confidence 56678888886543322 4699998 7999987 2335789999763
No 106
>KOG2068|consensus
Probab=86.84 E-value=0.53 Score=37.69 Aligned_cols=84 Identities=14% Similarity=0.314 Sum_probs=46.0
Q ss_pred CCccchhHHHHHhhcCC--CCCCCCCccccCCCC--ccccccchhHHHHHHHH-HHhhhh---hhcccCCccCHHHHHHH
Q psy17995 27 GHPLCEGCVDLLFLKGT--GNCYECNQPLRRGNF--RVQLFDDSSVEKEVEIR-KKLLKD---YNKVEEDFNSLAEYNDY 98 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~~~--~~CP~C~~~~~~~~~--~~~~f~d~~~~~e~~~r-k~~~k~---~~~~~~~~~~l~~y~~y 98 (120)
|-.+|..|+..+-.... +.||-|++++.+..+ ++...++... +...+ ++..++ ...++.+|.+++-.+..
T Consensus 1 ~yqIc~~cwh~i~~~~~~~grcpncr~ky~e~ki~~r~~~~~~l~~--~~n~~kk~e~e~k~~~~s~r~~ls~~rvVqkn 78 (327)
T KOG2068|consen 1 GYQICDSCWHHIATSAEKKGRCPNCRTKYKEEKIVLRRVQWESLVA--EKNKEKKKEQEIKRKLSSNRKHLSGVRVVQKN 78 (327)
T ss_pred CceeeHHHHhccccccccccCCccccCccchhhhccccccHHHHHH--hhhhhhhhHHHHhhhhhhcccccccchhhhhh
Confidence 44679999888766555 899999999975532 2222222211 11111 122222 22344668788877777
Q ss_pred HHHHHHHHHHHhcc
Q psy17995 99 LEEIEEIVFNLCNN 112 (120)
Q Consensus 99 le~~E~~i~~L~~~ 112 (120)
|+-+-.+=.+|-+.
T Consensus 79 lvyvvgl~~~~ade 92 (327)
T KOG2068|consen 79 LVYVVGLPLDLADE 92 (327)
T ss_pred hhhhhCCCccccch
Confidence 66654444444333
No 107
>PF12773 DZR: Double zinc ribbon
Probab=86.84 E-value=0.61 Score=26.55 Aligned_cols=29 Identities=17% Similarity=0.303 Sum_probs=20.2
Q ss_pred CCccchhHHHHHh--hcCCCCCCCCCccccC
Q psy17995 27 GHPLCEGCVDLLF--LKGTGNCYECNQPLRR 55 (120)
Q Consensus 27 GH~fC~~Ci~~~~--~~~~~~CP~C~~~~~~ 55 (120)
+-.||..|=..+. ......||.|++.+..
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGAENPP 41 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcCCCcC
Confidence 4678888876665 2334789999997643
No 108
>KOG0006|consensus
Probab=86.40 E-value=0.91 Score=36.62 Aligned_cols=37 Identities=24% Similarity=0.660 Sum_probs=27.3
Q ss_pred CCCccC--cccCCCcccCCCCcccc--cccCCccchhHHHH
Q psy17995 1 MDDQEC--PRCKTTKYRKPTLKLMV--NICGHPLCEGCVDL 37 (120)
Q Consensus 1 ~d~~~C--piC~~~~~~~p~~~~~~--~~CGH~fC~~Ci~~ 37 (120)
|+-..| |.|...++..|+.+-++ ..||-.||+.|...
T Consensus 313 ~gGVlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~C~e~ 353 (446)
T KOG0006|consen 313 MGGVLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCRECKEA 353 (446)
T ss_pred cCCEecCCCCCCcccccCCCCCcccCCCCchhHhHHHHHhh
Confidence 455667 46877788888765443 36999999999983
No 109
>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=86.34 E-value=0.58 Score=27.20 Aligned_cols=44 Identities=25% Similarity=0.483 Sum_probs=18.9
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhh----cCCCCCCCCCcc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFL----KGTGNCYECNQP 52 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~----~~~~~CP~C~~~ 52 (120)
+.||+... ....|. .-..|.|.-|-+= ..++. .+...||+|+++
T Consensus 3 L~CPls~~-~i~~P~---Rg~~C~H~~CFDl-~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQ-RIRIPV---RGKNCKHLQCFDL-ESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSS-B-SSEE---EETT--SS--EEH-HHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCC-EEEeCc---cCCcCcccceECH-HHHHHHhhccCCeECcCCcCc
Confidence 68999995 667771 1248999966332 22222 345789999864
No 110
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.61 E-value=0.64 Score=29.52 Aligned_cols=51 Identities=20% Similarity=0.402 Sum_probs=30.8
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCCCc
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNFR 59 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~ 59 (120)
.|--|-.++-.+..-.+ +-.=-|.||..|....+. ..||-|+..+.....+
T Consensus 7 nCECCDrDLpp~s~dA~-ICtfEcTFCadCae~~l~---g~CPnCGGelv~RP~R 57 (84)
T COG3813 7 NCECCDRDLPPDSTDAR-ICTFECTFCADCAENRLH---GLCPNCGGELVARPIR 57 (84)
T ss_pred CCcccCCCCCCCCCcee-EEEEeeehhHhHHHHhhc---CcCCCCCchhhcCcCC
Confidence 46666544322222221 212237899999987654 5899999988665444
No 111
>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=85.38 E-value=2.3 Score=30.83 Aligned_cols=15 Identities=13% Similarity=0.204 Sum_probs=12.0
Q ss_pred CCc-cCHHHHHHHHHH
Q psy17995 87 EDF-NSLAEYNDYLEE 101 (120)
Q Consensus 87 ~~~-~~l~~y~~yle~ 101 (120)
+.| |+-.++..|...
T Consensus 115 C~F~GtY~eLrKHar~ 130 (162)
T PF07800_consen 115 CSFSGTYSELRKHARS 130 (162)
T ss_pred cccccCHHHHHHHHHh
Confidence 678 888888888754
No 112
>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=85.09 E-value=1 Score=27.13 Aligned_cols=46 Identities=22% Similarity=0.612 Sum_probs=29.3
Q ss_pred cCcccCCCcccCCCCcccc-c-ccCCccchhHHHHHhhcCCCCCCCCCccccCC
Q psy17995 5 ECPRCKTTKYRKPTLKLMV-N-ICGHPLCEGCVDLLFLKGTGNCYECNQPLRRG 56 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~-~-~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~ 56 (120)
.|-.|..++-.+..-. ++ + .| .||..|....+. ..||-||..|.++
T Consensus 7 nCE~C~~dLp~~s~~A-~ICSfEC--TFC~~C~e~~l~---~~CPNCgGelv~R 54 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEA-YICSFEC--TFCADCAETMLN---GVCPNCGGELVRR 54 (57)
T ss_pred CccccCCCCCCCCCcc-eEEeEeC--cccHHHHHHHhc---CcCcCCCCccccC
Confidence 5777775543222111 22 2 33 699999998774 5799999887654
No 113
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=83.87 E-value=1.3 Score=35.88 Aligned_cols=25 Identities=24% Similarity=0.596 Sum_probs=20.0
Q ss_pred chhHHHHHhhc------------CCCCCCCCCccccC
Q psy17995 31 CEGCVDLLFLK------------GTGNCYECNQPLRR 55 (120)
Q Consensus 31 C~~Ci~~~~~~------------~~~~CP~C~~~~~~ 55 (120)
|-+|+.+.|.+ +..+||.||+.|.-
T Consensus 316 C~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi 352 (358)
T PF10272_consen 316 CLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI 352 (358)
T ss_pred HHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence 88999999873 23689999998863
No 114
>KOG3039|consensus
Probab=83.73 E-value=0.73 Score=35.83 Aligned_cols=31 Identities=16% Similarity=0.190 Sum_probs=26.0
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhh
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFL 40 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~ 40 (120)
-|+.|+ ..+.+| ++++=||.||+.||-..+-
T Consensus 45 cCsLtL-qPc~dP----vit~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 45 CCSLTL-QPCRDP----VITPDGYLFDREAILEYIL 75 (303)
T ss_pred eeeeec-ccccCC----ccCCCCeeeeHHHHHHHHH
Confidence 478888 488999 6899999999999987654
No 115
>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=83.41 E-value=1.1 Score=23.63 Aligned_cols=11 Identities=27% Similarity=0.612 Sum_probs=8.4
Q ss_pred CCCCCCCCCcc
Q psy17995 42 GTGNCYECNQP 52 (120)
Q Consensus 42 ~~~~CP~C~~~ 52 (120)
.+..||+|+.+
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 35789999873
No 116
>KOG2930|consensus
Probab=82.65 E-value=1.1 Score=30.38 Aligned_cols=28 Identities=18% Similarity=0.402 Sum_probs=23.9
Q ss_pred cccCCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 24 NICGHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 24 ~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
..|.|.|--.||.+.++.. ..||.|.+.
T Consensus 79 G~CNHaFH~hCisrWlktr-~vCPLdn~e 106 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTR-NVCPLDNKE 106 (114)
T ss_pred eecchHHHHHHHHHHHhhc-CcCCCcCcc
Confidence 3799999999999988864 689999764
No 117
>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=82.05 E-value=0.23 Score=27.78 Aligned_cols=28 Identities=25% Similarity=0.393 Sum_probs=16.1
Q ss_pred ccCCccchhHHHHHhhcCCCCCCCCCc-ccc
Q psy17995 25 ICGHPLCEGCVDLLFLKGTGNCYECNQ-PLR 54 (120)
Q Consensus 25 ~CGH~fC~~Ci~~~~~~~~~~CP~C~~-~~~ 54 (120)
.|||.|=..- .........||.|+. .++
T Consensus 10 ~Cg~~fe~~~--~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 10 ECGHEFEVLQ--SISEDDPVPCPECGSTEVR 38 (42)
T ss_pred CCCCEEEEEE--EcCCCCCCcCCCCCCCceE
Confidence 6888873221 111123478999998 443
No 118
>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=81.62 E-value=0.71 Score=26.94 Aligned_cols=40 Identities=25% Similarity=0.489 Sum_probs=24.7
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc-CCCCCCCCCccc
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK-GTGNCYECNQPL 53 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~-~~~~CP~C~~~~ 53 (120)
+.+.||.|.. -+. - ..+...|....... ....||+|...+
T Consensus 1 ~~f~CP~C~~-~~~-~----------~~L~~H~~~~H~~~~~~v~CPiC~~~~ 41 (54)
T PF05605_consen 1 DSFTCPYCGK-GFS-E----------SSLVEHCEDEHRSESKNVVCPICSSRV 41 (54)
T ss_pred CCcCCCCCCC-ccC-H----------HHHHHHHHhHCcCCCCCccCCCchhhh
Confidence 4689999996 322 1 24555555554443 346899998643
No 119
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=81.06 E-value=1.3 Score=35.62 Aligned_cols=48 Identities=21% Similarity=0.362 Sum_probs=33.5
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCC--CCCCCCCccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGT--GNCYECNQPL 53 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~--~~CP~C~~~~ 53 (120)
+.||+=++ ...+-+.+ +...|||++=..-++.+-+.|+ ..||-|-..-
T Consensus 337 FiCPVlKe-~~t~ENpP-~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~~ 386 (396)
T COG5109 337 FICPVLKE-LCTDENPP-VMLECGHVISKEALSVLSQNGVLSFKCPYCPEMS 386 (396)
T ss_pred eeccccHh-hhcccCCC-eeeeccceeeHHHHHHHhhcCcEEeeCCCCCcch
Confidence 57998775 33332323 2348999999999998877764 7899886543
No 120
>KOG1815|consensus
Probab=80.78 E-value=1 Score=37.18 Aligned_cols=49 Identities=27% Similarity=0.608 Sum_probs=32.1
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc----CC---CCCC--CCCccccC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK----GT---GNCY--ECNQPLRR 55 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~----~~---~~CP--~C~~~~~~ 55 (120)
...|.||.+ .+.. .+..-.|||.||..|+..++.. +. ..|| .|...+..
T Consensus 70 ~~~c~ic~~-~~~~---~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~ 127 (444)
T KOG1815|consen 70 DVQCGICVE-SYDG---EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGE 127 (444)
T ss_pred cccCCcccC-CCcc---hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCC
Confidence 368999996 3333 1223499999999999998764 22 2455 56665543
No 121
>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=80.42 E-value=1.4 Score=25.96 Aligned_cols=25 Identities=28% Similarity=0.794 Sum_probs=14.2
Q ss_pred ccCCccchhHHHHHhhcCCCCCCCCC
Q psy17995 25 ICGHPLCEGCVDLLFLKGTGNCYECN 50 (120)
Q Consensus 25 ~CGH~fC~~Ci~~~~~~~~~~CP~C~ 50 (120)
.|++.||-.| +.+....--.||.|.
T Consensus 26 ~C~~~FC~dC-D~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 26 KCKNHFCIDC-DVFIHETLHNCPGCE 50 (51)
T ss_dssp TTT--B-HHH-HHTTTTTS-SSSTT-
T ss_pred CCCCccccCc-ChhhhccccCCcCCC
Confidence 7999999999 333343446899985
No 122
>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=80.23 E-value=0.59 Score=25.32 Aligned_cols=13 Identities=38% Similarity=0.848 Sum_probs=9.7
Q ss_pred CCCCCCCCccccC
Q psy17995 43 TGNCYECNQPLRR 55 (120)
Q Consensus 43 ~~~CP~C~~~~~~ 55 (120)
...||.|+..+++
T Consensus 26 ~~~CP~Cg~~~~r 38 (41)
T smart00834 26 LATCPECGGDVRR 38 (41)
T ss_pred CCCCCCCCCccee
Confidence 4689999986543
No 123
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=79.66 E-value=0.42 Score=24.01 Aligned_cols=6 Identities=50% Similarity=1.436 Sum_probs=3.3
Q ss_pred cCcccC
Q psy17995 5 ECPRCK 10 (120)
Q Consensus 5 ~CpiC~ 10 (120)
.||.|.
T Consensus 4 ~Cp~Cg 9 (26)
T PF13248_consen 4 FCPNCG 9 (26)
T ss_pred CCcccC
Confidence 455555
No 124
>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=79.50 E-value=1.8 Score=25.04 Aligned_cols=36 Identities=17% Similarity=0.455 Sum_probs=22.3
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhh
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFL 40 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~ 40 (120)
..|++|.. .|.--..+..-..||+.||.+|......
T Consensus 3 ~~C~~C~~-~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGK-PFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCc-cccCCccccccCcCcCCcChHHcCCeee
Confidence 46899984 3322111111247999999999876543
No 125
>KOG2932|consensus
Probab=78.73 E-value=0.82 Score=36.67 Aligned_cols=27 Identities=22% Similarity=0.573 Sum_probs=20.2
Q ss_pred cccCCccchhHHHHHhhcCCCCCCCCCccc
Q psy17995 24 NICGHPLCEGCVDLLFLKGTGNCYECNQPL 53 (120)
Q Consensus 24 ~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~ 53 (120)
-+|.|+||-.|... .....||.|...+
T Consensus 107 IPCkHvFCl~CAr~---~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 107 IPCKHVFCLECARS---DSDKICPLCDDRV 133 (389)
T ss_pred cccchhhhhhhhhc---CccccCcCcccHH
Confidence 38999999999743 2236899997644
No 126
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=78.61 E-value=2.5 Score=25.60 Aligned_cols=30 Identities=23% Similarity=0.466 Sum_probs=20.9
Q ss_pred CCCCCCCccccCCCCccccccchhHHHHHHHHHH
Q psy17995 44 GNCYECNQPLRRGNFRVQLFDDSSVEKEVEIRKK 77 (120)
Q Consensus 44 ~~CP~C~~~~~~~~~~~~~f~d~~~~~e~~~rk~ 77 (120)
..||.||+++.. .+.|=+..++++...|++
T Consensus 4 kHC~~CG~~Ip~----~~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 4 KHCPVCGKPIPP----DESFCSPKCREEYRKRQK 33 (59)
T ss_pred CcCCcCCCcCCc----chhhhCHHHHHHHHHHHH
Confidence 569999998865 356777777766654444
No 127
>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 KOG2034|consensus
Probab=77.16 E-value=1.2 Score=40.02 Aligned_cols=35 Identities=29% Similarity=0.583 Sum_probs=26.9
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhh
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFL 40 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~ 40 (120)
...|.+|.-.++..| +++-+|||.|-.+|+.+...
T Consensus 817 ~d~C~~C~~~ll~~p---F~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 817 QDSCDHCGRPLLIKP---FYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred ccchHHhcchhhcCc---ceeeeccchHHHHHHHHHHH
Confidence 347999986555555 45679999999999988754
No 129
>KOG1952|consensus
Probab=77.15 E-value=1.6 Score=39.15 Aligned_cols=51 Identities=20% Similarity=0.347 Sum_probs=35.1
Q ss_pred CCccCcccCCCcccCCCCcccc-cccCCccchhHHHHHhhc------CCCCCCCCCcccc
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMV-NICGHPLCEGCVDLLFLK------GTGNCYECNQPLR 54 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~-~~CGH~fC~~Ci~~~~~~------~~~~CP~C~~~~~ 54 (120)
+.|.|.||.+.+-. ...+.. +.|.|+|--.||..+-++ ....||.|+....
T Consensus 190 ~~yeCmIC~e~I~~--t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 190 RKYECMICTERIKR--TAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred CceEEEEeeeeccc--cCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 46899999976532 222221 379999999999886543 2368999995443
No 130
>KOG2979|consensus
Probab=76.84 E-value=3.5 Score=32.05 Aligned_cols=45 Identities=18% Similarity=0.280 Sum_probs=33.6
Q ss_pred CccCcccCCCcccCCCCccccc-ccCCccchhHHHHHhhcC-CCCCCCCCcc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVN-ICGHPLCEGCVDLLFLKG-TGNCYECNQP 52 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~-~CGH~fC~~Ci~~~~~~~-~~~CP~C~~~ 52 (120)
+..||+-+. .+.|| +++ .|||+|=+.=|..++... ...||+=|..
T Consensus 176 s~rdPis~~-~I~nP----viSkkC~HvydrDsI~~~l~~~~~i~CPv~gC~ 222 (262)
T KOG2979|consen 176 SNRDPISKK-PIVNP----VISKKCGHVYDRDSIMQILCDEITIRCPVLGCE 222 (262)
T ss_pred cccCchhhh-hhhch----hhhcCcCcchhhhhHHHHhccCceeecccccCC
Confidence 357999884 77999 455 899999999888877652 4679975443
No 131
>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=76.38 E-value=1.9 Score=31.13 Aligned_cols=27 Identities=22% Similarity=0.632 Sum_probs=20.7
Q ss_pred CCccchhHHHHHhhcCCCCCCCCCccccCCC
Q psy17995 27 GHPLCEGCVDLLFLKGTGNCYECNQPLRRGN 57 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~ 57 (120)
-+.||..|=...+ ..||.|+.+++-..
T Consensus 27 ~~~fC~kCG~~tI----~~Cp~C~~~IrG~y 53 (158)
T PF10083_consen 27 REKFCSKCGAKTI----TSCPNCSTPIRGDY 53 (158)
T ss_pred HHHHHHHhhHHHH----HHCcCCCCCCCCce
Confidence 4789999976654 36999999997553
No 132
>KOG3842|consensus
Probab=75.73 E-value=2.7 Score=33.95 Aligned_cols=41 Identities=22% Similarity=0.442 Sum_probs=27.2
Q ss_pred cccCCccchhHHHHHhhcCC---------CCCCCCCcccc-CCCCccccccc
Q psy17995 24 NICGHPLCEGCVDLLFLKGT---------GNCYECNQPLR-RGNFRVQLFDD 65 (120)
Q Consensus 24 ~~CGH~fC~~Ci~~~~~~~~---------~~CP~C~~~~~-~~~~~~~~f~d 65 (120)
+||||. |..=--.+|++-+ ..||-|...+. ...+..-+|.+
T Consensus 376 ~PCGHv-~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge~~~ikliFq~ 426 (429)
T KOG3842|consen 376 NPCGHV-CSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGEQGYIKLIFQG 426 (429)
T ss_pred CCcccc-cchhhhhHhhcCcCCCccccccccCcchhhhhccCCceEEEEEec
Confidence 599996 6665666787521 46999998875 34454455554
No 133
>KOG2068|consensus
Probab=75.67 E-value=3.1 Score=33.37 Aligned_cols=51 Identities=25% Similarity=0.559 Sum_probs=34.0
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCC
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRG 56 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~ 56 (120)
-.||+|.+.... -...++--+|||..|-.|+...... ...||.|+++..+.
T Consensus 250 ~s~p~~~~~~~~-~d~~~lP~~~~~~~~l~~~~t~~~~-~~~~~~~rk~~~~~ 300 (327)
T KOG2068|consen 250 PSCPICYEDLDL-TDSNFLPCPCGFRLCLFCHKTISDG-DGRCPGCRKPYERN 300 (327)
T ss_pred CCCCCCCCcccc-cccccccccccccchhhhhhccccc-CCCCCccCCccccC
Confidence 369999864311 1111112489999999998876554 47999999876543
No 134
>PLN02248 cellulose synthase-like protein
Probab=75.50 E-value=2.2 Score=39.26 Aligned_cols=33 Identities=24% Similarity=0.654 Sum_probs=28.0
Q ss_pred ccCCccchhHHHHHhhcCCCCCCCCCccccCCCC
Q psy17995 25 ICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGNF 58 (120)
Q Consensus 25 ~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~ 58 (120)
+|++++|..|.-..... ...||.|+++.+..++
T Consensus 149 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 181 (1135)
T PLN02248 149 ECGFKICRDCYIDAVKS-GGICPGCKEPYKVTDL 181 (1135)
T ss_pred cccchhHHhHhhhhhhc-CCCCCCCccccccccc
Confidence 79999999998888776 4799999999976544
No 135
>KOG1100|consensus
Probab=75.25 E-value=1.5 Score=32.89 Aligned_cols=39 Identities=26% Similarity=0.658 Sum_probs=26.1
Q ss_pred CcccCCCcccCCCCcccccccCCc-cchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 6 CPRCKTTKYRKPTLKLMVNICGHP-LCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~~CGH~-fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
|-.|.+ ++ ..+++-||-|. +|..|-.. ...||+|+.+..
T Consensus 161 Cr~C~~----~~-~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGE----RE-ATVLLLPCRHLCLCGICDES-----LRICPICRSPKT 200 (207)
T ss_pred ceecCc----CC-ceEEeecccceEeccccccc-----CccCCCCcChhh
Confidence 777775 22 12234599997 89999542 357999998654
No 136
>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=74.52 E-value=2.6 Score=22.34 Aligned_cols=9 Identities=22% Similarity=0.623 Sum_probs=5.2
Q ss_pred ccCcccCCC
Q psy17995 4 QECPRCKTT 12 (120)
Q Consensus 4 ~~CpiC~~~ 12 (120)
|.|.-|...
T Consensus 1 Y~C~~Cg~~ 9 (32)
T PF03604_consen 1 YICGECGAE 9 (32)
T ss_dssp EBESSSSSS
T ss_pred CCCCcCCCe
Confidence 456666653
No 137
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=73.75 E-value=0.61 Score=22.88 Aligned_cols=7 Identities=29% Similarity=0.861 Sum_probs=3.1
Q ss_pred CCCCCCc
Q psy17995 45 NCYECNQ 51 (120)
Q Consensus 45 ~CP~C~~ 51 (120)
.||.||+
T Consensus 15 fC~~CG~ 21 (23)
T PF13240_consen 15 FCPNCGT 21 (23)
T ss_pred chhhhCC
Confidence 3444444
No 138
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=73.58 E-value=1.3 Score=29.88 Aligned_cols=10 Identities=30% Similarity=0.996 Sum_probs=4.8
Q ss_pred ccCCccchhH
Q psy17995 25 ICGHPLCEGC 34 (120)
Q Consensus 25 ~CGH~fC~~C 34 (120)
+|+|++|.+|
T Consensus 57 SCk~R~CP~C 66 (111)
T PF14319_consen 57 SCKNRHCPSC 66 (111)
T ss_pred cccCcCCCCC
Confidence 4555544444
No 139
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=73.43 E-value=0.92 Score=31.82 Aligned_cols=9 Identities=22% Similarity=0.379 Sum_probs=6.3
Q ss_pred CCCCCCCCc
Q psy17995 43 TGNCYECNQ 51 (120)
Q Consensus 43 ~~~CP~C~~ 51 (120)
.-.||+|+.
T Consensus 44 ~v~CPvC~~ 52 (131)
T COG1645 44 EVFCPVCGY 52 (131)
T ss_pred eEECCCCCc
Confidence 356888884
No 140
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=73.01 E-value=1.8 Score=25.31 Aligned_cols=33 Identities=21% Similarity=0.480 Sum_probs=20.6
Q ss_pred cCc--ccCCCcccC--CCCccccc-ccCCccchhHHHH
Q psy17995 5 ECP--RCKTTKYRK--PTLKLMVN-ICGHPLCEGCVDL 37 (120)
Q Consensus 5 ~Cp--iC~~~~~~~--p~~~~~~~-~CGH~fC~~Ci~~ 37 (120)
-|| -|...+... +....+.- .|||.||-.|...
T Consensus 20 ~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 20 WCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred CCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCc
Confidence 488 887544442 12333333 6999999999654
No 141
>PHA02862 5L protein; Provisional
Probab=72.31 E-value=4 Score=29.28 Aligned_cols=47 Identities=23% Similarity=0.484 Sum_probs=32.2
Q ss_pred CCCccCcccCCCcccCCCCcccccccCC-----ccchhHHHHHhhc-CCCCCCCCCcccc
Q psy17995 1 MDDQECPRCKTTKYRKPTLKLMVNICGH-----PLCEGCVDLLFLK-GTGNCYECNQPLR 54 (120)
Q Consensus 1 ~d~~~CpiC~~~~~~~p~~~~~~~~CGH-----~fC~~Ci~~~~~~-~~~~CP~C~~~~~ 54 (120)
|++ .|-||++. . ++. .+||+- ..-++|+.+.+.. +...||.|+.++.
T Consensus 1 ~~d-iCWIC~~~-~-~e~----~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 1 MSD-ICWICNDV-C-DER----NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CCC-EEEEecCc-C-CCC----cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 444 69999963 2 221 467653 3568999998875 4578999999774
No 142
>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=72.11 E-value=2 Score=29.15 Aligned_cols=48 Identities=19% Similarity=0.400 Sum_probs=25.9
Q ss_pred CCccCcccCCCc--ccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCc
Q psy17995 2 DDQECPRCKTTK--YRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQ 51 (120)
Q Consensus 2 d~~~CpiC~~~~--~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~ 51 (120)
++..|..|.... +.++. .+-..|+|++|..|-...-..+...|.+|.+
T Consensus 53 ~~~~C~~C~~~fg~l~~~~--~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG--RVCVDCKHRVCKKCGVYSKKEPIWLCKVCQK 102 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC--EEETTTTEEEETTSEEETSSSCCEEEHHHHH
T ss_pred CCcchhhhCCcccccCCCC--CcCCcCCccccCccCCcCCCCCCEEChhhHH
Confidence 356899998521 12221 1234799999999954311112345777754
No 143
>PRK11595 DNA utilization protein GntX; Provisional
Probab=71.65 E-value=3.7 Score=30.73 Aligned_cols=39 Identities=21% Similarity=0.417 Sum_probs=24.6
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
.|.+|...+ . + + ++.+|..|...+-.. ...||.|+.++.
T Consensus 7 ~C~~C~~~~-~-~------~--~~~lC~~C~~~l~~~-~~~C~~Cg~~~~ 45 (227)
T PRK11595 7 LCWLCRMPL-A-L------S--HWGICSVCSRALRTL-KTCCPQCGLPAT 45 (227)
T ss_pred cCccCCCcc-C-C------C--CCcccHHHHhhCCcc-cCcCccCCCcCC
Confidence 588998532 1 1 1 235899998765322 357999997653
No 144
>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=71.59 E-value=0.65 Score=24.32 Aligned_cols=24 Identities=21% Similarity=0.488 Sum_probs=10.6
Q ss_pred CccchhHHHHHhhcC---CCCCCCCCc
Q psy17995 28 HPLCEGCVDLLFLKG---TGNCYECNQ 51 (120)
Q Consensus 28 H~fC~~Ci~~~~~~~---~~~CP~C~~ 51 (120)
|+||..|=....... ...||.|+.
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 667776654433221 256777764
No 145
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=71.43 E-value=1.4 Score=25.31 Aligned_cols=9 Identities=33% Similarity=0.837 Sum_probs=7.4
Q ss_pred CCCCCCCCc
Q psy17995 43 TGNCYECNQ 51 (120)
Q Consensus 43 ~~~CP~C~~ 51 (120)
...||.|+.
T Consensus 26 ~~~CP~Cg~ 34 (52)
T TIGR02605 26 LATCPECGG 34 (52)
T ss_pred CCCCCCCCC
Confidence 357999997
No 146
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=70.86 E-value=1.6 Score=30.74 Aligned_cols=33 Identities=18% Similarity=0.342 Sum_probs=22.2
Q ss_pred ccCcccCCCcccCCCCcccccccC------CccchhHHHHH
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICG------HPLCEGCVDLL 38 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CG------H~fC~~Ci~~~ 38 (120)
..|.||.+.+ .+ +.-++.-+|| |.||.+|+.++
T Consensus 27 ~EC~IC~~~I-~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw 65 (134)
T PF05883_consen 27 VECQICFDRI-DN-NDGVVYVTDGGTLNLEKMFCADCDKRW 65 (134)
T ss_pred eeehhhhhhh-hc-CCCEEEEecCCeehHHHHHHHHHHHHH
Confidence 5799999755 33 2222222555 78999999986
No 147
>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=70.53 E-value=1.4 Score=26.66 Aligned_cols=35 Identities=20% Similarity=0.516 Sum_probs=15.9
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHh
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLF 39 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~ 39 (120)
-.|.+|.. .|.--..+..=..||+.||..|.....
T Consensus 10 ~~C~~C~~-~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 10 SNCMICGK-KFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp SB-TTT---B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CcCcCcCC-cCCCceeeEccCCCCCEECCchhCCEE
Confidence 47999995 452111111123799999999986543
No 148
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=69.61 E-value=5.7 Score=26.61 Aligned_cols=25 Identities=20% Similarity=0.562 Sum_probs=18.7
Q ss_pred CCccchhHHHHHhhc--------CCCCCCCCCc
Q psy17995 27 GHPLCEGCVDLLFLK--------GTGNCYECNQ 51 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~--------~~~~CP~C~~ 51 (120)
.=.||..||..-+.. +...||.|+.
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 778999998776542 3467999876
No 149
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=69.40 E-value=3.7 Score=31.33 Aligned_cols=28 Identities=21% Similarity=0.513 Sum_probs=21.5
Q ss_pred ccchhHHHHHhhcCCCCCCCCCccccCCC
Q psy17995 29 PLCEGCVDLLFLKGTGNCYECNQPLRRGN 57 (120)
Q Consensus 29 ~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~ 57 (120)
.-|.+|-..+ ..+.+.||.|+...+.++
T Consensus 195 K~C~sC~qqI-HRNAPiCPlCK~KsRSrn 222 (230)
T PF10146_consen 195 KTCQSCHQQI-HRNAPICPLCKAKSRSRN 222 (230)
T ss_pred chhHhHHHHH-hcCCCCCcccccccccCC
Confidence 4599997765 445689999999887655
No 150
>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=68.57 E-value=2 Score=24.13 Aligned_cols=11 Identities=55% Similarity=1.174 Sum_probs=7.1
Q ss_pred CCCccCcccCC
Q psy17995 1 MDDQECPRCKT 11 (120)
Q Consensus 1 ~d~~~CpiC~~ 11 (120)
|-...||.|..
T Consensus 15 ML~~~Cp~C~~ 25 (41)
T PF06677_consen 15 MLDEHCPDCGT 25 (41)
T ss_pred HhcCccCCCCC
Confidence 44557888864
No 151
>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=68.54 E-value=2.1 Score=28.93 Aligned_cols=27 Identities=19% Similarity=0.447 Sum_probs=17.4
Q ss_pred cchhHHHHHhh--cCCCCCCCCCccccCC
Q psy17995 30 LCEGCVDLLFL--KGTGNCYECNQPLRRG 56 (120)
Q Consensus 30 fC~~Ci~~~~~--~~~~~CP~C~~~~~~~ 56 (120)
.|.+|-.+++- +.+..||.||+.+...
T Consensus 11 ~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 45555555544 3457799999977543
No 152
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=68.21 E-value=2.1 Score=23.22 Aligned_cols=13 Identities=46% Similarity=1.313 Sum_probs=9.0
Q ss_pred ccCcccCCCcccCC
Q psy17995 4 QECPRCKTTKYRKP 17 (120)
Q Consensus 4 ~~CpiC~~~~~~~p 17 (120)
..||.|.. .|.-|
T Consensus 3 i~CP~C~~-~f~v~ 15 (37)
T PF13719_consen 3 ITCPNCQT-RFRVP 15 (37)
T ss_pred EECCCCCc-eEEcC
Confidence 47999995 66544
No 153
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=67.25 E-value=7.8 Score=28.11 Aligned_cols=46 Identities=24% Similarity=0.516 Sum_probs=31.8
Q ss_pred CccCcccCCCcccCCCCcccccccCC-----ccchhHHHHHhhc-CCCCCCCCCcccc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGH-----PLCEGCVDLLFLK-GTGNCYECNQPLR 54 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH-----~fC~~Ci~~~~~~-~~~~CP~C~~~~~ 54 (120)
+..|-||++. .++ ..+||.- ..-++|+.+.+.. +...|+.|+.++.
T Consensus 8 ~~~CRIC~~~--~~~----~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 8 DKCCWICKDE--YDV----VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCeeEecCCC--CCC----ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 3479999964 222 2356543 2378999998775 4578999999773
No 154
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=67.05 E-value=11 Score=22.59 Aligned_cols=31 Identities=10% Similarity=0.023 Sum_probs=17.5
Q ss_pred CCCCCCCccccCCCCccccccchhHHHHHHH
Q psy17995 44 GNCYECNQPLRRGNFRVQLFDDSSVEKEVEI 74 (120)
Q Consensus 44 ~~CP~C~~~~~~~~~~~~~f~d~~~~~e~~~ 74 (120)
..||.||.+........-.-+|...+--+.+
T Consensus 18 ~~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~ 48 (56)
T PRK13130 18 EICPVCGGKTKNPHPPRFSPEDKYGKYRRAL 48 (56)
T ss_pred ccCcCCCCCCCCCCCCCCCCCCccHHHHHHH
Confidence 5799999987655433323355444333333
No 155
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=66.55 E-value=3.5 Score=24.46 Aligned_cols=13 Identities=23% Similarity=0.659 Sum_probs=7.2
Q ss_pred CCCCCCCCccccC
Q psy17995 43 TGNCYECNQPLRR 55 (120)
Q Consensus 43 ~~~CP~C~~~~~~ 55 (120)
+..||+|+..++.
T Consensus 24 PatCP~C~a~~~~ 36 (54)
T PF09237_consen 24 PATCPICGAVIRQ 36 (54)
T ss_dssp -EE-TTT--EESS
T ss_pred CCCCCcchhhccc
Confidence 5789999998763
No 156
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=66.41 E-value=2 Score=25.03 Aligned_cols=11 Identities=45% Similarity=1.062 Sum_probs=6.0
Q ss_pred CCCCCCCcccc
Q psy17995 44 GNCYECNQPLR 54 (120)
Q Consensus 44 ~~CP~C~~~~~ 54 (120)
..||+|+.+|.
T Consensus 21 ~~CPlC~r~l~ 31 (54)
T PF04423_consen 21 GCCPLCGRPLD 31 (54)
T ss_dssp EE-TTT--EE-
T ss_pred CcCCCCCCCCC
Confidence 48999999885
No 157
>KOG1812|consensus
Probab=66.22 E-value=3.1 Score=33.96 Aligned_cols=42 Identities=31% Similarity=0.644 Sum_probs=24.0
Q ss_pred cCcccCCCcccCCCCccccc-ccCCccchhHHHHHhhcCCCCCCC
Q psy17995 5 ECPRCKTTKYRKPTLKLMVN-ICGHPLCEGCVDLLFLKGTGNCYE 48 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~-~CGH~fC~~Ci~~~~~~~~~~CP~ 48 (120)
.||.|+..+-+.-. =+.++ .|||-||-.|...+...+ ..|..
T Consensus 308 ~CpkC~~~ie~~~G-Cnhm~CrC~~~fcy~C~~~~~~~~-~~~~~ 350 (384)
T KOG1812|consen 308 QCPKCKFMIELSEG-CNHMTCRCGHQFCYMCGGDWKTHN-GECYE 350 (384)
T ss_pred cCcccceeeeecCC-cceEEeeccccchhhcCcchhhCC-ccccC
Confidence 69999954322221 11233 599999999986644332 33443
No 158
>KOG4185|consensus
Probab=66.11 E-value=1.8 Score=33.37 Aligned_cols=27 Identities=33% Similarity=0.787 Sum_probs=23.5
Q ss_pred cCCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 26 CGHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 26 CGH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
|||..|..|+..........||-|+..
T Consensus 239 c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 239 EGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHhcchHHHHHHhhhcCCcccce
Confidence 999999999999877654889999874
No 159
>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=64.82 E-value=3 Score=24.26 Aligned_cols=32 Identities=25% Similarity=0.630 Sum_probs=13.7
Q ss_pred cCcc--cCCCcccCCCCcc-ccc--ccCCccchhHHH
Q psy17995 5 ECPR--CKTTKYRKPTLKL-MVN--ICGHPLCEGCVD 36 (120)
Q Consensus 5 ~Cpi--C~~~~~~~p~~~~-~~~--~CGH~fC~~Ci~ 36 (120)
.||- |...+..+..... .++ .||+.||-.|-.
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~ 56 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGE 56 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEECSSSTS
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCc
Confidence 5766 8753323222221 133 388888888753
No 160
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=64.78 E-value=8.1 Score=26.38 Aligned_cols=25 Identities=24% Similarity=0.749 Sum_probs=16.3
Q ss_pred ccCCccchhHHHHHhhcCCCCCCCCC
Q psy17995 25 ICGHPLCEGCVDLLFLKGTGNCYECN 50 (120)
Q Consensus 25 ~CGH~fC~~Ci~~~~~~~~~~CP~C~ 50 (120)
.|++.||.+| +.++...-..||.|.
T Consensus 86 ~C~~~FC~dC-D~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 86 VCKNVFCVDC-DVFVHESLHCCPGCI 110 (112)
T ss_pred CCCCcccccc-chhhhhhccCCcCCC
Confidence 6888888888 333333335688886
No 161
>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=64.13 E-value=4.2 Score=22.03 Aligned_cols=8 Identities=38% Similarity=1.178 Sum_probs=6.2
Q ss_pred cCcccCCC
Q psy17995 5 ECPRCKTT 12 (120)
Q Consensus 5 ~CpiC~~~ 12 (120)
.|++|.+.
T Consensus 10 ~C~~C~~~ 17 (36)
T PF11781_consen 10 PCPVCGSR 17 (36)
T ss_pred cCCCCCCe
Confidence 39999964
No 162
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=63.68 E-value=8.7 Score=27.45 Aligned_cols=24 Identities=25% Similarity=0.466 Sum_probs=16.6
Q ss_pred ccCCccchhHHHHHhh----------cCCCCCCCCCccc
Q psy17995 25 ICGHPLCEGCVDLLFL----------KGTGNCYECNQPL 53 (120)
Q Consensus 25 ~CGH~fC~~Ci~~~~~----------~~~~~CP~C~~~~ 53 (120)
.+||.| +.+|. .+-..||+|+..-
T Consensus 9 ~~gH~F-----EgWF~ss~~fd~Q~~~glv~CP~Cgs~~ 42 (148)
T PF06676_consen 9 ENGHEF-----EGWFRSSAAFDRQQARGLVSCPVCGSTE 42 (148)
T ss_pred CCCCcc-----ceecCCHHHHHHHHHcCCccCCCCCCCe
Confidence 689999 34443 3446899999843
No 163
>KOG2169|consensus
Probab=63.42 E-value=3.5 Score=35.78 Aligned_cols=43 Identities=26% Similarity=0.430 Sum_probs=26.7
Q ss_pred CccCcccCCCcccCCCCcccccccCCccch--hHHHHHhh------cCCCCCCCCCcccc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCE--GCVDLLFL------KGTGNCYECNQPLR 54 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~--~Ci~~~~~------~~~~~CP~C~~~~~ 54 (120)
.+.||+++..+ .- +|-+..|+ .|.+..|- .++..||+|.+...
T Consensus 306 SL~CPl~~~Rm-~~--------P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC~~~~~ 356 (636)
T KOG2169|consen 306 SLNCPLSKMRM-SL--------PARGHTCKHLQCFDALSYLQMNEQKPTWRCPVCQKAAP 356 (636)
T ss_pred EecCCccccee-ec--------CCcccccccceecchhhhHHhccCCCeeeCccCCcccc
Confidence 46899998532 32 44444444 66666543 24578999998764
No 164
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=61.39 E-value=5.6 Score=21.84 Aligned_cols=24 Identities=21% Similarity=0.564 Sum_probs=12.7
Q ss_pred CcccCCCcccCCCCcccccccCCccch
Q psy17995 6 CPRCKTTKYRKPTLKLMVNICGHPLCE 32 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~~CGH~fC~ 32 (120)
|.+|....+..| +.-.-||..||.
T Consensus 1 C~~C~~~~~l~~---f~C~~C~~~FC~ 24 (39)
T smart00154 1 CHFCRKKVGLTG---FKCRHCGNLFCG 24 (39)
T ss_pred CcccCCcccccC---eECCccCCcccc
Confidence 566775333334 111248888875
No 165
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=60.83 E-value=5.4 Score=26.97 Aligned_cols=25 Identities=24% Similarity=0.554 Sum_probs=16.2
Q ss_pred ccccCCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 23 VNICGHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 23 ~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
-+.|||+|=.. +..+.+ -||.||..
T Consensus 5 CtrCG~vf~~g--~~~il~---GCp~CG~n 29 (112)
T COG3364 5 CTRCGEVFDDG--SEEILS---GCPKCGCN 29 (112)
T ss_pred ecccccccccc--cHHHHc---cCccccch
Confidence 46899998554 333333 39999864
No 166
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=60.62 E-value=3 Score=21.35 Aligned_cols=11 Identities=36% Similarity=0.763 Sum_probs=5.9
Q ss_pred CCCCCCccccC
Q psy17995 45 NCYECNQPLRR 55 (120)
Q Consensus 45 ~CP~C~~~~~~ 55 (120)
.||+|++.+.+
T Consensus 1 ~CP~C~s~l~~ 11 (28)
T PF03119_consen 1 TCPVCGSKLVR 11 (28)
T ss_dssp B-TTT--BEEE
T ss_pred CcCCCCCEeEc
Confidence 48999988764
No 167
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=60.42 E-value=2.1 Score=21.36 Aligned_cols=9 Identities=22% Similarity=0.467 Sum_probs=6.6
Q ss_pred CCCCCCCCc
Q psy17995 43 TGNCYECNQ 51 (120)
Q Consensus 43 ~~~CP~C~~ 51 (120)
...||.||.
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 367998874
No 168
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=58.98 E-value=3.7 Score=25.23 Aligned_cols=21 Identities=29% Similarity=0.621 Sum_probs=12.8
Q ss_pred chhHHHHHhhcCCCCCCCCCcc
Q psy17995 31 CEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 31 C~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
|..|. ++.......||+|+..
T Consensus 7 C~~Ck-~l~~~d~e~CP~Cgs~ 27 (64)
T COG2093 7 CKNCK-RLTPEDTEICPVCGST 27 (64)
T ss_pred Hhhcc-ccCCCCCccCCCCCCc
Confidence 55563 2233344679999986
No 169
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=58.89 E-value=8.9 Score=20.69 Aligned_cols=24 Identities=25% Similarity=0.642 Sum_probs=12.5
Q ss_pred cchhHHHHHhhc-------CCCCCCCCCccc
Q psy17995 30 LCEGCVDLLFLK-------GTGNCYECNQPL 53 (120)
Q Consensus 30 fC~~Ci~~~~~~-------~~~~CP~C~~~~ 53 (120)
+|..|+..+... ....|+.||-.+
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTNCGPRY 31 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTTCC-SC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCCCCCCE
Confidence 477777776542 235799998654
No 170
>PF13945 NST1: Salt tolerance down-regulator
Probab=58.87 E-value=12 Score=27.80 Aligned_cols=16 Identities=31% Similarity=0.561 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHHH
Q psy17995 93 AEYNDYLEEIEEIVFN 108 (120)
Q Consensus 93 ~~y~~yle~~E~~i~~ 108 (120)
..|+.|.+++|+.+..
T Consensus 160 ~ly~~~y~~l~~~~~~ 175 (190)
T PF13945_consen 160 RLYDAYYEELEQYANH 175 (190)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 4688888888876654
No 171
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=58.32 E-value=13 Score=28.01 Aligned_cols=43 Identities=28% Similarity=0.555 Sum_probs=27.7
Q ss_pred CcccCCCcccCCCCcccccccCCccchhHHHHHhhc-------CCCCCCCCCccccCCCC
Q psy17995 6 CPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK-------GTGNCYECNQPLRRGNF 58 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~-------~~~~CP~C~~~~~~~~~ 58 (120)
||.|... ..|. -..+|..|+-.-..- ....||.|++-+.+..|
T Consensus 1 C~~CG~~--~~~~--------~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~W 50 (236)
T PF04981_consen 1 CPRCGRE--IEPL--------IDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGGRW 50 (236)
T ss_pred CCCCCCC--CCCc--------ccccChHHhcccCCeeecCCccCceECCCCCCEECCCEe
Confidence 8999842 3341 136999998765431 12469999998776444
No 172
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=57.07 E-value=3.5 Score=33.97 Aligned_cols=42 Identities=29% Similarity=0.561 Sum_probs=0.0
Q ss_pred cccCCccchhHHHHHhhc-----CC----CCCCCCCcccc-CCCCccccccch
Q psy17995 24 NICGHPLCEGCVDLLFLK-----GT----GNCYECNQPLR-RGNFRVQLFDDS 66 (120)
Q Consensus 24 ~~CGH~fC~~Ci~~~~~~-----~~----~~CP~C~~~~~-~~~~~~~~f~d~ 66 (120)
+||||.- ..=.-++|++ +. ..||-|..+|. ...|..-+|.|.
T Consensus 363 ~PCGHv~-SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g~~g~vrLiFQ~~ 414 (416)
T PF04710_consen 363 NPCGHVC-SEKTAKYWSQIPLPHGTHAFHAACPFCATPLDGEQGYVRLIFQDP 414 (416)
T ss_dssp -----------------------------------------------------
T ss_pred ccccccc-chhhhhhhhcCCCCCCcccccccCCcccCcccCCCCceEEEEeCC
Confidence 5899974 3334466764 22 57999999996 456666667663
No 173
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.98 E-value=3.6 Score=26.34 Aligned_cols=30 Identities=23% Similarity=0.530 Sum_probs=18.3
Q ss_pred cccCCccchhHHHHHhhcCCCCCCCCCccccC
Q psy17995 24 NICGHPLCEGCVDLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 24 ~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~ 55 (120)
+.|||.| .=++..-..+-..||.|+..+++
T Consensus 16 ~~cg~~~--dvvq~~~ddplt~ce~c~a~~kk 45 (82)
T COG2331 16 TECGNRF--DVVQAMTDDPLTTCEECGARLKK 45 (82)
T ss_pred cccchHH--HHHHhcccCccccChhhChHHHH
Confidence 4799987 22222222233679999997764
No 174
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=56.92 E-value=7.4 Score=21.79 Aligned_cols=12 Identities=33% Similarity=0.911 Sum_probs=9.1
Q ss_pred CCCccCcccCCC
Q psy17995 1 MDDQECPRCKTT 12 (120)
Q Consensus 1 ~d~~~CpiC~~~ 12 (120)
|..|.|+.|...
T Consensus 1 ~~~y~C~~CG~~ 12 (46)
T PRK00398 1 MAEYKCARCGRE 12 (46)
T ss_pred CCEEECCCCCCE
Confidence 667888888853
No 175
>KOG4445|consensus
Probab=56.61 E-value=4 Score=32.70 Aligned_cols=49 Identities=18% Similarity=0.458 Sum_probs=34.0
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc-----------------C-----CCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK-----------------G-----TGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~-----------------~-----~~~CP~C~~~~~ 54 (120)
-.|.||+-.+-..| .+.+|+|.|-|-..|+.+++.. . ...||+|+..++
T Consensus 116 gqCvICLygfa~~~--~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~ 186 (368)
T KOG4445|consen 116 GQCVICLYGFASSP--AFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIK 186 (368)
T ss_pred CceEEEEEeecCCC--ceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcc
Confidence 36899984222333 2446899999999999988531 0 146999998775
No 176
>KOG2462|consensus
Probab=56.57 E-value=6.6 Score=30.85 Aligned_cols=51 Identities=20% Similarity=0.466 Sum_probs=31.4
Q ss_pred ccCcccCCCcccCCCCcccc---c-ccCCccchhHHHHHhhc----------CCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMV---N-ICGHPLCEGCVDLLFLK----------GTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~---~-~CGH~fC~~Ci~~~~~~----------~~~~CP~C~~~~~ 54 (120)
..|+.|......=|-++|.+ + +|--.||..=+.+.|-- .++.||.|++.|-
T Consensus 162 ~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFA 226 (279)
T KOG2462|consen 162 FSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFA 226 (279)
T ss_pred ccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhc
Confidence 46788875222445455543 2 56666777777776641 2478999998774
No 177
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=56.04 E-value=10 Score=25.39 Aligned_cols=34 Identities=15% Similarity=0.202 Sum_probs=16.5
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHh
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLF 39 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~ 39 (120)
++.|.+|...++...- ++-.=+-..--.|+..-.
T Consensus 2 kWkC~iCg~~I~~gql---FTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQL---FTFTKKGPVHYECFREKA 35 (101)
T ss_pred ceEEEecCCeeeecce---EEEecCCcEeHHHHHHHH
Confidence 3567777766655441 111112344556655433
No 178
>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=55.90 E-value=2 Score=33.44 Aligned_cols=44 Identities=23% Similarity=0.443 Sum_probs=18.4
Q ss_pred ccCcccCCCcccCCCCccccccc--CCc--cchhHHHHHhhcCCCCCCCCCcc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNIC--GHP--LCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~C--GH~--fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
-.||||.+ .|.+.++...= |++ +|.-|-.. |.-.-..||.|+..
T Consensus 173 g~CPvCGs----~P~~s~l~~~~~~G~R~L~Cs~C~t~-W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 173 GYCPVCGS----PPVLSVLRGGEREGKRYLHCSLCGTE-WRFVRIKCPYCGNT 220 (290)
T ss_dssp SS-TTT-------EEEEEEE------EEEEEETTT--E-EE--TTS-TTT---
T ss_pred CcCCCCCC----cCceEEEecCCCCccEEEEcCCCCCe-eeecCCCCcCCCCC
Confidence 47999995 44443333322 544 68888654 44434689999874
No 179
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=55.83 E-value=3.2 Score=30.19 Aligned_cols=20 Identities=25% Similarity=0.546 Sum_probs=14.0
Q ss_pred ccCCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 25 ICGHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 25 ~CGH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
.|||.+ ...+|.+||+|+.+
T Consensus 139 vCGy~~--------~ge~P~~CPiCga~ 158 (166)
T COG1592 139 VCGYTH--------EGEAPEVCPICGAP 158 (166)
T ss_pred CCCCcc--------cCCCCCcCCCCCCh
Confidence 688864 12346789999975
No 180
>PRK04023 DNA polymerase II large subunit; Validated
Probab=55.32 E-value=10 Score=34.93 Aligned_cols=45 Identities=20% Similarity=0.509 Sum_probs=28.4
Q ss_pred CccCcccCCCcccCCCCccccc-ccCC-----ccchhHHHHHhhcCCCCCCCCCccccCC
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVN-ICGH-----PLCEGCVDLLFLKGTGNCYECNQPLRRG 56 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~-~CGH-----~fC~~Ci~~~~~~~~~~CP~C~~~~~~~ 56 (120)
...||.|....+. ..- .||. .||..|-.. .++..||.|+......
T Consensus 626 ~RfCpsCG~~t~~------frCP~CG~~Te~i~fCP~CG~~---~~~y~CPKCG~El~~~ 676 (1121)
T PRK04023 626 RRKCPSCGKETFY------RRCPFCGTHTEPVYRCPRCGIE---VEEDECEKCGREPTPY 676 (1121)
T ss_pred CccCCCCCCcCCc------ccCCCCCCCCCcceeCccccCc---CCCCcCCCCCCCCCcc
Confidence 3479999853211 122 5884 599999322 2346799999877543
No 181
>PRK12495 hypothetical protein; Provisional
Probab=55.17 E-value=5.3 Score=30.44 Aligned_cols=11 Identities=36% Similarity=0.863 Sum_probs=6.2
Q ss_pred CCCCCCCcccc
Q psy17995 44 GNCYECNQPLR 54 (120)
Q Consensus 44 ~~CP~C~~~~~ 54 (120)
..||.|+..+.
T Consensus 59 ~~Cp~CQ~~~~ 69 (226)
T PRK12495 59 EFCPTCQQPVT 69 (226)
T ss_pred eECCCCCCccc
Confidence 45666665543
No 182
>PHA00626 hypothetical protein
Probab=55.10 E-value=9 Score=23.10 Aligned_cols=14 Identities=14% Similarity=0.368 Sum_probs=8.8
Q ss_pred CCCCCCCCccccCC
Q psy17995 43 TGNCYECNQPLRRG 56 (120)
Q Consensus 43 ~~~CP~C~~~~~~~ 56 (120)
...||.|+-.+.+.
T Consensus 23 rYkCkdCGY~ft~~ 36 (59)
T PHA00626 23 DYVCCDCGYNDSKD 36 (59)
T ss_pred ceEcCCCCCeechh
Confidence 35677777666543
No 183
>KOG3268|consensus
Probab=55.06 E-value=14 Score=27.60 Aligned_cols=49 Identities=22% Similarity=0.502 Sum_probs=33.5
Q ss_pred cCcccCCCcccCCCCcccc---cccCCccchhHHHHHhhc-----CC-----CCCCCCCcccc
Q psy17995 5 ECPRCKTTKYRKPTLKLMV---NICGHPLCEGCVDLLFLK-----GT-----GNCYECNQPLR 54 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~---~~CGH~fC~~Ci~~~~~~-----~~-----~~CP~C~~~~~ 54 (120)
-|.||.. ..++...+-++ ..||..|-+-|+..+++. .+ ..||-|..++.
T Consensus 167 ~cgicya-yqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 167 ACGICYA-YQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred cccceee-eecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 4788874 44444333333 379999999999988763 11 47999998774
No 184
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=54.96 E-value=7.4 Score=22.01 Aligned_cols=12 Identities=25% Similarity=0.747 Sum_probs=10.2
Q ss_pred CCCCCCCCcccc
Q psy17995 43 TGNCYECNQPLR 54 (120)
Q Consensus 43 ~~~CP~C~~~~~ 54 (120)
+..||+|+.+|.
T Consensus 8 ~K~C~~C~rpf~ 19 (42)
T PF10013_consen 8 SKICPVCGRPFT 19 (42)
T ss_pred CCcCcccCCcch
Confidence 478999999985
No 185
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=54.56 E-value=7.6 Score=29.54 Aligned_cols=26 Identities=15% Similarity=0.335 Sum_probs=15.6
Q ss_pred CccCcccCCCcccCCCCcccccccCCcc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPL 30 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~f 30 (120)
.+.||+|...+...+. -+.-+.||+|
T Consensus 2 ~~~CP~C~~~l~~~~~--~~~C~~~h~f 27 (272)
T PRK11088 2 SYQCPLCHQPLTLEEN--SWICPQNHQF 27 (272)
T ss_pred cccCCCCCcchhcCCC--EEEcCCCCCC
Confidence 3789999964432221 1233668887
No 186
>KOG4451|consensus
Probab=54.29 E-value=8.8 Score=29.64 Aligned_cols=28 Identities=21% Similarity=0.459 Sum_probs=20.9
Q ss_pred ccchhHHHHHhhcCCCCCCCCCccccCCC
Q psy17995 29 PLCEGCVDLLFLKGTGNCYECNQPLRRGN 57 (120)
Q Consensus 29 ~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~ 57 (120)
..|.+|-..+-+ +.+.||+|+...+.++
T Consensus 250 K~ClsChqqIHR-NAPiCPlCKaKsRSrN 277 (286)
T KOG4451|consen 250 KVCLSCHQQIHR-NAPICPLCKAKSRSRN 277 (286)
T ss_pred hHHHHHHHHHhc-CCCCCcchhhccccCC
Confidence 458899777554 4589999998877554
No 187
>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=54.01 E-value=3 Score=26.86 Aligned_cols=17 Identities=29% Similarity=0.681 Sum_probs=13.2
Q ss_pred ccccccCCccchhHHHH
Q psy17995 21 LMVNICGHPLCEGCVDL 37 (120)
Q Consensus 21 ~~~~~CGH~fC~~Ci~~ 37 (120)
+++.||||.|..+|+.+
T Consensus 93 f~~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 93 FVVFPCGHVVHYSCIKR 109 (109)
T ss_pred EEEeCCCeEEecccccC
Confidence 34569999999999753
No 188
>KOG3899|consensus
Probab=53.77 E-value=7.9 Score=30.97 Aligned_cols=30 Identities=20% Similarity=0.670 Sum_probs=22.0
Q ss_pred CCccchhHHHHHhh------------cCCCCCCCCCccccCC
Q psy17995 27 GHPLCEGCVDLLFL------------KGTGNCYECNQPLRRG 56 (120)
Q Consensus 27 GH~fC~~Ci~~~~~------------~~~~~CP~C~~~~~~~ 56 (120)
.---|.+|+.++|. .++.+||.|++.+.-.
T Consensus 326 rp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~ 367 (381)
T KOG3899|consen 326 RPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIR 367 (381)
T ss_pred ccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEe
Confidence 33457899988764 3567999999988643
No 189
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=53.62 E-value=6.2 Score=19.47 Aligned_cols=12 Identities=17% Similarity=0.437 Sum_probs=9.3
Q ss_pred CCCCCCCccccC
Q psy17995 44 GNCYECNQPLRR 55 (120)
Q Consensus 44 ~~CP~C~~~~~~ 55 (120)
.+||.|+..|..
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 479999987753
No 190
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=53.54 E-value=8.3 Score=21.79 Aligned_cols=12 Identities=25% Similarity=0.625 Sum_probs=7.6
Q ss_pred CCCCCCCCCccc
Q psy17995 42 GTGNCYECNQPL 53 (120)
Q Consensus 42 ~~~~CP~C~~~~ 53 (120)
++..||.||..+
T Consensus 18 ~~irC~~CG~rI 29 (44)
T smart00659 18 DVVRCRECGYRI 29 (44)
T ss_pred CceECCCCCceE
Confidence 346677777644
No 191
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=53.00 E-value=20 Score=27.81 Aligned_cols=47 Identities=19% Similarity=0.296 Sum_probs=32.3
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc-CCCCCC--CCCccc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK-GTGNCY--ECNQPL 53 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~-~~~~CP--~C~~~~ 53 (120)
+..|||-.. .+..| ++.+.|.|.|=..=|...+.. .+..|| .|...+
T Consensus 189 ~nrCpitl~-p~~~p---ils~kcnh~~e~D~I~~~lq~~~trvcp~~~Csq~~ 238 (275)
T COG5627 189 SNRCPITLN-PDFYP---ILSSKCNHKPEMDLINKKLQVECTRVCPRLICSQKE 238 (275)
T ss_pred cccCCcccC-cchhH---HHHhhhcccccHHHHHHHhcCCceeecchhhcchhe
Confidence 357999884 66666 223599999999888877663 246788 475444
No 192
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=52.71 E-value=11 Score=21.44 Aligned_cols=41 Identities=17% Similarity=0.506 Sum_probs=22.4
Q ss_pred CcccCCCcccCCCCcccccccCC-----ccchhHHHHHhhc-CCCCCCCC
Q psy17995 6 CPRCKTTKYRKPTLKLMVNICGH-----PLCEGCVDLLFLK-GTGNCYEC 49 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~~CGH-----~fC~~Ci~~~~~~-~~~~CP~C 49 (120)
|-||++....++ .+++||+= ..-.+|+.+.+.. +...|++|
T Consensus 1 CrIC~~~~~~~~---~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDE---PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS----EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCC---ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 568886432222 24567652 3466899998774 55778887
No 193
>KOG0309|consensus
Probab=52.38 E-value=10 Score=34.15 Aligned_cols=43 Identities=23% Similarity=0.518 Sum_probs=29.4
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCC-CCC
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCY-ECN 50 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP-~C~ 50 (120)
+.|.+|.-.+-... .+-..|||+.-.+|....|+.+ -.|| .||
T Consensus 1029 ~~C~~C~l~V~gss---~~Cg~C~Hv~H~sc~~eWf~~g-d~CpsGCG 1072 (1081)
T KOG0309|consen 1029 FQCAICHLAVRGSS---NFCGTCGHVGHTSCMMEWFRTG-DVCPSGCG 1072 (1081)
T ss_pred eeeeeEeeEeeccc---hhhccccccccHHHHHHHHhcC-CcCCCCCC
Confidence 46888874432222 1234799999999999999986 4788 344
No 194
>PRK12496 hypothetical protein; Provisional
Probab=52.21 E-value=4.1 Score=29.33 Aligned_cols=27 Identities=26% Similarity=0.610 Sum_probs=16.5
Q ss_pred chhHHHHHhhc-CCCCCCCCCccccCCC
Q psy17995 31 CEGCVDLLFLK-GTGNCYECNQPLRRGN 57 (120)
Q Consensus 31 C~~Ci~~~~~~-~~~~CP~C~~~~~~~~ 57 (120)
|..|-..+-.. ....||+||.+++++.
T Consensus 130 C~gC~~~~~~~~~~~~C~~CG~~~~r~~ 157 (164)
T PRK12496 130 CKGCKKKYPEDYPDDVCEICGSPVKRKM 157 (164)
T ss_pred CCCCCccccCCCCCCcCCCCCChhhhcc
Confidence 66675332121 1246999999987653
No 195
>PRK11032 hypothetical protein; Provisional
Probab=51.73 E-value=7.7 Score=28.05 Aligned_cols=23 Identities=22% Similarity=0.527 Sum_probs=14.0
Q ss_pred cccCCccchhHHHHHhhc-CCCCCCCCCcc
Q psy17995 24 NICGHPLCEGCVDLLFLK-GTGNCYECNQP 52 (120)
Q Consensus 24 ~~CGH~fC~~Ci~~~~~~-~~~~CP~C~~~ 52 (120)
..|||..+ +... ..++||.|+..
T Consensus 128 ~~Cg~~~~------~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 128 EKCHHHLA------FYTPEVLPLCPKCGHD 151 (160)
T ss_pred cCCCCEEE------ecCCCcCCCCCCCCCC
Confidence 46888751 1122 23799999863
No 196
>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=51.19 E-value=7.7 Score=19.39 Aligned_cols=9 Identities=22% Similarity=0.682 Sum_probs=7.5
Q ss_pred CCCCCCccc
Q psy17995 45 NCYECNQPL 53 (120)
Q Consensus 45 ~CP~C~~~~ 53 (120)
.||+|++.+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 699998876
No 197
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=50.48 E-value=11 Score=26.60 Aligned_cols=27 Identities=30% Similarity=0.855 Sum_probs=20.4
Q ss_pred CCCccCcccCCCcccCCCCcccccccCCccchhHHHH
Q psy17995 1 MDDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDL 37 (120)
Q Consensus 1 ~d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~ 37 (120)
|+--.||.|.. +|.. . |+.+|.+|...
T Consensus 1 m~l~nC~~Cgk-lF~~--------~-~~~iCp~C~~~ 27 (137)
T TIGR03826 1 MELANCPKCGR-LFVK--------T-GRDVCPSCYEE 27 (137)
T ss_pred CCCccccccch-hhhh--------c-CCccCHHHhHH
Confidence 67778999995 5442 2 88999999864
No 198
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=50.42 E-value=6.5 Score=26.85 Aligned_cols=10 Identities=40% Similarity=1.155 Sum_probs=8.5
Q ss_pred cccCCccchh
Q psy17995 24 NICGHPLCEG 33 (120)
Q Consensus 24 ~~CGH~fC~~ 33 (120)
..|||.||..
T Consensus 27 c~CGh~f~d~ 36 (112)
T PF08882_consen 27 CDCGHEFCDA 36 (112)
T ss_pred ccCCCeecCh
Confidence 4799999975
No 199
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=50.32 E-value=4.3 Score=31.95 Aligned_cols=27 Identities=19% Similarity=0.549 Sum_probs=19.3
Q ss_pred CCccchhHHHHHhhcC---CCCCCCCCccc
Q psy17995 27 GHPLCEGCVDLLFLKG---TGNCYECNQPL 53 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~~---~~~CP~C~~~~ 53 (120)
.|+||..|-.+..... ...||.|+...
T Consensus 110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 5899999977665432 26799998744
No 200
>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=49.13 E-value=10 Score=20.08 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=8.1
Q ss_pred CCCCCCCCcc
Q psy17995 43 TGNCYECNQP 52 (120)
Q Consensus 43 ~~~CP~C~~~ 52 (120)
+..||+|+.+
T Consensus 18 p~~CP~Cg~~ 27 (34)
T cd00729 18 PEKCPICGAP 27 (34)
T ss_pred CCcCcCCCCc
Confidence 4689999984
No 201
>KOG0825|consensus
Probab=49.00 E-value=12 Score=33.92 Aligned_cols=50 Identities=14% Similarity=0.232 Sum_probs=30.4
Q ss_pred CccCcccCCCcccCCCCccc---ccccCCccchhHHHHHhhc-----CCCCCCCCCccc
Q psy17995 3 DQECPRCKTTKYRKPTLKLM---VNICGHPLCEGCVDLLFLK-----GTGNCYECNQPL 53 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~---~~~CGH~fC~~Ci~~~~~~-----~~~~CP~C~~~~ 53 (120)
...|++|.. -+.+|.-.+- +..|||.||-.||..+... .+..|+.|..-|
T Consensus 96 s~Ss~~C~~-E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci 153 (1134)
T KOG0825|consen 96 SDTSPVCEK-EHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV 153 (1134)
T ss_pred ccccchhhe-ecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence 346778874 4455322221 3359999999999987553 223466665544
No 202
>KOG2231|consensus
Probab=48.92 E-value=14 Score=32.44 Aligned_cols=45 Identities=27% Similarity=0.696 Sum_probs=29.8
Q ss_pred cCcccCCCcccCCCCcccccccCC-ccchhHHHHHhhc-C----CCCCCCCCcccc
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGH-PLCEGCVDLLFLK-G----TGNCYECNQPLR 54 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH-~fC~~Ci~~~~~~-~----~~~CP~C~~~~~ 54 (120)
.|+||-. +|+.. ....||| ..|..|.-++... . ...||+|+..+.
T Consensus 2 ~c~ic~~----s~~~~-~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~ 52 (669)
T KOG2231|consen 2 SCAICAF----SPDFV-GRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVE 52 (669)
T ss_pred Ccceeec----Ccccc-ccccccccccchhhhhhhhhhcccccccccCccccccee
Confidence 4888874 33221 1248999 8999998886442 2 346799988553
No 203
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=48.86 E-value=5.8 Score=26.43 Aligned_cols=41 Identities=17% Similarity=0.318 Sum_probs=22.8
Q ss_pred CcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccc
Q psy17995 6 CPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPL 53 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~ 53 (120)
||+|..............+-+|+.+ .+..+...||.|+..+
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~-------~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESI-------TIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEE-------EEeeeeeECCCCCCEE
Confidence 8999842222221112234678765 1222346899999865
No 204
>PF06869 DUF1258: Protein of unknown function (DUF1258); InterPro: IPR009667 This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to Caenorhabditis elegans. Note that this family contains a number of conserved cysteine and histidine residues.
Probab=48.59 E-value=37 Score=26.46 Aligned_cols=21 Identities=24% Similarity=0.686 Sum_probs=13.5
Q ss_pred CCccchhHHHHHhhcCCCCCCCC
Q psy17995 27 GHPLCEGCVDLLFLKGTGNCYEC 49 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~~~~~CP~C 49 (120)
-|.||..|-.. ... ...|-.|
T Consensus 17 ~h~~CN~CG~~-~~~-~~kC~~c 37 (258)
T PF06869_consen 17 THFICNSCGKV-VES-NEKCSCC 37 (258)
T ss_pred eehhhhhhhhh-hcc-Cceeecc
Confidence 49999999883 332 2456444
No 205
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.36 E-value=9.4 Score=23.57 Aligned_cols=13 Identities=31% Similarity=0.662 Sum_probs=10.5
Q ss_pred CCCCCCCCccccC
Q psy17995 43 TGNCYECNQPLRR 55 (120)
Q Consensus 43 ~~~CP~C~~~~~~ 55 (120)
+.+||+||+++..
T Consensus 7 ~v~CP~Cgkpv~w 19 (65)
T COG3024 7 TVPCPTCGKPVVW 19 (65)
T ss_pred cccCCCCCCcccc
Confidence 3689999998854
No 206
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=47.17 E-value=8.5 Score=27.22 Aligned_cols=16 Identities=19% Similarity=0.551 Sum_probs=10.9
Q ss_pred CCCccccc-ccCCccchh
Q psy17995 17 PTLKLMVN-ICGHPLCEG 33 (120)
Q Consensus 17 p~~~~~~~-~CGH~fC~~ 33 (120)
|+.+ ++. .|||+||..
T Consensus 66 ~~~r-v~rcecghsf~d~ 82 (165)
T COG4647 66 AQKR-VIRCECGHSFGDY 82 (165)
T ss_pred cccc-EEEEeccccccCh
Confidence 4444 343 899999975
No 207
>PRK01343 zinc-binding protein; Provisional
Probab=47.10 E-value=12 Score=22.54 Aligned_cols=12 Identities=42% Similarity=0.869 Sum_probs=9.8
Q ss_pred CCCCCCCCcccc
Q psy17995 43 TGNCYECNQPLR 54 (120)
Q Consensus 43 ~~~CP~C~~~~~ 54 (120)
...||+|++++.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 468999999864
No 208
>KOG4080|consensus
Probab=46.71 E-value=16 Score=26.72 Aligned_cols=14 Identities=29% Similarity=0.676 Sum_probs=10.8
Q ss_pred CCccchhHHHHHhh
Q psy17995 27 GHPLCEGCVDLLFL 40 (120)
Q Consensus 27 GH~fC~~Ci~~~~~ 40 (120)
.|++|..|...+..
T Consensus 105 a~~LC~~Cy~kV~k 118 (176)
T KOG4080|consen 105 AHTLCDYCYAKVHK 118 (176)
T ss_pred ccccHHHHHHHHHH
Confidence 37899999887643
No 209
>COG1773 Rubredoxin [Energy production and conversion]
Probab=46.42 E-value=7.7 Score=23.21 Aligned_cols=13 Identities=31% Similarity=0.685 Sum_probs=10.6
Q ss_pred CCCccCcccCCCcc
Q psy17995 1 MDDQECPRCKTTKY 14 (120)
Q Consensus 1 ~d~~~CpiC~~~~~ 14 (120)
|..++|.+|. .+|
T Consensus 1 m~~~~C~~CG-~vY 13 (55)
T COG1773 1 MKRWRCSVCG-YVY 13 (55)
T ss_pred CCceEecCCc-eEe
Confidence 6788999999 465
No 210
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=46.31 E-value=10 Score=25.42 Aligned_cols=28 Identities=32% Similarity=0.691 Sum_probs=18.7
Q ss_pred ccchhHHHHHhhc---CCCCCCCCCccccCC
Q psy17995 29 PLCEGCVDLLFLK---GTGNCYECNQPLRRG 56 (120)
Q Consensus 29 ~fC~~Ci~~~~~~---~~~~CP~C~~~~~~~ 56 (120)
++|..|...+-.. ....||-|+.+|..+
T Consensus 63 iiCGvC~~~LT~~EY~~~~~Cp~C~spFNp~ 93 (105)
T COG4357 63 IICGVCRKLLTRAEYGMCGSCPYCQSPFNPG 93 (105)
T ss_pred EEhhhhhhhhhHHHHhhcCCCCCcCCCCCcc
Confidence 5677787665332 246799999998643
No 211
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=46.11 E-value=12 Score=20.05 Aligned_cols=12 Identities=42% Similarity=1.118 Sum_probs=8.3
Q ss_pred ccCcccCCCcccC
Q psy17995 4 QECPRCKTTKYRK 16 (120)
Q Consensus 4 ~~CpiC~~~~~~~ 16 (120)
..||-|.. .|.=
T Consensus 3 i~Cp~C~~-~y~i 14 (36)
T PF13717_consen 3 ITCPNCQA-KYEI 14 (36)
T ss_pred EECCCCCC-EEeC
Confidence 47999985 5643
No 212
>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=46.02 E-value=8.5 Score=30.61 Aligned_cols=44 Identities=20% Similarity=0.526 Sum_probs=27.5
Q ss_pred ccCcccCCCcccCCCCccccc---ccCCc--cchhHHHHHhhcCCCCCCCCCcc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVN---ICGHP--LCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~---~CGH~--fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
-.||||.+ .|.+.++.. .=|++ .|.-|-.. |...-..||.|+..
T Consensus 185 ~~CPvCGs----~P~~s~~~~~~~~~G~RyL~CslC~te-W~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 185 TLCPACGS----PPVASMVRQGGKETGLRYLSCSLCATE-WHYVRVKCSHCEES 233 (305)
T ss_pred CcCCCCCC----hhhhhhhcccCCCCCceEEEcCCCCCc-ccccCccCCCCCCC
Confidence 37999995 343332221 34655 58888544 54444789999975
No 213
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=45.54 E-value=6.1 Score=30.97 Aligned_cols=24 Identities=25% Similarity=0.605 Sum_probs=15.1
Q ss_pred ccchhHHHHHhhcCCCCCCCCCccc
Q psy17995 29 PLCEGCVDLLFLKGTGNCYECNQPL 53 (120)
Q Consensus 29 ~fC~~Ci~~~~~~~~~~CP~C~~~~ 53 (120)
-+|..|+..+-+. +..||+|++.|
T Consensus 256 yvCs~Clsi~C~~-p~~C~~Cgt~f 279 (279)
T TIGR00627 256 FVCSVCLSVLCQY-TPICKTCKTAF 279 (279)
T ss_pred EECCCccCCcCCC-CCCCCCCCCCC
Confidence 4566666655443 35888888753
No 214
>KOG2807|consensus
Probab=44.55 E-value=13 Score=30.08 Aligned_cols=10 Identities=30% Similarity=1.009 Sum_probs=5.0
Q ss_pred ccCCccchhH
Q psy17995 25 ICGHPLCEGC 34 (120)
Q Consensus 25 ~CGH~fC~~C 34 (120)
.|.|.||-.|
T Consensus 350 ~Ck~~FCldC 359 (378)
T KOG2807|consen 350 SCKNVFCLDC 359 (378)
T ss_pred hccceeeccc
Confidence 3455555555
No 215
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=43.00 E-value=7.1 Score=18.10 Aligned_cols=11 Identities=18% Similarity=0.664 Sum_probs=8.0
Q ss_pred CCCCCCccccC
Q psy17995 45 NCYECNQPLRR 55 (120)
Q Consensus 45 ~CP~C~~~~~~ 55 (120)
.||.|++.+..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 58888887753
No 216
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=42.74 E-value=42 Score=27.59 Aligned_cols=42 Identities=17% Similarity=0.299 Sum_probs=21.5
Q ss_pred CCc-cchhHH--HHHhhcCCCCCCCCCccccCC-CCccccccchhH
Q psy17995 27 GHP-LCEGCV--DLLFLKGTGNCYECNQPLRRG-NFRVQLFDDSSV 68 (120)
Q Consensus 27 GH~-fC~~Ci--~~~~~~~~~~CP~C~~~~~~~-~~~~~~f~d~~~ 68 (120)
||. +|..|. ...+......||.|+..+.-. .+|.-.+.|..+
T Consensus 238 g~~~~c~~cg~~~~~~~~~~~~c~~Cg~~~~~~GPlW~GpL~d~~f 283 (380)
T COG1867 238 GYIYHCSRCGEIVGSFREVDEKCPHCGGKVHLAGPLWLGPLHDEEF 283 (380)
T ss_pred CcEEEcccccceecccccccccCCcccccceeccCcccCcccCHHH
Confidence 444 577774 222223347899999654322 233333445443
No 217
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=42.45 E-value=13 Score=22.72 Aligned_cols=10 Identities=20% Similarity=0.471 Sum_probs=8.0
Q ss_pred CCCCCCCccc
Q psy17995 44 GNCYECNQPL 53 (120)
Q Consensus 44 ~~CP~C~~~~ 53 (120)
..||.|+..-
T Consensus 16 ~~CP~Cgs~~ 25 (61)
T PRK08351 16 DRCPVCGSRD 25 (61)
T ss_pred CcCCCCcCCc
Confidence 4799999854
No 218
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=42.42 E-value=25 Score=20.43 Aligned_cols=30 Identities=23% Similarity=0.473 Sum_probs=18.3
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHH
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLL 38 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~ 38 (120)
.|+||..-+-. +..+-..=| .+|.+|+..+
T Consensus 1 ~C~iCg~kigl---~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGL---FKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCcccccccc---ccceeccCc-cchHHHHHHh
Confidence 48999853221 110113457 7999999886
No 219
>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=42.07 E-value=13 Score=20.53 Aligned_cols=8 Identities=38% Similarity=1.310 Sum_probs=5.7
Q ss_pred ccCcccCC
Q psy17995 4 QECPRCKT 11 (120)
Q Consensus 4 ~~CpiC~~ 11 (120)
+.||.|..
T Consensus 1 m~Cp~Cg~ 8 (43)
T PF08271_consen 1 MKCPNCGS 8 (43)
T ss_dssp ESBTTTSS
T ss_pred CCCcCCcC
Confidence 36888875
No 220
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=41.77 E-value=24 Score=33.76 Aligned_cols=14 Identities=21% Similarity=0.759 Sum_probs=11.6
Q ss_pred CCCCCCCccccCCC
Q psy17995 44 GNCYECNQPLRRGN 57 (120)
Q Consensus 44 ~~CP~C~~~~~~~~ 57 (120)
..||.|++++.+.+
T Consensus 934 k~Cp~Cg~~~~kdg 947 (1437)
T PRK00448 934 KDCPKCGTKLKKDG 947 (1437)
T ss_pred ccCccccccccccC
Confidence 67999999987654
No 221
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=40.99 E-value=19 Score=22.04 Aligned_cols=11 Identities=36% Similarity=0.969 Sum_probs=8.7
Q ss_pred CCCCCCCcccc
Q psy17995 44 GNCYECNQPLR 54 (120)
Q Consensus 44 ~~CP~C~~~~~ 54 (120)
..||+|++++.
T Consensus 7 v~CP~C~k~~~ 17 (62)
T PRK00418 7 VNCPTCGKPVE 17 (62)
T ss_pred ccCCCCCCccc
Confidence 57999999763
No 222
>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=40.95 E-value=11 Score=17.08 Aligned_cols=10 Identities=30% Similarity=0.896 Sum_probs=5.5
Q ss_pred CCCCCCcccc
Q psy17995 45 NCYECNQPLR 54 (120)
Q Consensus 45 ~CP~C~~~~~ 54 (120)
.||.|+..+.
T Consensus 2 ~C~~C~~~~~ 11 (24)
T PF13894_consen 2 QCPICGKSFR 11 (24)
T ss_dssp E-SSTS-EES
T ss_pred CCcCCCCcCC
Confidence 4788877664
No 223
>PF15616 TerY-C: TerY-C metal binding domain
Probab=40.63 E-value=13 Score=26.04 Aligned_cols=39 Identities=31% Similarity=0.679 Sum_probs=25.6
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
--||-|... + .+++-.||+.||- +. .+...||-|+....
T Consensus 78 PgCP~CGn~-~-----~fa~C~CGkl~Ci---~g---~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 78 PGCPHCGNQ-Y-----AFAVCGCGKLFCI---DG---EGEVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCcCh-h-----cEEEecCCCEEEe---CC---CCCEECCCCCCeee
Confidence 469999852 1 1234489999863 22 23478999998654
No 224
>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=40.58 E-value=13 Score=24.55 Aligned_cols=21 Identities=33% Similarity=0.906 Sum_probs=17.0
Q ss_pred CCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 27 GHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
.|++|..|...+ ..|+.|+++
T Consensus 70 Yh~iC~~Ca~~~-----~vCaKC~k~ 90 (92)
T PF10217_consen 70 YHVICDPCAKEL-----KVCAKCGKP 90 (92)
T ss_pred HHHHHHHHHHhh-----ccCcccCCC
Confidence 599999998753 679999874
No 225
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=40.44 E-value=15 Score=34.65 Aligned_cols=48 Identities=27% Similarity=0.596 Sum_probs=29.2
Q ss_pred ccCcccCCCcccCCCCcccccccCCcc-----chhHHHHHhhc--CCCCCCCCCccccCC
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPL-----CEGCVDLLFLK--GTGNCYECNQPLRRG 56 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~f-----C~~Ci~~~~~~--~~~~CP~C~~~~~~~ 56 (120)
..||-|....+. . +-..||++. |.+|=..+-.. +...||.|+.++...
T Consensus 668 rkCPkCG~~t~~-~----fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~~ 722 (1337)
T PRK14714 668 RRCPSCGTETYE-N----RCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTPY 722 (1337)
T ss_pred EECCCCCCcccc-c----cCcccCCcCCCceeCccCCCccCCCccccccCCCCCCccccc
Confidence 589999963211 1 123688774 88885443221 124799999887654
No 226
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=39.75 E-value=28 Score=32.79 Aligned_cols=14 Identities=29% Similarity=0.949 Sum_probs=11.8
Q ss_pred CCCCCCCccccCCC
Q psy17995 44 GNCYECNQPLRRGN 57 (120)
Q Consensus 44 ~~CP~C~~~~~~~~ 57 (120)
..||.|++++.+.+
T Consensus 709 k~cp~c~~~~~~dg 722 (1213)
T TIGR01405 709 KDCPKCGAPLKKDG 722 (1213)
T ss_pred ccCccccccccccC
Confidence 67999999987764
No 227
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.19 E-value=11 Score=22.15 Aligned_cols=11 Identities=27% Similarity=0.778 Sum_probs=9.6
Q ss_pred CCCCCCCcccc
Q psy17995 44 GNCYECNQPLR 54 (120)
Q Consensus 44 ~~CP~C~~~~~ 54 (120)
..||+|+.+|.
T Consensus 13 KICpvCqRPFs 23 (54)
T COG4338 13 KICPVCQRPFS 23 (54)
T ss_pred hhhhhhcCchH
Confidence 57999999984
No 228
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=39.08 E-value=32 Score=28.89 Aligned_cols=108 Identities=22% Similarity=0.266 Sum_probs=57.2
Q ss_pred ccCcccCCCcccCCCCccccc--ccCCccchhHHHHHhhc-------C-------CCCCCCCCccccCCCCccccccchh
Q psy17995 4 QECPRCKTTKYRKPTLKLMVN--ICGHPLCEGCVDLLFLK-------G-------TGNCYECNQPLRRGNFRVQLFDDSS 67 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~--~CGH~fC~~Ci~~~~~~-------~-------~~~CP~C~~~~~~~~~~~~~f~d~~ 67 (120)
-+|+||.. .-.+.+.-..+. .|||.=--.|.-+.... | ...|..|+....-=+++..+|.--
T Consensus 129 C~C~iC~k-fD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~seLlG~vk~vf~~c- 206 (446)
T PF07227_consen 129 CMCCICSK-FDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSELLGFVKKVFQTC- 206 (446)
T ss_pred CCccccCC-cccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhhHHHHHHHHHHHH-
Confidence 47999984 322222222233 69998878886553311 1 135888987543222222233111
Q ss_pred HHHHHHHHHHhhhhhhcccCCc-cCHH-HHHHHHHHHHHHHHHHhcc-cch
Q psy17995 68 VEKEVEIRKKLLKDYNKVEEDF-NSLA-EYNDYLEEIEEIVFNLCNN-IDI 115 (120)
Q Consensus 68 ~~~e~~~rk~~~k~~~~~~~~~-~~l~-~y~~yle~~E~~i~~L~~~-~d~ 115 (120)
++..-+..+.+.++-...-| +|-. .+...++.+|+++..|-++ ++.
T Consensus 207 --a~~~~~d~L~~eL~l~~rIf~GSed~rgk~L~~~~e~al~KL~~~~~~~ 255 (446)
T PF07227_consen 207 --AKAWRVDVLCKELDLVRRIFRGSEDYRGKELHEKVEEALAKLENGVIDS 255 (446)
T ss_pred --HhhhhHHHHHHHHHHHHHHhhCccchhHHHHHHHHHHHHHHHhCCCCCH
Confidence 11111122233333333445 3432 4788899999999999988 455
No 229
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=39.02 E-value=10 Score=22.68 Aligned_cols=8 Identities=38% Similarity=1.153 Sum_probs=3.9
Q ss_pred ccCcccCC
Q psy17995 4 QECPRCKT 11 (120)
Q Consensus 4 ~~CpiC~~ 11 (120)
.+||-|..
T Consensus 8 VkCp~C~~ 15 (55)
T PF01667_consen 8 VKCPGCYN 15 (55)
T ss_dssp EE-TTT-S
T ss_pred EECCCCCC
Confidence 46777763
No 230
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.96 E-value=17 Score=24.63 Aligned_cols=14 Identities=29% Similarity=0.973 Sum_probs=11.2
Q ss_pred CCCCCCCCCccccC
Q psy17995 42 GTGNCYECNQPLRR 55 (120)
Q Consensus 42 ~~~~CP~C~~~~~~ 55 (120)
|...||.||.++..
T Consensus 48 G~t~CP~Cg~~~e~ 61 (115)
T COG1885 48 GSTSCPKCGEPFES 61 (115)
T ss_pred ccccCCCCCCccce
Confidence 45689999998854
No 231
>KOG4718|consensus
Probab=38.90 E-value=14 Score=28.21 Aligned_cols=43 Identities=16% Similarity=0.472 Sum_probs=29.4
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
.|.+|+..+...- .-..||=.+-.+|+...+.+ ...||.|+--
T Consensus 183 ~Cn~Ch~LvIqg~----rCg~c~i~~h~~c~qty~q~-~~~cphc~d~ 225 (235)
T KOG4718|consen 183 NCNLCHCLVIQGI----RCGSCNIQYHRGCIQTYLQR-RDICPHCGDL 225 (235)
T ss_pred HHhHhHHHhheee----ccCcccchhhhHHHHHHhcc-cCcCCchhcc
Confidence 6888886322211 01267777788999999887 5789999753
No 232
>KOG3579|consensus
Probab=38.06 E-value=14 Score=29.47 Aligned_cols=36 Identities=14% Similarity=0.390 Sum_probs=24.9
Q ss_pred CccCcccCCCcccCCCCcccc--cccCCccchhHHHHHhhc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMV--NICGHPLCEGCVDLLFLK 41 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~--~~CGH~fC~~Ci~~~~~~ 41 (120)
.+.|-+|++ .+.|-. +|+ +.=.|.||-.|-...++.
T Consensus 268 pLcCTLC~E-RLEDTH--FVQCPSVp~HKFCFPCSResIK~ 305 (352)
T KOG3579|consen 268 PLCCTLCHE-RLEDTH--FVQCPSVPSHKFCFPCSRESIKQ 305 (352)
T ss_pred ceeehhhhh-hhccCc--eeecCCCcccceecccCHHHHHh
Confidence 467999997 445543 233 234899999998887764
No 233
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=36.96 E-value=69 Score=26.06 Aligned_cols=49 Identities=22% Similarity=0.356 Sum_probs=31.7
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc---C----CCCCCCCCccccCCCCcc
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK---G----TGNCYECNQPLRRGNFRV 60 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~---~----~~~CP~C~~~~~~~~~~~ 60 (120)
..-.|+.|... .+| =.|.+|..|+-.-... + ...|+.|+....++.|..
T Consensus 5 ~~~~C~~CGr~--~~~--------~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga~~~~~~W~~ 60 (355)
T COG1499 5 STILCVRCGRS--VDP--------LIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGAYRIRGRWVD 60 (355)
T ss_pred cccEeccCCCc--Cch--------hhccccHHHHhccCccccCCCceEEEECCcCCCccCCCccee
Confidence 34579999842 223 3689999998763221 1 146999997666665543
No 234
>KOG1829|consensus
Probab=36.89 E-value=16 Score=31.69 Aligned_cols=23 Identities=17% Similarity=0.511 Sum_probs=17.4
Q ss_pred ccCCccchhHHHHHhhcCCCCCCCCCc
Q psy17995 25 ICGHPLCEGCVDLLFLKGTGNCYECNQ 51 (120)
Q Consensus 25 ~CGH~fC~~Ci~~~~~~~~~~CP~C~~ 51 (120)
.||+.|-..|+.+ .++.||.|-.
T Consensus 536 ~C~avfH~~C~~r----~s~~CPrC~R 558 (580)
T KOG1829|consen 536 TCLAVFHKKCLRR----KSPCCPRCER 558 (580)
T ss_pred HHHHHHHHHHHhc----cCCCCCchHH
Confidence 6999999988764 4455999943
No 235
>PHA00616 hypothetical protein
Probab=36.81 E-value=11 Score=21.55 Aligned_cols=12 Identities=25% Similarity=0.730 Sum_probs=9.8
Q ss_pred CCCCCCCccccC
Q psy17995 44 GNCYECNQPLRR 55 (120)
Q Consensus 44 ~~CP~C~~~~~~ 55 (120)
.+||.||..|..
T Consensus 2 YqC~~CG~~F~~ 13 (44)
T PHA00616 2 YQCLRCGGIFRK 13 (44)
T ss_pred CccchhhHHHhh
Confidence 579999998864
No 236
>PF14353 CpXC: CpXC protein
Probab=36.61 E-value=14 Score=24.93 Aligned_cols=11 Identities=18% Similarity=0.639 Sum_probs=7.5
Q ss_pred CCCCCCccccC
Q psy17995 45 NCYECNQPLRR 55 (120)
Q Consensus 45 ~CP~C~~~~~~ 55 (120)
.||.|+..+..
T Consensus 3 tCP~C~~~~~~ 13 (128)
T PF14353_consen 3 TCPHCGHEFEF 13 (128)
T ss_pred CCCCCCCeeEE
Confidence 57777776653
No 237
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=36.54 E-value=25 Score=23.03 Aligned_cols=21 Identities=14% Similarity=0.341 Sum_probs=14.1
Q ss_pred CCCCCCCCccccCCCCccccc
Q psy17995 43 TGNCYECNQPLRRGNFRVQLF 63 (120)
Q Consensus 43 ~~~CP~C~~~~~~~~~~~~~f 63 (120)
...|..|+..+.-..+.+.+-
T Consensus 53 IW~C~kCg~~fAGgay~P~t~ 73 (89)
T COG1997 53 IWKCRKCGAKFAGGAYTPVTP 73 (89)
T ss_pred eEEcCCCCCeeccccccccch
Confidence 456777888777666666543
No 238
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=36.09 E-value=14 Score=20.15 Aligned_cols=12 Identities=25% Similarity=0.589 Sum_probs=8.8
Q ss_pred CCCCCCccccCC
Q psy17995 45 NCYECNQPLRRG 56 (120)
Q Consensus 45 ~CP~C~~~~~~~ 56 (120)
.||.|+..+...
T Consensus 1 ~CP~C~~~l~~~ 12 (41)
T PF13453_consen 1 KCPRCGTELEPV 12 (41)
T ss_pred CcCCCCcccceE
Confidence 589998876543
No 239
>KOG3476|consensus
Probab=36.08 E-value=3.7 Score=26.96 Aligned_cols=35 Identities=29% Similarity=0.755 Sum_probs=22.9
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
.|-||+. ....| |-.+|+.|... ...|..|++.+.
T Consensus 56 kC~iCk~-~vHQ~---------GshYC~tCAY~-----KgiCAMCGKki~ 90 (100)
T KOG3476|consen 56 KCRICKQ-LVHQP---------GSHYCQTCAYK-----KGICAMCGKKIL 90 (100)
T ss_pred hhHHHHH-HhcCC---------cchhHhHhhhh-----hhHHHHhhhHhh
Confidence 4666763 33333 77789998653 357889988663
No 240
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=35.89 E-value=75 Score=19.22 Aligned_cols=13 Identities=15% Similarity=0.373 Sum_probs=9.4
Q ss_pred CCCCCCCccccCC
Q psy17995 44 GNCYECNQPLRRG 56 (120)
Q Consensus 44 ~~CP~C~~~~~~~ 56 (120)
-.||+||......
T Consensus 18 e~Cp~CG~~t~~~ 30 (59)
T COG2260 18 EKCPVCGGDTKVP 30 (59)
T ss_pred ccCCCCCCccccC
Confidence 3799999876543
No 241
>PRK11827 hypothetical protein; Provisional
Probab=35.79 E-value=22 Score=21.57 Aligned_cols=12 Identities=25% Similarity=0.742 Sum_probs=8.2
Q ss_pred ccCcccCCCccc
Q psy17995 4 QECPRCKTTKYR 15 (120)
Q Consensus 4 ~~CpiC~~~~~~ 15 (120)
+.||+|+..+..
T Consensus 9 LaCP~ckg~L~~ 20 (60)
T PRK11827 9 IACPVCNGKLWY 20 (60)
T ss_pred eECCCCCCcCeE
Confidence 579999864433
No 242
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=35.61 E-value=17 Score=29.02 Aligned_cols=45 Identities=24% Similarity=0.507 Sum_probs=27.6
Q ss_pred CccCcccCCCcccCCCCcccc--cccCCc--cchhHHHHHhhcCCCCCCCCCcc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMV--NICGHP--LCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~--~~CGH~--fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
+-.||+|.+ .|.+.++. ..=|++ .|.-|-.. |.-.-..||-|+..
T Consensus 187 ~~~CPvCGs----~P~~s~v~~~~~~G~RyL~CslC~te-W~~~R~~C~~Cg~~ 235 (309)
T PRK03564 187 RQFCPVCGS----MPVSSVVQIGTTQGLRYLHCNLCESE-WHVVRVKCSNCEQS 235 (309)
T ss_pred CCCCCCCCC----cchhheeeccCCCCceEEEcCCCCCc-ccccCccCCCCCCC
Confidence 357999995 34333221 134655 58888544 44444789999973
No 243
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=35.51 E-value=19 Score=26.81 Aligned_cols=43 Identities=23% Similarity=0.641 Sum_probs=26.1
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHH-HHHhhc---CCCCCCCCCc
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCV-DLLFLK---GTGNCYECNQ 51 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci-~~~~~~---~~~~CP~C~~ 51 (120)
+.-.|..|.. +-. ....|-|++|..|- +...+. ....|+.|++
T Consensus 59 ~~~~C~nCg~----~GH---~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~ 105 (190)
T COG5082 59 ENPVCFNCGQ----NGH---LRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGE 105 (190)
T ss_pred cccccchhcc----cCc---ccccCChhHhhhcCCCCcccccCCcccccccccc
Confidence 4557888984 222 13589999999992 111111 1256888876
No 244
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=35.49 E-value=19 Score=21.79 Aligned_cols=11 Identities=27% Similarity=0.712 Sum_probs=7.8
Q ss_pred CCCCCCCcccc
Q psy17995 44 GNCYECNQPLR 54 (120)
Q Consensus 44 ~~CP~C~~~~~ 54 (120)
-.|+.|+..|.
T Consensus 31 V~C~~Cg~~L~ 41 (59)
T PRK00415 31 VRCLVCGKTLA 41 (59)
T ss_pred EECcccCCCcc
Confidence 46888887773
No 245
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=35.21 E-value=10 Score=23.17 Aligned_cols=25 Identities=20% Similarity=0.408 Sum_probs=21.6
Q ss_pred CCccchhHHHHHhhcCCCCCCCCCc
Q psy17995 27 GHPLCEGCVDLLFLKGTGNCYECNQ 51 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~~~~~CP~C~~ 51 (120)
-|.+|..|=...+......|..|+-
T Consensus 16 tHt~CrRCG~~syh~qK~~CasCGy 40 (62)
T PRK04179 16 THIRCRRCGRHSYNVRKKYCAACGF 40 (62)
T ss_pred ccchhcccCcccccccccchhhcCC
Confidence 5999999988888876789999987
No 246
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=35.08 E-value=15 Score=32.61 Aligned_cols=24 Identities=25% Similarity=0.427 Sum_probs=16.3
Q ss_pred CCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 27 GHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
|.-+|..|-.. +..+..||.|+..
T Consensus 461 ~~L~CH~Cg~~--~~~p~~Cp~Cgs~ 484 (730)
T COG1198 461 GQLRCHYCGYQ--EPIPQSCPECGSE 484 (730)
T ss_pred CeeEeCCCCCC--CCCCCCCCCCCCC
Confidence 55667777443 2335789999986
No 247
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=35.07 E-value=19 Score=19.07 Aligned_cols=11 Identities=18% Similarity=0.709 Sum_probs=7.2
Q ss_pred CCCccCcccCC
Q psy17995 1 MDDQECPRCKT 11 (120)
Q Consensus 1 ~d~~~CpiC~~ 11 (120)
|+...|+.|..
T Consensus 1 ~~~~~C~~C~~ 11 (33)
T PF08792_consen 1 SNLKKCSKCGG 11 (33)
T ss_pred CCceEcCCCCC
Confidence 45567777764
No 248
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=34.86 E-value=21 Score=31.67 Aligned_cols=50 Identities=20% Similarity=0.398 Sum_probs=33.2
Q ss_pred ccCcccCCCcccCCCCccc----c--cccCCcc--------------------chhHHHHHhhc-------CCCCCCCCC
Q psy17995 4 QECPRCKTTKYRKPTLKLM----V--NICGHPL--------------------CEGCVDLLFLK-------GTGNCYECN 50 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~----~--~~CGH~f--------------------C~~Ci~~~~~~-------~~~~CP~C~ 50 (120)
-.|+-|+..+ .||+-+-+ + |.||=+| |..|-+.+-.. .+..||.||
T Consensus 102 a~C~~Cl~Ei-~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfHAQp~aCp~CG 180 (750)
T COG0068 102 ATCEDCLEEI-FDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFHAQPIACPKCG 180 (750)
T ss_pred hhhHHHHHHh-cCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccccccccccCcccC
Confidence 4789998644 56654422 2 4688766 99998876432 245799999
Q ss_pred cccc
Q psy17995 51 QPLR 54 (120)
Q Consensus 51 ~~~~ 54 (120)
-.+.
T Consensus 181 P~~~ 184 (750)
T COG0068 181 PHLF 184 (750)
T ss_pred CCeE
Confidence 7653
No 249
>PF14164 YqzH: YqzH-like protein
Probab=34.83 E-value=39 Score=20.78 Aligned_cols=16 Identities=25% Similarity=0.557 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHhcc
Q psy17995 97 DYLEEIEEIVFNLCNN 112 (120)
Q Consensus 97 ~yle~~E~~i~~L~~~ 112 (120)
|..|-|||+||+-|-|
T Consensus 49 Dl~eiVeDvVY~yiTg 64 (64)
T PF14164_consen 49 DLHEIVEDVVYDYITG 64 (64)
T ss_pred hHHHHHHHHHHHHhcC
Confidence 5678899999987643
No 250
>KOG1729|consensus
Probab=34.78 E-value=11 Score=29.80 Aligned_cols=52 Identities=25% Similarity=0.508 Sum_probs=29.6
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHHHhhc-----CC-CCCCCCCcccc
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLK-----GT-GNCYECNQPLR 54 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~-----~~-~~CP~C~~~~~ 54 (120)
...|.+|...-|.--..+-..-.||++||..|-...+.. ++ ..|+.|=..+.
T Consensus 168 a~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~~~l~~~~~k~~rvC~~CF~el~ 225 (288)
T KOG1729|consen 168 ATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNRFLLPNLSTKPIRVCDICFEELE 225 (288)
T ss_pred ceecccCCCccccHHHHHHHHHhcchHhhhhhhcCcccccccCCCCceecHHHHHHHh
Confidence 357999985322111111112369999999998774432 12 25787755553
No 251
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.62 E-value=23 Score=24.92 Aligned_cols=27 Identities=19% Similarity=0.580 Sum_probs=17.8
Q ss_pred ccchhHHHHHhhcCCCCCCCCCccccCCCCc
Q psy17995 29 PLCEGCVDLLFLKGTGNCYECNQPLRRGNFR 59 (120)
Q Consensus 29 ~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~~~ 59 (120)
.||..|-..- ..+||.|..+++-..+.
T Consensus 29 afcskcgeat----i~qcp~csasirgd~~v 55 (160)
T COG4306 29 AFCSKCGEAT----ITQCPICSASIRGDYYV 55 (160)
T ss_pred HHHhhhchHH----HhcCCccCCccccccee
Confidence 4777774432 25799999988765443
No 252
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=34.54 E-value=11 Score=18.51 Aligned_cols=12 Identities=17% Similarity=0.506 Sum_probs=9.0
Q ss_pred CCCCCCCCcccc
Q psy17995 43 TGNCYECNQPLR 54 (120)
Q Consensus 43 ~~~CP~C~~~~~ 54 (120)
+..||.|++.|.
T Consensus 14 ~~~C~~C~k~F~ 25 (26)
T PF13465_consen 14 PYKCPYCGKSFS 25 (26)
T ss_dssp SEEESSSSEEES
T ss_pred CCCCCCCcCeeC
Confidence 467999987663
No 253
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=34.51 E-value=19 Score=22.15 Aligned_cols=16 Identities=6% Similarity=0.131 Sum_probs=11.1
Q ss_pred CCCCCCCCccccCCCC
Q psy17995 43 TGNCYECNQPLRRGNF 58 (120)
Q Consensus 43 ~~~CP~C~~~~~~~~~ 58 (120)
...||+|+..-...+|
T Consensus 17 ~~~Cp~Cgs~~~S~~w 32 (64)
T PRK06393 17 EKTCPVHGDEKTTTEW 32 (64)
T ss_pred CCcCCCCCCCcCCcCc
Confidence 3589999987544444
No 254
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=33.71 E-value=62 Score=19.22 Aligned_cols=43 Identities=28% Similarity=0.774 Sum_probs=27.4
Q ss_pred ccCcccCCCcccCCCCcccc-cccCCccchhHHHHHhhcCCCCCCC--CCccc
Q psy17995 4 QECPRCKTTKYRKPTLKLMV-NICGHPLCEGCVDLLFLKGTGNCYE--CNQPL 53 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~-~~CGH~fC~~Ci~~~~~~~~~~CP~--C~~~~ 53 (120)
..|++|.. .+++..- +|+ ..||-..-++|.... ..|-. |++++
T Consensus 6 ~~C~~Cg~-~~~~~dD-iVvCp~CgapyHR~C~~~~-----g~C~~~~c~~~~ 51 (54)
T PF14446_consen 6 CKCPVCGK-KFKDGDD-IVVCPECGAPYHRDCWEKA-----GGCINYSCGTGF 51 (54)
T ss_pred ccChhhCC-cccCCCC-EEECCCCCCcccHHHHhhC-----CceEeccCCCCc
Confidence 57999996 5543322 233 479988888887652 45655 66654
No 255
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=33.64 E-value=14 Score=27.58 Aligned_cols=15 Identities=13% Similarity=0.439 Sum_probs=11.4
Q ss_pred CCCCCCCCccccCCC
Q psy17995 43 TGNCYECNQPLRRGN 57 (120)
Q Consensus 43 ~~~CP~C~~~~~~~~ 57 (120)
...||+|++.|+.+.
T Consensus 5 ~~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 5 KITCPVCGKEFKTKK 19 (214)
T ss_pred ceECCCCCCeeeeeE
Confidence 468999999886543
No 256
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.49 E-value=22 Score=24.09 Aligned_cols=8 Identities=25% Similarity=0.837 Sum_probs=6.7
Q ss_pred CCCCCCcc
Q psy17995 45 NCYECNQP 52 (120)
Q Consensus 45 ~CP~C~~~ 52 (120)
.||.|+..
T Consensus 90 ~CP~Cgs~ 97 (117)
T PRK00564 90 VCEKCHSK 97 (117)
T ss_pred cCcCCCCC
Confidence 59999975
No 257
>KOG3475|consensus
Probab=33.25 E-value=17 Score=23.71 Aligned_cols=28 Identities=25% Similarity=0.618 Sum_probs=23.5
Q ss_pred CCccchhHHHHHhhcCCCCCCCCCcccc
Q psy17995 27 GHPLCEGCVDLLFLKGTGNCYECNQPLR 54 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~~~~~CP~C~~~~~ 54 (120)
.|.+|..|=...+......|..|+-+-.
T Consensus 15 shtlC~RCG~~syH~QKstC~~CGYpaa 42 (92)
T KOG3475|consen 15 SHTLCRRCGRRSYHIQKSTCSSCGYPAA 42 (92)
T ss_pred chHHHHHhCchhhhhhcccccccCCcch
Confidence 4899999998888876688999998764
No 258
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=32.94 E-value=45 Score=18.30 Aligned_cols=35 Identities=20% Similarity=0.541 Sum_probs=18.1
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhh
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFL 40 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~ 40 (120)
..|+-|... .+...+|+..+=|=.+|..|+.....
T Consensus 2 ~~CSFCgr~--~~~v~~li~g~~~~~IC~~Cv~~~~~ 36 (41)
T PF06689_consen 2 KRCSFCGRP--ESEVGRLISGPNGAYICDECVEQAYE 36 (41)
T ss_dssp -B-TTT--B--TTTSSSEEEES-SEEEEHHHHHHHHH
T ss_pred CCccCCCCC--HHHHhceecCCCCcEECHHHHHHHHH
Confidence 468999852 23323333334355689999987643
No 259
>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=32.89 E-value=34 Score=23.96 Aligned_cols=27 Identities=4% Similarity=0.090 Sum_probs=15.5
Q ss_pred cchhHHHHHhh--cCCCCCCCCCccccCC
Q psy17995 30 LCEGCVDLLFL--KGTGNCYECNQPLRRG 56 (120)
Q Consensus 30 fC~~Ci~~~~~--~~~~~CP~C~~~~~~~ 56 (120)
.|.+|-.+++- +.+..||.||..+...
T Consensus 11 ~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCccccccCCCCccCCCcCCccCcc
Confidence 34444444433 3467899998876443
No 260
>KOG3507|consensus
Probab=32.79 E-value=19 Score=21.89 Aligned_cols=8 Identities=38% Similarity=0.804 Sum_probs=4.0
Q ss_pred CCCCCCCc
Q psy17995 44 GNCYECNQ 51 (120)
Q Consensus 44 ~~CP~C~~ 51 (120)
..|-.||-
T Consensus 38 irCReCG~ 45 (62)
T KOG3507|consen 38 IRCRECGY 45 (62)
T ss_pred Eehhhcch
Confidence 44555543
No 261
>KOG3970|consensus
Probab=32.71 E-value=41 Score=26.08 Aligned_cols=45 Identities=20% Similarity=0.401 Sum_probs=30.0
Q ss_pred cCcccCCCcccCCCCcccc-cccCCccchhHHHHHhhc---C----CCCCCCCCccc
Q psy17995 5 ECPRCKTTKYRKPTLKLMV-NICGHPLCEGCVDLLFLK---G----TGNCYECNQPL 53 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~-~~CGH~fC~~Ci~~~~~~---~----~~~CP~C~~~~ 53 (120)
.|..|.+. +-.... + ..|.|.|--.|+..--.. + .-+||.|...+
T Consensus 52 NC~LC~t~-La~gdt---~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei 104 (299)
T KOG3970|consen 52 NCRLCNTP-LASGDT---TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI 104 (299)
T ss_pred CCceeCCc-cccCcc---eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence 68888853 222211 2 279999999999876543 1 25799997755
No 262
>PF14149 YhfH: YhfH-like protein
Probab=32.68 E-value=15 Score=20.19 Aligned_cols=16 Identities=25% Similarity=0.723 Sum_probs=10.3
Q ss_pred Hhhc-CCCCCCCCCccc
Q psy17995 38 LFLK-GTGNCYECNQPL 53 (120)
Q Consensus 38 ~~~~-~~~~CP~C~~~~ 53 (120)
+|++ +...|+.||+.+
T Consensus 7 FfrnLp~K~C~~CG~~i 23 (37)
T PF14149_consen 7 FFRNLPPKKCTECGKEI 23 (37)
T ss_pred HHHhCCCcccHHHHHHH
Confidence 3443 446788888754
No 263
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=32.47 E-value=15 Score=21.42 Aligned_cols=9 Identities=22% Similarity=0.471 Sum_probs=5.4
Q ss_pred CCCCCCCcc
Q psy17995 44 GNCYECNQP 52 (120)
Q Consensus 44 ~~CP~C~~~ 52 (120)
..||-|+.-
T Consensus 25 irCp~Cg~r 33 (49)
T COG1996 25 IRCPYCGSR 33 (49)
T ss_pred eeCCCCCcE
Confidence 456666653
No 264
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=32.35 E-value=14 Score=22.22 Aligned_cols=12 Identities=25% Similarity=0.689 Sum_probs=6.2
Q ss_pred CCCCCCCccccC
Q psy17995 44 GNCYECNQPLRR 55 (120)
Q Consensus 44 ~~CP~C~~~~~~ 55 (120)
..||+|++++..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 469999998753
No 265
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=32.21 E-value=47 Score=24.32 Aligned_cols=16 Identities=31% Similarity=0.673 Sum_probs=12.6
Q ss_pred cCCCCCCCCCccccCC
Q psy17995 41 KGTGNCYECNQPLRRG 56 (120)
Q Consensus 41 ~~~~~CP~C~~~~~~~ 56 (120)
.|-+.||.|+.++...
T Consensus 152 AGRP~CPlCg~PlDP~ 167 (171)
T PF11290_consen 152 AGRPPCPLCGEPLDPE 167 (171)
T ss_pred CCCCCCCCCCCCCCCC
Confidence 3568999999998643
No 266
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=32.16 E-value=53 Score=18.23 Aligned_cols=20 Identities=20% Similarity=0.343 Sum_probs=12.2
Q ss_pred hHHHHHhhc---CCCCCCCCCcc
Q psy17995 33 GCVDLLFLK---GTGNCYECNQP 52 (120)
Q Consensus 33 ~Ci~~~~~~---~~~~CP~C~~~ 52 (120)
+|+.-+... +.+.||.|+..
T Consensus 5 ~c~~~l~~~RW~~g~~CP~Cg~~ 27 (46)
T PF12760_consen 5 ACREYLEEIRWPDGFVCPHCGST 27 (46)
T ss_pred HHHHHHHHhcCCCCCCCCCCCCe
Confidence 455544332 33779999974
No 267
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=32.13 E-value=38 Score=17.07 Aligned_cols=10 Identities=40% Similarity=1.045 Sum_probs=6.9
Q ss_pred CCCCCCCccc
Q psy17995 44 GNCYECNQPL 53 (120)
Q Consensus 44 ~~CP~C~~~~ 53 (120)
..|..|+.+|
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 5677787765
No 268
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=31.94 E-value=34 Score=20.80 Aligned_cols=30 Identities=27% Similarity=0.428 Sum_probs=17.0
Q ss_pred CccCcccCCCcccCCCCcccccccCCccchhHHHH
Q psy17995 3 DQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDL 37 (120)
Q Consensus 3 ~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~ 37 (120)
+..||+|+......+ ..+=.++-|-.|-..
T Consensus 2 k~~CPlCkt~~n~gs-----k~~pNyntCT~Ck~~ 31 (61)
T PF05715_consen 2 KSLCPLCKTTLNVGS-----KDPPNYNTCTECKSQ 31 (61)
T ss_pred CccCCcccchhhcCC-----CCCCCccHHHHHhhh
Confidence 468999996432111 112356777777543
No 269
>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=31.86 E-value=22 Score=21.08 Aligned_cols=11 Identities=18% Similarity=0.643 Sum_probs=8.2
Q ss_pred CCCCCCCcccc
Q psy17995 44 GNCYECNQPLR 54 (120)
Q Consensus 44 ~~CP~C~~~~~ 54 (120)
..||.|++.+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 47888888764
No 270
>PF07807 RED_C: RED-like protein C-terminal region; InterPro: IPR012492 This family contains sequences that are similar to the C-terminal region of Red protein (Q13123 from SWISSPROT). This and related proteins are thought to be localised to the nucleus, and contain a RED repeat which consists of a number of RE and RD sequence elements []. The region in question has several conserved NLS sequences []. The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated or that the protein self-aggregates extremely efficiently [].
Probab=31.11 E-value=32 Score=23.65 Aligned_cols=21 Identities=33% Similarity=0.610 Sum_probs=17.9
Q ss_pred ccCCccCHHHHHHHHHHHHHH
Q psy17995 85 VEEDFNSLAEYNDYLEEIEEI 105 (120)
Q Consensus 85 ~~~~~~~l~~y~~yle~~E~~ 105 (120)
.+=||.|-.+|.+|.+++|-+
T Consensus 37 ~RwDFdT~EEy~~Y~~~kEal 57 (118)
T PF07807_consen 37 GRWDFDTEEEYSKYMEQKEAL 57 (118)
T ss_pred ccCCCCCHHHHHHHHhhhhhC
Confidence 345899999999999999974
No 271
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=30.97 E-value=24 Score=23.80 Aligned_cols=9 Identities=22% Similarity=0.755 Sum_probs=7.2
Q ss_pred CCCCCCCcc
Q psy17995 44 GNCYECNQP 52 (120)
Q Consensus 44 ~~CP~C~~~ 52 (120)
..||.|+..
T Consensus 88 ~~CP~Cgs~ 96 (114)
T PRK03681 88 RRCPQCHGD 96 (114)
T ss_pred CcCcCcCCC
Confidence 569999964
No 272
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=30.97 E-value=29 Score=20.42 Aligned_cols=10 Identities=20% Similarity=0.394 Sum_probs=8.0
Q ss_pred CCCCCCCccc
Q psy17995 44 GNCYECNQPL 53 (120)
Q Consensus 44 ~~CP~C~~~~ 53 (120)
..||.|++.-
T Consensus 25 IKCpRC~tiN 34 (51)
T PF10122_consen 25 IKCPRCKTIN 34 (51)
T ss_pred EECCCCCccc
Confidence 5799999854
No 273
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=30.56 E-value=20 Score=19.56 Aligned_cols=11 Identities=36% Similarity=0.911 Sum_probs=7.9
Q ss_pred CCCCCCCcccc
Q psy17995 44 GNCYECNQPLR 54 (120)
Q Consensus 44 ~~CP~C~~~~~ 54 (120)
..||.|+..+.
T Consensus 2 ~~CP~Cg~~lv 12 (39)
T PF01396_consen 2 EKCPKCGGPLV 12 (39)
T ss_pred cCCCCCCceeE
Confidence 36888887664
No 274
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=30.43 E-value=53 Score=24.20 Aligned_cols=16 Identities=25% Similarity=0.663 Sum_probs=12.6
Q ss_pred cCCCCCCCCCccccCC
Q psy17995 41 KGTGNCYECNQPLRRG 56 (120)
Q Consensus 41 ~~~~~CP~C~~~~~~~ 56 (120)
.|-+.||.|+.++...
T Consensus 154 AGRP~CPlCg~PldP~ 169 (177)
T TIGR03847 154 AGRPPCPLCGRPIDPD 169 (177)
T ss_pred CCCCCCCCCCCCCCCC
Confidence 4568999999998643
No 275
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=30.38 E-value=72 Score=18.81 Aligned_cols=29 Identities=17% Similarity=0.256 Sum_probs=15.4
Q ss_pred CCCCCCccccCCCCccccccchhHHHHHH
Q psy17995 45 NCYECNQPLRRGNFRVQLFDDSSVEKEVE 73 (120)
Q Consensus 45 ~CP~C~~~~~~~~~~~~~f~d~~~~~e~~ 73 (120)
.||.||..........-.-+|...+--+.
T Consensus 19 ~cp~cG~~T~~ahPaRFSPdDky~~yRi~ 47 (53)
T PF04135_consen 19 KCPPCGGPTESAHPARFSPDDKYSKYRIA 47 (53)
T ss_dssp BBTTTSSBSEESSSSSS-TTTTTCHHHHH
T ss_pred ccCCCCCCCcCCcCCCCCCCCccHHHHHH
Confidence 79999987765543222234544333333
No 276
>PRK02224 chromosome segregation protein; Provisional
Probab=30.22 E-value=81 Score=27.99 Aligned_cols=15 Identities=40% Similarity=0.953 Sum_probs=12.1
Q ss_pred CCCCCCCCccccCCC
Q psy17995 43 TGNCYECNQPLRRGN 57 (120)
Q Consensus 43 ~~~CP~C~~~~~~~~ 57 (120)
...||+|+.++....
T Consensus 451 ~~~Cp~C~r~~~~~~ 465 (880)
T PRK02224 451 AGKCPECGQPVEGSP 465 (880)
T ss_pred cccCCCCCCcCCCcc
Confidence 368999999997654
No 277
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=30.11 E-value=12 Score=28.66 Aligned_cols=27 Identities=19% Similarity=0.438 Sum_probs=16.0
Q ss_pred CCccchhHHHHHhhc-C--CCCCCCCCccc
Q psy17995 27 GHPLCEGCVDLLFLK-G--TGNCYECNQPL 53 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~-~--~~~CP~C~~~~ 53 (120)
.|+||..|=...... + ...||.|+...
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCCEE
Confidence 377787776554322 1 25688887643
No 278
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=30.07 E-value=30 Score=24.26 Aligned_cols=24 Identities=29% Similarity=0.729 Sum_probs=13.7
Q ss_pred cccCCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 24 NICGHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 24 ~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
+.||+.|=..=.. +- .-||.||..
T Consensus 5 t~Cg~~f~dgs~e--il---~GCP~CGg~ 28 (131)
T PF09845_consen 5 TKCGRVFEDGSKE--IL---SGCPECGGN 28 (131)
T ss_pred CcCCCCcCCCcHH--HH---ccCcccCCc
Confidence 5788887332221 11 349999874
No 279
>KOG3053|consensus
Probab=30.03 E-value=31 Score=27.07 Aligned_cols=53 Identities=19% Similarity=0.317 Sum_probs=33.9
Q ss_pred CCccCcccCCCcccCCCCcccccccC-----CccchhHHHHHhhcC-------CCCCCCCCccccC
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICG-----HPLCEGCVDLLFLKG-------TGNCYECNQPLRR 55 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CG-----H~fC~~Ci~~~~~~~-------~~~CP~C~~~~~~ 55 (120)
.+-.|-||..+- .|....-.+.||- |-.-++|+.+.+... +-.||.|++....
T Consensus 19 ~eR~CWiCF~Td-eDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYii 83 (293)
T KOG3053|consen 19 LERCCWICFATD-EDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYII 83 (293)
T ss_pred cceeEEEEeccC-cccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhee
Confidence 455799998632 3322222355664 446789999988642 2369999997654
No 280
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=29.88 E-value=34 Score=21.27 Aligned_cols=13 Identities=15% Similarity=0.713 Sum_probs=8.7
Q ss_pred ccchhHHHHHhhc
Q psy17995 29 PLCEGCVDLLFLK 41 (120)
Q Consensus 29 ~fC~~Ci~~~~~~ 41 (120)
-||+.|+.+....
T Consensus 11 gFCRNCLskWy~~ 23 (68)
T PF06844_consen 11 GFCRNCLSKWYRE 23 (68)
T ss_dssp S--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 5999999997763
No 281
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=29.12 E-value=25 Score=22.82 Aligned_cols=10 Identities=30% Similarity=0.561 Sum_probs=5.9
Q ss_pred CCCCCCCccc
Q psy17995 44 GNCYECNQPL 53 (120)
Q Consensus 44 ~~CP~C~~~~ 53 (120)
-.|..|+..|
T Consensus 55 V~C~~Cg~~L 64 (85)
T PTZ00083 55 VLCGGCSSQL 64 (85)
T ss_pred EEccccCCEe
Confidence 3466666655
No 282
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.48 E-value=32 Score=26.64 Aligned_cols=21 Identities=33% Similarity=0.648 Sum_probs=15.0
Q ss_pred HhhcCCCCCCCCCccccCCCC
Q psy17995 38 LFLKGTGNCYECNQPLRRGNF 58 (120)
Q Consensus 38 ~~~~~~~~CP~C~~~~~~~~~ 58 (120)
++......||+|++.|.+..+
T Consensus 14 ~f~kk~ieCPvC~tkFkkeev 34 (267)
T COG1655 14 LFYKKTIECPVCNTKFKKEEV 34 (267)
T ss_pred HHhhceeccCcccchhhhhhe
Confidence 344445789999999977643
No 283
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=28.35 E-value=27 Score=19.10 Aligned_cols=23 Identities=17% Similarity=0.547 Sum_probs=13.1
Q ss_pred CCCCCCCCccc-cCCCCccccccc
Q psy17995 43 TGNCYECNQPL-RRGNFRVQLFDD 65 (120)
Q Consensus 43 ~~~CP~C~~~~-~~~~~~~~~f~d 65 (120)
+..||.|+..- ...++....+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~g~~~r~i~~ 25 (47)
T PF14690_consen 2 PPRCPHCGSPSVHRHGYKTRRIRH 25 (47)
T ss_pred CccCCCcCCCceECCceEEEEEee
Confidence 35799999754 333444444444
No 284
>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=28.18 E-value=44 Score=18.78 Aligned_cols=40 Identities=28% Similarity=0.792 Sum_probs=19.8
Q ss_pred CcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccCCC
Q psy17995 6 CPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRRGN 57 (120)
Q Consensus 6 CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~~~ 57 (120)
|+.|...+.... +++..-|..|...|+ .|-.|+++|....
T Consensus 1 C~~C~~~I~~~~---~~~~~~~~~~H~~Cf---------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGTE---IVIKAMGKFWHPECF---------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSSS---EEEEETTEEEETTTS---------BETTTTCBTTTSS
T ss_pred CCCCCCCccCcE---EEEEeCCcEEEcccc---------ccCCCCCccCCCe
Confidence 556665433222 111244555555555 3556666666554
No 285
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=28.08 E-value=19 Score=21.88 Aligned_cols=26 Identities=19% Similarity=0.382 Sum_probs=22.2
Q ss_pred CCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 27 GHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
-|..|..|=...+......|..|+-+
T Consensus 15 tH~~CRRCGr~syhv~k~~CaaCGfg 40 (61)
T COG2126 15 THIRCRRCGRRSYHVRKKYCAACGFG 40 (61)
T ss_pred ceehhhhccchheeeccceecccCCC
Confidence 58999999888887767899999876
No 286
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=27.86 E-value=42 Score=21.21 Aligned_cols=8 Identities=38% Similarity=1.099 Sum_probs=6.1
Q ss_pred cCcccCCC
Q psy17995 5 ECPRCKTT 12 (120)
Q Consensus 5 ~CpiC~~~ 12 (120)
.||||+..
T Consensus 1 iCPVC~~~ 8 (82)
T PF14768_consen 1 ICPVCQKG 8 (82)
T ss_pred CCCccCCC
Confidence 49999853
No 287
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=27.86 E-value=34 Score=20.69 Aligned_cols=14 Identities=29% Similarity=0.691 Sum_probs=10.9
Q ss_pred CCCCCCCCccccCC
Q psy17995 43 TGNCYECNQPLRRG 56 (120)
Q Consensus 43 ~~~CP~C~~~~~~~ 56 (120)
.+.||.|+.+..+.
T Consensus 39 ~p~CPlC~s~M~~~ 52 (59)
T PF14169_consen 39 EPVCPLCKSPMVSG 52 (59)
T ss_pred CccCCCcCCccccc
Confidence 47899999987643
No 288
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=27.56 E-value=34 Score=31.47 Aligned_cols=11 Identities=18% Similarity=0.386 Sum_probs=8.8
Q ss_pred CCCCCCCCccc
Q psy17995 43 TGNCYECNQPL 53 (120)
Q Consensus 43 ~~~CP~C~~~~ 53 (120)
.-|||+||..-
T Consensus 503 GePCPVCGS~~ 513 (1047)
T PRK10246 503 GQPCPLCGSTS 513 (1047)
T ss_pred CCCcCCCCccc
Confidence 37899999854
No 289
>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=27.45 E-value=11 Score=26.71 Aligned_cols=24 Identities=21% Similarity=0.455 Sum_probs=13.8
Q ss_pred cccCCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 24 NICGHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 24 ~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
..|||...- .. ...-++||.|+..
T Consensus 116 ~~Cg~~~~~---~~--~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 116 ENCGHEVEL---TH--PERLPPCPKCGHT 139 (146)
T ss_pred ccCCCEEEe---cC--CCcCCCCCCCCCC
Confidence 468887521 11 1123799999863
No 290
>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=27.43 E-value=35 Score=28.78 Aligned_cols=8 Identities=38% Similarity=0.924 Sum_probs=4.4
Q ss_pred ccCcccCC
Q psy17995 4 QECPRCKT 11 (120)
Q Consensus 4 ~~CpiC~~ 11 (120)
+-||.|+.
T Consensus 27 ~yCp~CL~ 34 (483)
T PF05502_consen 27 YYCPNCLF 34 (483)
T ss_pred eECccccc
Confidence 44666664
No 291
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=27.19 E-value=25 Score=21.47 Aligned_cols=37 Identities=16% Similarity=0.213 Sum_probs=20.0
Q ss_pred CCCCccccc--ccCCccchhHHHHHhhc-CCCCCCCCCccc
Q psy17995 16 KPTLKLMVN--ICGHPLCEGCVDLLFLK-GTGNCYECNQPL 53 (120)
Q Consensus 16 ~p~~~~~~~--~CGH~fC~~Ci~~~~~~-~~~~CP~C~~~~ 53 (120)
+|.-+++.. |||.+|=-+ +..++.. ....||.|.-.+
T Consensus 15 ~~e~~~ftyPCPCGDRFeIs-LeDl~~GE~VArCPSCSLiv 54 (67)
T COG5216 15 SREEKTFTYPCPCGDRFEIS-LEDLRNGEVVARCPSCSLIV 54 (67)
T ss_pred cCCCceEEecCCCCCEeEEE-HHHhhCCceEEEcCCceEEE
Confidence 344444443 899998332 2222221 136899997644
No 292
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=27.06 E-value=22 Score=29.09 Aligned_cols=29 Identities=14% Similarity=0.260 Sum_probs=17.5
Q ss_pred cCCccchhHHHHHhhc-CCCCCCCCCccccC
Q psy17995 26 CGHPLCEGCVDLLFLK-GTGNCYECNQPLRR 55 (120)
Q Consensus 26 CGH~fC~~Ci~~~~~~-~~~~CP~C~~~~~~ 55 (120)
-||+-|..+++.--.. ....|| ||+.+++
T Consensus 241 ~~c~~C~~~~~~~~~~~~~~~Cp-CG~~i~~ 270 (374)
T TIGR00375 241 TACEACGEPAVSEDAETACANCP-CGGRIKK 270 (374)
T ss_pred hhhcccCCcCCchhhhhcCCCCC-CCCccee
Confidence 4666666666533221 126899 9998754
No 293
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=27.02 E-value=24 Score=26.71 Aligned_cols=15 Identities=20% Similarity=0.512 Sum_probs=9.5
Q ss_pred CCCCCCCccccCCCC
Q psy17995 44 GNCYECNQPLRRGNF 58 (120)
Q Consensus 44 ~~CP~C~~~~~~~~~ 58 (120)
..||.|++.|+-..|
T Consensus 78 ~~C~lc~KlFkg~eF 92 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEF 92 (214)
T ss_dssp EEE-SSS-EESSHHH
T ss_pred ECCCCCCcccCChHH
Confidence 579999998875443
No 294
>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=26.92 E-value=24 Score=19.42 Aligned_cols=10 Identities=30% Similarity=0.840 Sum_probs=5.8
Q ss_pred ccCCccchhH
Q psy17995 25 ICGHPLCEGC 34 (120)
Q Consensus 25 ~CGH~fC~~C 34 (120)
.||..||..=
T Consensus 18 ~C~~~FC~~H 27 (43)
T PF01428_consen 18 HCGKSFCLKH 27 (43)
T ss_dssp TTS-EE-TTT
T ss_pred CCCcccCccc
Confidence 4999998654
No 295
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=26.59 E-value=24 Score=21.03 Aligned_cols=12 Identities=25% Similarity=0.672 Sum_probs=9.7
Q ss_pred CCCCCCCCcccc
Q psy17995 43 TGNCYECNQPLR 54 (120)
Q Consensus 43 ~~~CP~C~~~~~ 54 (120)
...||.||.+.-
T Consensus 14 ~~~Cp~cGipth 25 (55)
T PF13824_consen 14 NFECPDCGIPTH 25 (55)
T ss_pred CCcCCCCCCcCc
Confidence 478999998764
No 296
>PLN00209 ribosomal protein S27; Provisional
Probab=26.47 E-value=29 Score=22.63 Aligned_cols=10 Identities=30% Similarity=0.554 Sum_probs=6.1
Q ss_pred CCCCCCCccc
Q psy17995 44 GNCYECNQPL 53 (120)
Q Consensus 44 ~~CP~C~~~~ 53 (120)
-.|..|+..|
T Consensus 56 V~C~~Cg~~L 65 (86)
T PLN00209 56 VVCGSCQTVL 65 (86)
T ss_pred EEccccCCEe
Confidence 3566666655
No 297
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=26.30 E-value=62 Score=23.89 Aligned_cols=42 Identities=19% Similarity=0.425 Sum_probs=25.2
Q ss_pred ccCcccCCCcccCCCCc-ccc--cccCCccchhHHHHHhhcCCCCCCCCCc
Q psy17995 4 QECPRCKTTKYRKPTLK-LMV--NICGHPLCEGCVDLLFLKGTGNCYECNQ 51 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~-~~~--~~CGH~fC~~Ci~~~~~~~~~~CP~C~~ 51 (120)
+.|.+|.++-..=|-.. -++ ..||-.|-..|... ..||.|..
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~------~~CpkC~R 197 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK------KSCPKCAR 197 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC------CCCCCcHh
Confidence 57888885322223111 112 26888888888752 56999964
No 298
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=26.10 E-value=46 Score=19.14 Aligned_cols=23 Identities=26% Similarity=0.501 Sum_probs=10.9
Q ss_pred ccCCccchhHHHHHhhcCCCCCCCC
Q psy17995 25 ICGHPLCEGCVDLLFLKGTGNCYEC 49 (120)
Q Consensus 25 ~CGH~fC~~Ci~~~~~~~~~~CP~C 49 (120)
.|||.+=.+=-.+. .+...||.|
T Consensus 33 ~Cgh~w~~~v~~R~--~~~~~CP~C 55 (55)
T PF14311_consen 33 KCGHEWKASVNDRT--RRGKGCPYC 55 (55)
T ss_pred CCCCeeEccHhhhc--cCCCCCCCC
Confidence 46776632222222 233567766
No 299
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=25.99 E-value=41 Score=30.76 Aligned_cols=34 Identities=24% Similarity=0.493 Sum_probs=21.0
Q ss_pred cCcccCCCcccCCC----CcccccccCCccchhHHHHH
Q psy17995 5 ECPRCKTTKYRKPT----LKLMVNICGHPLCEGCVDLL 38 (120)
Q Consensus 5 ~CpiC~~~~~~~p~----~~~~~~~CGH~fC~~Ci~~~ 38 (120)
.|..|....+.... .+-.-..||++||..|-..-
T Consensus 462 tC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnR 499 (1374)
T PTZ00303 462 SCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKR 499 (1374)
T ss_pred cccCcCCcccccccccccccccccCCccccCccccCCc
Confidence 59999963323210 11112379999999997653
No 300
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=25.94 E-value=51 Score=28.95 Aligned_cols=38 Identities=18% Similarity=0.472 Sum_probs=21.9
Q ss_pred ccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcCCCCCCCCCccccC
Q psy17995 4 QECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~ 55 (120)
-.|+-|... +... .-..||+. ...+...||.||..+..
T Consensus 16 kFC~~CG~~-l~~~----~Cp~CG~~---------~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 16 RFCQKCGTS-LTHK----PCPQCGTE---------VPVDEAHCPNCGAETGT 53 (645)
T ss_pred ccccccCCC-CCCC----cCCCCCCC---------CCcccccccccCCcccc
Confidence 369999853 2111 11245654 22345789999987754
No 302
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=25.55 E-value=51 Score=18.33 Aligned_cols=11 Identities=18% Similarity=0.289 Sum_probs=6.5
Q ss_pred CCCCCCCcccc
Q psy17995 44 GNCYECNQPLR 54 (120)
Q Consensus 44 ~~CP~C~~~~~ 54 (120)
..||.|+....
T Consensus 21 ~vC~~Cg~~~~ 31 (52)
T smart00661 21 FVCRKCGYEEP 31 (52)
T ss_pred EECCcCCCeEE
Confidence 45777765443
No 303
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=25.38 E-value=30 Score=18.48 Aligned_cols=10 Identities=40% Similarity=0.996 Sum_probs=4.8
Q ss_pred CCCCCCcccc
Q psy17995 45 NCYECNQPLR 54 (120)
Q Consensus 45 ~CP~C~~~~~ 54 (120)
.||.|+.++.
T Consensus 2 fC~~CG~~l~ 11 (34)
T PF14803_consen 2 FCPQCGGPLE 11 (34)
T ss_dssp B-TTT--B-E
T ss_pred ccccccChhh
Confidence 5999999875
No 304
>PRK03922 hypothetical protein; Provisional
Probab=25.33 E-value=39 Score=23.03 Aligned_cols=15 Identities=27% Similarity=0.760 Sum_probs=11.4
Q ss_pred CCCCCCCCCccccCC
Q psy17995 42 GTGNCYECNQPLRRG 56 (120)
Q Consensus 42 ~~~~CP~C~~~~~~~ 56 (120)
|...||.|+.++...
T Consensus 48 G~~~cP~cge~~~~a 62 (113)
T PRK03922 48 GLTICPKCGEPFDSA 62 (113)
T ss_pred CcccCCCCCCcCCcE
Confidence 346799999988653
No 305
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=25.16 E-value=18 Score=26.70 Aligned_cols=24 Identities=38% Similarity=0.957 Sum_probs=14.6
Q ss_pred chhHHHHHhhcCCCCCCCCCccccC
Q psy17995 31 CEGCVDLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 31 C~~Ci~~~~~~~~~~CP~C~~~~~~ 55 (120)
|..|-.. |..+...||.||.++++
T Consensus 142 C~GC~~~-f~~~~~~Cp~CG~~~~~ 165 (177)
T COG1439 142 CHGCKRI-FPEPKDFCPICGSPLKR 165 (177)
T ss_pred EecCcee-cCCCCCcCCCCCCceEE
Confidence 5555433 22334679999998754
No 306
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=24.90 E-value=54 Score=24.71 Aligned_cols=22 Identities=27% Similarity=0.736 Sum_probs=15.7
Q ss_pred cCcccCCCcccCCCCcccccccCCccchhHHHHHh
Q psy17995 5 ECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLF 39 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~ 39 (120)
.||+|.. .-.+-+|..|+..-+
T Consensus 1 ~C~iC~~-------------~~~~~~C~~C~~~~L 22 (302)
T PF10186_consen 1 QCPICHN-------------SRRRFYCANCVNNRL 22 (302)
T ss_pred CCCCCCC-------------CCCCeECHHHHHHHH
Confidence 5999992 124678999998743
No 307
>smart00570 AWS associated with SET domains. subdomain of PRESET
Probab=24.79 E-value=1.1e+02 Score=17.78 Aligned_cols=24 Identities=25% Similarity=0.815 Sum_probs=16.4
Q ss_pred cccCCccchhHHHHHhhcC-CCCCCCCCcc
Q psy17995 24 NICGHPLCEGCVDLLFLKG-TGNCYECNQP 52 (120)
Q Consensus 24 ~~CGH~fC~~Ci~~~~~~~-~~~CP~C~~~ 52 (120)
.+|| +.||.+++..- +..|| |+..
T Consensus 16 ~~Cg----sdClNR~l~~EC~~~C~-~G~~ 40 (51)
T smart00570 16 GACG----SDCLNRMLLIECSSDCP-CGSY 40 (51)
T ss_pred CCcc----hHHHHHHHhhhcCCCCC-CCcC
Confidence 4899 78999987642 35677 4443
No 308
>KOG3726|consensus
Probab=24.68 E-value=51 Score=29.23 Aligned_cols=42 Identities=17% Similarity=0.416 Sum_probs=27.6
Q ss_pred cCcccCCCcccCCCCccc-ccccCCccchhHHHHHhhcCCCCCCCCCcc
Q psy17995 5 ECPRCKTTKYRKPTLKLM-VNICGHPLCEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 5 ~CpiC~~~~~~~p~~~~~-~~~CGH~fC~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
.|-+|+. ..+|.+-+- .+.|+-.+|.+|.... ...||+|+--
T Consensus 656 ~C~vcq~--pedse~~v~rt~~C~~~~C~~c~~~~----~~~~~vC~~~ 698 (717)
T KOG3726|consen 656 TCKVCQL--PEDSETDVCRTTFCYTPYCVACSLDY----ASISEVCGPD 698 (717)
T ss_pred HHHHhcC--CcCccccccCccccCCcchHhhhhhh----hccCcccCch
Confidence 4778883 355533211 2379999999997654 3569999853
No 309
>PRK10220 hypothetical protein; Provisional
Probab=24.59 E-value=55 Score=22.29 Aligned_cols=29 Identities=24% Similarity=0.652 Sum_probs=15.8
Q ss_pred CCCccCcccCCCcccCCCCccccc-ccCCcc
Q psy17995 1 MDDQECPRCKTTKYRKPTLKLMVN-ICGHPL 30 (120)
Q Consensus 1 ~d~~~CpiC~~~~~~~p~~~~~~~-~CGH~f 30 (120)
|.--.||.|.. -|.=+.-.+++- .|||-+
T Consensus 1 m~lP~CP~C~s-eytY~d~~~~vCpeC~hEW 30 (111)
T PRK10220 1 MSLPHCPKCNS-EYTYEDNGMYICPECAHEW 30 (111)
T ss_pred CCCCcCCCCCC-cceEcCCCeEECCcccCcC
Confidence 56678999985 332222222343 566653
No 310
>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=24.42 E-value=9.6 Score=25.15 Aligned_cols=48 Identities=19% Similarity=0.322 Sum_probs=15.0
Q ss_pred ccCcccCCCcc-cCCCCcccccccCCccchhHHHHHhhc---CCCCCCCCCcccc
Q psy17995 4 QECPRCKTTKY-RKPTLKLMVNICGHPLCEGCVDLLFLK---GTGNCYECNQPLR 54 (120)
Q Consensus 4 ~~CpiC~~~~~-~~p~~~~~~~~CGH~fC~~Ci~~~~~~---~~~~CP~C~~~~~ 54 (120)
..|++|.+.+- .++ ...+.+=||.| ..|.-.++.- +...|++|+..+.
T Consensus 15 E~C~~C~~~i~~~~~--~~~~C~~GH~w-~RC~lT~l~i~~~~~r~C~~C~~~~l 66 (99)
T PF12660_consen 15 EKCPICGAPIPFDDL--DEAQCENGHVW-PRCALTFLPIQTPGVRVCPVCGRRAL 66 (99)
T ss_dssp --------------S--SEEE-TTS-EE-EB-SSS-SBS-SS-EEE-TTT--EEE
T ss_pred ccccccccccccCCc--CEeECCCCCEE-eeeeeeeeeeccCCeeEcCCCCCEEe
Confidence 47999997442 333 22234669997 4554444332 2367999997654
No 311
>KOG1814|consensus
Probab=24.41 E-value=42 Score=28.04 Aligned_cols=35 Identities=31% Similarity=0.822 Sum_probs=23.9
Q ss_pred ccCcccCCCcccCCC--CcccccccCCccchhHHHHHh
Q psy17995 4 QECPRCKTTKYRKPT--LKLMVNICGHPLCEGCVDLLF 39 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~--~~~~~~~CGH~fC~~Ci~~~~ 39 (120)
-.||.|.. +...+. -+|.-+.|||.||--|-..+.
T Consensus 369 krCP~C~v-~IEr~eGCnKM~C~~c~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 369 KRCPKCKV-VIERSEGCNKMHCTKCGTYFCWICAELLY 405 (445)
T ss_pred CCCCcccc-eeecCCCccceeeccccccceeehhhhcC
Confidence 37999995 443332 255567899999888876655
No 312
>KOG4021|consensus
Probab=24.33 E-value=41 Score=25.44 Aligned_cols=22 Identities=14% Similarity=0.161 Sum_probs=14.6
Q ss_pred hhHHHHHhhcCCCCCCCCCccc
Q psy17995 32 EGCVDLLFLKGTGNCYECNQPL 53 (120)
Q Consensus 32 ~~Ci~~~~~~~~~~CP~C~~~~ 53 (120)
..||.+.-..-..+||+|+-..
T Consensus 97 ktCIrkn~~~~gnpCPICRDey 118 (239)
T KOG4021|consen 97 KTCIRKNGRFLGNPCPICRDEY 118 (239)
T ss_pred hHHHhhcCeecCCCCCccccce
Confidence 3577765443236899998754
No 313
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=24.31 E-value=40 Score=18.17 Aligned_cols=10 Identities=60% Similarity=1.477 Sum_probs=7.2
Q ss_pred CccCcccCCC
Q psy17995 3 DQECPRCKTT 12 (120)
Q Consensus 3 ~~~CpiC~~~ 12 (120)
++.||-|..+
T Consensus 5 ~v~CP~C~s~ 14 (36)
T PF03811_consen 5 DVHCPRCQST 14 (36)
T ss_pred eeeCCCCCCC
Confidence 3579999853
No 314
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=24.16 E-value=85 Score=23.14 Aligned_cols=14 Identities=36% Similarity=0.714 Sum_probs=11.1
Q ss_pred CCCCCCCCccccCC
Q psy17995 43 TGNCYECNQPLRRG 56 (120)
Q Consensus 43 ~~~CP~C~~~~~~~ 56 (120)
.+.||.|+..++..
T Consensus 130 ~p~C~~Cgg~lrp~ 143 (224)
T cd01412 130 LPRCPKCGGLLRPG 143 (224)
T ss_pred CCCCCCCCCccCCc
Confidence 47899999887654
No 315
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=23.95 E-value=15 Score=23.09 Aligned_cols=22 Identities=18% Similarity=0.526 Sum_probs=6.4
Q ss_pred chhHHHHHhhcCCCCCCCCCcc
Q psy17995 31 CEGCVDLLFLKGTGNCYECNQP 52 (120)
Q Consensus 31 C~~Ci~~~~~~~~~~CP~C~~~ 52 (120)
|.+|...........||.||-.
T Consensus 12 C~aCf~~t~~~~k~FCp~CGn~ 33 (73)
T PF08772_consen 12 CHACFKITKDMTKQFCPKCGNA 33 (73)
T ss_dssp -SSS--EES-SS--S-SSS--S
T ss_pred ccccccCcCCCCceeCcccCCC
Confidence 4444433222233568888763
No 316
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=23.31 E-value=38 Score=23.12 Aligned_cols=8 Identities=38% Similarity=0.870 Sum_probs=5.6
Q ss_pred CCCCCccc
Q psy17995 46 CYECNQPL 53 (120)
Q Consensus 46 CP~C~~~~ 53 (120)
||+|+..+
T Consensus 1 CPvCg~~l 8 (113)
T PF09862_consen 1 CPVCGGEL 8 (113)
T ss_pred CCCCCCce
Confidence 77777755
No 317
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=23.20 E-value=87 Score=22.21 Aligned_cols=12 Identities=25% Similarity=0.489 Sum_probs=10.3
Q ss_pred CCCCCCCCcccc
Q psy17995 43 TGNCYECNQPLR 54 (120)
Q Consensus 43 ~~~CP~C~~~~~ 54 (120)
.+.||.||.++.
T Consensus 128 ~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 128 NFTCPRCGAMLD 139 (158)
T ss_pred CCcCCCCCCEee
Confidence 489999999885
No 318
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=23.08 E-value=30 Score=17.98 Aligned_cols=7 Identities=43% Similarity=1.426 Sum_probs=2.5
Q ss_pred cCcccCC
Q psy17995 5 ECPRCKT 11 (120)
Q Consensus 5 ~CpiC~~ 11 (120)
.||.|..
T Consensus 4 ~Cp~C~s 10 (30)
T PF08274_consen 4 KCPLCGS 10 (30)
T ss_dssp --TTT--
T ss_pred CCCCCCC
Confidence 5888875
No 319
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=22.82 E-value=92 Score=18.97 Aligned_cols=12 Identities=17% Similarity=0.650 Sum_probs=9.6
Q ss_pred CCCCCCCccccC
Q psy17995 44 GNCYECNQPLRR 55 (120)
Q Consensus 44 ~~CP~C~~~~~~ 55 (120)
..||+|++++..
T Consensus 9 ~HC~VCg~aIp~ 20 (64)
T COG4068 9 RHCVVCGKAIPP 20 (64)
T ss_pred ccccccCCcCCC
Confidence 569999998864
No 320
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=22.67 E-value=95 Score=22.86 Aligned_cols=14 Identities=29% Similarity=0.591 Sum_probs=11.2
Q ss_pred CCCCCCCCccccCC
Q psy17995 43 TGNCYECNQPLRRG 56 (120)
Q Consensus 43 ~~~CP~C~~~~~~~ 56 (120)
.+.||.|+..++..
T Consensus 133 ~p~C~~Cg~~lrP~ 146 (218)
T cd01407 133 VPRCPKCGGLLRPD 146 (218)
T ss_pred CCcCCCCCCccCCC
Confidence 47899999987754
No 321
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.55 E-value=72 Score=22.01 Aligned_cols=13 Identities=15% Similarity=0.468 Sum_probs=10.1
Q ss_pred CCCCCCCCccccC
Q psy17995 43 TGNCYECNQPLRR 55 (120)
Q Consensus 43 ~~~CP~C~~~~~~ 55 (120)
...|+.|+..|..
T Consensus 53 RyrC~~C~~tf~~ 65 (129)
T COG3677 53 RYKCKSCGSTFTV 65 (129)
T ss_pred ccccCCcCcceee
Confidence 3789999988753
No 322
>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=22.38 E-value=43 Score=19.14 Aligned_cols=8 Identities=50% Similarity=1.149 Sum_probs=3.3
Q ss_pred CccCcccC
Q psy17995 3 DQECPRCK 10 (120)
Q Consensus 3 ~~~CpiC~ 10 (120)
++.||+|.
T Consensus 34 ~w~CP~C~ 41 (47)
T PF00301_consen 34 DWVCPVCG 41 (47)
T ss_dssp T-B-TTTS
T ss_pred CCcCcCCC
Confidence 44555555
No 323
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=22.23 E-value=31 Score=32.63 Aligned_cols=31 Identities=29% Similarity=0.714 Sum_probs=20.2
Q ss_pred CCccchhHHHHHhhc----------CCCCCCCCCccccCCC
Q psy17995 27 GHPLCEGCVDLLFLK----------GTGNCYECNQPLRRGN 57 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~----------~~~~CP~C~~~~~~~~ 57 (120)
.|-.|..|-.--+.. +...||.|++++++.+
T Consensus 913 PHY~Cp~Cky~Ef~~d~svgsGfDLpdK~CPkCg~pl~kDG 953 (1444)
T COG2176 913 PHYLCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTPLKKDG 953 (1444)
T ss_pred ccccCCCCceeeeecCCCcCCCCCCCCCCCCcCCCccccCC
Confidence 377777775433322 1257999999998763
No 324
>KOG1818|consensus
Probab=22.12 E-value=35 Score=29.91 Aligned_cols=51 Identities=27% Similarity=0.601 Sum_probs=32.5
Q ss_pred CCccCcccCCCcccCCCCcccccccCCccchhHHHHHhhcC-------CCCCCCCCccc
Q psy17995 2 DDQECPRCKTTKYRKPTLKLMVNICGHPLCEGCVDLLFLKG-------TGNCYECNQPL 53 (120)
Q Consensus 2 d~~~CpiC~~~~~~~p~~~~~~~~CGH~fC~~Ci~~~~~~~-------~~~CP~C~~~~ 53 (120)
|...|-.|.. .|..=+.+-.-..||.+||..|...-+..+ ...|=.|-+.+
T Consensus 164 D~~~C~rCr~-~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l 221 (634)
T KOG1818|consen 164 DSEECLRCRV-KFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELL 221 (634)
T ss_pred cccccceeee-eeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHh
Confidence 3457888884 665444333334799999999987765431 24577774444
No 325
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=22.11 E-value=41 Score=18.27 Aligned_cols=26 Identities=19% Similarity=0.422 Sum_probs=17.8
Q ss_pred CccchhHHHHHhh--cCCCCCCCCCccc
Q psy17995 28 HPLCEGCVDLLFL--KGTGNCYECNQPL 53 (120)
Q Consensus 28 H~fC~~Ci~~~~~--~~~~~CP~C~~~~ 53 (120)
-.+|..|-..+|. .....|+.|+...
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~~~ 38 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKVKC 38 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCCch
Confidence 4578888777775 2346788887654
No 326
>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=21.88 E-value=40 Score=17.71 Aligned_cols=11 Identities=18% Similarity=0.440 Sum_probs=7.6
Q ss_pred CCCCCCCcccc
Q psy17995 44 GNCYECNQPLR 54 (120)
Q Consensus 44 ~~CP~C~~~~~ 54 (120)
..||.|+..|.
T Consensus 26 v~C~~C~~~~~ 36 (38)
T TIGR02098 26 VRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEE
Confidence 46888887653
No 327
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=21.83 E-value=45 Score=22.68 Aligned_cols=25 Identities=20% Similarity=0.551 Sum_probs=12.9
Q ss_pred ccCcccCCCcccCCCCccccc-ccCCc
Q psy17995 4 QECPRCKTTKYRKPTLKLMVN-ICGHP 29 (120)
Q Consensus 4 ~~CpiC~~~~~~~p~~~~~~~-~CGH~ 29 (120)
-.||.|.+ -|.=+.-.+++- .|||-
T Consensus 3 p~CP~C~s-eytY~dg~~~iCpeC~~E 28 (109)
T TIGR00686 3 PPCPKCNS-EYTYHDGTQLICPSCLYE 28 (109)
T ss_pred CcCCcCCC-cceEecCCeeECcccccc
Confidence 36999985 332222222343 56665
No 328
>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=21.74 E-value=52 Score=19.29 Aligned_cols=6 Identities=33% Similarity=1.016 Sum_probs=3.0
Q ss_pred CCCCCC
Q psy17995 45 NCYECN 50 (120)
Q Consensus 45 ~CP~C~ 50 (120)
.||.||
T Consensus 41 vc~~cG 46 (56)
T PF01783_consen 41 VCPSCG 46 (56)
T ss_dssp BCTTTB
T ss_pred eeCCCC
Confidence 455554
No 329
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=21.70 E-value=56 Score=22.79 Aligned_cols=12 Identities=25% Similarity=0.742 Sum_probs=9.6
Q ss_pred CCCCCCCCCccc
Q psy17995 42 GTGNCYECNQPL 53 (120)
Q Consensus 42 ~~~~CP~C~~~~ 53 (120)
|...||.|++.+
T Consensus 109 GeK~C~~C~tGi 120 (128)
T PF11682_consen 109 GEKYCPKCGTGI 120 (128)
T ss_pred cCEecCCCCCcc
Confidence 457899999866
No 330
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=21.52 E-value=50 Score=19.13 Aligned_cols=8 Identities=50% Similarity=1.149 Sum_probs=4.0
Q ss_pred CccCcccC
Q psy17995 3 DQECPRCK 10 (120)
Q Consensus 3 ~~~CpiC~ 10 (120)
++.||+|.
T Consensus 34 ~w~CP~C~ 41 (50)
T cd00730 34 DWVCPVCG 41 (50)
T ss_pred CCCCCCCC
Confidence 34555554
No 331
>PF14165 YtzH: YtzH-like protein
Probab=21.32 E-value=81 Score=20.57 Aligned_cols=27 Identities=30% Similarity=0.370 Sum_probs=22.0
Q ss_pred CCccCHHHHHHHHHHHHHHHHHHhcccchhh
Q psy17995 87 EDFNSLAEYNDYLEEIEEIVFNLCNNIDILE 117 (120)
Q Consensus 87 ~~~~~l~~y~~yle~~E~~i~~L~~~~d~~~ 117 (120)
+-+||..+| |+||++|..|..+.++..
T Consensus 20 DccgTvsEc----EQieRLvksLm~n~~i~~ 46 (87)
T PF14165_consen 20 DCCGTVSEC----EQIERLVKSLMANPNIDA 46 (87)
T ss_pred hccCcHHHH----HHHHHHHHHHHcCCCcCH
Confidence 556998887 579999999999887753
No 332
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=21.30 E-value=33 Score=28.49 Aligned_cols=31 Identities=23% Similarity=0.334 Sum_probs=21.9
Q ss_pred ccCCccchhHHHHHhhcCCCCCCCCCccccC
Q psy17995 25 ICGHPLCEGCVDLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 25 ~CGH~fC~~Ci~~~~~~~~~~CP~C~~~~~~ 55 (120)
+=|-+-|..|....-....+.||.|+.++..
T Consensus 217 ~~~~~~C~~C~~~~~~~~~~~CpRC~~~Ly~ 247 (418)
T COG2995 217 REGLRSCLCCHYILPHDAEPRCPRCGSKLYV 247 (418)
T ss_pred cccceecccccccCCHhhCCCCCCCCChhhc
Confidence 3456678888665444345799999998854
No 333
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=21.27 E-value=47 Score=18.91 Aligned_cols=11 Identities=27% Similarity=0.733 Sum_probs=8.5
Q ss_pred CCCCCCCCCcc
Q psy17995 42 GTGNCYECNQP 52 (120)
Q Consensus 42 ~~~~CP~C~~~ 52 (120)
+...||.|++.
T Consensus 10 GirkCp~CGt~ 20 (44)
T PF14952_consen 10 GIRKCPKCGTY 20 (44)
T ss_pred ccccCCcCcCc
Confidence 55789999873
No 334
>smart00355 ZnF_C2H2 zinc finger.
Probab=21.19 E-value=50 Score=14.70 Aligned_cols=10 Identities=30% Similarity=0.952 Sum_probs=7.2
Q ss_pred CCCCCCcccc
Q psy17995 45 NCYECNQPLR 54 (120)
Q Consensus 45 ~CP~C~~~~~ 54 (120)
.|+.|+..+.
T Consensus 2 ~C~~C~~~f~ 11 (26)
T smart00355 2 RCPECGKVFK 11 (26)
T ss_pred CCCCCcchhC
Confidence 5888887664
No 335
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=21.15 E-value=66 Score=23.60 Aligned_cols=19 Identities=26% Similarity=0.468 Sum_probs=13.1
Q ss_pred HHHhhcCCCCCCCCCccccC
Q psy17995 36 DLLFLKGTGNCYECNQPLRR 55 (120)
Q Consensus 36 ~~~~~~~~~~CP~C~~~~~~ 55 (120)
+.++..+ +.||.||..+..
T Consensus 126 deA~~~~-F~Cp~Cg~~L~~ 144 (176)
T COG1675 126 DEAMELG-FTCPKCGEDLEE 144 (176)
T ss_pred HHHHHhC-CCCCCCCchhhh
Confidence 3344433 899999998864
No 336
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=21.10 E-value=26 Score=23.01 Aligned_cols=27 Identities=30% Similarity=0.632 Sum_probs=22.4
Q ss_pred CCccchhHHHHHhhcCCCCCCCCCccc
Q psy17995 27 GHPLCEGCVDLLFLKGTGNCYECNQPL 53 (120)
Q Consensus 27 GH~fC~~Ci~~~~~~~~~~CP~C~~~~ 53 (120)
-|.+|..|=...|......|..|+-+-
T Consensus 15 tHtlCrRCG~~syH~qK~~CasCGyps 41 (91)
T PTZ00073 15 THTLCRRCGKRSFHVQKKRCASCGYPS 41 (91)
T ss_pred CcchhcccCccccccccccchhcCCch
Confidence 599999998888877668899998754
No 337
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=21.08 E-value=78 Score=19.16 Aligned_cols=13 Identities=38% Similarity=0.700 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHhc
Q psy17995 99 LEEIEEIVFNLCN 111 (120)
Q Consensus 99 le~~E~~i~~L~~ 111 (120)
-++||++|.+|..
T Consensus 30 ~~eVe~~I~klak 42 (60)
T PF08069_consen 30 PEEVEELIVKLAK 42 (60)
T ss_dssp HHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHH
Confidence 4789999999864
No 338
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=21.01 E-value=39 Score=20.18 Aligned_cols=9 Identities=22% Similarity=0.497 Sum_probs=6.9
Q ss_pred CCCCCCccc
Q psy17995 45 NCYECNQPL 53 (120)
Q Consensus 45 ~CP~C~~~~ 53 (120)
.||+||..-
T Consensus 6 ~CP~CgnKT 14 (55)
T PF14205_consen 6 LCPICGNKT 14 (55)
T ss_pred ECCCCCCcc
Confidence 599998654
No 339
>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=20.86 E-value=38 Score=19.06 Aligned_cols=6 Identities=50% Similarity=1.303 Sum_probs=5.2
Q ss_pred ccCCcc
Q psy17995 25 ICGHPL 30 (120)
Q Consensus 25 ~CGH~f 30 (120)
.|||.|
T Consensus 32 ~Cg~tf 37 (47)
T PF04606_consen 32 ECGHTF 37 (47)
T ss_pred cCCCEE
Confidence 699987
No 340
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=20.58 E-value=42 Score=18.57 Aligned_cols=9 Identities=33% Similarity=0.803 Sum_probs=4.7
Q ss_pred CCCCCCCcc
Q psy17995 44 GNCYECNQP 52 (120)
Q Consensus 44 ~~CP~C~~~ 52 (120)
.+||.|+..
T Consensus 4 ~pCP~CGG~ 12 (40)
T PF08273_consen 4 GPCPICGGK 12 (40)
T ss_dssp E--TTTT-T
T ss_pred CCCCCCcCc
Confidence 579999874
No 341
>KOG3460|consensus
Probab=20.57 E-value=47 Score=21.59 Aligned_cols=25 Identities=16% Similarity=0.414 Sum_probs=17.5
Q ss_pred hhhhcccC--Cc-cCHHHHHHHHHHHHH
Q psy17995 80 KDYNKVEE--DF-NSLAEYNDYLEEIEE 104 (120)
Q Consensus 80 k~~~~~~~--~~-~~l~~y~~yle~~E~ 104 (120)
.+|-|.+. .. |+|..|+.|+..|--
T Consensus 17 rVyVKlr~drel~G~L~afD~HlNmvL~ 44 (91)
T KOG3460|consen 17 RVYVKLRSDRELRGTLHAFDEHLNMVLG 44 (91)
T ss_pred eEEEEecCChhhhcchhhhHHhhhhhhh
Confidence 34556663 34 999999999877543
No 342
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=20.54 E-value=74 Score=17.41 Aligned_cols=17 Identities=24% Similarity=0.669 Sum_probs=8.2
Q ss_pred HHHHhhcCCCCCCCCCc
Q psy17995 35 VDLLFLKGTGNCYECNQ 51 (120)
Q Consensus 35 i~~~~~~~~~~CP~C~~ 51 (120)
++.+++..+..||+|.+
T Consensus 5 lelll~~H~~dC~~C~~ 21 (41)
T PF10588_consen 5 LELLLANHPLDCPTCDK 21 (41)
T ss_dssp HHHHHTT----TTT-TT
T ss_pred HHHHHhCCCCcCcCCCC
Confidence 45566666788999975
No 343
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=20.34 E-value=69 Score=20.72 Aligned_cols=12 Identities=33% Similarity=0.924 Sum_probs=7.0
Q ss_pred CCCCCCCccccC
Q psy17995 44 GNCYECNQPLRR 55 (120)
Q Consensus 44 ~~CP~C~~~~~~ 55 (120)
..||.|+++++-
T Consensus 34 S~C~~C~~~L~~ 45 (92)
T PF06750_consen 34 SHCPHCGHPLSW 45 (92)
T ss_pred CcCcCCCCcCcc
Confidence 456666666653
No 344
>PF10170 C6_DPF: Cysteine-rich domain; InterPro: IPR018785 This entry represents the N-terminal approximately 100 amino acids of a family of proteins found in a range of organisms, including human, chicken and Drosophila [, , ]. It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed.
Probab=20.30 E-value=95 Score=20.65 Aligned_cols=11 Identities=27% Similarity=0.576 Sum_probs=5.4
Q ss_pred CccchhHHHHH
Q psy17995 28 HPLCEGCVDLL 38 (120)
Q Consensus 28 H~fC~~Ci~~~ 38 (120)
-+||..|+...
T Consensus 71 krFC~pC~~~~ 81 (97)
T PF10170_consen 71 KRFCLPCVKRN 81 (97)
T ss_pred CceeHHHHHHH
Confidence 34555555443
No 345
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=20.10 E-value=59 Score=21.80 Aligned_cols=15 Identities=27% Similarity=0.654 Sum_probs=11.2
Q ss_pred CCCCCCCCCccccCC
Q psy17995 42 GTGNCYECNQPLRRG 56 (120)
Q Consensus 42 ~~~~CP~C~~~~~~~ 56 (120)
|...||.|+.++...
T Consensus 46 G~~~cP~Cge~~~~a 60 (102)
T PF04475_consen 46 GDTICPKCGEELDSA 60 (102)
T ss_pred CcccCCCCCCccCce
Confidence 346799999988653
No 346
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=20.05 E-value=1.4e+02 Score=21.64 Aligned_cols=13 Identities=23% Similarity=0.516 Sum_probs=10.9
Q ss_pred CCCCCCCCccccC
Q psy17995 43 TGNCYECNQPLRR 55 (120)
Q Consensus 43 ~~~CP~C~~~~~~ 55 (120)
.+.||.||..+..
T Consensus 136 ~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 136 GFRCPQCGEMLEE 148 (178)
T ss_pred CCcCCCCCCCCee
Confidence 5899999998863
No 347
>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=20.05 E-value=1e+02 Score=25.99 Aligned_cols=10 Identities=20% Similarity=0.707 Sum_probs=7.9
Q ss_pred CCCCCCCCcc
Q psy17995 43 TGNCYECNQP 52 (120)
Q Consensus 43 ~~~CP~C~~~ 52 (120)
+..||.|+..
T Consensus 253 ~~~Cp~C~s~ 262 (505)
T TIGR00595 253 PKTCPQCGSE 262 (505)
T ss_pred CCCCCCCCCC
Confidence 4689999874
Done!