Query psy509
Match_columns 158
No_of_seqs 231 out of 1152
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 17:02:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy509.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/509hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1818|consensus 100.0 2E-34 4.3E-39 256.5 6.6 136 1-154 137-272 (634)
2 PF01363 FYVE: FYVE zinc finge 99.8 2.3E-21 4.9E-26 129.0 2.4 63 24-86 1-68 (69)
3 smart00064 FYVE Protein presen 99.8 2.3E-19 5.1E-24 118.9 3.9 63 24-86 2-67 (68)
4 cd00065 FYVE FYVE domain; Zinc 99.6 1.6E-16 3.4E-21 101.7 2.6 55 29-83 2-56 (57)
5 KOG1729|consensus 99.6 2.7E-16 5.8E-21 130.6 2.3 69 18-87 154-226 (288)
6 KOG1819|consensus 99.6 3.2E-16 7E-21 137.4 1.6 63 22-84 891-961 (990)
7 PTZ00303 phosphatidylinositol 99.5 3.3E-15 7.1E-20 135.8 4.1 71 17-87 444-531 (1374)
8 KOG1842|consensus 99.0 1.9E-11 4.1E-16 105.8 -1.2 65 23-87 171-260 (505)
9 KOG1409|consensus 99.0 7.8E-11 1.7E-15 99.5 1.8 70 21-90 274-354 (404)
10 KOG1841|consensus 99.0 2.2E-10 4.9E-15 107.6 1.8 49 19-67 544-595 (1287)
11 KOG1843|consensus 98.8 2.7E-09 5.8E-14 91.8 2.0 66 21-86 149-219 (473)
12 KOG1811|consensus 98.0 5.6E-07 1.2E-11 81.5 -1.5 55 31-85 328-383 (1141)
13 KOG4424|consensus 97.9 2.7E-06 5.9E-11 76.2 0.5 65 23-88 408-474 (623)
14 PF02318 FYVE_2: FYVE-type zin 97.7 3.1E-05 6.8E-10 56.5 2.8 53 28-87 53-106 (118)
15 smart00726 UIM Ubiquitin-inter 97.6 6.8E-05 1.5E-09 40.9 2.4 22 135-156 1-22 (26)
16 PF02809 UIM: Ubiquitin intera 97.5 5.5E-05 1.2E-09 37.8 1.4 17 135-151 2-18 (18)
17 KOG0230|consensus 97.5 6.4E-05 1.4E-09 73.4 2.6 48 29-87 5-52 (1598)
18 KOG0230|consensus 97.1 0.00039 8.6E-09 68.1 3.0 55 29-92 97-151 (1598)
19 KOG2199|consensus 95.9 0.0049 1.1E-07 53.7 2.3 27 130-156 159-185 (462)
20 KOG1841|consensus 93.6 0.072 1.6E-06 51.7 3.7 54 21-87 646-702 (1287)
21 PF07975 C1_4: TFIIH C1-like d 93.1 0.02 4.2E-07 36.1 -0.6 44 31-82 1-50 (51)
22 KOG0993|consensus 92.7 0.0057 1.2E-07 53.5 -4.6 58 28-87 467-526 (542)
23 KOG4275|consensus 92.1 0.042 9.1E-07 46.3 -0.0 48 29-85 44-91 (350)
24 KOG1729|consensus 90.3 0.078 1.7E-06 44.5 -0.1 56 29-84 20-81 (288)
25 PF09538 FYDLN_acid: Protein o 89.9 0.22 4.9E-06 35.9 2.0 33 23-55 3-36 (108)
26 smart00154 ZnF_AN1 AN1-like Zi 89.7 0.2 4.3E-06 29.6 1.3 26 32-59 1-26 (39)
27 PF13717 zinc_ribbon_4: zinc-r 89.4 0.2 4.4E-06 29.0 1.2 25 31-55 4-35 (36)
28 PRK00464 nrdR transcriptional 88.7 0.22 4.7E-06 38.2 1.2 25 31-55 2-38 (154)
29 TIGR02300 FYDLN_acid conserved 88.7 0.28 6.2E-06 36.4 1.8 33 23-55 3-36 (129)
30 PF13719 zinc_ribbon_5: zinc-r 87.8 0.31 6.6E-06 28.3 1.2 25 31-55 4-35 (37)
31 TIGR00622 ssl1 transcription f 86.8 0.46 9.9E-06 34.6 1.9 45 30-82 56-110 (112)
32 PF14634 zf-RING_5: zinc-RING 86.3 0.14 3.1E-06 30.6 -0.8 33 31-64 1-33 (44)
33 KOG0320|consensus 84.7 0.084 1.8E-06 41.4 -3.0 46 31-87 133-179 (187)
34 PHA02768 hypothetical protein; 84.4 0.43 9.4E-06 30.4 0.7 26 30-55 6-41 (55)
35 PF07282 OrfB_Zn_ribbon: Putat 84.3 0.86 1.9E-05 29.5 2.2 31 25-55 24-56 (69)
36 PRK03564 formate dehydrogenase 83.2 1.3 2.8E-05 37.6 3.3 72 20-92 178-269 (309)
37 KOG3576|consensus 83.0 0.35 7.7E-06 39.1 -0.1 28 30-57 118-157 (267)
38 KOG2164|consensus 82.3 0.4 8.8E-06 43.1 -0.1 52 29-87 186-237 (513)
39 PF13639 zf-RING_2: Ring finge 82.0 0.33 7.2E-06 28.7 -0.5 34 30-64 1-34 (44)
40 PRK00398 rpoP DNA-directed RNA 81.5 0.89 1.9E-05 27.4 1.3 25 31-55 5-31 (46)
41 PRK00420 hypothetical protein; 80.9 1.1 2.3E-05 32.7 1.8 26 29-54 23-49 (112)
42 PF01485 IBR: IBR domain; Int 80.9 1.2 2.7E-05 27.7 1.9 33 31-63 20-58 (64)
43 PF10571 UPF0547: Uncharacteri 80.1 1.1 2.3E-05 24.2 1.2 23 31-55 2-24 (26)
44 KOG0823|consensus 79.9 0.71 1.5E-05 37.6 0.6 34 49-87 63-96 (230)
45 PF12773 DZR: Double zinc ribb 78.9 1.4 2.9E-05 26.7 1.5 26 29-54 12-38 (50)
46 TIGR02098 MJ0042_CXXC MJ0042 f 76.6 1.5 3.2E-05 25.1 1.1 25 31-55 4-35 (38)
47 KOG3799|consensus 76.2 1.1 2.4E-05 33.9 0.6 53 28-85 64-117 (169)
48 KOG3173|consensus 74.7 1.4 3E-05 34.2 0.8 27 30-59 106-132 (167)
49 KOG0153|consensus 74.5 0.56 1.2E-05 40.4 -1.5 17 29-45 41-57 (377)
50 smart00647 IBR In Between Ring 74.1 2.7 5.9E-05 26.2 2.0 22 42-63 37-58 (64)
51 KOG0978|consensus 74.1 0.29 6.3E-06 45.6 -3.5 44 30-84 644-687 (698)
52 PF07191 zinc-ribbons_6: zinc- 74.1 1.1 2.5E-05 29.9 0.2 32 31-62 3-39 (70)
53 PLN03208 E3 ubiquitin-protein 73.4 0.43 9.3E-06 37.9 -2.3 54 30-87 19-80 (193)
54 KOG1814|consensus 73.3 1.5 3.3E-05 38.6 0.9 40 24-63 361-404 (445)
55 TIGR00570 cdk7 CDK-activating 73.0 0.8 1.7E-05 38.9 -0.9 50 28-86 2-54 (309)
56 PF13923 zf-C3HC4_2: Zinc fing 72.7 1 2.3E-05 25.9 -0.2 29 32-63 1-29 (39)
57 PF14803 Nudix_N_2: Nudix N-te 71.9 2.3 4.9E-05 24.4 1.1 27 55-82 2-29 (34)
58 KOG4739|consensus 71.4 1.8 3.9E-05 35.4 0.8 44 31-86 5-48 (233)
59 cd00162 RING RING-finger (Real 71.4 1.1 2.4E-05 25.3 -0.3 31 31-64 1-31 (45)
60 PF12760 Zn_Tnp_IS1595: Transp 71.1 3 6.5E-05 25.1 1.6 30 24-53 13-45 (46)
61 PF13901 DUF4206: Domain of un 71.0 3.1 6.8E-05 32.9 2.1 46 47-92 2-52 (202)
62 TIGR02605 CxxC_CxxC_SSSS putat 70.7 2 4.4E-05 26.2 0.8 23 31-53 7-34 (52)
63 PF06750 DiS_P_DiS: Bacterial 70.4 2.6 5.7E-05 29.4 1.4 30 25-54 29-67 (92)
64 PF11781 RRN7: RNA polymerase 69.9 2.8 6.1E-05 24.2 1.2 30 25-54 2-34 (36)
65 PF13445 zf-RING_UBOX: RING-ty 69.7 1.3 2.8E-05 26.6 -0.2 31 32-63 1-31 (43)
66 PF03107 C1_2: C1 domain; Int 69.5 4.3 9.4E-05 22.2 1.9 29 31-60 2-30 (30)
67 TIGR00100 hypA hydrogenase nic 68.9 2.4 5.2E-05 30.7 1.0 24 30-53 71-94 (115)
68 PF08271 TF_Zn_Ribbon: TFIIB z 67.8 3.4 7.3E-05 24.4 1.3 25 31-55 2-29 (43)
69 KOG1829|consensus 66.8 3.6 7.9E-05 37.8 1.9 63 30-92 341-410 (580)
70 TIGR01562 FdhE formate dehydro 66.3 6.1 0.00013 33.5 3.0 66 26-92 181-269 (305)
71 KOG0317|consensus 65.7 1.3 2.8E-05 37.2 -1.1 46 29-86 239-284 (293)
72 PF02591 DUF164: Putative zinc 65.2 3.9 8.5E-05 25.5 1.3 28 27-54 20-55 (56)
73 PF01155 HypA: Hydrogenase exp 64.4 2.2 4.8E-05 30.7 0.0 24 30-53 71-94 (113)
74 smart00659 RPOLCX RNA polymera 64.3 3.9 8.5E-05 24.7 1.1 23 31-53 4-27 (44)
75 KOG2462|consensus 64.2 3 6.6E-05 34.9 0.8 12 75-86 243-254 (279)
76 PRK14559 putative protein seri 64.2 4.2 9E-05 37.9 1.8 30 29-62 15-50 (645)
77 PRK00432 30S ribosomal protein 64.0 4.6 0.0001 25.0 1.4 26 30-55 21-47 (50)
78 PF06221 zf-C2HC5: Putative zi 63.6 2.6 5.6E-05 27.1 0.2 18 41-58 14-31 (57)
79 smart00834 CxxC_CXXC_SSSS Puta 63.5 3.6 7.7E-05 23.6 0.8 13 31-43 7-19 (41)
80 PF10367 Vps39_2: Vacuolar sor 63.1 6.1 0.00013 27.1 2.1 31 29-61 78-108 (109)
81 COG1996 RPC10 DNA-directed RNA 63.0 3.5 7.6E-05 25.7 0.7 23 31-53 8-32 (49)
82 COG1439 Predicted nucleic acid 61.5 3.8 8.3E-05 32.1 0.9 21 31-53 141-161 (177)
83 COG5151 SSL1 RNA polymerase II 60.6 3.5 7.5E-05 35.4 0.5 34 29-62 362-405 (421)
84 PF00097 zf-C3HC4: Zinc finger 60.2 2.7 5.8E-05 24.1 -0.1 30 32-64 1-30 (41)
85 PRK00564 hypA hydrogenase nick 59.7 4.5 9.8E-05 29.3 1.0 24 30-53 72-96 (117)
86 COG0675 Transposase and inacti 59.5 5.5 0.00012 32.4 1.5 24 29-55 309-332 (364)
87 PRK12380 hydrogenase nickel in 59.4 4.5 9.9E-05 29.1 0.9 24 30-53 71-94 (113)
88 PF14353 CpXC: CpXC protein 59.4 4.8 0.0001 29.2 1.1 11 45-55 38-48 (128)
89 KOG1356|consensus 59.3 4.8 0.0001 38.5 1.2 46 17-64 212-262 (889)
90 PF01529 zf-DHHC: DHHC palmito 59.1 4.7 0.0001 30.2 1.0 24 30-55 49-72 (174)
91 PF09889 DUF2116: Uncharacteri 58.8 5.7 0.00012 25.6 1.2 27 45-87 3-30 (59)
92 PRK12496 hypothetical protein; 58.6 5.8 0.00013 30.5 1.4 13 43-55 125-137 (164)
93 cd02341 ZZ_ZZZ3 Zinc finger, Z 58.2 4.4 9.5E-05 25.0 0.6 31 31-62 2-35 (48)
94 PHA02926 zinc finger-like prot 57.8 1.6 3.5E-05 35.6 -1.8 57 29-87 170-231 (242)
95 PF09538 FYDLN_acid: Protein o 57.6 5.3 0.00011 28.8 1.0 32 42-86 6-37 (108)
96 PF04438 zf-HIT: HIT zinc fing 57.5 6.1 0.00013 21.9 1.0 22 31-57 4-25 (30)
97 PF09723 Zn-ribbon_8: Zinc rib 57.2 5 0.00011 23.7 0.7 12 31-42 7-18 (42)
98 COG5574 PEX10 RING-finger-cont 57.0 2.5 5.5E-05 35.1 -0.8 48 29-86 215-262 (271)
99 KOG2884|consensus 56.4 6.7 0.00015 32.1 1.5 22 133-154 212-233 (259)
100 PF09947 DUF2180: Uncharacteri 55.9 6.6 0.00014 26.1 1.1 41 46-86 17-67 (68)
101 cd02340 ZZ_NBR1_like Zinc fing 54.9 6.1 0.00013 23.6 0.8 30 31-62 2-32 (43)
102 PF15135 UPF0515: Uncharacteri 54.9 7.5 0.00016 32.3 1.5 30 28-57 131-167 (278)
103 PF03604 DNA_RNApol_7kD: DNA d 54.6 7.8 0.00017 21.9 1.2 23 31-53 2-25 (32)
104 COG1773 Rubredoxin [Energy pro 54.1 5.8 0.00013 25.3 0.6 13 44-56 2-14 (55)
105 PRK03824 hypA hydrogenase nick 54.0 6.4 0.00014 29.3 1.0 12 31-42 72-83 (135)
106 COG4855 Uncharacterized protei 53.6 2.7 5.8E-05 28.0 -1.0 64 24-87 2-75 (76)
107 PF09297 zf-NADH-PPase: NADH p 53.2 6.4 0.00014 21.8 0.6 25 54-82 4-28 (32)
108 KOG3576|consensus 53.0 3.8 8.3E-05 33.2 -0.4 53 30-82 146-219 (267)
109 PRK14873 primosome assembly pr 51.8 8.6 0.00019 36.0 1.6 40 31-70 394-439 (665)
110 TIGR02300 FYDLN_acid conserved 51.8 7.7 0.00017 28.9 1.1 31 42-85 6-36 (129)
111 smart00531 TFIIE Transcription 51.4 7.9 0.00017 29.0 1.1 25 31-55 101-133 (147)
112 COG3357 Predicted transcriptio 51.2 7.7 0.00017 27.3 0.9 15 41-55 54-68 (97)
113 smart00291 ZnF_ZZ Zinc-binding 51.1 7.2 0.00015 23.2 0.7 21 30-52 5-25 (44)
114 PF01428 zf-AN1: AN1-like Zinc 50.7 8.5 0.00018 22.8 1.0 16 45-60 13-28 (43)
115 KOG3362|consensus 50.5 8 0.00017 29.5 1.0 31 23-58 111-142 (156)
116 cd02249 ZZ Zinc finger, ZZ typ 50.3 6.9 0.00015 23.4 0.5 30 31-62 2-32 (46)
117 KOG2462|consensus 50.2 6 0.00013 33.1 0.3 26 30-55 188-225 (279)
118 COG1645 Uncharacterized Zn-fin 50.0 8.6 0.00019 28.8 1.1 25 29-61 28-52 (131)
119 TIGR01384 TFS_arch transcripti 49.8 9.4 0.0002 26.6 1.2 24 31-54 2-25 (104)
120 PF04981 NMD3: NMD3 family ; 49.7 7.7 0.00017 31.3 0.9 28 30-57 14-47 (236)
121 PF10013 DUF2256: Uncharacteri 49.6 6.9 0.00015 23.6 0.4 16 28-43 7-22 (42)
122 PF09845 DUF2072: Zn-ribbon co 49.6 7.6 0.00016 29.0 0.7 24 30-53 2-27 (131)
123 PRK03681 hypA hydrogenase nick 49.5 8.2 0.00018 27.8 0.9 24 30-53 71-95 (114)
124 KOG1311|consensus 49.3 8 0.00017 32.0 0.9 24 30-55 114-137 (299)
125 PF10170 C6_DPF: Cysteine-rich 49.1 9.7 0.00021 27.0 1.2 35 42-86 46-82 (97)
126 PF13920 zf-C3HC4_3: Zinc fing 48.4 1 2.2E-05 27.3 -3.5 44 30-85 3-47 (50)
127 PRK11595 DNA utilization prote 48.2 4.6 0.0001 32.3 -0.7 31 30-62 21-57 (227)
128 PF15227 zf-C3HC4_4: zinc fing 47.9 4.4 9.6E-05 23.9 -0.6 16 49-64 14-29 (42)
129 TIGR00595 priA primosomal prot 47.6 13 0.00027 33.5 2.0 39 31-69 224-269 (505)
130 PF15616 TerY-C: TerY-C metal 47.6 9.8 0.00021 28.4 1.1 23 30-57 78-100 (131)
131 PRK04023 DNA polymerase II lar 47.4 12 0.00027 36.7 1.9 30 29-62 626-660 (1121)
132 PRK06266 transcription initiat 47.4 8.1 0.00018 30.1 0.6 25 31-55 119-146 (178)
133 PF04277 OAD_gamma: Oxaloaceta 47.1 29 0.00064 22.7 3.3 19 136-154 61-79 (79)
134 PHA02942 putative transposase; 47.1 15 0.00033 31.9 2.4 28 28-55 324-352 (383)
135 PF01286 XPA_N: XPA protein N- 47.0 8.2 0.00018 22.2 0.5 8 75-82 24-31 (34)
136 KOG2935|consensus 47.0 16 0.00034 30.5 2.3 17 135-151 217-233 (315)
137 PF10263 SprT-like: SprT-like 46.8 10 0.00022 28.0 1.1 25 31-55 125-153 (157)
138 KOG3795|consensus 46.4 8.8 0.00019 30.4 0.7 24 38-61 8-34 (230)
139 PF02150 RNA_POL_M_15KD: RNA p 46.0 10 0.00022 21.6 0.8 7 55-61 3-9 (35)
140 PHA02929 N1R/p28-like protein; 45.6 2.7 6E-05 34.4 -2.3 51 29-87 174-228 (238)
141 PRK04179 rpl37e 50S ribosomal 45.6 10 0.00022 24.8 0.8 22 31-53 19-40 (62)
142 TIGR00373 conserved hypothetic 44.9 11 0.00023 28.8 0.9 25 31-55 111-138 (158)
143 cd02342 ZZ_UBA_plant Zinc fing 44.7 10 0.00022 23.0 0.6 29 31-60 2-31 (43)
144 PF14835 zf-RING_6: zf-RING of 44.1 15 0.00032 24.2 1.4 29 31-63 9-38 (65)
145 smart00184 RING Ring finger. E 44.1 5.6 0.00012 21.3 -0.6 15 49-63 14-28 (39)
146 PF13248 zf-ribbon_3: zinc-rib 44.0 13 0.00028 19.6 0.9 6 32-37 5-10 (26)
147 PF09332 Mcm10: Mcm10 replicat 43.9 9.3 0.0002 33.0 0.5 10 74-83 302-311 (344)
148 PHA00732 hypothetical protein 42.5 18 0.0004 24.4 1.7 10 31-40 3-12 (79)
149 PF02148 zf-UBP: Zn-finger in 41.8 14 0.00031 23.4 1.1 24 32-58 1-24 (63)
150 PF00569 ZZ: Zinc finger, ZZ t 41.7 7.1 0.00015 23.5 -0.4 22 30-52 5-26 (46)
151 COG1198 PriA Primosomal protei 41.3 17 0.00036 34.6 1.8 34 31-64 446-486 (730)
152 PTZ00218 40S ribosomal protein 41.2 20 0.00043 22.8 1.6 22 62-87 25-46 (54)
153 PF06677 Auto_anti-p27: Sjogre 41.2 16 0.00034 21.8 1.1 11 29-39 17-27 (41)
154 cd02345 ZZ_dah Zinc finger, ZZ 41.0 12 0.00026 22.9 0.6 21 31-53 2-23 (49)
155 smart00661 RPOL9 RNA polymeras 40.7 23 0.0005 21.2 1.8 10 74-83 19-28 (52)
156 KOG1818|consensus 40.5 5.7 0.00012 36.9 -1.3 55 30-85 55-110 (634)
157 PF13465 zf-H2C2_2: Zinc-finge 40.5 14 0.0003 19.4 0.7 13 43-55 12-24 (26)
158 PF13912 zf-C2H2_6: C2H2-type 40.2 6.9 0.00015 20.2 -0.5 11 31-41 3-13 (27)
159 KOG2593|consensus 40.1 13 0.00028 33.0 0.8 33 30-62 129-170 (436)
160 PRK12496 hypothetical protein; 40.0 14 0.00031 28.3 1.0 25 30-54 128-152 (164)
161 PF00301 Rubredoxin: Rubredoxi 39.7 14 0.0003 22.7 0.7 13 45-57 1-13 (47)
162 PF04216 FdhE: Protein involve 39.6 11 0.00023 31.3 0.2 64 25-89 169-252 (290)
163 PF05458 Siva: Cd27 binding pr 39.3 13 0.00028 29.0 0.7 29 48-81 142-170 (175)
164 COG1579 Zn-ribbon protein, pos 39.2 12 0.00026 30.7 0.4 28 28-55 196-231 (239)
165 KOG1813|consensus 39.0 24 0.00053 29.9 2.3 30 30-63 242-271 (313)
166 PF01927 Mut7-C: Mut7-C RNAse 38.7 18 0.00039 27.0 1.3 10 30-39 92-101 (147)
167 TIGR00599 rad18 DNA repair pro 38.5 11 0.00024 33.2 0.1 31 29-63 26-56 (397)
168 PF13453 zf-TFIIB: Transcripti 37.9 20 0.00044 20.8 1.2 9 46-54 20-28 (41)
169 COG1998 RPS31 Ribosomal protei 37.8 18 0.00038 22.7 0.9 24 30-53 20-45 (51)
170 PF12172 DUF35_N: Rubredoxin-l 37.7 18 0.0004 20.4 1.0 8 47-54 13-20 (37)
171 COG1545 Predicted nucleic-acid 36.6 13 0.00028 27.8 0.3 10 46-55 30-39 (140)
172 PRK04136 rpl40e 50S ribosomal 36.4 20 0.00043 22.2 1.0 22 30-53 15-36 (48)
173 COG1779 C4-type Zn-finger prot 36.3 32 0.00069 27.6 2.4 46 31-76 16-66 (201)
174 PRK05580 primosome assembly pr 36.2 22 0.00048 33.2 1.8 34 31-64 392-432 (679)
175 KOG1314|consensus 36.0 8.8 0.00019 33.4 -0.8 33 20-54 74-114 (414)
176 KOG2932|consensus 35.6 14 0.00031 31.7 0.4 45 30-87 91-135 (389)
177 PRK04351 hypothetical protein; 35.1 21 0.00045 27.1 1.2 9 31-39 114-122 (149)
178 PF05191 ADK_lid: Adenylate ki 34.8 20 0.00042 20.7 0.8 9 47-55 3-11 (36)
179 TIGR00311 aIF-2beta translatio 34.8 20 0.00043 26.8 1.0 24 31-54 99-127 (133)
180 PF00096 zf-C2H2: Zinc finger, 34.7 18 0.00038 17.8 0.5 9 47-55 2-10 (23)
181 PF07649 C1_3: C1-like domain; 34.6 9 0.0002 20.8 -0.7 27 31-58 2-28 (30)
182 PF13913 zf-C2HC_2: zinc-finge 34.5 8.9 0.00019 20.2 -0.7 11 31-41 4-14 (25)
183 KOG3896|consensus 34.5 19 0.00041 31.3 1.0 28 35-63 15-42 (449)
184 PF13005 zf-IS66: zinc-finger 34.2 26 0.00057 20.6 1.3 11 30-40 3-13 (47)
185 PF07754 DUF1610: Domain of un 34.1 28 0.00061 18.4 1.2 9 45-53 16-24 (24)
186 cd02339 ZZ_Mind_bomb Zinc fing 33.9 21 0.00045 21.6 0.8 30 31-61 2-32 (45)
187 PF11023 DUF2614: Protein of u 33.9 17 0.00036 26.6 0.4 24 31-54 71-94 (114)
188 KOG2935|consensus 33.8 27 0.00059 29.2 1.7 19 133-151 233-251 (315)
189 COG5148 RPN10 26S proteasome r 33.7 24 0.00053 28.3 1.4 17 137-153 207-223 (243)
190 smart00731 SprT SprT homologue 33.5 27 0.00059 25.9 1.6 25 31-55 114-143 (146)
191 PRK14559 putative protein seri 33.1 34 0.00074 32.0 2.4 47 31-87 3-53 (645)
192 PRK06260 threonine synthase; V 32.6 25 0.00054 30.4 1.4 24 31-54 5-28 (397)
193 COG1327 Predicted transcriptio 32.4 23 0.00049 27.2 1.0 15 41-55 24-38 (156)
194 PRK11788 tetratricopeptide rep 32.4 32 0.0007 28.5 2.0 26 46-71 355-386 (389)
195 COG2126 RPL37A Ribosomal prote 32.2 19 0.00042 23.2 0.5 6 48-53 19-24 (61)
196 PHA00733 hypothetical protein 32.0 25 0.00054 25.8 1.1 10 31-40 75-84 (128)
197 KOG3183|consensus 31.8 18 0.0004 29.7 0.4 19 133-151 200-218 (250)
198 COG1997 RPL43A Ribosomal prote 31.6 31 0.00068 24.1 1.5 27 30-57 36-65 (89)
199 PF02945 Endonuclease_7: Recom 31.4 16 0.00034 25.0 -0.0 26 29-54 22-50 (81)
200 cd00202 ZnF_GATA Zinc finger D 31.4 42 0.00092 20.9 2.0 33 56-88 2-34 (54)
201 PF05443 ROS_MUCR: ROS/MUCR tr 31.2 14 0.0003 27.6 -0.3 16 30-46 73-88 (132)
202 KOG2807|consensus 30.9 31 0.00068 29.8 1.7 44 30-82 331-374 (378)
203 PRK05978 hypothetical protein; 30.9 27 0.00058 26.6 1.2 34 22-55 21-62 (148)
204 cd02335 ZZ_ADA2 Zinc finger, Z 30.4 57 0.0012 19.7 2.4 31 31-62 2-33 (49)
205 COG5152 Uncharacterized conser 30.3 11 0.00024 30.4 -1.1 29 31-63 198-226 (259)
206 PRK07591 threonine synthase; V 30.0 29 0.00063 30.4 1.4 25 30-55 19-43 (421)
207 PRK03988 translation initiatio 30.0 26 0.00057 26.2 1.0 24 31-54 104-132 (138)
208 smart00504 Ubox Modified RING 30.0 22 0.00048 21.8 0.5 12 50-61 18-29 (63)
209 PF10497 zf-4CXXC_R1: Zinc-fin 29.9 18 0.00039 25.8 0.1 55 29-85 7-71 (105)
210 COG4338 Uncharacterized protei 29.7 8.6 0.00019 24.0 -1.4 18 27-44 10-27 (54)
211 PRK14890 putative Zn-ribbon RN 29.0 33 0.00071 22.2 1.1 25 30-54 8-34 (59)
212 KOG4323|consensus 28.2 27 0.00059 31.4 0.9 58 30-87 169-227 (464)
213 smart00653 eIF2B_5 domain pres 28.0 30 0.00064 24.9 0.9 23 31-53 82-109 (110)
214 COG3364 Zn-ribbon containing p 28.0 22 0.00048 25.6 0.3 11 45-55 2-12 (112)
215 cd07153 Fur_like Ferric uptake 28.0 27 0.00058 24.3 0.7 15 46-60 74-88 (116)
216 PF14471 DUF4428: Domain of un 27.9 44 0.00095 20.7 1.6 12 76-87 21-32 (51)
217 PRK08359 transcription factor; 27.9 2.2E+02 0.0047 22.2 5.8 15 73-87 28-42 (176)
218 KOG1734|consensus 27.6 21 0.00046 30.1 0.2 54 28-87 223-282 (328)
219 TIGR01195 oadG_fam sodium pump 27.1 91 0.002 21.1 3.2 20 135-154 61-80 (82)
220 cd02338 ZZ_PCMF_like Zinc fing 27.0 61 0.0013 19.6 2.1 20 31-52 2-22 (49)
221 KOG0006|consensus 27.0 17 0.00036 31.5 -0.6 33 30-62 316-353 (446)
222 cd02336 ZZ_RSC8 Zinc finger, Z 26.9 29 0.00063 21.0 0.6 10 75-84 23-32 (45)
223 PF09862 DUF2089: Protein of u 26.8 37 0.00081 24.7 1.3 27 32-60 1-27 (113)
224 cd04476 RPA1_DBD_C RPA1_DBD_C: 26.6 32 0.0007 25.8 1.0 57 30-87 35-95 (166)
225 PF06397 Desulfoferrod_N: Desu 26.6 29 0.00062 20.1 0.5 11 45-55 6-16 (36)
226 cd00350 rubredoxin_like Rubred 26.5 40 0.00086 18.7 1.1 10 46-55 2-11 (33)
227 PF11238 DUF3039: Protein of u 26.2 60 0.0013 20.9 2.0 15 73-87 42-56 (58)
228 PF00130 C1_1: Phorbol esters/ 26.2 54 0.0012 19.6 1.8 33 30-62 12-45 (53)
229 PF01873 eIF-5_eIF-2B: Domain 26.1 34 0.00075 25.1 1.0 24 31-54 95-123 (125)
230 COG0498 ThrC Threonine synthas 26.1 27 0.00058 30.9 0.5 26 30-55 6-31 (411)
231 COG3791 Uncharacterized conser 25.9 30 0.00065 25.4 0.6 10 31-40 28-37 (133)
232 PF03966 Trm112p: Trm112p-like 25.8 40 0.00087 21.7 1.2 15 41-55 49-63 (68)
233 cd00730 rubredoxin Rubredoxin; 25.8 34 0.00073 21.2 0.8 12 45-56 1-12 (50)
234 PF10164 DUF2367: Uncharacteri 25.7 28 0.00061 24.7 0.4 14 42-55 85-98 (98)
235 PRK09678 DNA-binding transcrip 25.7 46 0.00099 22.3 1.4 14 42-55 24-39 (72)
236 PF13894 zf-C2H2_4: C2H2-type 25.7 34 0.00073 16.3 0.7 9 47-55 2-10 (24)
237 TIGR00244 transcriptional regu 25.6 39 0.00085 25.7 1.2 14 42-55 25-38 (147)
238 cd00021 BBOX B-Box-type zinc f 25.6 26 0.00056 19.4 0.2 18 45-62 12-29 (39)
239 PRK08197 threonine synthase; V 25.1 41 0.00088 29.1 1.4 24 30-54 8-31 (394)
240 PF01667 Ribosomal_S27e: Ribos 25.1 43 0.00093 21.3 1.2 27 31-57 9-38 (55)
241 PLN02400 cellulose synthase 24.9 42 0.0009 33.3 1.6 53 29-88 36-91 (1085)
242 PRK12495 hypothetical protein; 24.9 39 0.00086 27.5 1.2 11 30-40 43-53 (226)
243 PF12251 zf-SNAP50_C: snRNA-ac 24.8 36 0.00078 26.9 0.9 39 44-87 138-177 (196)
244 COG5273 Uncharacterized protei 24.7 26 0.00057 29.6 0.2 23 30-54 110-132 (309)
245 PRK12336 translation initiatio 24.7 36 0.00079 26.9 1.0 25 31-55 100-129 (201)
246 PRK08329 threonine synthase; V 24.6 45 0.00097 28.3 1.6 23 31-55 3-25 (347)
247 KOG2272|consensus 24.2 35 0.00076 28.6 0.8 33 25-57 216-266 (332)
248 PF12171 zf-C2H2_jaz: Zinc-fin 24.1 41 0.00088 17.4 0.8 10 46-55 2-11 (27)
249 COG1499 NMD3 NMD protein affec 24.1 32 0.00069 29.8 0.6 30 54-83 22-51 (355)
250 KOG1315|consensus 24.1 25 0.00054 29.9 -0.1 22 31-54 111-132 (307)
251 cd00729 rubredoxin_SM Rubredox 24.0 45 0.00098 18.7 1.0 10 46-55 3-12 (34)
252 PF03833 PolC_DP2: DNA polymer 24.0 26 0.00056 33.9 0.0 7 31-37 657-663 (900)
253 PF06689 zf-C4_ClpX: ClpX C4-t 23.7 34 0.00073 20.1 0.5 15 74-88 23-37 (41)
254 KOG2177|consensus 23.7 16 0.00035 28.4 -1.2 34 28-65 12-45 (386)
255 COG4530 Uncharacterized protei 23.6 41 0.00089 24.6 1.0 26 30-55 10-36 (129)
256 PF14446 Prok-RING_1: Prokaryo 23.5 46 0.001 21.1 1.1 25 30-54 6-30 (54)
257 KOG4317|consensus 23.4 39 0.00085 29.1 1.0 23 31-57 9-31 (383)
258 PRK00762 hypA hydrogenase nick 23.4 40 0.00086 24.6 0.9 11 30-41 71-81 (124)
259 PF14445 Prok-RING_2: Prokaryo 23.1 15 0.00032 23.2 -1.2 45 30-86 8-52 (57)
260 PF12647 RNHCP: RNHCP domain; 23.0 48 0.001 23.3 1.2 24 30-53 5-32 (92)
261 PF10892 DUF2688: Protein of u 22.9 27 0.00059 22.4 -0.1 11 45-55 10-20 (60)
262 KOG0804|consensus 22.9 30 0.00066 31.0 0.2 28 28-59 227-254 (493)
263 PRK14892 putative transcriptio 22.6 60 0.0013 23.0 1.7 14 50-63 39-52 (99)
264 PF00643 zf-B_box: B-box zinc 22.5 19 0.00042 20.6 -0.8 28 31-62 5-32 (42)
265 PRK08351 DNA-directed RNA poly 22.5 42 0.0009 21.8 0.7 9 47-55 5-13 (61)
266 PRK06450 threonine synthase; V 22.3 51 0.0011 28.0 1.5 23 31-54 5-27 (338)
267 KOG2463|consensus 22.0 35 0.00076 29.5 0.4 23 31-54 244-266 (376)
268 COG0353 RecR Recombinational D 22.0 56 0.0012 26.1 1.5 21 43-63 52-76 (198)
269 KOG1074|consensus 21.9 55 0.0012 31.7 1.7 52 30-82 606-669 (958)
270 smart00290 ZnF_UBP Ubiquitin C 21.8 57 0.0012 19.2 1.3 24 32-59 2-25 (50)
271 TIGR03826 YvyF flagellar opero 21.8 35 0.00075 25.6 0.3 26 46-86 4-29 (137)
272 PRK06393 rpoE DNA-directed RNA 21.8 41 0.0009 22.0 0.6 16 47-62 7-26 (64)
273 PF14279 HNH_5: HNH endonuclea 21.7 83 0.0018 20.8 2.1 11 77-87 32-42 (71)
274 KOG2879|consensus 21.4 50 0.0011 27.9 1.2 32 29-63 239-270 (298)
275 PF05225 HTH_psq: helix-turn-h 21.4 71 0.0015 19.0 1.6 9 137-145 2-10 (45)
276 KOG1812|consensus 21.4 42 0.00091 29.3 0.8 32 31-63 308-341 (384)
277 PRK14714 DNA polymerase II lar 21.3 57 0.0012 33.0 1.7 48 30-86 668-720 (1337)
278 PF11682 DUF3279: Protein of u 21.1 66 0.0014 23.9 1.7 46 5-53 67-118 (128)
279 cd02344 ZZ_HERC2 Zinc finger, 21.0 51 0.0011 19.9 0.9 31 31-62 2-33 (45)
280 PLN02569 threonine synthase 20.9 55 0.0012 29.4 1.4 26 29-55 49-74 (484)
281 PRK13130 H/ACA RNA-protein com 20.8 74 0.0016 20.2 1.6 22 30-55 6-27 (56)
282 PLN02189 cellulose synthase 20.8 57 0.0012 32.3 1.6 53 28-87 33-88 (1040)
283 PRK12286 rpmF 50S ribosomal pr 20.7 54 0.0012 20.8 1.0 20 30-52 28-47 (57)
284 cd02337 ZZ_CBP Zinc finger, ZZ 20.5 37 0.00081 20.0 0.2 28 31-61 2-30 (41)
285 PRK05638 threonine synthase; V 20.5 55 0.0012 28.8 1.3 23 31-55 3-25 (442)
286 COG4098 comFA Superfamily II D 20.3 41 0.00089 29.6 0.5 10 52-61 59-68 (441)
287 PF02132 RecR: RecR protein; 20.3 17 0.00038 21.3 -1.3 12 43-54 15-26 (41)
288 PTZ00073 60S ribosomal protein 20.3 50 0.0011 23.1 0.8 22 31-53 18-39 (91)
No 1
>KOG1818|consensus
Probab=100.00 E-value=2e-34 Score=256.47 Aligned_cols=136 Identities=56% Similarity=0.926 Sum_probs=122.9
Q ss_pred CccCCCcCCCCCcccccccCCCCCCcccCCCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChh
Q psy509 1 MKAEGFQFPVLKESDAMFSADTAPEWMDGDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCED 80 (158)
Q Consensus 1 l~~~g~~fp~~~~s~~~~~~~~~p~W~~~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~ 80 (158)
||.+||+||+.++.|+||+++++|.|+|...|..|.++|++|+||||||+||+|||..|+++.++||.+|+.++||||+.
T Consensus 137 lk~~g~~Fpe~~e~d~mf~~~~~pdW~D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~ 216 (634)
T KOG1818|consen 137 LKGGGHVFPELDENDAMFDAETAPDWIDSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDS 216 (634)
T ss_pred HhcCCccccccccchhhhcccCCcccccccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhh
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHhcccCCCCCCCCCCCCCCCCchhhhccccCCCCCCCCCCCCCCCchhhhcchHHHHHHHHhcHHHHhhc
Q psy509 81 CHEKFTNYYRSPTPGAAGSKSEEMLPAEYLNSSLALQPQVPPPKATGGKTEEELKEEEELQLALALSQSEAESN 154 (158)
Q Consensus 81 C~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~s~~~~~~~~~~~~a~~~~~~~~~~eeedl~~aia~Sl~e~e~~ 154 (158)
||+.+.+. +.+. .+.++++...++...+.+ .....++|+|||++||+||++|+++.
T Consensus 217 C~E~l~~~----s~~~---------~~~~~~s~~s~~~~~k~r-----~~~~~~keeed~~lAi~lSq~E~~~~ 272 (634)
T KOG1818|consen 217 CYELLTRA----SVGE---------KAAALNSKLSPQKTKKDR-----AKALEEKEEEDLSLAIALSQSEAEAA 272 (634)
T ss_pred hHHHhhhc----ccch---------hhhhhhcccchhhhcccc-----cccccchhhHHHHHHHHHhHHHHHHh
Confidence 99999872 1111 267778888777777666 56778899999999999999999986
No 2
>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=99.82 E-value=2.3e-21 Score=128.98 Aligned_cols=63 Identities=44% Similarity=1.043 Sum_probs=45.9
Q ss_pred CCccc---CCCccccCccccccccccccccccceecCCCCCCccccC--CCCCCCceeeChhhHHHHh
Q psy509 24 PEWMD---GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLP--KFGIEKEVRVCEDCHEKFT 86 (158)
Q Consensus 24 p~W~~---~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp--~~~~~~~~RVC~~C~~~l~ 86 (158)
|.|++ ...|+.|+++|++|+||||||.||.+||..|+.+++.++ ..+...++|||+.|+..|+
T Consensus 1 ~~W~~d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~~~~~~RvC~~C~~~~~ 68 (69)
T PF01363_consen 1 PHWVPDSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIPLPTPSSGSGEPVRVCDSCYSKLQ 68 (69)
T ss_dssp --SSSGGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEEET--GGTESEEEEE-HHHHHHHH
T ss_pred CCcCCCCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEcccccccCCCCcCEECHHHHHHhc
Confidence 78997 479999999999999999999999999999999998887 5666799999999999886
No 3
>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 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=99.62 E-value=1.6e-16 Score=101.68 Aligned_cols=55 Identities=47% Similarity=1.112 Sum_probs=50.7
Q ss_pred CCCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHH
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHE 83 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~ 83 (158)
...|..|++.|+++.|+|||+.||.+||..|+.+...++..+..+++|||..||.
T Consensus 2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~~~~~~~~~~rvC~~C~~ 56 (57)
T cd00065 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSCYE 56 (57)
T ss_pred cCcCcccCccccCCccccccCcCcCCcChHHcCCeeecCcccCCCccEeChHHhC
Confidence 4679999999999999999999999999999999998887566799999999985
No 5
>KOG1729|consensus
Probab=99.60 E-value=2.7e-16 Score=130.63 Aligned_cols=69 Identities=36% Similarity=0.890 Sum_probs=61.6
Q ss_pred ccCCCCCCcccC---CCccccCc-cccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 18 FSADTAPEWMDG---DTCHRCRT-TFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 18 ~~~~~~p~W~~~---~~C~~C~~-~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
.....++.|+|+ ..|+.|++ .|+++.||||||+||.|||..|+.++..+|... .+++|||+.||..+..
T Consensus 154 ~~~~~~~~W~PD~ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~~~l~~~~-~k~~rvC~~CF~el~~ 226 (288)
T KOG1729|consen 154 PSNNSAAVWLPDSEATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNRFLLPNLS-TKPIRVCDICFEELEK 226 (288)
T ss_pred CCCCcCCcccCcccceecccCCCccccHHHHHHHHHhcchHhhhhhhcCcccccccC-CCCceecHHHHHHHhc
Confidence 345568999985 68999999 999999999999999999999999998888665 7899999999999975
No 6
>KOG1819|consensus
Probab=99.58 E-value=3.2e-16 Score=137.41 Aligned_cols=63 Identities=40% Similarity=1.099 Sum_probs=58.5
Q ss_pred CCCCcccC---CCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeCh-----hhHHH
Q psy509 22 TAPEWMDG---DTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCE-----DCHEK 84 (158)
Q Consensus 22 ~~p~W~~~---~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~-----~C~~~ 84 (158)
.+|.|+++ ..|+.|..+|+.|+||||||+||.|||+.|+...+++|.+|+.+.+|||. .||..
T Consensus 891 sppawipd~~a~~cmacq~pf~afrrrhhcrncggifcg~cs~asapip~~gl~ka~rvcrpqsnldc~~r 961 (990)
T KOG1819|consen 891 SPPAWIPDEDAEQCMACQMPFNAFRRRHHCRNCGGIFCGKCSCASAPIPEHGLDKAPRVCRPQSNLDCLTR 961 (990)
T ss_pred CCcccCCCCcchhhhhccCcHHHHHHhhhhcccCceeecccccCCCCCcccccccCceecCCcccccceee
Confidence 48899974 68999999999999999999999999999999999999999999999999 77764
No 7
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=99.54 E-value=3.3e-15 Score=135.79 Aligned_cols=71 Identities=31% Similarity=0.775 Sum_probs=54.1
Q ss_pred cccCCCCCCcccC----CCccccCcccccc-----ccccccccccceecCCCCCCccccC-----CCCC---CCceeeCh
Q psy509 17 MFSADTAPEWMDG----DTCHRCRTTFSLV-----QRKHHCRACGQVFCQLCSSKSTSLP-----KFGI---EKEVRVCE 79 (158)
Q Consensus 17 ~~~~~~~p~W~~~----~~C~~C~~~F~~~-----~RkhhCr~CG~vfC~~Cs~~~~~lp-----~~~~---~~~~RVC~ 79 (158)
|-.....|.|+++ +.|+.|++.|+++ .||||||+||++||..||++++.+| ..+. ..+.|||+
T Consensus 444 l~k~LhAPvWqpDDEaSdtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs~yp~aKLpKPgsseE~ppRRVCD 523 (1374)
T PTZ00303 444 LTKLLHNPSWQKDDESSDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRAHYSFAKLAKPGSSDEAEERLVCD 523 (1374)
T ss_pred hhhhccCCCCCCCcccCCcccCcCCcccccccccccccccccCCccccCccccCCcccCcccccCCCCCcccccccchhH
Confidence 3334568999963 4699999999864 6999999999999999999876533 2221 23678999
Q ss_pred hhHHHHhc
Q psy509 80 DCHEKFTN 87 (158)
Q Consensus 80 ~C~~~l~~ 87 (158)
.||+.+..
T Consensus 524 ~CYdq~En 531 (1374)
T PTZ00303 524 TCYKEYET 531 (1374)
T ss_pred HHHHHHHh
Confidence 99976654
No 8
>KOG1842|consensus
Probab=99.05 E-value=1.9e-11 Score=105.76 Aligned_cols=65 Identities=32% Similarity=0.885 Sum_probs=50.1
Q ss_pred CCCcccC---CCccccCccccccccccccccccceecCCCCCCcc-------------cc---CC-----C-CCCCceee
Q psy509 23 APEWMDG---DTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKST-------------SL---PK-----F-GIEKEVRV 77 (158)
Q Consensus 23 ~p~W~~~---~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~-------------~l---p~-----~-~~~~~~RV 77 (158)
-..|.|+ .-|..|+.+|++.+||||||.||.|+|..|+..-. .. |. + ....+.|+
T Consensus 171 vVpW~DDs~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~~C~k~iSle~a~~ltsss~~dt~~e~~qq~~~lH~~~~~iRl 250 (505)
T KOG1842|consen 171 VVPWLDDSSVQFCPECANSFGLTRRRHHCRLCGRVMCRDCSKFISLEIAIGLTSSSASDTHFEPNQQKDDLHQHPQPIRL 250 (505)
T ss_pred cccccCCCcccccccccchhhhHHHhhhhhhcchHHHHHHHHhcChHHHHHHhhccCCCCCcCcccCcccccCChhHhHH
Confidence 4579975 47999999999999999999999999999987632 00 00 0 11356899
Q ss_pred ChhhHHHHhc
Q psy509 78 CEDCHEKFTN 87 (158)
Q Consensus 78 C~~C~~~l~~ 87 (158)
|..|...|-.
T Consensus 251 C~hCl~~L~~ 260 (505)
T KOG1842|consen 251 CMHCLDNLFR 260 (505)
T ss_pred HHHHHHHHHH
Confidence 9999988754
No 9
>KOG1409|consensus
Probab=99.03 E-value=7.8e-11 Score=99.54 Aligned_cols=70 Identities=41% Similarity=0.954 Sum_probs=62.7
Q ss_pred CCCCCcccCCCccccCccccc-----------cccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhccc
Q psy509 21 DTAPEWMDGDTCHRCRTTFSL-----------VQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTNYY 89 (158)
Q Consensus 21 ~~~p~W~~~~~C~~C~~~F~~-----------~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~~~ 89 (158)
...|.|.+++.|..|..+|.+ -.|.||||.||+.||..|++++...|..|+.-.+|+|+.||..+....
T Consensus 274 ~etpewl~s~~cQ~c~qpffwn~~~m~~~k~~glr~h~crkcg~avc~~c~s~~~~~p~mg~e~~vR~~~~c~~~i~~~~ 353 (404)
T KOG1409|consen 274 VETPEWLDSDSCQKCNQPFFWNFRQMWDRKQLGLRQHHCRKCGKAVCGKCSSNRSSYPTMGFEFSVRVCDSCYPTIKDEE 353 (404)
T ss_pred ecCccccccchhhhhCchHHHHHHHHHhhhhhhhhhhhhhhhhhhcCcccccCccccccccceeEEEEecccchhhhcCC
Confidence 458999999999999999952 368899999999999999999999999999999999999999998744
Q ss_pred C
Q psy509 90 R 90 (158)
Q Consensus 90 ~ 90 (158)
+
T Consensus 354 ~ 354 (404)
T KOG1409|consen 354 R 354 (404)
T ss_pred C
Confidence 3
No 10
>KOG1841|consensus
Probab=98.95 E-value=2.2e-10 Score=107.55 Aligned_cols=49 Identities=35% Similarity=0.998 Sum_probs=43.1
Q ss_pred cCCCCCCcccC---CCccccCccccccccccccccccceecCCCCCCccccC
Q psy509 19 SADTAPEWMDG---DTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLP 67 (158)
Q Consensus 19 ~~~~~p~W~~~---~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp 67 (158)
...+.|.|+++ ..||.|..+|++++||||||+||+|+|+.|++.+..+-
T Consensus 544 lgkkqP~wvpdse~pncm~clqkft~ikrrhhcRacgkVlcgvccnek~~le 595 (1287)
T KOG1841|consen 544 LGKKQPSWVPDSEAPNCMDCLQKFTPIKRRHHCRACGKVLCGVCCNEKSALE 595 (1287)
T ss_pred cCCCCCccCccccCchHHHHHhhcccccccccchhccceeehhhcchhhhhh
Confidence 35569999985 57889999999999999999999999999999887653
No 11
>KOG1843|consensus
Probab=98.77 E-value=2.7e-09 Score=91.83 Aligned_cols=66 Identities=21% Similarity=0.331 Sum_probs=55.5
Q ss_pred CCCCCcccC---CCccccCcccc-ccccccccccccceecCCCCCCccccC-CCCCCCceeeChhhHHHHh
Q psy509 21 DTAPEWMDG---DTCHRCRTTFS-LVQRKHHCRACGQVFCQLCSSKSTSLP-KFGIEKEVRVCEDCHEKFT 86 (158)
Q Consensus 21 ~~~p~W~~~---~~C~~C~~~F~-~~~RkhhCr~CG~vfC~~Cs~~~~~lp-~~~~~~~~RVC~~C~~~l~ 86 (158)
-.+|.|..+ ..|+.|...|+ ++.||||||.|+.+||..|+.....+| ++....+.|||+.|+..+.
T Consensus 149 ~~ap~f~yskskglfagvSvegsaI~erR~anR~~yg~~cra~~ilsg~vp~p~a~d~l~RVldS~~~nl~ 219 (473)
T KOG1843|consen 149 GEAPVFLYSKSKGLFAGVSVEGSAIIERREANRKFYGIFCRAKSILSGLVPVPFAADPLQRVLDSCAFNLE 219 (473)
T ss_pred CcCccccccccccceeeeecccceeeecchhhhhhcCccchhhhhhccCCCCCcccCCHHHHHhhHhhccC
Confidence 358999975 47999999999 678999999999999999998765554 3445688999999999883
No 12
>KOG1811|consensus
Probab=98.04 E-value=5.6e-07 Score=81.54 Aligned_cols=55 Identities=35% Similarity=0.778 Sum_probs=48.9
Q ss_pred Cccc-cCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHH
Q psy509 31 TCHR-CRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKF 85 (158)
Q Consensus 31 ~C~~-C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l 85 (158)
-|+. |+..|..|+||||||.||...|..|...+....+-|...|.++|+.|+..-
T Consensus 328 ~~~a~~R~~~kd~~Rk~~~~g~Ga~e~aa~ea~kgiqEd~gse~~Adg~Dq~psvs 383 (1141)
T KOG1811|consen 328 ICMACCREHFKDFNRKHHCRGCGALECAACEAKKGIQEDCGSENPADGCDQCPSVS 383 (1141)
T ss_pred HHHHHHHHHHHHHHHhhhccccchHHHhHHHHhhhhhhcccccCcccccccccchh
Confidence 5774 678999999999999999999999999988888888789999999999653
No 13
>KOG4424|consensus
Probab=97.91 E-value=2.7e-06 Score=76.17 Aligned_cols=65 Identities=31% Similarity=0.618 Sum_probs=53.8
Q ss_pred CCCccc-CCCccccCcccc-ccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhcc
Q psy509 23 APEWMD-GDTCHRCRTTFS-LVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTNY 88 (158)
Q Consensus 23 ~p~W~~-~~~C~~C~~~F~-~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~~ 88 (158)
.|.|.. ...|+.|+..|+ ...|||||+.||.++|+.|+.+...+. +......|||..||......
T Consensus 408 ~~r~~~k~~~c~~c~e~~~s~t~~R~~~k~~~~vlc~~cs~~~~~l~-~~~s~ssrv~~~~~~~~~~a 474 (623)
T KOG4424|consen 408 APRRDNKVTSCDSCEETFNSITFRRHRCKAKGAVLCDKCSDFMAKLS-YDNSRSSRVCMDRYLTPSGA 474 (623)
T ss_pred CcccccccccchhhcCchhhHHHhhhhhhhccceeeccccchhhhhc-ccccchhhhhhhhccCCCCC
Confidence 668843 578999999997 567999999999999999999976654 24467889999999987653
No 14
>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=97.67 E-value=3.1e-05 Score=56.52 Aligned_cols=53 Identities=23% Similarity=0.640 Sum_probs=42.5
Q ss_pred cCCCccccCcccccc-ccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 28 DGDTCHRCRTTFSLV-QRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 28 ~~~~C~~C~~~F~~~-~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
....|..|+++|+++ ++.+.|..|+..||..|..+. ...+.-+|..|+....-
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~-------~~~~~WlC~vC~k~rel 106 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYS-------KKEPIWLCKVCQKQREL 106 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEET-------SSSCCEEEHHHHHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCcC-------CCCCCEEChhhHHHHHH
Confidence 456899999999976 689999999999999998771 24678999999987543
No 15
>smart00726 UIM Ubiquitin-interacting motif. Present in proteasome subunit S5a and other ubiquitin-associated proteins.
Probab=97.56 E-value=6.8e-05 Score=40.87 Aligned_cols=22 Identities=55% Similarity=0.699 Sum_probs=19.0
Q ss_pred cchHHHHHHHHhcHHHHhhcCC
Q psy509 135 KEEEELQLALALSQSEAESNKP 156 (158)
Q Consensus 135 ~eeedl~~aia~Sl~e~e~~~~ 156 (158)
+||++|++||++|+.|++....
T Consensus 1 ~EDe~Lq~Ai~lSl~e~e~~~~ 22 (26)
T smart00726 1 DEDEDLQLALELSLQEAEESXX 22 (26)
T ss_pred ChHHHHHHHHHHhHHHhhhccc
Confidence 4799999999999999987643
No 16
>PF02809 UIM: Ubiquitin interaction motif; InterPro: IPR003903 The Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a stretch of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin [,]. In addition, the UIM is found, often in tandem or triplet arrays, in a variety of proteins either involved in ubiquitination and ubiquitin metabolism, or known to interact with ubiquitin-like modifiers. Among the UIM proteins are two different subgroups of the UBP (ubiquitin carboxy-terminal hydrolase) family of deubiquitinating enzymes, one F-box protein, one family of HECT-containing ubiquitin-ligases (E3s) from plants, and several proteins containing ubiquitin-associated UBA and/or UBX domains []. In most of these proteins, the UIM occurs in multiple copies and in association with other domains such as UBA (IPR015940 from INTERPRO), UBX (IPR001012 from INTERPRO), ENTH, EH (IPR000261 from INTERPRO), VHS (IPR002014 from INTERPRO), SH3 (IPR001452 from INTERPRO), HECT (IPR000569 from INTERPRO), VWFA (IPR002035 from INTERPRO), EF-hand calcium-binding, WD-40 (IPR001680 from INTERPRO), F-box (IPR001810 from INTERPRO), LIM (IPR001781 from INTERPRO), protein kinase (IPR000719 from INTERPRO), ankyrin (IPR002110 from INTERPRO), PX (IPR001683 from INTERPRO), phosphatidylinositol 3- and 4-kinase (IPR000403 from INTERPRO), C2 (IPR000008 from INTERPRO), OTU (IPR003323 from INTERPRO), dnaJ (IPR001623 from INTERPRO), RING-finger (IPR001841 from INTERPRO) or FYVE-finger (IPR017455 from INTERPRO). UIMs have been shown to bind ubiquitin and to serve as a specific targeting signal important for monoubiquitination. Thus, UIMs may have several functions in ubiquitin metabolism each of which may require different numbers of UIMs [, , ]. The UIM is unlikely to form an independent folding domain. Instead, based on the spacing of the conserved residues, the motif probably forms a short alpha-helix that can be embedded into different protein folds []. Some proteins known to contain an UIM are listed below: Eukaryotic PSD4/RPN-10/S5, a multi-ubiquitin binding subunit of the 26S proteasome. Vertebrate Machado-Joseph disease protein 1 (Ataxin-3), which acts as a histone-binding protein that regulates transcription; defects in Ataxin-3 cause the neurodegenerative disorder Machado-Joseph disease (MJD). Vertebrate epsin and epsin2. Vertebrate hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). Mammalian epidermal growth factor receptor substrate 15 (EPS15), which is involved in cell growth regulation. Mammalian epidermal growth factor receptor substrate EPS15R. Drosophila melanogaster (Fruit fly) liquid facets (lqf), an epsin. Yeast VPS27 vacuolar sorting protein, which is required for membrane traffic to the vacuole. ; PDB: 2KDE_A 2KDF_A 1YX6_A 1YX5_A 1YX4_A 1P9C_A 1UEL_B 1P9D_S 2KLZ_A.
Probab=97.49 E-value=5.5e-05 Score=37.77 Aligned_cols=17 Identities=53% Similarity=0.659 Sum_probs=15.2
Q ss_pred cchHHHHHHHHhcHHHH
Q psy509 135 KEEEELQLALALSQSEA 151 (158)
Q Consensus 135 ~eeedl~~aia~Sl~e~ 151 (158)
+||++|++||++|++|+
T Consensus 2 ~Ed~~L~~Al~~S~~e~ 18 (18)
T PF02809_consen 2 DEDEDLQRALEMSLEEA 18 (18)
T ss_dssp HHHHHHHHHHHHHHHHC
T ss_pred chHHHHHHHHHhhhccC
Confidence 57999999999999874
No 17
>KOG0230|consensus
Probab=97.47 E-value=6.4e-05 Score=73.41 Aligned_cols=48 Identities=40% Similarity=1.120 Sum_probs=39.7
Q ss_pred CCCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
...|..|+ +.++|+|||+.||++||++|.... ....|||..|+.....
T Consensus 5 ~~~~~~~~---t~~~~~~~~~~~g~~~~~~~~~~~--------~~~i~~~~~~~~~~~~ 52 (1598)
T KOG0230|consen 5 SNVCYDCD---TSVNRRHHCRVCGRVFCSKCQDSP--------ETSIRVCNECRGQWEQ 52 (1598)
T ss_pred ccchhccc---cccccCCCCcccCceeccccCCCC--------ccceeehhhhhhhccc
Confidence 45677888 788999999999999999999332 2378999999998764
No 18
>KOG0230|consensus
Probab=97.05 E-value=0.00039 Score=68.12 Aligned_cols=55 Identities=31% Similarity=0.791 Sum_probs=40.0
Q ss_pred CCCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhcccCCC
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTNYYRSP 92 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~~~~~~ 92 (158)
+..|..|+..|..|+|+||| ||++||..|- ..-.++..... +.|......+..+.
T Consensus 97 ~~ec~~~~~~~~t~Rr~~~~--~gqi~~ss~~----~~~~~~~~~e~---d~c~~~~~~~~~ss 151 (1598)
T KOG0230|consen 97 SKECYDCEQKFETFRRKHHC--CGQIFCSSCI----DGMSIRCDGEL---DYCSRYVEDFAKSS 151 (1598)
T ss_pred cchhhhhccchhhhhccccc--CccccCCccc----CCccccccccc---chhHHHhhhhhccC
Confidence 46899999999999999999 9999999991 11112222222 88888887665443
No 19
>KOG2199|consensus
Probab=95.90 E-value=0.0049 Score=53.65 Aligned_cols=27 Identities=37% Similarity=0.430 Sum_probs=23.1
Q ss_pred chhhhcchHHHHHHHHhcHHHHhhcCC
Q psy509 130 TEEELKEEEELQLALALSQSEAESNKP 156 (158)
Q Consensus 130 ~~~~~~eeedl~~aia~Sl~e~e~~~~ 156 (158)
.....+|||||+.||+|||+|.|.|+.
T Consensus 159 ~v~~k~EeEdiaKAi~lSL~E~~~Q~k 185 (462)
T KOG2199|consen 159 TVSSKQEEEDIAKAIELSLKEQEKQKK 185 (462)
T ss_pred cccccccHHHHHHHHHhhHHHHhhchh
Confidence 345568999999999999999999864
No 20
>KOG1841|consensus
Probab=93.60 E-value=0.072 Score=51.66 Aligned_cols=54 Identities=26% Similarity=0.532 Sum_probs=43.0
Q ss_pred CCCCCcccC---CCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 21 DTAPEWMDG---DTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 21 ~~~p~W~~~---~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
++++.|+.+ ..|+.|.+.|.++.++|||| |.+| + .+...+..|+|..|...+.+
T Consensus 646 e~ksVw~aDg~aPng~la~t~~~~~~e~~hsr--~~ls----------~-~~~s~~~~~~~n~t~s~~rn 702 (1287)
T KOG1841|consen 646 EVKSVWFADGIAPNGELAETRFTFTGERHHSR--GKLS----------L-LYSSRKEARPCNITHSVLRN 702 (1287)
T ss_pred eecceeccCCcCCCceecccceeeeccccccc--cccc----------c-cccccccCCCCcccCccchh
Confidence 568999974 68999999999999999999 8887 1 11124567899999988776
No 21
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=93.10 E-value=0.02 Score=36.08 Aligned_cols=44 Identities=23% Similarity=0.647 Sum_probs=25.8
Q ss_pred CccccCcccccc------ccccccccccceecCCCCCCccccCCCCCCCceeeChhhH
Q psy509 31 TCHRCRTTFSLV------QRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCH 82 (158)
Q Consensus 31 ~C~~C~~~F~~~------~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~ 82 (158)
.|.+|.++|... ..++.|..|+++||..|=.+. ...+..|..|.
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fi--------HE~LH~CPGC~ 50 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFI--------HETLHNCPGCE 50 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT--B-HHHHHTT--------TTTS-SSSTT-
T ss_pred CCccCCCCCCCcccccccCCeEECCCCCCccccCcChhh--------hccccCCcCCC
Confidence 388999999875 468999999999999995442 34456666663
No 22
>KOG0993|consensus
Probab=92.68 E-value=0.0057 Score=53.50 Aligned_cols=58 Identities=26% Similarity=0.625 Sum_probs=50.3
Q ss_pred cCCCccccCcccccccccccccc--ccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 28 DGDTCHRCRTTFSLVQRKHHCRA--CGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 28 ~~~~C~~C~~~F~~~~RkhhCr~--CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
+...|..|..+|..++-+-||-+ ||++||.+|+.-. +|.+....+..||..|+..+.+
T Consensus 467 ~ve~c~~~~aS~~slk~e~erl~qq~eqi~~~~~~Kat--vp~l~~e~~akv~rlq~eL~~s 526 (542)
T KOG0993|consen 467 DVEQCSNCDASFASLKVEPERLHQQCEQIFCMNCLKAT--VPSLPNERPAKVCRLQHELLNS 526 (542)
T ss_pred HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhHHHhh--cccccccchHHHHHHHHHHhhh
Confidence 35789999999999999999988 9999999999764 5666667899999999998775
No 23
>KOG4275|consensus
Probab=92.10 E-value=0.042 Score=46.25 Aligned_cols=48 Identities=29% Similarity=0.731 Sum_probs=41.0
Q ss_pred CCCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHH
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKF 85 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l 85 (158)
+.+|..|+..|..+.+||.|-.|.+-||..||.. ....|.|..|...-
T Consensus 44 ~p~ckacg~~f~~~~~k~~c~dckk~fc~tcs~v---------~~~lr~c~~c~r~~ 91 (350)
T KOG4275|consen 44 APHCKACGEEFEDAQSKSDCEDCKKEFCATCSRV---------SISLRTCTSCRRVN 91 (350)
T ss_pred cchhhhhchhHhhhhhhhhhhhhhHHHHHHHHHh---------cccchhhhHHHHHH
Confidence 4589999999999999999999999999999933 23468899998753
No 24
>KOG1729|consensus
Probab=90.32 E-value=0.078 Score=44.54 Aligned_cols=56 Identities=21% Similarity=0.528 Sum_probs=42.5
Q ss_pred CCCccccCccccccccccccccccceecCCCCC-Cc---cccCCC--CCCCceeeChhhHHH
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSS-KS---TSLPKF--GIEKEVRVCEDCHEK 84 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~-~~---~~lp~~--~~~~~~RVC~~C~~~ 84 (158)
+..|..|...|.++.|.|||+.||++||..|+. +. .+-+.+ -......+|..|+..
T Consensus 20 ~~s~~~~~~e~~~~~r~~~~~~~grv~~~q~~~~k~~rk~~q~r~~~l~~D~~~~~~~~~~~ 81 (288)
T KOG1729|consen 20 ANSCRNCKVEFCFGRRGHPCRECGRVLCRQGTLVKRCRKKLQSRSFFLFNDILVYGNIVSDN 81 (288)
T ss_pred chhhhhhcccchhhhccCcccccchhhhhhhhhHHHHhcccccccccccccchhhcccccCH
Confidence 568999999999999999999999999999988 21 111111 124567788888776
No 25
>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=89.86 E-value=0.22 Score=35.94 Aligned_cols=33 Identities=30% Similarity=0.658 Sum_probs=25.6
Q ss_pred CCCcccCCCccccCccccccccc-ccccccccee
Q psy509 23 APEWMDGDTCHRCRTTFSLVQRK-HHCRACGQVF 55 (158)
Q Consensus 23 ~p~W~~~~~C~~C~~~F~~~~Rk-hhCr~CG~vf 55 (158)
.|.|--=..|..|+++|==|+|. -+|..||.+|
T Consensus 3 kpelGtKR~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 3 KPELGTKRTCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred ccccCCcccCCCCcchhccCCCCCccCCCCCCcc
Confidence 46676667999999999766654 5588888876
No 26
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=89.73 E-value=0.2 Score=29.58 Aligned_cols=26 Identities=42% Similarity=1.076 Sum_probs=19.6
Q ss_pred ccccCccccccccccccccccceecCCC
Q psy509 32 CHRCRTTFSLVQRKHHCRACGQVFCQLC 59 (158)
Q Consensus 32 C~~C~~~F~~~~RkhhCr~CG~vfC~~C 59 (158)
|..|++.-.++ ...|+.||.+||...
T Consensus 1 C~~C~~~~~l~--~f~C~~C~~~FC~~H 26 (39)
T smart00154 1 CHFCRKKVGLT--GFKCRHCGNLFCGEH 26 (39)
T ss_pred CcccCCccccc--CeECCccCCcccccc
Confidence 56677765554 678999999998754
No 27
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=89.45 E-value=0.2 Score=29.02 Aligned_cols=25 Identities=40% Similarity=1.058 Sum_probs=18.9
Q ss_pred CccccCccccc-------ccccccccccccee
Q psy509 31 TCHRCRTTFSL-------VQRKHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~-------~~RkhhCr~CG~vf 55 (158)
.|..|++.|.+ -.++..|.+||++|
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 58888888864 34667888888876
No 28
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=88.69 E-value=0.22 Score=38.21 Aligned_cols=25 Identities=32% Similarity=0.832 Sum_probs=19.4
Q ss_pred CccccCcccc------------cccccccccccccee
Q psy509 31 TCHRCRTTFS------------LVQRKHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~------------~~~RkhhCr~CG~vf 55 (158)
.|..|+.+++ ..+|+++|.+||..|
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 4888887772 356679999999987
No 29
>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=88.68 E-value=0.28 Score=36.45 Aligned_cols=33 Identities=18% Similarity=0.310 Sum_probs=25.7
Q ss_pred CCCcccCCCccccCcccccc-cccccccccccee
Q psy509 23 APEWMDGDTCHRCRTTFSLV-QRKHHCRACGQVF 55 (158)
Q Consensus 23 ~p~W~~~~~C~~C~~~F~~~-~RkhhCr~CG~vf 55 (158)
.|.|---..|..|+++|--+ ++-.+|..||.+|
T Consensus 3 k~elGtKr~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 3 KPDLGTKRICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred chhhCccccCCCcCccccccCCCCccCCCcCCcc
Confidence 46777777999999999755 4567888888875
No 30
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=87.78 E-value=0.31 Score=28.33 Aligned_cols=25 Identities=48% Similarity=1.055 Sum_probs=19.7
Q ss_pred CccccCccccc-------ccccccccccccee
Q psy509 31 TCHRCRTTFSL-------VQRKHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~-------~~RkhhCr~CG~vf 55 (158)
.|..|++.|.+ -.++..|..||.+|
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 58899998863 35688888888887
No 31
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=86.79 E-value=0.46 Score=34.61 Aligned_cols=45 Identities=24% Similarity=0.685 Sum_probs=33.1
Q ss_pred CCccccCcccccc----------ccccccccccceecCCCCCCccccCCCCCCCceeeChhhH
Q psy509 30 DTCHRCRTTFSLV----------QRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCH 82 (158)
Q Consensus 30 ~~C~~C~~~F~~~----------~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~ 82 (158)
..|.+|.+.|.-. ..++-|..|+++||-.|=.+. ...+..|-.|.
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fi--------He~Lh~CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFV--------HESLHCCPGCI 110 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhh--------hhhccCCcCCC
Confidence 4699999999742 446889999999999997553 23445566664
No 32
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=86.28 E-value=0.14 Score=30.56 Aligned_cols=33 Identities=30% Similarity=0.837 Sum_probs=23.2
Q ss_pred CccccCccccccccccccccccceecCCCCCCcc
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKST 64 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~ 64 (158)
.|..|...|+ -.++-.=-.||++||..|.....
T Consensus 1 ~C~~C~~~~~-~~~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 1 HCNICFEKYS-EERRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CCcCcCcccc-CCCCeEEcccCCHHHHHHHHhhc
Confidence 4778888882 22334445899999999987754
No 33
>KOG0320|consensus
Probab=84.74 E-value=0.084 Score=41.44 Aligned_cols=46 Identities=33% Similarity=0.761 Sum_probs=31.7
Q ss_pred CccccCcccccccccc-ccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 31 TCHRCRTTFSLVQRKH-HCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 31 ~C~~C~~~F~~~~Rkh-hCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
.|.+|--.|+ .|. .--.||+|||..|....+ +..++|..|..+|..
T Consensus 133 ~CPiCl~~~s---ek~~vsTkCGHvFC~~Cik~al--------k~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 133 KCPICLDSVS---EKVPVSTKCGHVFCSQCIKDAL--------KNTNKCPTCRKKITH 179 (187)
T ss_pred CCCceecchh---hccccccccchhHHHHHHHHHH--------HhCCCCCCcccccch
Confidence 5666665553 222 446899999999987642 445789999877654
No 34
>PHA02768 hypothetical protein; Provisional
Probab=84.41 E-value=0.43 Score=30.45 Aligned_cols=26 Identities=15% Similarity=0.346 Sum_probs=17.8
Q ss_pred CCccccCcccccc------cc----cccccccccee
Q psy509 30 DTCHRCRTTFSLV------QR----KHHCRACGQVF 55 (158)
Q Consensus 30 ~~C~~C~~~F~~~------~R----khhCr~CG~vf 55 (158)
-.|..|++.|+.. .| .+.|-.||++|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f 41 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRIS 41 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcCCcccCCccccee
Confidence 3799999999732 23 34477777766
No 35
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=84.33 E-value=0.86 Score=29.51 Aligned_cols=31 Identities=29% Similarity=0.535 Sum_probs=23.9
Q ss_pred CcccCCCccccCccccc--ccccccccccccee
Q psy509 25 EWMDGDTCHRCRTTFSL--VQRKHHCRACGQVF 55 (158)
Q Consensus 25 ~W~~~~~C~~C~~~F~~--~~RkhhCr~CG~vf 55 (158)
.|..+..|..|+..-.. -.|.++|..||..+
T Consensus 24 ~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 24 EAYTSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CCCCccCccCcccccccccccceEEcCCCCCEE
Confidence 33457789999876654 78899999999874
No 36
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=83.17 E-value=1.3 Score=37.63 Aligned_cols=72 Identities=22% Similarity=0.409 Sum_probs=46.3
Q ss_pred CCCCCCcccCCCccccCcc--ccc-------cccccccccccc------eecCCCCCCccccCC--CCC---CCceeeCh
Q psy509 20 ADTAPEWMDGDTCHRCRTT--FSL-------VQRKHHCRACGQ------VFCQLCSSKSTSLPK--FGI---EKEVRVCE 79 (158)
Q Consensus 20 ~~~~p~W~~~~~C~~C~~~--F~~-------~~RkhhCr~CG~------vfC~~Cs~~~~~lp~--~~~---~~~~RVC~ 79 (158)
....+.|.....|..||.. .++ -.|..||..||. +-|..|.+.. .+-- +.. ...+-+|+
T Consensus 178 ~~~~~~~~~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~-~l~y~~~~~~~~~~r~e~C~ 256 (309)
T PRK03564 178 KARAEYGEQRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSG-KLHYWSLDSEQAAVKAESCG 256 (309)
T ss_pred ccccccccCCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCCC-ceeeeeecCCCcceEeeecc
Confidence 3345556667899999975 232 357889999985 4788887642 2211 111 23467999
Q ss_pred hhHHHHhcccCCC
Q psy509 80 DCHEKFTNYYRSP 92 (158)
Q Consensus 80 ~C~~~l~~~~~~~ 92 (158)
.|...+.-.+...
T Consensus 257 ~C~~YlK~~~~~~ 269 (309)
T PRK03564 257 DCGTYLKILYQEK 269 (309)
T ss_pred cccccceeccccc
Confidence 9999887754443
No 37
>KOG3576|consensus
Probab=82.99 E-value=0.35 Score=39.05 Aligned_cols=28 Identities=36% Similarity=0.876 Sum_probs=21.6
Q ss_pred CCccccCccccc---cc---------cccccccccceecC
Q psy509 30 DTCHRCRTTFSL---VQ---------RKHHCRACGQVFCQ 57 (158)
Q Consensus 30 ~~C~~C~~~F~~---~~---------RkhhCr~CG~vfC~ 57 (158)
-.|..|++.|++ ++ |||-|+.||+-|=.
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfnd 157 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFND 157 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccc
Confidence 479999999983 43 47888899988733
No 38
>KOG2164|consensus
Probab=82.32 E-value=0.4 Score=43.05 Aligned_cols=52 Identities=25% Similarity=0.465 Sum_probs=38.3
Q ss_pred CCCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
+..|.+|=..+.+-.|- +||+|||..|.-...-.+ -....+-|..|+..+..
T Consensus 186 ~~~CPICL~~~~~p~~t----~CGHiFC~~CiLqy~~~s---~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRT----NCGHIFCGPCILQYWNYS---AIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCCCCccccc----ccCceeeHHHHHHHHhhh---cccCCccCCchhhhccc
Confidence 46899998877755443 499999999976543333 23556889999999875
No 39
>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=82.00 E-value=0.33 Score=28.72 Aligned_cols=34 Identities=26% Similarity=0.549 Sum_probs=24.4
Q ss_pred CCccccCccccccccccccccccceecCCCCCCcc
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKST 64 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~ 64 (158)
+.|.+|...|..-..-.-. .||++||..|...++
T Consensus 1 d~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~~~ 34 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKL-PCGHVFHRSCIKEWL 34 (44)
T ss_dssp -CETTTTCBHHTTSCEEEE-TTSEEEEHHHHHHHH
T ss_pred CCCcCCChhhcCCCeEEEc-cCCCeeCHHHHHHHH
Confidence 4689999988653333333 499999999987764
No 40
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=81.55 E-value=0.89 Score=27.39 Aligned_cols=25 Identities=28% Similarity=0.644 Sum_probs=17.6
Q ss_pred CccccCcccccccc--cccccccccee
Q psy509 31 TCHRCRTTFSLVQR--KHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~~~R--khhCr~CG~vf 55 (158)
.|..|+..|.+-.. ..+|..||.-+
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEECCCCCceECCCCCCeE
Confidence 58888888865443 57888887643
No 41
>PRK00420 hypothetical protein; Validated
Probab=80.94 E-value=1.1 Score=32.67 Aligned_cols=26 Identities=19% Similarity=0.399 Sum_probs=17.1
Q ss_pred CCCccccCccccc-cccccccccccce
Q psy509 29 GDTCHRCRTTFSL-VQRKHHCRACGQV 54 (158)
Q Consensus 29 ~~~C~~C~~~F~~-~~RkhhCr~CG~v 54 (158)
+..|..|+.+|.- -..+..|.+||.+
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCe
Confidence 4789999987764 3445555555554
No 42
>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=80.91 E-value=1.2 Score=27.73 Aligned_cols=33 Identities=24% Similarity=0.588 Sum_probs=20.1
Q ss_pred Cccc--cCcccccccc----ccccccccceecCCCCCCc
Q psy509 31 TCHR--CRTTFSLVQR----KHHCRACGQVFCQLCSSKS 63 (158)
Q Consensus 31 ~C~~--C~~~F~~~~R----khhCr~CG~vfC~~Cs~~~ 63 (158)
.|.. |+..|..-.. ...|..||..||..|...+
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 5654 8877754332 2689999999999998654
No 43
>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=80.14 E-value=1.1 Score=24.19 Aligned_cols=23 Identities=30% Similarity=0.748 Sum_probs=12.5
Q ss_pred CccccCcccccccccccccccccee
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~vf 55 (158)
.|..|++.-.... .-|.+||..|
T Consensus 2 ~CP~C~~~V~~~~--~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESA--KFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhc--CcCCCCCCCC
Confidence 4666666443332 2466677665
No 44
>KOG0823|consensus
Probab=79.95 E-value=0.71 Score=37.58 Aligned_cols=34 Identities=21% Similarity=0.549 Sum_probs=26.1
Q ss_pred ccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 49 RACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 49 r~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
-.||+.||+-|.-+|..+. .....|-.|...+..
T Consensus 63 TlCGHLFCWpClyqWl~~~-----~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 63 TLCGHLFCWPCLYQWLQTR-----PNSKECPVCKAEVSI 96 (230)
T ss_pred eecccceehHHHHHHHhhc-----CCCeeCCcccccccc
Confidence 3799999999999986542 334677888887765
No 45
>PF12773 DZR: Double zinc ribbon
Probab=78.94 E-value=1.4 Score=26.74 Aligned_cols=26 Identities=31% Similarity=0.648 Sum_probs=16.8
Q ss_pred CCCccccCcccc-ccccccccccccce
Q psy509 29 GDTCHRCRTTFS-LVQRKHHCRACGQV 54 (158)
Q Consensus 29 ~~~C~~C~~~F~-~~~RkhhCr~CG~v 54 (158)
+..|..|+.++. .......|..||..
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCC
Confidence 567888888776 23345667777763
No 46
>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=76.58 E-value=1.5 Score=25.11 Aligned_cols=25 Identities=40% Similarity=1.027 Sum_probs=14.5
Q ss_pred CccccCcccccc-------cccccccccccee
Q psy509 31 TCHRCRTTFSLV-------QRKHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~~-------~RkhhCr~CG~vf 55 (158)
.|..|++.|.+- ..+-.|.+||..|
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 477777777532 2235566666654
No 47
>KOG3799|consensus
Probab=76.23 E-value=1.1 Score=33.88 Aligned_cols=53 Identities=32% Similarity=0.685 Sum_probs=38.7
Q ss_pred cCCCccccCc-cccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHH
Q psy509 28 DGDTCHRCRT-TFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKF 85 (158)
Q Consensus 28 ~~~~C~~C~~-~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l 85 (158)
++..|.+|.+ +|.--. -|.|..|.--||..|.-+- .+ ..++-..||..|....
T Consensus 64 ddatC~IC~KTKFADG~-GH~C~YCq~r~CARCGGrv-~l---rsNKv~wvcnlc~k~q 117 (169)
T KOG3799|consen 64 DDATCGICHKTKFADGC-GHNCSYCQTRFCARCGGRV-SL---RSNKVMWVCNLCRKQQ 117 (169)
T ss_pred cCcchhhhhhccccccc-CcccchhhhhHHHhcCCee-ee---ccCceEEeccCCcHHH
Confidence 4668999975 664333 4999999999999998663 22 2256678999997654
No 48
>KOG3173|consensus
Probab=74.68 E-value=1.4 Score=34.19 Aligned_cols=27 Identities=37% Similarity=1.045 Sum_probs=22.7
Q ss_pred CCccccCccccccccccccccccceecCCC
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVFCQLC 59 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vfC~~C 59 (158)
..|..|+++-++.. .||| ||.+||+..
T Consensus 106 ~rC~~C~kk~gltg--f~Cr-CG~~fC~~H 132 (167)
T KOG3173|consen 106 KRCFKCRKKVGLTG--FKCR-CGNTFCGTH 132 (167)
T ss_pred hhhhhhhhhhcccc--cccc-cCCcccccc
Confidence 36999999888887 8886 999998854
No 49
>KOG0153|consensus
Probab=74.46 E-value=0.56 Score=40.39 Aligned_cols=17 Identities=24% Similarity=0.714 Sum_probs=14.4
Q ss_pred CCCccccCccccccccc
Q psy509 29 GDTCHRCRTTFSLVQRK 45 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~Rk 45 (158)
+..|.+|.++|++|+.+
T Consensus 41 gkECKICtrPfT~Frw~ 57 (377)
T KOG0153|consen 41 GKECKICTRPFTIFRWC 57 (377)
T ss_pred CCccceecCcceEEEec
Confidence 46899999999988654
No 50
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=74.15 E-value=2.7 Score=26.17 Aligned_cols=22 Identities=27% Similarity=0.608 Sum_probs=18.5
Q ss_pred cccccccccccceecCCCCCCc
Q psy509 42 VQRKHHCRACGQVFCQLCSSKS 63 (158)
Q Consensus 42 ~~RkhhCr~CG~vfC~~Cs~~~ 63 (158)
......|..||..||..|...+
T Consensus 37 ~~~~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 37 GCNRVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred CCCeeECCCCCCeECCCCCCcC
Confidence 4678899999999999997654
No 51
>KOG0978|consensus
Probab=74.14 E-value=0.29 Score=45.63 Aligned_cols=44 Identities=30% Similarity=0.738 Sum_probs=31.2
Q ss_pred CCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHH
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEK 84 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~ 84 (158)
-.|..|.+.+- ---=..||++||..|...+. ....|-|..|-.-
T Consensus 644 LkCs~Cn~R~K----d~vI~kC~H~FC~~Cvq~r~-------etRqRKCP~Cn~a 687 (698)
T KOG0978|consen 644 LKCSVCNTRWK----DAVITKCGHVFCEECVQTRY-------ETRQRKCPKCNAA 687 (698)
T ss_pred eeCCCccCchh----hHHHHhcchHHHHHHHHHHH-------HHhcCCCCCCCCC
Confidence 36999987653 11124799999999998762 4567889888643
No 52
>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=74.07 E-value=1.1 Score=29.89 Aligned_cols=32 Identities=31% Similarity=0.834 Sum_probs=19.1
Q ss_pred CccccCccccccccccccccccce-----ecCCCCCC
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQV-----FCQLCSSK 62 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~v-----fC~~Cs~~ 62 (158)
.|..|+....+...+.||..|+.- +|..|-..
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~ 39 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQP 39 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccH
Confidence 588888888877788888888765 45555443
No 53
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=73.37 E-value=0.43 Score=37.93 Aligned_cols=54 Identities=22% Similarity=0.498 Sum_probs=35.9
Q ss_pred CCccccCccccccccccccccccceecCCCCCCccccCC--------CCCCCceeeChhhHHHHhc
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPK--------FGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~--------~~~~~~~RVC~~C~~~l~~ 87 (158)
-.|.+|...|.- -.--.||++||..|...+..... ....+....|-.|...+..
T Consensus 19 ~~CpICld~~~d----PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 19 FDCNICLDQVRD----PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred cCCccCCCcCCC----cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 579999887642 22357999999999976643211 1112345689999988764
No 54
>KOG1814|consensus
Probab=73.31 E-value=1.5 Score=38.61 Aligned_cols=40 Identities=28% Similarity=0.928 Sum_probs=32.6
Q ss_pred CCccc--CCCccccCccccccc--cccccccccceecCCCCCCc
Q psy509 24 PEWMD--GDTCHRCRTTFSLVQ--RKHHCRACGQVFCQLCSSKS 63 (158)
Q Consensus 24 p~W~~--~~~C~~C~~~F~~~~--RkhhCr~CG~vfC~~Cs~~~ 63 (158)
-.|+. +..|..|........ -|+||-.||..||+-|+...
T Consensus 361 ekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l 404 (445)
T KOG1814|consen 361 EKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELL 404 (445)
T ss_pred HHHHHhcCCCCCcccceeecCCCccceeeccccccceeehhhhc
Confidence 37875 678999998776553 58999999999999998654
No 55
>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=72.98 E-value=0.8 Score=38.88 Aligned_cols=50 Identities=24% Similarity=0.594 Sum_probs=30.4
Q ss_pred cCCCccccCcc--cccccc-ccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHh
Q psy509 28 DGDTCHRCRTT--FSLVQR-KHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFT 86 (158)
Q Consensus 28 ~~~~C~~C~~~--F~~~~R-khhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~ 86 (158)
++..|..|.+. ++.-.+ -.+ .||+.||..|....... +...|..|...+.
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~--~CGH~~C~sCv~~l~~~-------~~~~CP~C~~~lr 54 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVN--VCGHTLCESCVDLLFVR-------GSGSCPECDTPLR 54 (309)
T ss_pred CCCCCCcCCCCCccCcccccccC--CCCCcccHHHHHHHhcC-------CCCCCCCCCCccc
Confidence 44689999873 321111 123 79999999998874221 1236777755544
No 56
>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=72.68 E-value=1 Score=25.89 Aligned_cols=29 Identities=28% Similarity=0.686 Sum_probs=19.2
Q ss_pred ccccCccccccccccccccccceecCCCCCCc
Q psy509 32 CHRCRTTFSLVQRKHHCRACGQVFCQLCSSKS 63 (158)
Q Consensus 32 C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~ 63 (158)
|.+|.. .+.....-..||++||..|...+
T Consensus 1 C~iC~~---~~~~~~~~~~CGH~fC~~C~~~~ 29 (39)
T PF13923_consen 1 CPICLD---ELRDPVVVTPCGHSFCKECIEKY 29 (39)
T ss_dssp ETTTTS---B-SSEEEECTTSEEEEHHHHHHH
T ss_pred CCCCCC---cccCcCEECCCCCchhHHHHHHH
Confidence 445544 33334567889999999997664
No 57
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=71.92 E-value=2.3 Score=24.39 Aligned_cols=27 Identities=33% Similarity=0.821 Sum_probs=12.2
Q ss_pred ecCCCCCC-ccccCCCCCCCceeeChhhH
Q psy509 55 FCQLCSSK-STSLPKFGIEKEVRVCEDCH 82 (158)
Q Consensus 55 fC~~Cs~~-~~~lp~~~~~~~~RVC~~C~ 82 (158)
||..|... ...+| .|.+++..||..|-
T Consensus 2 fC~~CG~~l~~~ip-~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 2 FCPQCGGPLERRIP-EGDDRERLVCPACG 29 (34)
T ss_dssp B-TTT--B-EEE---TT-SS-EEEETTTT
T ss_pred ccccccChhhhhcC-CCCCccceECCCCC
Confidence 44555443 22334 33468889999884
No 58
>KOG4739|consensus
Probab=71.44 E-value=1.8 Score=35.41 Aligned_cols=44 Identities=32% Similarity=0.698 Sum_probs=29.4
Q ss_pred CccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHh
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFT 86 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~ 86 (158)
+|..|+..=+ ....+=-.|++|||..|.....+ ++|..|...+.
T Consensus 5 hCn~C~~~~~--~~~f~LTaC~HvfC~~C~k~~~~----------~~C~lCkk~ir 48 (233)
T KOG4739|consen 5 HCNKCFRFPS--QDPFFLTACRHVFCEPCLKASSP----------DVCPLCKKSIR 48 (233)
T ss_pred EeccccccCC--CCceeeeechhhhhhhhcccCCc----------cccccccceee
Confidence 6777765322 34444458999999999866311 28999987643
No 59
>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=71.41 E-value=1.1 Score=25.29 Aligned_cols=31 Identities=32% Similarity=0.724 Sum_probs=21.2
Q ss_pred CccccCccccccccccccccccceecCCCCCCcc
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKST 64 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~ 64 (158)
.|.+|...| .....-..||+.||..|...+.
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~ 31 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWL 31 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHH
Confidence 367777766 3334445699999999987653
No 60
>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=71.14 E-value=3 Score=25.09 Aligned_cols=30 Identities=33% Similarity=0.881 Sum_probs=19.9
Q ss_pred CCcccCCCccccCcc--cccc-ccccccccccc
Q psy509 24 PEWMDGDTCHRCRTT--FSLV-QRKHHCRACGQ 53 (158)
Q Consensus 24 p~W~~~~~C~~C~~~--F~~~-~RkhhCr~CG~ 53 (158)
-.|-++-.|..|+.. +.+- ..++.|+.|++
T Consensus 13 ~RW~~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 13 IRWPDGFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred hcCCCCCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 468788889999852 2222 25677888764
No 61
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=71.05 E-value=3.1 Score=32.94 Aligned_cols=46 Identities=15% Similarity=0.354 Sum_probs=35.5
Q ss_pred ccccccceecCCCCCC-ccccCCC----CCCCceeeChhhHHHHhcccCCC
Q psy509 47 HCRACGQVFCQLCSSK-STSLPKF----GIEKEVRVCEDCHEKFTNYYRSP 92 (158)
Q Consensus 47 hCr~CG~vfC~~Cs~~-~~~lp~~----~~~~~~RVC~~C~~~l~~~~~~~ 92 (158)
.|...|+.||..|-.. ...||.. .--++..||+..+..|......|
T Consensus 2 ~C~Y~G~yyC~~CH~~~~~vIParil~~WDf~~~pVs~~a~~~L~~~~~~P 52 (202)
T PF13901_consen 2 FCDYTGKYYCSSCHWNDTSVIPARILHNWDFRPYPVSRFAKQFLDQIWSKP 52 (202)
T ss_pred ccCCCCCcCCCCCCCCCceeccHHHHHhcCCCccHHHHHHHHHHHHhccCC
Confidence 5889999999999877 4556631 11378899999999998866555
No 62
>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=70.66 E-value=2 Score=26.20 Aligned_cols=23 Identities=30% Similarity=0.904 Sum_probs=13.8
Q ss_pred CccccCcccccccccc-----ccccccc
Q psy509 31 TCHRCRTTFSLVQRKH-----HCRACGQ 53 (158)
Q Consensus 31 ~C~~C~~~F~~~~Rkh-----hCr~CG~ 53 (158)
.|..|+..|..+..-+ .|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 5777888787664322 3555554
No 63
>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=70.40 E-value=2.6 Score=29.37 Aligned_cols=30 Identities=23% Similarity=0.568 Sum_probs=20.0
Q ss_pred CcccCCCccccCcccc---------ccccccccccccce
Q psy509 25 EWMDGDTCHRCRTTFS---------LVQRKHHCRACGQV 54 (158)
Q Consensus 25 ~W~~~~~C~~C~~~F~---------~~~RkhhCr~CG~v 54 (158)
-|.+...|..|+++.. ++.-|.+||.|+.-
T Consensus 29 i~~~rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~ 67 (92)
T PF06750_consen 29 IIFPRSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAP 67 (92)
T ss_pred ccCCCCcCcCCCCcCcccccchHHHHHHhCCCCcccCCC
Confidence 3445677888887654 44567778888763
No 64
>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=69.93 E-value=2.8 Score=24.24 Aligned_cols=30 Identities=30% Similarity=0.720 Sum_probs=19.0
Q ss_pred CcccCCC--ccccCcccc-ccccccccccccce
Q psy509 25 EWMDGDT--CHRCRTTFS-LVQRKHHCRACGQV 54 (158)
Q Consensus 25 ~W~~~~~--C~~C~~~F~-~~~RkhhCr~CG~v 54 (158)
.|..... |..|+..|. .-..+.-|..||.+
T Consensus 2 e~~~~~~~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 2 EWMRGPNEPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cccccCCCcCCCCCCeEeEccCCEEEhhhCceE
Confidence 3555444 888886643 34567777777765
No 65
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=69.70 E-value=1.3 Score=26.63 Aligned_cols=31 Identities=35% Similarity=0.802 Sum_probs=14.1
Q ss_pred ccccCccccccccccccccccceecCCCCCCc
Q psy509 32 CHRCRTTFSLVQRKHHCRACGQVFCQLCSSKS 63 (158)
Q Consensus 32 C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~ 63 (158)
|.+|.. |+--...--=-.||++||..|..+.
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l 31 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKL 31 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHH
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHH
Confidence 556666 6543333333458998888887653
No 66
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=69.49 E-value=4.3 Score=22.22 Aligned_cols=29 Identities=24% Similarity=0.533 Sum_probs=23.0
Q ss_pred CccccCccccccccccccccccceecCCCC
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQVFCQLCS 60 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs 60 (158)
.|..|++..+-+. -++|..|+-.+-..|.
T Consensus 2 ~C~~C~~~~~~~~-~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-FYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCcCCCE-eEEeCCCCCeEcCccC
Confidence 5888998887776 8999999877766663
No 67
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=68.95 E-value=2.4 Score=30.67 Aligned_cols=24 Identities=21% Similarity=0.430 Sum_probs=17.3
Q ss_pred CCccccCccccccccccccccccc
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQ 53 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~ 53 (158)
-.|..|+..|........|..||.
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (115)
T TIGR00100 71 CECEDCSEEVSPEIDLYRCPKCHG 94 (115)
T ss_pred EEcccCCCEEecCCcCccCcCCcC
Confidence 378889988877655556777764
No 68
>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=67.77 E-value=3.4 Score=24.45 Aligned_cols=25 Identities=24% Similarity=0.574 Sum_probs=11.2
Q ss_pred CccccCcccc---cccccccccccccee
Q psy509 31 TCHRCRTTFS---LVQRKHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~---~~~RkhhCr~CG~vf 55 (158)
.|..|+.... ..+....|..||.|+
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence 3666665442 223334455555443
No 69
>KOG1829|consensus
Probab=66.84 E-value=3.6 Score=37.82 Aligned_cols=63 Identities=25% Similarity=0.471 Sum_probs=45.6
Q ss_pred CCccccCcccc--ccccccccccccceecCCCCCCccc-cCCCCC----CCceeeChhhHHHHhcccCCC
Q psy509 30 DTCHRCRTTFS--LVQRKHHCRACGQVFCQLCSSKSTS-LPKFGI----EKEVRVCEDCHEKFTNYYRSP 92 (158)
Q Consensus 30 ~~C~~C~~~F~--~~~RkhhCr~CG~vfC~~Cs~~~~~-lp~~~~----~~~~RVC~~C~~~l~~~~~~~ 92 (158)
-.|.+|++.++ ++.|-.-|+.+|..||..|-..-.. ||.-.+ -.+..||+.=+..|......|
T Consensus 341 ~~CAgC~~~i~~~~~~~~R~C~y~G~y~C~~Ch~~~~svIPARVl~~WDf~~y~Vs~~a~~~L~~ir~~P 410 (580)
T KOG1829|consen 341 FRCAGCGHTIGPDLEQRPRLCRYLGKYFCDCCHQNDKSVIPARVLHNWDFTKYPVSNFAKQFLDEIREQP 410 (580)
T ss_pred ceecccCCCcccccccchhHhhhhhhhhCchhcccCcccccccceecccCcccccchhHHHHHHHHhccc
Confidence 37999999998 5678889999999999999876433 342211 256778887777776544433
No 70
>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=66.28 E-value=6.1 Score=33.52 Aligned_cols=66 Identities=20% Similarity=0.509 Sum_probs=41.4
Q ss_pred cccCCCccccCccc--cc--------cccccccccccc------eecCCCCCCccccCCCCC-----CCcee--eChhhH
Q psy509 26 WMDGDTCHRCRTTF--SL--------VQRKHHCRACGQ------VFCQLCSSKSTSLPKFGI-----EKEVR--VCEDCH 82 (158)
Q Consensus 26 W~~~~~C~~C~~~F--~~--------~~RkhhCr~CG~------vfC~~Cs~~~~~lp~~~~-----~~~~R--VC~~C~ 82 (158)
|.....|..||..= ++ -.|..||..|+. +-|..|.+.. .+-.+.+ ...+| +|..|.
T Consensus 181 ~~~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~ 259 (305)
T TIGR01562 181 RESRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQ 259 (305)
T ss_pred cCCCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccc
Confidence 34456899998642 22 247789999985 5788887653 2221111 22344 999999
Q ss_pred HHHhcccCCC
Q psy509 83 EKFTNYYRSP 92 (158)
Q Consensus 83 ~~l~~~~~~~ 92 (158)
..+.-.+...
T Consensus 260 ~YlK~~~~~~ 269 (305)
T TIGR01562 260 GYLKILYQEK 269 (305)
T ss_pred cchhhhcccc
Confidence 9887754433
No 71
>KOG0317|consensus
Probab=65.71 E-value=1.3 Score=37.20 Aligned_cols=46 Identities=30% Similarity=0.659 Sum_probs=30.9
Q ss_pred CCCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHh
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFT 86 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~ 86 (158)
...|..|=. .++---|--||++||+.|..-|..- ++ -|.-|....+
T Consensus 239 ~~kC~LCLe----~~~~pSaTpCGHiFCWsCI~~w~~e------k~--eCPlCR~~~~ 284 (293)
T KOG0317|consen 239 TRKCSLCLE----NRSNPSATPCGHIFCWSCILEWCSE------KA--ECPLCREKFQ 284 (293)
T ss_pred CCceEEEec----CCCCCCcCcCcchHHHHHHHHHHcc------cc--CCCcccccCC
Confidence 467888854 2234568899999999998766422 11 1777776654
No 72
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=65.18 E-value=3.9 Score=25.53 Aligned_cols=28 Identities=25% Similarity=0.809 Sum_probs=19.6
Q ss_pred ccCCCccccCcccc-----cc---ccccccccccce
Q psy509 27 MDGDTCHRCRTTFS-----LV---QRKHHCRACGQV 54 (158)
Q Consensus 27 ~~~~~C~~C~~~F~-----~~---~RkhhCr~CG~v 54 (158)
+++..|.+|+...+ .+ ..-.+|.+||++
T Consensus 20 v~~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 20 VEGGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred eeCCccCCCCEEcCHHHHHHHHcCCCeEECcCCCcc
Confidence 34679999998765 12 235788888876
No 73
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=64.36 E-value=2.2 Score=30.69 Aligned_cols=24 Identities=25% Similarity=0.700 Sum_probs=16.9
Q ss_pred CCccccCccccccccccccccccc
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQ 53 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~ 53 (158)
-.|..|+..|..-.....|..||.
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFDFSCPRCGS 94 (113)
T ss_dssp EEETTTS-EEECHHCCHH-SSSSS
T ss_pred EECCCCCCEEecCCCCCCCcCCcC
Confidence 379999999987666677777776
No 74
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=64.30 E-value=3.9 Score=24.71 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=14.0
Q ss_pred CccccCcccccc-ccccccccccc
Q psy509 31 TCHRCRTTFSLV-QRKHHCRACGQ 53 (158)
Q Consensus 31 ~C~~C~~~F~~~-~RkhhCr~CG~ 53 (158)
.|..|+..|.+- .-.-.|+.||.
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCc
Confidence 488888888765 23344555544
No 75
>KOG2462|consensus
Probab=64.18 E-value=3 Score=34.86 Aligned_cols=12 Identities=25% Similarity=0.753 Sum_probs=7.1
Q ss_pred eeeChhhHHHHh
Q psy509 75 VRVCEDCHEKFT 86 (158)
Q Consensus 75 ~RVC~~C~~~l~ 86 (158)
.--|..|...+.
T Consensus 243 ~~qC~~C~KsFs 254 (279)
T KOG2462|consen 243 KHQCPRCGKSFA 254 (279)
T ss_pred cccCcchhhHHH
Confidence 456777766543
No 76
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=64.17 E-value=4.2 Score=37.91 Aligned_cols=30 Identities=27% Similarity=0.865 Sum_probs=22.5
Q ss_pred CCCccccCccccccccccccccccce------ecCCCCCC
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQV------FCQLCSSK 62 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~v------fC~~Cs~~ 62 (158)
+..|..|+.++.. ..|..||.. ||..|...
T Consensus 15 akFC~~CG~~l~~----~~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 15 NRFCQKCGTSLTH----KPCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CccccccCCCCCC----CcCCCCCCCCCcccccccccCCc
Confidence 4578888888753 368888887 78888765
No 77
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=64.04 E-value=4.6 Score=25.05 Aligned_cols=26 Identities=31% Similarity=0.689 Sum_probs=16.8
Q ss_pred CCccccCcccc-cccccccccccccee
Q psy509 30 DTCHRCRTTFS-LVQRKHHCRACGQVF 55 (158)
Q Consensus 30 ~~C~~C~~~F~-~~~RkhhCr~CG~vf 55 (158)
..|..|+..|- .-..+.+|..||..+
T Consensus 21 ~fCP~Cg~~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 21 KFCPRCGSGFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred CcCcCCCcchheccCCcEECCCcCCEE
Confidence 47888887432 224577888888754
No 78
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=63.57 E-value=2.6 Score=27.07 Aligned_cols=18 Identities=28% Similarity=0.853 Sum_probs=13.1
Q ss_pred ccccccccccccceecCC
Q psy509 41 LVQRKHHCRACGQVFCQL 58 (158)
Q Consensus 41 ~~~RkhhCr~CG~vfC~~ 58 (158)
+|.---+|-+||+|+|..
T Consensus 14 L~~~~~NCl~CGkIiC~~ 31 (57)
T PF06221_consen 14 LFPYAPNCLNCGKIICEQ 31 (57)
T ss_pred CccccccccccChhhccc
Confidence 333356899999999873
No 79
>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=63.49 E-value=3.6 Score=23.59 Aligned_cols=13 Identities=38% Similarity=0.963 Sum_probs=8.8
Q ss_pred CccccCccccccc
Q psy509 31 TCHRCRTTFSLVQ 43 (158)
Q Consensus 31 ~C~~C~~~F~~~~ 43 (158)
.|..|+..|.++.
T Consensus 7 ~C~~Cg~~fe~~~ 19 (41)
T smart00834 7 RCEDCGHTFEVLQ 19 (41)
T ss_pred EcCCCCCEEEEEE
Confidence 5777888776543
No 80
>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=63.09 E-value=6.1 Score=27.09 Aligned_cols=31 Identities=19% Similarity=0.436 Sum_probs=22.6
Q ss_pred CCCccccCccccccccccccccccceecCCCCC
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSS 61 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~ 61 (158)
+..|..|+++|+. ....--.||.+|-..|..
T Consensus 78 ~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 5689999998863 334445778888888864
No 81
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=62.97 E-value=3.5 Score=25.67 Aligned_cols=23 Identities=35% Similarity=0.808 Sum_probs=15.7
Q ss_pred CccccCcccccc--ccccccccccc
Q psy509 31 TCHRCRTTFSLV--QRKHHCRACGQ 53 (158)
Q Consensus 31 ~C~~C~~~F~~~--~RkhhCr~CG~ 53 (158)
.|..|++.|.+. .+-..|..||.
T Consensus 8 ~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 8 KCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EhhhcCCeeehhhccCceeCCCCCc
Confidence 588999999744 34455666665
No 82
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=61.47 E-value=3.8 Score=32.15 Aligned_cols=21 Identities=38% Similarity=1.102 Sum_probs=10.9
Q ss_pred CccccCccccccccccccccccc
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQ 53 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~ 53 (158)
.|.+|.+.|. .-++.|..||.
T Consensus 141 rC~GC~~~f~--~~~~~Cp~CG~ 161 (177)
T COG1439 141 RCHGCKRIFP--EPKDFCPICGS 161 (177)
T ss_pred EEecCceecC--CCCCcCCCCCC
Confidence 4555555555 34445555544
No 83
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=60.64 E-value=3.5 Score=35.37 Aligned_cols=34 Identities=24% Similarity=0.698 Sum_probs=28.0
Q ss_pred CCCccccCcccc----------ccccccccccccceecCCCCCC
Q psy509 29 GDTCHRCRTTFS----------LVQRKHHCRACGQVFCQLCSSK 62 (158)
Q Consensus 29 ~~~C~~C~~~F~----------~~~RkhhCr~CG~vfC~~Cs~~ 62 (158)
+..|..|+-+|- +...++.|..|..-||..|-..
T Consensus 362 s~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvf 405 (421)
T COG5151 362 STHCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVF 405 (421)
T ss_pred CccceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHH
Confidence 467999999883 3467899999999999999654
No 84
>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=60.21 E-value=2.7 Score=24.07 Aligned_cols=30 Identities=30% Similarity=0.597 Sum_probs=18.5
Q ss_pred ccccCccccccccccccccccceecCCCCCCcc
Q psy509 32 CHRCRTTFSLVQRKHHCRACGQVFCQLCSSKST 64 (158)
Q Consensus 32 C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~ 64 (158)
|.+|...|.... .=..||+.||..|.....
T Consensus 1 C~iC~~~~~~~~---~~~~C~H~fC~~C~~~~~ 30 (41)
T PF00097_consen 1 CPICLEPFEDPV---ILLPCGHSFCRDCLRKWL 30 (41)
T ss_dssp ETTTSSBCSSEE---EETTTSEEEEHHHHHHHH
T ss_pred CCcCCccccCCC---EEecCCCcchHHHHHHHH
Confidence 455655554332 345788888888876653
No 85
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=59.75 E-value=4.5 Score=29.34 Aligned_cols=24 Identities=21% Similarity=0.515 Sum_probs=16.3
Q ss_pred CCccccCcccccccccc-ccccccc
Q psy509 30 DTCHRCRTTFSLVQRKH-HCRACGQ 53 (158)
Q Consensus 30 ~~C~~C~~~F~~~~Rkh-hCr~CG~ 53 (158)
-.|..|+..|....... +|..||.
T Consensus 72 ~~C~~Cg~~~~~~~~~~~~CP~Cgs 96 (117)
T PRK00564 72 LECKDCSHVFKPNALDYGVCEKCHS 96 (117)
T ss_pred EEhhhCCCccccCCccCCcCcCCCC
Confidence 36889998887754333 4777765
No 86
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=59.47 E-value=5.5 Score=32.39 Aligned_cols=24 Identities=38% Similarity=0.773 Sum_probs=19.0
Q ss_pred CCCccccCcccccccccccccccccee
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVF 55 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vf 55 (158)
+..|..|+. +..|.+.|..||..+
T Consensus 309 S~~C~~cg~---~~~r~~~C~~cg~~~ 332 (364)
T COG0675 309 SKTCPCCGH---LSGRLFKCPRCGFVH 332 (364)
T ss_pred cccccccCC---ccceeEECCCCCCee
Confidence 478999999 446778888888765
No 87
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=59.40 E-value=4.5 Score=29.14 Aligned_cols=24 Identities=21% Similarity=0.585 Sum_probs=16.8
Q ss_pred CCccccCccccccccccccccccc
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQ 53 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~ 53 (158)
-.|..|+..|..-.+..-|..||.
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVEIHQHDAQCPHCHG 94 (113)
T ss_pred EEcccCCCEEecCCcCccCcCCCC
Confidence 368888888876555555777774
No 88
>PF14353 CpXC: CpXC protein
Probab=59.38 E-value=4.8 Score=29.16 Aligned_cols=11 Identities=36% Similarity=1.090 Sum_probs=8.5
Q ss_pred cccccccccee
Q psy509 45 KHHCRACGQVF 55 (158)
Q Consensus 45 khhCr~CG~vf 55 (158)
.+.|..||..|
T Consensus 38 ~~~CP~Cg~~~ 48 (128)
T PF14353_consen 38 SFTCPSCGHKF 48 (128)
T ss_pred EEECCCCCCce
Confidence 57888888865
No 89
>KOG1356|consensus
Probab=59.31 E-value=4.8 Score=38.51 Aligned_cols=46 Identities=30% Similarity=0.644 Sum_probs=36.3
Q ss_pred cccCCCCCCccc-----CCCccccCccccccccccccccccceecCCCCCCcc
Q psy509 17 MFSADTAPEWMD-----GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKST 64 (158)
Q Consensus 17 ~~~~~~~p~W~~-----~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~ 64 (158)
|....+.+.|.. ...|..|.+ ++|+-.-.|+.||..||-.|...+-
T Consensus 212 ~~~~~~~~a~k~a~~g~~~mC~~C~~--tlfn~hw~C~~C~~~~Cl~C~r~~~ 262 (889)
T KOG1356|consen 212 MQRPDQKVAWKRAVKGIREMCDRCET--TLFNIHWRCPRCGFGVCLDCYRKWY 262 (889)
T ss_pred ccCcccccchhhcccCcchhhhhhcc--cccceeEEccccCCeeeecchhhcc
Confidence 566667788874 357999998 4566567799999999999998874
No 90
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=59.11 E-value=4.7 Score=30.18 Aligned_cols=24 Identities=33% Similarity=0.905 Sum_probs=18.4
Q ss_pred CCccccCcccccccccccccccccee
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVF 55 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vf 55 (158)
..|..|... .-.|-|||+.||+.+
T Consensus 49 ~~C~~C~~~--kp~Rs~HC~~C~~CV 72 (174)
T PF01529_consen 49 KYCSTCKII--KPPRSHHCRVCNRCV 72 (174)
T ss_pred EECcccCCc--CCCcceecccccccc
Confidence 578888753 556899999998764
No 91
>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=58.82 E-value=5.7 Score=25.63 Aligned_cols=27 Identities=30% Similarity=0.968 Sum_probs=18.4
Q ss_pred ccccccccceecCCCCCCccccCCCCCCCceeeC-hhhHHHHhc
Q psy509 45 KHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVC-EDCHEKFTN 87 (158)
Q Consensus 45 khhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC-~~C~~~l~~ 87 (158)
..||.+||..+ | ...+.| ..|.+.+.+
T Consensus 3 HkHC~~CG~~I-----------p-----~~~~fCS~~C~~~~~k 30 (59)
T PF09889_consen 3 HKHCPVCGKPI-----------P-----PDESFCSPKCREEYRK 30 (59)
T ss_pred CCcCCcCCCcC-----------C-----cchhhhCHHHHHHHHH
Confidence 46999998742 2 246788 588877654
No 92
>PRK12496 hypothetical protein; Provisional
Probab=58.57 E-value=5.8 Score=30.47 Aligned_cols=13 Identities=15% Similarity=0.800 Sum_probs=8.0
Q ss_pred cccccccccccee
Q psy509 43 QRKHHCRACGQVF 55 (158)
Q Consensus 43 ~RkhhCr~CG~vf 55 (158)
+.++.|..||+.|
T Consensus 125 ~w~~~C~gC~~~~ 137 (164)
T PRK12496 125 KWRKVCKGCKKKY 137 (164)
T ss_pred eeeEECCCCCccc
Confidence 3456677777665
No 93
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=58.24 E-value=4.4 Score=24.96 Aligned_cols=31 Identities=29% Similarity=0.759 Sum_probs=21.0
Q ss_pred CccccCcccccccccccccccc---ceecCCCCCC
Q psy509 31 TCHRCRTTFSLVQRKHHCRACG---QVFCQLCSSK 62 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG---~vfC~~Cs~~ 62 (158)
.|..|+.. .+...|+||..|. .-+|..|-..
T Consensus 2 ~Cd~C~~~-pI~G~R~~C~~C~~~d~DlC~~C~~~ 35 (48)
T cd02341 2 KCDSCGIE-PIPGTRYHCSECDDGDFDLCQDCVVK 35 (48)
T ss_pred CCCCCCCC-ccccceEECCCCCCCCCccCHHHHhC
Confidence 47788872 2457889999997 4466666443
No 94
>PHA02926 zinc finger-like protein; Provisional
Probab=57.78 E-value=1.6 Score=35.58 Aligned_cols=57 Identities=19% Similarity=0.416 Sum_probs=33.9
Q ss_pred CCCccccCccc-cc---c-ccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 29 GDTCHRCRTTF-SL---V-QRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 29 ~~~C~~C~~~F-~~---~-~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
...|.+|-... .- - +|-..=..|+++||..|-..|..... + ..-.+.|..|...+..
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~-~-~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRR-E-TGASDNCPICRTRFRN 231 (242)
T ss_pred CCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhcc-c-cCcCCcCCCCcceeee
Confidence 46899997432 10 0 01112248999999999988754321 1 2345778888765543
No 95
>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=57.55 E-value=5.3 Score=28.79 Aligned_cols=32 Identities=31% Similarity=0.862 Sum_probs=18.7
Q ss_pred cccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHh
Q psy509 42 VQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFT 86 (158)
Q Consensus 42 ~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~ 86 (158)
+..|+.|..||.-| |.+++.--||-.|-..+.
T Consensus 6 lGtKR~Cp~CG~kF-------------YDLnk~PivCP~CG~~~~ 37 (108)
T PF09538_consen 6 LGTKRTCPSCGAKF-------------YDLNKDPIVCPKCGTEFP 37 (108)
T ss_pred cCCcccCCCCcchh-------------ccCCCCCccCCCCCCccC
Confidence 34567777777765 333444456777755443
No 96
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=57.49 E-value=6.1 Score=21.89 Aligned_cols=22 Identities=32% Similarity=0.946 Sum_probs=14.6
Q ss_pred CccccCccccccccccccccccceecC
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQVFCQ 57 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~vfC~ 57 (158)
.|.+|+. ..++.|..||..+|+
T Consensus 4 ~C~vC~~-----~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 4 LCSVCGN-----PAKYRCPRCGARYCS 25 (30)
T ss_dssp EETSSSS-----EESEE-TTT--EESS
T ss_pred CCccCcC-----CCEEECCCcCCceeC
Confidence 5777776 467889999999886
No 97
>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=57.17 E-value=5 Score=23.72 Aligned_cols=12 Identities=25% Similarity=0.916 Sum_probs=6.6
Q ss_pred CccccCcccccc
Q psy509 31 TCHRCRTTFSLV 42 (158)
Q Consensus 31 ~C~~C~~~F~~~ 42 (158)
.|..|+..|..+
T Consensus 7 ~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 7 RCEECGHEFEVL 18 (42)
T ss_pred EeCCCCCEEEEE
Confidence 455666666543
No 98
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.04 E-value=2.5 Score=35.13 Aligned_cols=48 Identities=27% Similarity=0.595 Sum_probs=30.7
Q ss_pred CCCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHh
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFT 86 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~ 86 (158)
+-.|..|-..- -.--|..||++||..|.-... ..+..-.|..|.++..
T Consensus 215 d~kC~lC~e~~----~~ps~t~CgHlFC~~Cl~~~~------t~~k~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEEP----EVPSCTPCGHLFCLSCLLISW------TKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeeccc----CCcccccccchhhHHHHHHHH------HhhccccCchhhhhcc
Confidence 45788886533 234688999999999975510 1233345777776643
No 99
>KOG2884|consensus
Probab=56.44 E-value=6.7 Score=32.05 Aligned_cols=22 Identities=36% Similarity=0.524 Sum_probs=16.6
Q ss_pred hhcchHHHHHHHHhcHHHHhhc
Q psy509 133 ELKEEEELQLALALSQSEAESN 154 (158)
Q Consensus 133 ~~~eeedl~~aia~Sl~e~e~~ 154 (158)
+..+|.||.+||++|+.|..++
T Consensus 212 dp~~DPELAlALRlSMEEer~r 233 (259)
T KOG2884|consen 212 DPEDDPELALALRLSMEEERAR 233 (259)
T ss_pred CcccCHHHHHHHHhhHHHHHHH
Confidence 4456888999999998876554
No 100
>PF09947 DUF2180: Uncharacterized protein conserved in archaea (DUF2180); InterPro: IPR017211 This group represents a predicted zinc finger protein, AF1427 type.
Probab=55.92 E-value=6.6 Score=26.11 Aligned_cols=41 Identities=24% Similarity=0.588 Sum_probs=26.1
Q ss_pred cccccccceecCCCCCCcc-cc-------C--CCCCCCceeeChhhHHHHh
Q psy509 46 HHCRACGQVFCQLCSSKST-SL-------P--KFGIEKEVRVCEDCHEKFT 86 (158)
Q Consensus 46 hhCr~CG~vfC~~Cs~~~~-~l-------p--~~~~~~~~RVC~~C~~~l~ 86 (158)
--|..||.-+|...+.... ++ | .....-|.-+|..|+..+.
T Consensus 17 avCivCG~GlC~~H~~~e~~~~~~g~yp~~~~~~~~~l~RilC~~C~~a~~ 67 (68)
T PF09947_consen 17 AVCIVCGAGLCMDHSKREEIPVWEGGYPFPSKKLKKPLPRILCPECHAALK 67 (68)
T ss_pred ehHHhcCchhhHHHHhhhheeeeccCCCCccccccCCCCeeecHHHHHHhh
Confidence 4588999999998877521 11 1 1111235568999998653
No 101
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=54.89 E-value=6.1 Score=23.60 Aligned_cols=30 Identities=27% Similarity=0.804 Sum_probs=22.5
Q ss_pred CccccCccccccccccccccc-cceecCCCCCC
Q psy509 31 TCHRCRTTFSLVQRKHHCRAC-GQVFCQLCSSK 62 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~C-G~vfC~~Cs~~ 62 (158)
.|.+|++ .++..|++|..| ..-+|..|-..
T Consensus 2 ~Cd~C~~--~i~G~ry~C~~C~d~dLC~~C~~~ 32 (43)
T cd02340 2 ICDGCQG--PIVGVRYKCLVCPDYDLCESCEAK 32 (43)
T ss_pred CCCCCCC--cCcCCeEECCCCCCccchHHhhCc
Confidence 5888988 456778999999 45677777554
No 102
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=54.88 E-value=7.5 Score=32.26 Aligned_cols=30 Identities=23% Similarity=0.670 Sum_probs=23.5
Q ss_pred cCCCccccCcccc-------ccccccccccccceecC
Q psy509 28 DGDTCHRCRTTFS-------LVQRKHHCRACGQVFCQ 57 (158)
Q Consensus 28 ~~~~C~~C~~~F~-------~~~RkhhCr~CG~vfC~ 57 (158)
+...|..|.++|. +-.-..||..||+.|=+
T Consensus 131 eVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 131 EVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred ccccccccccccCCCccccccceeeeecccccccchh
Confidence 4678999999986 34567999999998743
No 103
>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=54.55 E-value=7.8 Score=21.86 Aligned_cols=23 Identities=26% Similarity=0.735 Sum_probs=13.7
Q ss_pred CccccCccccccc-cccccccccc
Q psy509 31 TCHRCRTTFSLVQ-RKHHCRACGQ 53 (158)
Q Consensus 31 ~C~~C~~~F~~~~-RkhhCr~CG~ 53 (158)
.|..|+..|.+-. -...|+.||.
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeEcCCCCcEECCcCCC
Confidence 4778888877432 2457777775
No 104
>COG1773 Rubredoxin [Energy production and conversion]
Probab=54.05 E-value=5.8 Score=25.27 Aligned_cols=13 Identities=31% Similarity=0.981 Sum_probs=11.0
Q ss_pred cccccccccceec
Q psy509 44 RKHHCRACGQVFC 56 (158)
Q Consensus 44 RkhhCr~CG~vfC 56 (158)
+++.|+.||.||=
T Consensus 2 ~~~~C~~CG~vYd 14 (55)
T COG1773 2 KRWRCSVCGYVYD 14 (55)
T ss_pred CceEecCCceEec
Confidence 5789999999973
No 105
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=54.05 E-value=6.4 Score=29.28 Aligned_cols=12 Identities=33% Similarity=0.875 Sum_probs=7.2
Q ss_pred CccccCcccccc
Q psy509 31 TCHRCRTTFSLV 42 (158)
Q Consensus 31 ~C~~C~~~F~~~ 42 (158)
.|..|+..|.+-
T Consensus 72 ~C~~CG~~~~~~ 83 (135)
T PRK03824 72 KCRNCGNEWSLK 83 (135)
T ss_pred ECCCCCCEEecc
Confidence 466666666543
No 106
>COG4855 Uncharacterized protein conserved in archaea [Function unknown]
Probab=53.60 E-value=2.7 Score=28.02 Aligned_cols=64 Identities=22% Similarity=0.458 Sum_probs=38.9
Q ss_pred CCcccCCCccccCccccccccccccccccceecCCCCCCc-ccc-------C--CCCCCCceeeChhhHHHHhc
Q psy509 24 PEWMDGDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKS-TSL-------P--KFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 24 p~W~~~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~-~~l-------p--~~~~~~~~RVC~~C~~~l~~ 87 (158)
+.|-+--.|..|...=.-..----|-.||.-+|....-+. .++ | ...-.-|.-+|..|++.+..
T Consensus 2 ~~~~~~mKCY~C~eeGKDtdAV~iCIVCG~GlC~EHli~eE~p~w~G~YP~p~k~~K~~lpRilC~~C~~a~~e 75 (76)
T COG4855 2 LRWSNMMKCYDCAEEGKDTDAVGICIVCGMGLCMEHLIREETPMWGGGYPFPAKKLKKTLPRILCVECHEAIKE 75 (76)
T ss_pred cchhhhhHHHHHHHhCCCcccEEEEEEeCchHHHHHHHhhhcccccCCCCCcchhhhccCCceeeHHHHHHhhc
Confidence 4566666677775432233334568899999988776542 111 1 11223567899999998753
No 107
>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=53.15 E-value=6.4 Score=21.76 Aligned_cols=25 Identities=28% Similarity=0.698 Sum_probs=12.5
Q ss_pred eecCCCCCCccccCCCCCCCceeeChhhH
Q psy509 54 VFCQLCSSKSTSLPKFGIEKEVRVCEDCH 82 (158)
Q Consensus 54 vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~ 82 (158)
-||..|.......+ ..-.|+|..|-
T Consensus 4 rfC~~CG~~t~~~~----~g~~r~C~~Cg 28 (32)
T PF09297_consen 4 RFCGRCGAPTKPAP----GGWARRCPSCG 28 (32)
T ss_dssp SB-TTT--BEEE-S----SSS-EEESSSS
T ss_pred cccCcCCccccCCC----CcCEeECCCCc
Confidence 36777766654443 24578888874
No 108
>KOG3576|consensus
Probab=52.96 E-value=3.8 Score=33.23 Aligned_cols=53 Identities=30% Similarity=0.630 Sum_probs=35.3
Q ss_pred CCccccCccccc------------cccccccccccceecCCCCCCc--cccCC----CC---CCCceeeChhhH
Q psy509 30 DTCHRCRTTFSL------------VQRKHHCRACGQVFCQLCSSKS--TSLPK----FG---IEKEVRVCEDCH 82 (158)
Q Consensus 30 ~~C~~C~~~F~~------------~~RkhhCr~CG~vfC~~Cs~~~--~~lp~----~~---~~~~~RVC~~C~ 82 (158)
..|..|++.|+- -.|-+.|..|++.|-..|+-.. ..+-+ +. ....+-||..|-
T Consensus 146 ~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg 219 (267)
T KOG3576|consen 146 HLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCG 219 (267)
T ss_pred HHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccC
Confidence 469999999962 2456789999999999998531 01111 11 134578999984
No 109
>PRK14873 primosome assembly protein PriA; Provisional
Probab=51.83 E-value=8.6 Score=35.96 Aligned_cols=40 Identities=28% Similarity=0.651 Sum_probs=25.6
Q ss_pred CccccCcccccc--ccccccccccce----ecCCCCCCccccCCCC
Q psy509 31 TCHRCRTTFSLV--QRKHHCRACGQV----FCQLCSSKSTSLPKFG 70 (158)
Q Consensus 31 ~C~~C~~~F~~~--~RkhhCr~CG~v----fC~~Cs~~~~~lp~~~ 70 (158)
.|..|+...++- .+.-.|++||.. .|..|.+..+..-++|
T Consensus 394 ~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~~l~~~g~G 439 (665)
T PRK14873 394 RCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSDRLRAVVVG 439 (665)
T ss_pred ECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCCcceeeecc
Confidence 455666655553 335779999985 6889988754443433
No 110
>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=51.81 E-value=7.7 Score=28.90 Aligned_cols=31 Identities=23% Similarity=0.475 Sum_probs=19.9
Q ss_pred cccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHH
Q psy509 42 VQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKF 85 (158)
Q Consensus 42 ~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l 85 (158)
+..|+.|..||.-| |.+++.-.||..|-...
T Consensus 6 lGtKr~Cp~cg~kF-------------YDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 6 LGTKRICPNTGSKF-------------YDLNRRPAVSPYTGEQF 36 (129)
T ss_pred hCccccCCCcCccc-------------cccCCCCccCCCcCCcc
Confidence 34577888888765 33455566777776554
No 111
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=51.44 E-value=7.9 Score=28.97 Aligned_cols=25 Identities=20% Similarity=0.870 Sum_probs=15.4
Q ss_pred CccccCcccccc--------cccccccccccee
Q psy509 31 TCHRCRTTFSLV--------QRKHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~~--------~RkhhCr~CG~vf 55 (158)
.|..|+..|++. .++..|..||..+
T Consensus 101 ~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 101 KCPNCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred ECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 588888888742 2235666666554
No 112
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=51.24 E-value=7.7 Score=27.34 Aligned_cols=15 Identities=40% Similarity=0.946 Sum_probs=10.4
Q ss_pred cccccccccccccee
Q psy509 41 LVQRKHHCRACGQVF 55 (158)
Q Consensus 41 ~~~RkhhCr~CG~vf 55 (158)
++.+--.|+.||..|
T Consensus 54 Llv~Pa~CkkCGfef 68 (97)
T COG3357 54 LLVRPARCKKCGFEF 68 (97)
T ss_pred EEecChhhcccCccc
Confidence 455666777777776
No 113
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=51.10 E-value=7.2 Score=23.20 Aligned_cols=21 Identities=29% Similarity=0.795 Sum_probs=14.6
Q ss_pred CCccccCcccccccccccccccc
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACG 52 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG 52 (158)
..|..|++. +...+++|..|.
T Consensus 5 ~~C~~C~~~--i~g~ry~C~~C~ 25 (44)
T smart00291 5 YSCDTCGKP--IVGVRYHCLVCP 25 (44)
T ss_pred cCCCCCCCC--CcCCEEECCCCC
Confidence 368888883 456677888773
No 114
>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=50.73 E-value=8.5 Score=22.78 Aligned_cols=16 Identities=31% Similarity=0.941 Sum_probs=10.2
Q ss_pred ccccccccceecCCCC
Q psy509 45 KHHCRACGQVFCQLCS 60 (158)
Q Consensus 45 khhCr~CG~vfC~~Cs 60 (158)
...|+.||..||...-
T Consensus 13 ~~~C~~C~~~FC~~Hr 28 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKHR 28 (43)
T ss_dssp HEE-TTTS-EE-TTTH
T ss_pred CeECCCCCcccCcccc
Confidence 4679999999998653
No 115
>KOG3362|consensus
Probab=50.48 E-value=8 Score=29.50 Aligned_cols=31 Identities=26% Similarity=0.753 Sum_probs=21.9
Q ss_pred CCCccc-CCCccccCccccccccccccccccceecCC
Q psy509 23 APEWMD-GDTCHRCRTTFSLVQRKHHCRACGQVFCQL 58 (158)
Q Consensus 23 ~p~W~~-~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~ 58 (158)
+|...| ...|.+|| +-.++-|-+||.-+|.-
T Consensus 111 ~p~~KP~r~fCaVCG-----~~S~ysC~~CG~kyCsv 142 (156)
T KOG3362|consen 111 KPSFKPLRKFCAVCG-----YDSKYSCVNCGTKYCSV 142 (156)
T ss_pred CCCCCCcchhhhhcC-----CCchhHHHhcCCceeec
Confidence 344444 46899998 23567899999988863
No 116
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=50.27 E-value=6.9 Score=23.42 Aligned_cols=30 Identities=30% Similarity=0.800 Sum_probs=19.9
Q ss_pred CccccCcccccccccccccccc-ceecCCCCCC
Q psy509 31 TCHRCRTTFSLVQRKHHCRACG-QVFCQLCSSK 62 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG-~vfC~~Cs~~ 62 (158)
.|..|++ .+...+.+|..|. ..+|..|-..
T Consensus 2 ~C~~C~~--~i~g~r~~C~~C~d~dLC~~Cf~~ 32 (46)
T cd02249 2 SCDGCLK--PIVGVRYHCLVCEDFDLCSSCYAK 32 (46)
T ss_pred CCcCCCC--CCcCCEEECCCCCCCcCHHHHHCc
Confidence 4888888 3455788888886 3355555443
No 117
>KOG2462|consensus
Probab=50.24 E-value=6 Score=33.14 Aligned_cols=26 Identities=35% Similarity=0.904 Sum_probs=18.7
Q ss_pred CCccccCcccc---cc---------cccccccccccee
Q psy509 30 DTCHRCRTTFS---LV---------QRKHHCRACGQVF 55 (158)
Q Consensus 30 ~~C~~C~~~F~---~~---------~RkhhCr~CG~vf 55 (158)
-.|.+|++.|+ ++ .+-.-|..||+.|
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAF 225 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAF 225 (279)
T ss_pred cccccccccccchHHhhcccccccCCCCccCCcccchh
Confidence 37889999998 22 3446688888877
No 118
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=50.00 E-value=8.6 Score=28.76 Aligned_cols=25 Identities=32% Similarity=0.915 Sum_probs=16.8
Q ss_pred CCCccccCccccccccccccccccceecCCCCC
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSS 61 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~ 61 (158)
+.+|..|+.+. |. .=|.|||..|-.
T Consensus 28 ~~hCp~Cg~PL--F~------KdG~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTPL--FR------KDGEVFCPVCGY 52 (131)
T ss_pred HhhCcccCCcc--ee------eCCeEECCCCCc
Confidence 46899999863 32 347777777764
No 119
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=49.76 E-value=9.4 Score=26.62 Aligned_cols=24 Identities=21% Similarity=0.566 Sum_probs=14.8
Q ss_pred CccccCccccccccccccccccce
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQV 54 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~v 54 (158)
.|..|+..+....-...|+.||..
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCc
Confidence 477788776544445566666654
No 120
>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=49.69 E-value=7.7 Score=31.29 Aligned_cols=28 Identities=21% Similarity=0.634 Sum_probs=15.3
Q ss_pred CCccccC-ccccccc-----cccccccccceecC
Q psy509 30 DTCHRCR-TTFSLVQ-----RKHHCRACGQVFCQ 57 (158)
Q Consensus 30 ~~C~~C~-~~F~~~~-----RkhhCr~CG~vfC~ 57 (158)
..|..|- +.|.++. .-.+|+.||..+..
T Consensus 14 ~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 14 GLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIG 47 (236)
T ss_pred ccChHHhcccCCeeecCCccCceECCCCCCEECC
Confidence 4566664 2333332 33567777777655
No 121
>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=49.63 E-value=6.9 Score=23.57 Aligned_cols=16 Identities=19% Similarity=0.536 Sum_probs=12.8
Q ss_pred cCCCccccCccccccc
Q psy509 28 DGDTCHRCRTTFSLVQ 43 (158)
Q Consensus 28 ~~~~C~~C~~~F~~~~ 43 (158)
+...|..|+++|++-.
T Consensus 7 p~K~C~~C~rpf~WRK 22 (42)
T PF10013_consen 7 PSKICPVCGRPFTWRK 22 (42)
T ss_pred CCCcCcccCCcchHHH
Confidence 4678999999998653
No 122
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=49.58 E-value=7.6 Score=29.05 Aligned_cols=24 Identities=25% Similarity=0.664 Sum_probs=12.3
Q ss_pred CCccccCcccccc--ccccccccccc
Q psy509 30 DTCHRCRTTFSLV--QRKHHCRACGQ 53 (158)
Q Consensus 30 ~~C~~C~~~F~~~--~RkhhCr~CG~ 53 (158)
+.|..|++.|--- .=...|..||.
T Consensus 2 H~Ct~Cg~~f~dgs~eil~GCP~CGg 27 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKEILSGCPECGG 27 (131)
T ss_pred cccCcCCCCcCCCcHHHHccCcccCC
Confidence 3566666666421 22345666654
No 123
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=49.53 E-value=8.2 Score=27.84 Aligned_cols=24 Identities=21% Similarity=0.672 Sum_probs=15.0
Q ss_pred CCccccCccccccccc-cccccccc
Q psy509 30 DTCHRCRTTFSLVQRK-HHCRACGQ 53 (158)
Q Consensus 30 ~~C~~C~~~F~~~~Rk-hhCr~CG~ 53 (158)
-.|..|+..|....+. ..|..||.
T Consensus 71 ~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 71 CWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred EEcccCCCeeecCCccCCcCcCcCC
Confidence 3688888777654332 44776664
No 124
>KOG1311|consensus
Probab=49.34 E-value=8 Score=32.03 Aligned_cols=24 Identities=25% Similarity=0.703 Sum_probs=18.4
Q ss_pred CCccccCcccccccccccccccccee
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVF 55 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vf 55 (158)
..|..|..- .-.|-|||+.|+.-+
T Consensus 114 ~~C~~C~~~--rPpRs~HCsvC~~CV 137 (299)
T KOG1311|consen 114 KYCDTCQLY--RPPRSSHCSVCNNCV 137 (299)
T ss_pred EEcCcCccc--CCCCcccchhhcccc
Confidence 578888763 567889999998754
No 125
>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=49.11 E-value=9.7 Score=27.05 Aligned_cols=35 Identities=26% Similarity=0.529 Sum_probs=25.9
Q ss_pred cccccccccccceecCC--CCCCccccCCCCCCCceeeChhhHHHHh
Q psy509 42 VQRKHHCRACGQVFCQL--CSSKSTSLPKFGIEKEVRVCEDCHEKFT 86 (158)
Q Consensus 42 ~~RkhhCr~CG~vfC~~--Cs~~~~~lp~~~~~~~~RVC~~C~~~l~ 86 (158)
+.---+|..||+.+|.. ||-+. ..|.|..|...-.
T Consensus 46 LvLGa~CS~C~~~VC~~~~CSlFY----------tkrFC~pC~~~~~ 82 (97)
T PF10170_consen 46 LVLGAPCSICGKPVCVGQDCSLFY----------TKRFCLPCVKRNL 82 (97)
T ss_pred EEECccccccCCceEcCCCccEEe----------eCceeHHHHHHHH
Confidence 33346899999999964 88664 3589999987643
No 126
>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=48.36 E-value=1 Score=27.33 Aligned_cols=44 Identities=20% Similarity=0.608 Sum_probs=26.7
Q ss_pred CCccccCccccccccccccccccce-ecCCCCCCccccCCCCCCCceeeChhhHHHH
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQV-FCQLCSSKSTSLPKFGIEKEVRVCEDCHEKF 85 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~v-fC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l 85 (158)
..|.+|...+. ...-..||+. ||..|...... ..+.|..|...+
T Consensus 3 ~~C~iC~~~~~----~~~~~pCgH~~~C~~C~~~~~~--------~~~~CP~Cr~~i 47 (50)
T PF13920_consen 3 EECPICFENPR----DVVLLPCGHLCFCEECAERLLK--------RKKKCPICRQPI 47 (50)
T ss_dssp SB-TTTSSSBS----SEEEETTCEEEEEHHHHHHHHH--------TTSBBTTTTBB-
T ss_pred CCCccCCccCC----ceEEeCCCChHHHHHHhHHhcc--------cCCCCCcCChhh
Confidence 46888877653 2344569999 99999876532 234555555433
No 127
>PRK11595 DNA utilization protein GntX; Provisional
Probab=48.19 E-value=4.6 Score=32.30 Aligned_cols=31 Identities=29% Similarity=0.718 Sum_probs=23.2
Q ss_pred CCccccCccccccccccccccccce------ecCCCCCC
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQV------FCQLCSSK 62 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~v------fC~~Cs~~ 62 (158)
..|..|...|.++ .++|..||.. +|..|...
T Consensus 21 ~lC~~C~~~l~~~--~~~C~~Cg~~~~~~~~~C~~C~~~ 57 (227)
T PRK11595 21 GICSVCSRALRTL--KTCCPQCGLPATHPHLPCGRCLQK 57 (227)
T ss_pred cccHHHHhhCCcc--cCcCccCCCcCCCCCCCcHHHHcC
Confidence 3688888888765 5789999974 48888654
No 128
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=47.89 E-value=4.4 Score=23.95 Aligned_cols=16 Identities=31% Similarity=0.854 Sum_probs=12.5
Q ss_pred ccccceecCCCCCCcc
Q psy509 49 RACGQVFCQLCSSKST 64 (158)
Q Consensus 49 r~CG~vfC~~Cs~~~~ 64 (158)
-.||++||..|.....
T Consensus 14 l~CGH~FC~~Cl~~~~ 29 (42)
T PF15227_consen 14 LPCGHSFCRSCLERLW 29 (42)
T ss_dssp -SSSSEEEHHHHHHHH
T ss_pred cCCcCHHHHHHHHHHH
Confidence 4799999999977653
No 129
>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=47.63 E-value=13 Score=33.54 Aligned_cols=39 Identities=23% Similarity=0.654 Sum_probs=24.6
Q ss_pred CccccCccccc--cccccccccccce-----ecCCCCCCccccCCC
Q psy509 31 TCHRCRTTFSL--VQRKHHCRACGQV-----FCQLCSSKSTSLPKF 69 (158)
Q Consensus 31 ~C~~C~~~F~~--~~RkhhCr~CG~v-----fC~~Cs~~~~~lp~~ 69 (158)
.|..|+...++ -.++-.|..||.. .|..|.+..+...++
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~ 269 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGY 269 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeEeecc
Confidence 35566654443 3456788888887 688888765443333
No 130
>PF15616 TerY-C: TerY-C metal binding domain
Probab=47.58 E-value=9.8 Score=28.42 Aligned_cols=23 Identities=30% Similarity=1.107 Sum_probs=18.7
Q ss_pred CCccccCccccccccccccccccceecC
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVFCQ 57 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vfC~ 57 (158)
..|..|+..|.|. -| .||+++|.
T Consensus 78 PgCP~CGn~~~fa----~C-~CGkl~Ci 100 (131)
T PF15616_consen 78 PGCPHCGNQYAFA----VC-GCGKLFCI 100 (131)
T ss_pred CCCCCCcChhcEE----Ee-cCCCEEEe
Confidence 5799999988775 35 79999985
No 131
>PRK04023 DNA polymerase II large subunit; Validated
Probab=47.42 E-value=12 Score=36.67 Aligned_cols=30 Identities=23% Similarity=0.609 Sum_probs=22.5
Q ss_pred CCCccccCccccccccccccccccce-----ecCCCCCC
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQV-----FCQLCSSK 62 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~v-----fC~~Cs~~ 62 (158)
...|..|++.. -...|..||.. ||..|-..
T Consensus 626 ~RfCpsCG~~t----~~frCP~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 626 RRKCPSCGKET----FYRRCPFCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred CccCCCCCCcC----CcccCCCCCCCCCcceeCccccCc
Confidence 46899999974 23589999964 89998443
No 132
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=47.39 E-value=8.1 Score=30.09 Aligned_cols=25 Identities=24% Similarity=0.866 Sum_probs=19.0
Q ss_pred CccccCccccc---ccccccccccccee
Q psy509 31 TCHRCRTTFSL---VQRKHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~---~~RkhhCr~CG~vf 55 (158)
.|..|+..|++ +.--.+|..||...
T Consensus 119 ~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L 146 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEYGFRCPQCGEML 146 (178)
T ss_pred ECCCCCcEEeHHHHhhcCCcCCCCCCCC
Confidence 69999999985 35567888888753
No 133
>PF04277 OAD_gamma: Oxaloacetate decarboxylase, gamma chain ; InterPro: IPR005899 This family comprises distantly related, low complexity, hydrophobic small subunits of several related sodium ion-pumping decarboxylases. These include oxaloacetate decarboxylase gamma subunit and methylmalonyl-CoA decarboxylase delta subunit [].; GO: 0008948 oxaloacetate decarboxylase activity, 0015081 sodium ion transmembrane transporter activity, 0071436 sodium ion export, 0016020 membrane
Probab=47.12 E-value=29 Score=22.75 Aligned_cols=19 Identities=21% Similarity=0.268 Sum_probs=16.9
Q ss_pred chHHHHHHHHhcHHHHhhc
Q psy509 136 EEEELQLALALSQSEAESN 154 (158)
Q Consensus 136 eeedl~~aia~Sl~e~e~~ 154 (158)
+|+++-+||+++++.++.|
T Consensus 61 ~~~~~vAaI~AAi~~~~~~ 79 (79)
T PF04277_consen 61 DDPELVAAIAAAIAAYRRQ 79 (79)
T ss_pred CChHHHHHHHHHHHHHHhC
Confidence 6899999999999988765
No 134
>PHA02942 putative transposase; Provisional
Probab=47.08 E-value=15 Score=31.89 Aligned_cols=28 Identities=25% Similarity=0.719 Sum_probs=19.7
Q ss_pred cCCCccccCccc-ccccccccccccccee
Q psy509 28 DGDTCHRCRTTF-SLVQRKHHCRACGQVF 55 (158)
Q Consensus 28 ~~~~C~~C~~~F-~~~~RkhhCr~CG~vf 55 (158)
.+..|..|+..= .+-.|.+.|..||...
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCCEe
Confidence 467899998532 2345778899998864
No 135
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=47.04 E-value=8.2 Score=22.16 Aligned_cols=8 Identities=38% Similarity=1.294 Sum_probs=2.7
Q ss_pred eeeChhhH
Q psy509 75 VRVCEDCH 82 (158)
Q Consensus 75 ~RVC~~C~ 82 (158)
.+||+.|.
T Consensus 24 ~~VCD~CR 31 (34)
T PF01286_consen 24 LPVCDKCR 31 (34)
T ss_dssp -S--TTT-
T ss_pred cccccccc
Confidence 46777664
No 136
>KOG2935|consensus
Probab=46.97 E-value=16 Score=30.54 Aligned_cols=17 Identities=53% Similarity=0.718 Sum_probs=10.6
Q ss_pred cchHHHHHHHHhcHHHH
Q psy509 135 KEEEELQLALALSQSEA 151 (158)
Q Consensus 135 ~eeedl~~aia~Sl~e~ 151 (158)
++|+||++|+|+|..|.
T Consensus 217 q~e~d~a~a~a~s~~et 233 (315)
T KOG2935|consen 217 QDEEDLARALALSRQET 233 (315)
T ss_pred cchHHHHHHHHHHHhhh
Confidence 56666666666665443
No 137
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=46.77 E-value=10 Score=28.03 Aligned_cols=25 Identities=24% Similarity=0.743 Sum_probs=14.8
Q ss_pred CccccCcccccccc----cccccccccee
Q psy509 31 TCHRCRTTFSLVQR----KHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~~~R----khhCr~CG~vf 55 (158)
.|..|+..+...+| ++.|+.||..+
T Consensus 125 ~C~~C~~~~~r~~~~~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 125 RCPSCGREYKRHRRSKRKRYRCGRCGGPL 153 (157)
T ss_pred EcCCCCCEeeeecccchhhEECCCCCCEE
Confidence 57777766543322 45677777654
No 138
>KOG3795|consensus
Probab=46.39 E-value=8.8 Score=30.39 Aligned_cols=24 Identities=25% Similarity=0.784 Sum_probs=19.1
Q ss_pred cccccccccccccccce---ecCCCCC
Q psy509 38 TFSLVQRKHHCRACGQV---FCQLCSS 61 (158)
Q Consensus 38 ~F~~~~RkhhCr~CG~v---fC~~Cs~ 61 (158)
.|.....||.|+.||.. ||-.|.-
T Consensus 8 ~~d~ieGRs~C~~C~~SRkFfCY~C~V 34 (230)
T KOG3795|consen 8 SFDPIEGRSTCPGCKSSRKFFCYDCRV 34 (230)
T ss_pred ccCcccccccCCCCCCcceEEEEeecc
Confidence 45667889999999875 9998864
No 139
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=45.96 E-value=10 Score=21.62 Aligned_cols=7 Identities=43% Similarity=1.345 Sum_probs=3.1
Q ss_pred ecCCCCC
Q psy509 55 FCQLCSS 61 (158)
Q Consensus 55 fC~~Cs~ 61 (158)
||..|.+
T Consensus 3 FCp~C~n 9 (35)
T PF02150_consen 3 FCPECGN 9 (35)
T ss_dssp BETTTTS
T ss_pred eCCCCCc
Confidence 4444443
No 140
>PHA02929 N1R/p28-like protein; Provisional
Probab=45.65 E-value=2.7 Score=34.39 Aligned_cols=51 Identities=22% Similarity=0.436 Sum_probs=32.0
Q ss_pred CCCccccCccccccc---c-ccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 29 GDTCHRCRTTFSLVQ---R-KHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~---R-khhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
+..|.+|...|.--. + -..=..||++||..|...+.. ....|..|...+..
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~--------~~~tCPlCR~~~~~ 228 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK--------EKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh--------cCCCCCCCCCEeeE
Confidence 468999988764211 0 112237999999999987642 12357777655443
No 141
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=45.62 E-value=10 Score=24.76 Aligned_cols=22 Identities=45% Similarity=0.911 Sum_probs=10.5
Q ss_pred CccccCccccccccccccccccc
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQ 53 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~ 53 (158)
.|..|++. ++-.+++.|..||.
T Consensus 19 ~CrRCG~~-syh~qK~~CasCGy 40 (62)
T PRK04179 19 RCRRCGRH-SYNVRKKYCAACGF 40 (62)
T ss_pred hhcccCcc-cccccccchhhcCC
Confidence 35555543 34444555555544
No 142
>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=44.93 E-value=11 Score=28.78 Aligned_cols=25 Identities=20% Similarity=0.671 Sum_probs=19.8
Q ss_pred CccccCccccc---ccccccccccccee
Q psy509 31 TCHRCRTTFSL---VQRKHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~---~~RkhhCr~CG~vf 55 (158)
.|..|+..|++ +.--.+|..||...
T Consensus 111 ~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L 138 (158)
T TIGR00373 111 ICPNMCVRFTFNEAMELNFTCPRCGAML 138 (158)
T ss_pred ECCCCCcEeeHHHHHHcCCcCCCCCCEe
Confidence 69999999985 45568899998763
No 143
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=44.72 E-value=10 Score=22.97 Aligned_cols=29 Identities=14% Similarity=0.574 Sum_probs=17.2
Q ss_pred CccccCccccccccccccccccce-ecCCCC
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQV-FCQLCS 60 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~v-fC~~Cs 60 (158)
.|-+|+. +.+...|++|..|... +|..|-
T Consensus 2 ~CDgCg~-~PI~G~RykC~~C~dyDLC~~C~ 31 (43)
T cd02342 2 QCDGCGV-LPITGPRYKSKVKEDYDLCTICF 31 (43)
T ss_pred CCCCCCC-CcccccceEeCCCCCCccHHHHh
Confidence 4667775 3456677777777443 444443
No 144
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=44.13 E-value=15 Score=24.24 Aligned_cols=29 Identities=24% Similarity=0.829 Sum_probs=13.4
Q ss_pred CccccCcccccccccccc-ccccceecCCCCCCc
Q psy509 31 TCHRCRTTFSLVQRKHHC-RACGQVFCQLCSSKS 63 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhC-r~CG~vfC~~Cs~~~ 63 (158)
.|..|. ++ .|.-+| -.|.++||+.|.+..
T Consensus 9 rCs~C~---~~-l~~pv~l~~CeH~fCs~Ci~~~ 38 (65)
T PF14835_consen 9 RCSICF---DI-LKEPVCLGGCEHIFCSSCIRDC 38 (65)
T ss_dssp S-SSS----S---SS-B---SSS--B-TTTGGGG
T ss_pred CCcHHH---HH-hcCCceeccCccHHHHHHhHHh
Confidence 344444 34 355666 799999999998664
No 145
>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=44.12 E-value=5.6 Score=21.28 Aligned_cols=15 Identities=40% Similarity=0.992 Sum_probs=11.3
Q ss_pred ccccceecCCCCCCc
Q psy509 49 RACGQVFCQLCSSKS 63 (158)
Q Consensus 49 r~CG~vfC~~Cs~~~ 63 (158)
..||++||..|...+
T Consensus 14 ~~C~H~~c~~C~~~~ 28 (39)
T smart00184 14 LPCGHTFCRSCIRKW 28 (39)
T ss_pred ecCCChHHHHHHHHH
Confidence 458888888887654
No 146
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=43.97 E-value=13 Score=19.63 Aligned_cols=6 Identities=33% Similarity=1.210 Sum_probs=2.2
Q ss_pred ccccCc
Q psy509 32 CHRCRT 37 (158)
Q Consensus 32 C~~C~~ 37 (158)
|..|++
T Consensus 5 Cp~Cg~ 10 (26)
T PF13248_consen 5 CPNCGA 10 (26)
T ss_pred CcccCC
Confidence 333333
No 147
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=43.88 E-value=9.3 Score=33.00 Aligned_cols=10 Identities=20% Similarity=0.757 Sum_probs=2.9
Q ss_pred ceeeChhhHH
Q psy509 74 EVRVCEDCHE 83 (158)
Q Consensus 74 ~~RVC~~C~~ 83 (158)
|...|..|-.
T Consensus 302 P~~~C~~Cg~ 311 (344)
T PF09332_consen 302 PKKHCSNCGS 311 (344)
T ss_dssp --S--TTT-S
T ss_pred CCCCCCcCCc
Confidence 4456666654
No 148
>PHA00732 hypothetical protein
Probab=42.53 E-value=18 Score=24.40 Aligned_cols=10 Identities=30% Similarity=0.524 Sum_probs=8.1
Q ss_pred CccccCcccc
Q psy509 31 TCHRCRTTFS 40 (158)
Q Consensus 31 ~C~~C~~~F~ 40 (158)
.|..|++.|.
T Consensus 3 ~C~~Cgk~F~ 12 (79)
T PHA00732 3 KCPICGFTTV 12 (79)
T ss_pred cCCCCCCccC
Confidence 5888888886
No 149
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=41.77 E-value=14 Score=23.45 Aligned_cols=24 Identities=33% Similarity=0.696 Sum_probs=15.1
Q ss_pred ccccCccccccccccccccccceecCC
Q psy509 32 CHRCRTTFSLVQRKHHCRACGQVFCQL 58 (158)
Q Consensus 32 C~~C~~~F~~~~RkhhCr~CG~vfC~~ 58 (158)
|..|+.. -.+..-|-.||.++|+.
T Consensus 1 C~~C~~~---~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGST---NSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTC---SSSEEEETTTS-EEETT
T ss_pred CCCCCCc---CCceEEeCCCCcccccC
Confidence 4455532 34566799999999985
No 150
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=41.75 E-value=7.1 Score=23.49 Aligned_cols=22 Identities=32% Similarity=0.798 Sum_probs=12.3
Q ss_pred CCccccCcccccccccccccccc
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACG 52 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG 52 (158)
..|..|+.. .+...|++|..|.
T Consensus 5 ~~C~~C~~~-~i~g~Ry~C~~C~ 26 (46)
T PF00569_consen 5 YTCDGCGTD-PIIGVRYHCLVCP 26 (46)
T ss_dssp CE-SSS-SS-SEESSEEEESSSS
T ss_pred eECcCCCCC-cCcCCeEECCCCC
Confidence 357788773 3345667777773
No 151
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=41.26 E-value=17 Score=34.56 Aligned_cols=34 Identities=26% Similarity=0.730 Sum_probs=24.2
Q ss_pred CccccCccccc--cccccccccccce-----ecCCCCCCcc
Q psy509 31 TCHRCRTTFSL--VQRKHHCRACGQV-----FCQLCSSKST 64 (158)
Q Consensus 31 ~C~~C~~~F~~--~~RkhhCr~CG~v-----fC~~Cs~~~~ 64 (158)
.|..|...+++ ..+.-.|+.||+. .|..|.+..+
T Consensus 446 ~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L 486 (730)
T COG1198 446 ECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEHL 486 (730)
T ss_pred cCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCee
Confidence 56667666553 4567788888887 8888887743
No 152
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=41.20 E-value=20 Score=22.76 Aligned_cols=22 Identities=23% Similarity=0.694 Sum_probs=13.6
Q ss_pred CccccCCCCCCCceeeChhhHHHHhc
Q psy509 62 KSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 62 ~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
....+..+| ..+|..|+..+..
T Consensus 25 ~~gliRkyg----L~~CRqCFRe~A~ 46 (54)
T PTZ00218 25 RHGLIRKYG----LNVCRQCFRENAE 46 (54)
T ss_pred cchhhhhcC----cchhhHHHHHhhH
Confidence 444555554 3578888877654
No 153
>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=41.18 E-value=16 Score=21.76 Aligned_cols=11 Identities=27% Similarity=0.839 Sum_probs=7.7
Q ss_pred CCCccccCccc
Q psy509 29 GDTCHRCRTTF 39 (158)
Q Consensus 29 ~~~C~~C~~~F 39 (158)
+..|..|+.+.
T Consensus 17 ~~~Cp~C~~PL 27 (41)
T PF06677_consen 17 DEHCPDCGTPL 27 (41)
T ss_pred cCccCCCCCee
Confidence 56788887654
No 154
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=41.04 E-value=12 Score=22.88 Aligned_cols=21 Identities=29% Similarity=0.861 Sum_probs=13.8
Q ss_pred CccccCc-cccccccccccccccc
Q psy509 31 TCHRCRT-TFSLVQRKHHCRACGQ 53 (158)
Q Consensus 31 ~C~~C~~-~F~~~~RkhhCr~CG~ 53 (158)
.|..|.+ .+. ..|.+|-.|..
T Consensus 2 ~C~~C~~~~i~--g~R~~C~~C~d 23 (49)
T cd02345 2 SCSACRKQDIS--GIRFPCQVCRD 23 (49)
T ss_pred cCCCCCCCCce--EeeEECCCCCC
Confidence 5778877 554 45667777754
No 155
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=40.75 E-value=23 Score=21.19 Aligned_cols=10 Identities=30% Similarity=0.614 Sum_probs=6.9
Q ss_pred ceeeChhhHH
Q psy509 74 EVRVCEDCHE 83 (158)
Q Consensus 74 ~~RVC~~C~~ 83 (158)
...||..|--
T Consensus 19 ~~~vC~~Cg~ 28 (52)
T smart00661 19 RRFVCRKCGY 28 (52)
T ss_pred CEEECCcCCC
Confidence 4677888853
No 156
>KOG1818|consensus
Probab=40.49 E-value=5.7 Score=36.90 Aligned_cols=55 Identities=24% Similarity=0.383 Sum_probs=38.6
Q ss_pred CCccccCcccccccccccccccc-ceecCCCCCCccccCCCCCCCceeeChhhHHHH
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACG-QVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKF 85 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG-~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l 85 (158)
+.|..|-..|++..+.|+|++|| .++|.-|+.-.+-.-... ...+|+|..=..++
T Consensus 55 ~h~np~~~~~~~~~~d~cvkn~G~gv~~ei~tre~m~~~~~~-l~~~~~~e~v~~~~ 110 (634)
T KOG1818|consen 55 DHENPNVQLFTLKLTDHCVKNCGHGVHCEIATREFMDLLKSL-LESQRIHEEVKNKI 110 (634)
T ss_pred hccCCCcccchhhhHHHHHhcCCcchhHHHHHHHHHHHHHhh-hccccccchHHHHH
Confidence 47889999999999999999999 888888887654432222 23344555444443
No 157
>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=40.47 E-value=14 Score=19.37 Aligned_cols=13 Identities=31% Similarity=0.927 Sum_probs=9.0
Q ss_pred cccccccccccee
Q psy509 43 QRKHHCRACGQVF 55 (158)
Q Consensus 43 ~RkhhCr~CG~vf 55 (158)
.|.+.|..||+.|
T Consensus 12 ~k~~~C~~C~k~F 24 (26)
T PF13465_consen 12 EKPYKCPYCGKSF 24 (26)
T ss_dssp SSSEEESSSSEEE
T ss_pred CCCCCCCCCcCee
Confidence 3567777777766
No 158
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=40.18 E-value=6.9 Score=20.24 Aligned_cols=11 Identities=45% Similarity=0.981 Sum_probs=8.1
Q ss_pred CccccCccccc
Q psy509 31 TCHRCRTTFSL 41 (158)
Q Consensus 31 ~C~~C~~~F~~ 41 (158)
.|..|++.|+.
T Consensus 3 ~C~~C~~~F~~ 13 (27)
T PF13912_consen 3 ECDECGKTFSS 13 (27)
T ss_dssp EETTTTEEESS
T ss_pred CCCccCCccCC
Confidence 47788888863
No 159
>KOG2593|consensus
Probab=40.06 E-value=13 Score=33.02 Aligned_cols=33 Identities=18% Similarity=0.565 Sum_probs=27.5
Q ss_pred CCccccCccccc------c---ccccccccccceecCCCCCC
Q psy509 30 DTCHRCRTTFSL------V---QRKHHCRACGQVFCQLCSSK 62 (158)
Q Consensus 30 ~~C~~C~~~F~~------~---~RkhhCr~CG~vfC~~Cs~~ 62 (158)
-.|..|+++|+. | ....||-+||.-+=..|+..
T Consensus 129 Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~~ 170 (436)
T KOG2593|consen 129 YVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENKL 170 (436)
T ss_pred ccCCccccchhhhHHHHhhcccCceEEEecCCCchhcccccC
Confidence 479999999973 2 46899999999988888765
No 160
>PRK12496 hypothetical protein; Provisional
Probab=39.96 E-value=14 Score=28.27 Aligned_cols=25 Identities=20% Similarity=0.663 Sum_probs=18.4
Q ss_pred CCccccCccccccccccccccccce
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQV 54 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~v 54 (158)
..|.+|++.|..-.-.-.|..||.-
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~ 152 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSP 152 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCCh
Confidence 3599999998755455678888864
No 161
>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=39.71 E-value=14 Score=22.66 Aligned_cols=13 Identities=38% Similarity=0.881 Sum_probs=10.0
Q ss_pred ccccccccceecC
Q psy509 45 KHHCRACGQVFCQ 57 (158)
Q Consensus 45 khhCr~CG~vfC~ 57 (158)
|+.|+.||.|+=.
T Consensus 1 ky~C~~CgyvYd~ 13 (47)
T PF00301_consen 1 KYQCPVCGYVYDP 13 (47)
T ss_dssp EEEETTTSBEEET
T ss_pred CcCCCCCCEEEcC
Confidence 5789999988743
No 162
>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=39.64 E-value=11 Score=31.33 Aligned_cols=64 Identities=28% Similarity=0.607 Sum_probs=32.6
Q ss_pred CcccCCCccccCccc--cc-------cccccccccccce------ecCCCCCCccc-cCCC----CCCCceeeChhhHHH
Q psy509 25 EWMDGDTCHRCRTTF--SL-------VQRKHHCRACGQV------FCQLCSSKSTS-LPKF----GIEKEVRVCEDCHEK 84 (158)
Q Consensus 25 ~W~~~~~C~~C~~~F--~~-------~~RkhhCr~CG~v------fC~~Cs~~~~~-lp~~----~~~~~~RVC~~C~~~ 84 (158)
.|.. ..|..||..= +. -.|..||..||.- -|..|.+.... +..+ .....+-||+.|...
T Consensus 169 ~w~~-g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Y 247 (290)
T PF04216_consen 169 GWQR-GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSY 247 (290)
T ss_dssp -TT--SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEE
T ss_pred CccC-CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccch
Confidence 3443 5899998742 21 2488899999864 78999775321 1111 113457899999998
Q ss_pred Hhccc
Q psy509 85 FTNYY 89 (158)
Q Consensus 85 l~~~~ 89 (158)
+.-..
T Consensus 248 lK~vd 252 (290)
T PF04216_consen 248 LKTVD 252 (290)
T ss_dssp EEEEE
T ss_pred HHHHh
Confidence 87755
No 163
>PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 [].
Probab=39.33 E-value=13 Score=28.99 Aligned_cols=29 Identities=38% Similarity=1.032 Sum_probs=15.7
Q ss_pred cccccceecCCCCCCccccCCCCCCCceeeChhh
Q psy509 48 CRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDC 81 (158)
Q Consensus 48 Cr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C 81 (158)
|..|+.+||..|+... ++.....-.|..|
T Consensus 142 C~~C~~~~Cs~Cs~~~-----y~~~~e~~lC~~C 170 (175)
T PF05458_consen 142 CSSCSEVFCSLCSTVN-----YSDQYERVLCLSC 170 (175)
T ss_pred hhchhhhhhcCccccc-----cCCcccccccCCC
Confidence 6666777777776432 2223344456555
No 164
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=39.21 E-value=12 Score=30.75 Aligned_cols=28 Identities=25% Similarity=0.757 Sum_probs=17.4
Q ss_pred cCCCccccCccccc-----c---cccccccccccee
Q psy509 28 DGDTCHRCRTTFSL-----V---QRKHHCRACGQVF 55 (158)
Q Consensus 28 ~~~~C~~C~~~F~~-----~---~RkhhCr~CG~vf 55 (158)
.+..|.+|+...+. + ..-.+|.+||+|.
T Consensus 196 ~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRIL 231 (239)
T COG1579 196 EGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRIL 231 (239)
T ss_pred cCCcccCCeeeecHHHHHHHhcCCCCccCCccchHH
Confidence 46788888876641 1 2235677777764
No 165
>KOG1813|consensus
Probab=39.03 E-value=24 Score=29.93 Aligned_cols=30 Identities=33% Similarity=0.805 Sum_probs=22.7
Q ss_pred CCccccCccccccccccccccccceecCCCCCCc
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKS 63 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~ 63 (158)
..|.+|++.|-. -.=-.||+.||..|+...
T Consensus 242 f~c~icr~~f~~----pVvt~c~h~fc~~ca~~~ 271 (313)
T KOG1813|consen 242 FKCFICRKYFYR----PVVTKCGHYFCEVCALKP 271 (313)
T ss_pred cccccccccccc----chhhcCCceeehhhhccc
Confidence 369999998842 222479999999998764
No 166
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=38.71 E-value=18 Score=26.98 Aligned_cols=10 Identities=20% Similarity=0.873 Sum_probs=6.7
Q ss_pred CCccccCccc
Q psy509 30 DTCHRCRTTF 39 (158)
Q Consensus 30 ~~C~~C~~~F 39 (158)
..|..|+..+
T Consensus 92 sRC~~CN~~L 101 (147)
T PF01927_consen 92 SRCPKCNGPL 101 (147)
T ss_pred CccCCCCcEe
Confidence 4677777655
No 167
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.48 E-value=11 Score=33.19 Aligned_cols=31 Identities=29% Similarity=0.828 Sum_probs=23.0
Q ss_pred CCCccccCccccccccccccccccceecCCCCCCc
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKS 63 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~ 63 (158)
.-.|.+|...|.- ..--.||+.||..|....
T Consensus 26 ~l~C~IC~d~~~~----PvitpCgH~FCs~CI~~~ 56 (397)
T TIGR00599 26 SLRCHICKDFFDV----PVLTSCSHTFCSLCIRRC 56 (397)
T ss_pred ccCCCcCchhhhC----ccCCCCCCchhHHHHHHH
Confidence 4589999887742 223589999999998754
No 168
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=37.86 E-value=20 Score=20.79 Aligned_cols=9 Identities=33% Similarity=1.121 Sum_probs=4.2
Q ss_pred cccccccce
Q psy509 46 HHCRACGQV 54 (158)
Q Consensus 46 hhCr~CG~v 54 (158)
++|..||.+
T Consensus 20 d~C~~C~G~ 28 (41)
T PF13453_consen 20 DVCPSCGGI 28 (41)
T ss_pred EECCCCCeE
Confidence 344555444
No 169
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=37.77 E-value=18 Score=22.66 Aligned_cols=24 Identities=29% Similarity=0.717 Sum_probs=11.1
Q ss_pred CCccccCc-ccc-ccccccccccccc
Q psy509 30 DTCHRCRT-TFS-LVQRKHHCRACGQ 53 (158)
Q Consensus 30 ~~C~~C~~-~F~-~~~RkhhCr~CG~ 53 (158)
..|..|+- .|- .-.-|.+|-.||.
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred ccCCCCCCcchhhhcCceeEeccccc
Confidence 35666663 232 1223455555554
No 170
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=37.68 E-value=18 Score=20.40 Aligned_cols=8 Identities=63% Similarity=1.643 Sum_probs=2.6
Q ss_pred ccccccce
Q psy509 47 HCRACGQV 54 (158)
Q Consensus 47 hCr~CG~v 54 (158)
+|+.||.+
T Consensus 13 rC~~Cg~~ 20 (37)
T PF12172_consen 13 RCRDCGRV 20 (37)
T ss_dssp E-TTT--E
T ss_pred EcCCCCCE
Confidence 45555554
No 171
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=36.58 E-value=13 Score=27.78 Aligned_cols=10 Identities=40% Similarity=1.404 Sum_probs=6.0
Q ss_pred ccccccccee
Q psy509 46 HHCRACGQVF 55 (158)
Q Consensus 46 hhCr~CG~vf 55 (158)
.-|..||++|
T Consensus 30 ~kC~~CG~v~ 39 (140)
T COG1545 30 TKCKKCGRVY 39 (140)
T ss_pred EEcCCCCeEE
Confidence 3466666664
No 172
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=36.40 E-value=20 Score=22.20 Aligned_cols=22 Identities=36% Similarity=0.851 Sum_probs=14.7
Q ss_pred CCccccCccccccccccccccccc
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQ 53 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~ 53 (158)
..|..|+..- --|-..||.||.
T Consensus 15 ~ICrkC~ARn--p~~A~~CRKCg~ 36 (48)
T PRK04136 15 KICMRCNARN--PWRATKCRKCGY 36 (48)
T ss_pred cchhcccCCC--CccccccccCCC
Confidence 4677777643 335678888875
No 173
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=36.31 E-value=32 Score=27.56 Aligned_cols=46 Identities=22% Similarity=0.377 Sum_probs=21.3
Q ss_pred CccccCccccccccccccccccce-----ecCCCCCCccccCCCCCCCcee
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQV-----FCQLCSSKSTSLPKFGIEKEVR 76 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~v-----fC~~Cs~~~~~lp~~~~~~~~R 76 (158)
.|..|+..|-...+.+.=.+=|.| +|..|.-+...+-..+-..|.|
T Consensus 16 ~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e~~eP~r 66 (201)
T COG1779 16 DCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLEEREPRR 66 (201)
T ss_pred cCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccceeecccCCCeE
Confidence 566666655544444444444444 4555544433333333333433
No 174
>PRK05580 primosome assembly protein PriA; Validated
Probab=36.15 E-value=22 Score=33.18 Aligned_cols=34 Identities=32% Similarity=0.847 Sum_probs=22.6
Q ss_pred CccccCccccc--cccccccccccce-----ecCCCCCCcc
Q psy509 31 TCHRCRTTFSL--VQRKHHCRACGQV-----FCQLCSSKST 64 (158)
Q Consensus 31 ~C~~C~~~F~~--~~RkhhCr~CG~v-----fC~~Cs~~~~ 64 (158)
.|..|+..+++ ..+.-.|+.||.. .|..|.+..+
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l 432 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDL 432 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCee
Confidence 45566665543 3455679999987 6888877643
No 175
>KOG1314|consensus
Probab=36.05 E-value=8.8 Score=33.43 Aligned_cols=33 Identities=27% Similarity=0.796 Sum_probs=22.6
Q ss_pred CCCCCCcccC--------CCccccCccccccccccccccccce
Q psy509 20 ADTAPEWMDG--------DTCHRCRTTFSLVQRKHHCRACGQV 54 (158)
Q Consensus 20 ~~~~p~W~~~--------~~C~~C~~~F~~~~RkhhCr~CG~v 54 (158)
.-.++.|.|- .-|..|+. | ---|.||||.|.+.
T Consensus 74 G~vp~~wkPe~~~D~~~lqfCk~Cqg-Y-KapRSHHCrkCnrC 114 (414)
T KOG1314|consen 74 GFVPLGWKPENPKDEMFLQFCKKCQG-Y-KAPRSHHCRKCNRC 114 (414)
T ss_pred CCCCCCCCCCCChhHHHHHHHhhccC-c-CCCccccchHHHHH
Confidence 4457788861 25888864 1 23589999999875
No 176
>KOG2932|consensus
Probab=35.55 E-value=14 Score=31.69 Aligned_cols=45 Identities=24% Similarity=0.716 Sum_probs=30.6
Q ss_pred CCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
+.|..|+.+.-++.|-.- |.+|||-+|.... +.++|-.|-+.+++
T Consensus 91 HfCd~Cd~PI~IYGRmIP---CkHvFCl~CAr~~----------~dK~Cp~C~d~Vqr 135 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIP---CKHVFCLECARSD----------SDKICPLCDDRVQR 135 (389)
T ss_pred EeecccCCcceeeecccc---cchhhhhhhhhcC----------ccccCcCcccHHHH
Confidence 468899988877766644 5678999997543 24566666655554
No 177
>PRK04351 hypothetical protein; Provisional
Probab=35.07 E-value=21 Score=27.07 Aligned_cols=9 Identities=22% Similarity=1.036 Sum_probs=4.5
Q ss_pred CccccCccc
Q psy509 31 TCHRCRTTF 39 (158)
Q Consensus 31 ~C~~C~~~F 39 (158)
.|..|+..+
T Consensus 114 ~C~~Cg~~~ 122 (149)
T PRK04351 114 ECQSCGQQY 122 (149)
T ss_pred ECCCCCCEe
Confidence 455555444
No 178
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=34.84 E-value=20 Score=20.66 Aligned_cols=9 Identities=33% Similarity=1.324 Sum_probs=4.8
Q ss_pred cccccccee
Q psy509 47 HCRACGQVF 55 (158)
Q Consensus 47 hCr~CG~vf 55 (158)
-|..||.+|
T Consensus 3 ~C~~Cg~~Y 11 (36)
T PF05191_consen 3 ICPKCGRIY 11 (36)
T ss_dssp EETTTTEEE
T ss_pred CcCCCCCcc
Confidence 355555554
No 179
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=34.81 E-value=20 Score=26.77 Aligned_cols=24 Identities=25% Similarity=0.686 Sum_probs=17.7
Q ss_pred CccccCcccccccc-----ccccccccce
Q psy509 31 TCHRCRTTFSLVQR-----KHHCRACGQV 54 (158)
Q Consensus 31 ~C~~C~~~F~~~~R-----khhCr~CG~v 54 (158)
.|..|+.+-+.+.+ -.+|..||..
T Consensus 99 lC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 99 ICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred ECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 69999998886655 2477777764
No 180
>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=34.65 E-value=18 Score=17.80 Aligned_cols=9 Identities=44% Similarity=1.331 Sum_probs=5.4
Q ss_pred cccccccee
Q psy509 47 HCRACGQVF 55 (158)
Q Consensus 47 hCr~CG~vf 55 (158)
.|..||+.|
T Consensus 2 ~C~~C~~~f 10 (23)
T PF00096_consen 2 KCPICGKSF 10 (23)
T ss_dssp EETTTTEEE
T ss_pred CCCCCCCcc
Confidence 466666655
No 181
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=34.62 E-value=9 Score=20.77 Aligned_cols=27 Identities=15% Similarity=0.352 Sum_probs=8.6
Q ss_pred CccccCccccccccccccccccceecCC
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQVFCQL 58 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~vfC~~ 58 (158)
.|..|+++... ..-++|..|...+...
T Consensus 2 ~C~~C~~~~~~-~~~Y~C~~Cdf~lH~~ 28 (30)
T PF07649_consen 2 RCDACGKPIDG-GWFYRCSECDFDLHEE 28 (30)
T ss_dssp --TTTS----S---EEE-TTT-----HH
T ss_pred cCCcCCCcCCC-CceEECccCCCccChh
Confidence 47777776654 4557777776665433
No 182
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=34.54 E-value=8.9 Score=20.15 Aligned_cols=11 Identities=27% Similarity=0.730 Sum_probs=7.9
Q ss_pred CccccCccccc
Q psy509 31 TCHRCRTTFSL 41 (158)
Q Consensus 31 ~C~~C~~~F~~ 41 (158)
.|..|++.|..
T Consensus 4 ~C~~CgR~F~~ 14 (25)
T PF13913_consen 4 PCPICGRKFNP 14 (25)
T ss_pred cCCCCCCEECH
Confidence 57778887764
No 183
>KOG3896|consensus
Probab=34.52 E-value=19 Score=31.33 Aligned_cols=28 Identities=25% Similarity=0.598 Sum_probs=23.6
Q ss_pred cCccccccccccccccccceecCCCCCCc
Q psy509 35 CRTTFSLVQRKHHCRACGQVFCQLCSSKS 63 (158)
Q Consensus 35 C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~ 63 (158)
|+ .|..+.--..||+|-++-|..|+.+.
T Consensus 15 cg-~~~pl~~L~FCRyC~klrc~~Cv~hE 42 (449)
T KOG3896|consen 15 CG-KFRPLPDLVFCRYCFKLRCDDCVLHE 42 (449)
T ss_pred cc-ccccccceeeeecccccccccccccc
Confidence 55 68888888999999999888888774
No 184
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=34.20 E-value=26 Score=20.60 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=6.0
Q ss_pred CCccccCcccc
Q psy509 30 DTCHRCRTTFS 40 (158)
Q Consensus 30 ~~C~~C~~~F~ 40 (158)
..|..|+..+.
T Consensus 3 ~~C~~Cg~~l~ 13 (47)
T PF13005_consen 3 RACPDCGGELK 13 (47)
T ss_pred CcCCCCCceee
Confidence 35556665554
No 185
>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=34.13 E-value=28 Score=18.39 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=5.9
Q ss_pred ccccccccc
Q psy509 45 KHHCRACGQ 53 (158)
Q Consensus 45 khhCr~CG~ 53 (158)
.+.|.+||.
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 466777773
No 186
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=33.93 E-value=21 Score=21.57 Aligned_cols=30 Identities=23% Similarity=0.806 Sum_probs=20.1
Q ss_pred CccccCccccccccccccccc-cceecCCCCC
Q psy509 31 TCHRCRTTFSLVQRKHHCRAC-GQVFCQLCSS 61 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~C-G~vfC~~Cs~ 61 (158)
.|.+|++. .+...|++|..| ..-+|..|-.
T Consensus 2 ~Cd~C~~~-~i~G~RykC~~C~dyDLC~~C~~ 32 (45)
T cd02339 2 ICDTCRKQ-GIIGIRWKCAECPNYDLCTTCYH 32 (45)
T ss_pred CCCCCCCC-CcccCeEECCCCCCccchHHHhC
Confidence 47778753 455677888888 3557777754
No 187
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=33.90 E-value=17 Score=26.58 Aligned_cols=24 Identities=21% Similarity=0.620 Sum_probs=20.3
Q ss_pred CccccCccccccccccccccccce
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQV 54 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~v 54 (158)
.|..|++..-.+.|..-|-+|++.
T Consensus 71 ~CP~C~K~TKmLGr~D~CM~C~~p 94 (114)
T PF11023_consen 71 ECPNCGKQTKMLGRVDACMHCKEP 94 (114)
T ss_pred ECCCCCChHhhhchhhccCcCCCc
Confidence 699999988888888888888774
No 188
>KOG2935|consensus
Probab=33.77 E-value=27 Score=29.20 Aligned_cols=19 Identities=37% Similarity=0.438 Sum_probs=15.2
Q ss_pred hhcchHHHHHHHHhcHHHH
Q psy509 133 ELKEEEELQLALALSQSEA 151 (158)
Q Consensus 133 ~~~eeedl~~aia~Sl~e~ 151 (158)
.+.|||+|+.||++|+..+
T Consensus 233 t~~ede~lrsaie~s~~~~ 251 (315)
T KOG2935|consen 233 TEMEDEDLRSAIELSMQSA 251 (315)
T ss_pred hhcccHHHHHHHHhhhhhh
Confidence 3567999999999998543
No 189
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=33.67 E-value=24 Score=28.31 Aligned_cols=17 Identities=41% Similarity=0.450 Sum_probs=13.3
Q ss_pred hHHHHHHHHhcHHHHhh
Q psy509 137 EEELQLALALSQSEAES 153 (158)
Q Consensus 137 eedl~~aia~Sl~e~e~ 153 (158)
|-||..||.||+.|-..
T Consensus 207 DpELA~AlrLSmeEek~ 223 (243)
T COG5148 207 DPELAEALRLSMEEEKK 223 (243)
T ss_pred CHHHHHHHHhhHHHHHH
Confidence 78899999999876543
No 190
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=33.51 E-value=27 Score=25.86 Aligned_cols=25 Identities=24% Similarity=0.725 Sum_probs=14.9
Q ss_pred CccccCccccccc-----ccccccccccee
Q psy509 31 TCHRCRTTFSLVQ-----RKHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~~~-----RkhhCr~CG~vf 55 (158)
.|..|+..+...+ ++..|+.||..+
T Consensus 114 ~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 114 RCTGCGQRYLRVRRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred ECCCCCCCCceEccccCcceEEcCCCCCEE
Confidence 5777877664222 345677776654
No 191
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=33.05 E-value=34 Score=32.01 Aligned_cols=47 Identities=19% Similarity=0.612 Sum_probs=30.8
Q ss_pred CccccCccccccccccccccccce----ecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQV----FCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~v----fC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
.|..|+..- -..-..|..||.. +|..|.... ....+.|..|-..+..
T Consensus 3 ~Cp~Cg~~n--~~~akFC~~CG~~l~~~~Cp~CG~~~--------~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 3 ICPQCQFEN--PNNNRFCQKCGTSLTHKPCPQCGTEV--------PVDEAHCPNCGAETGT 53 (645)
T ss_pred cCCCCCCcC--CCCCccccccCCCCCCCcCCCCCCCC--------CcccccccccCCcccc
Confidence 588887753 2333468888876 477776542 3456889999777654
No 192
>PRK06260 threonine synthase; Validated
Probab=32.58 E-value=25 Score=30.39 Aligned_cols=24 Identities=21% Similarity=0.624 Sum_probs=19.1
Q ss_pred CccccCccccccccccccccccce
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQV 54 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~v 54 (158)
.|..|++.|..-...+.|..||..
T Consensus 5 ~C~~cg~~~~~~~~~~~Cp~cg~~ 28 (397)
T PRK06260 5 KCIECGKEYDPDEIIYTCPECGGL 28 (397)
T ss_pred EECCCCCCCCCCCccccCCCCCCe
Confidence 689999999866566779889865
No 193
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=32.42 E-value=23 Score=27.24 Aligned_cols=15 Identities=33% Similarity=1.019 Sum_probs=9.4
Q ss_pred cccccccccccccee
Q psy509 41 LVQRKHHCRACGQVF 55 (158)
Q Consensus 41 ~~~RkhhCr~CG~vf 55 (158)
.++|+.+|..||.-|
T Consensus 24 aIRRRReC~~C~~RF 38 (156)
T COG1327 24 AIRRRRECLECGERF 38 (156)
T ss_pred hhhhhhccccccccc
Confidence 356666666666655
No 194
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=32.36 E-value=32 Score=28.45 Aligned_cols=26 Identities=35% Similarity=0.751 Sum_probs=16.3
Q ss_pred cccccccce------ecCCCCCCccccCCCCC
Q psy509 46 HHCRACGQV------FCQLCSSKSTSLPKFGI 71 (158)
Q Consensus 46 hhCr~CG~v------fC~~Cs~~~~~lp~~~~ 71 (158)
+.|.+||.+ .|..|.+.-...|..|.
T Consensus 355 ~~c~~cg~~~~~~~~~c~~c~~~~~~~~~~~~ 386 (389)
T PRK11788 355 YRCRNCGFTARTLYWHCPSCKAWETIKPIRGL 386 (389)
T ss_pred EECCCCCCCCccceeECcCCCCccCcCCcccC
Confidence 556667665 67777766555555443
No 195
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=32.19 E-value=19 Score=23.25 Aligned_cols=6 Identities=67% Similarity=1.951 Sum_probs=3.0
Q ss_pred cccccc
Q psy509 48 CRACGQ 53 (158)
Q Consensus 48 Cr~CG~ 53 (158)
||.||.
T Consensus 19 CRRCGr 24 (61)
T COG2126 19 CRRCGR 24 (61)
T ss_pred hhhccc
Confidence 555554
No 196
>PHA00733 hypothetical protein
Probab=32.05 E-value=25 Score=25.83 Aligned_cols=10 Identities=40% Similarity=0.873 Sum_probs=6.2
Q ss_pred CccccCcccc
Q psy509 31 TCHRCRTTFS 40 (158)
Q Consensus 31 ~C~~C~~~F~ 40 (158)
.|..|++.|.
T Consensus 75 ~C~~Cgk~Fs 84 (128)
T PHA00733 75 VCPLCLMPFS 84 (128)
T ss_pred cCCCCCCcCC
Confidence 5666666664
No 197
>KOG3183|consensus
Probab=31.85 E-value=18 Score=29.74 Aligned_cols=19 Identities=16% Similarity=0.094 Sum_probs=11.6
Q ss_pred hhcchHHHHHHHHhcHHHH
Q psy509 133 ELKEEEELQLALALSQSEA 151 (158)
Q Consensus 133 ~~~eeedl~~aia~Sl~e~ 151 (158)
...+++-|.+++.++.-|+
T Consensus 200 ~n~~~~~l~Rs~~~~~~e~ 218 (250)
T KOG3183|consen 200 LNVKSSTLTRSLSQDKGEL 218 (250)
T ss_pred cccchHHHHHHhhhhhhhh
Confidence 3455677777766665554
No 198
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=31.61 E-value=31 Score=24.05 Aligned_cols=27 Identities=30% Similarity=0.728 Sum_probs=14.6
Q ss_pred CCccccCccccc---cccccccccccceecC
Q psy509 30 DTCHRCRTTFSL---VQRKHHCRACGQVFCQ 57 (158)
Q Consensus 30 ~~C~~C~~~F~~---~~RkhhCr~CG~vfC~ 57 (158)
..|..|++. .. -...-.|+.||..|=+
T Consensus 36 ~~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 36 HVCPFCGRT-TVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred CcCCCCCCc-ceeeeccCeEEcCCCCCeecc
Confidence 467777765 21 1223456666666633
No 199
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=31.44 E-value=16 Score=24.98 Aligned_cols=26 Identities=31% Similarity=0.566 Sum_probs=14.0
Q ss_pred CCCccccCccccccccc---cccccccce
Q psy509 29 GDTCHRCRTTFSLVQRK---HHCRACGQV 54 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~Rk---hhCr~CG~v 54 (158)
+..|.+|+.++....++ -||..+|.|
T Consensus 22 ~~~C~iC~~~~~~~~~~~~vDHdH~tG~v 50 (81)
T PF02945_consen 22 GGRCAICGKPLPGESRKLVVDHDHKTGRV 50 (81)
T ss_dssp TTE-TTT-SEEETTCGGCEEEE-TTTTBE
T ss_pred CCcCcCCCCCcccCCCcceecCCCCCCCc
Confidence 45899999855433332 577777764
No 200
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=31.42 E-value=42 Score=20.93 Aligned_cols=33 Identities=21% Similarity=0.482 Sum_probs=18.2
Q ss_pred cCCCCCCccccCCCCCCCceeeChhhHHHHhcc
Q psy509 56 CQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTNY 88 (158)
Q Consensus 56 C~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~~ 88 (158)
|..|.....++=..+......+|..|-.....+
T Consensus 2 C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~ 34 (54)
T cd00202 2 CSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKH 34 (54)
T ss_pred CCCCCCCCCcccccCCCCcchHHHHHHHHHHhc
Confidence 444444433332223245667888888777653
No 201
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=31.16 E-value=14 Score=27.60 Aligned_cols=16 Identities=25% Similarity=0.735 Sum_probs=10.2
Q ss_pred CCccccCcccccccccc
Q psy509 30 DTCHRCRTTFSLVQRKH 46 (158)
Q Consensus 30 ~~C~~C~~~F~~~~Rkh 46 (158)
-.|..||+.|..+ +||
T Consensus 73 i~clecGk~~k~L-krH 88 (132)
T PF05443_consen 73 IICLECGKKFKTL-KRH 88 (132)
T ss_dssp EE-TBT--EESBH-HHH
T ss_pred eEEccCCcccchH-HHH
Confidence 4799999999988 444
No 202
>KOG2807|consensus
Probab=30.91 E-value=31 Score=29.80 Aligned_cols=44 Identities=25% Similarity=0.702 Sum_probs=30.2
Q ss_pred CCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhH
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCH 82 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~ 82 (158)
..|..|+.. ..-.-++.|+.|..+||..|-... ....-+|..|.
T Consensus 331 ~~Cf~C~~~-~~~~~~y~C~~Ck~~FCldCDv~i--------HesLh~CpgCe 374 (378)
T KOG2807|consen 331 RFCFACQGE-LLSSGRYRCESCKNVFCLDCDVFI--------HESLHNCPGCE 374 (378)
T ss_pred cceeeeccc-cCCCCcEEchhccceeeccchHHH--------HhhhhcCCCcC
Confidence 459999321 134567899999999999996542 23455676664
No 203
>PRK05978 hypothetical protein; Provisional
Probab=30.88 E-value=27 Score=26.61 Aligned_cols=34 Identities=29% Similarity=0.687 Sum_probs=23.4
Q ss_pred CCCCccc-----CCCccccCc--ccc-cccccccccccccee
Q psy509 22 TAPEWMD-----GDTCHRCRT--TFS-LVQRKHHCRACGQVF 55 (158)
Q Consensus 22 ~~p~W~~-----~~~C~~C~~--~F~-~~~RkhhCr~CG~vf 55 (158)
.+|.|.. .-.|..|++ -|. ++.=+.+|..||.-|
T Consensus 21 ~r~~~~~~~rGl~grCP~CG~G~LF~g~Lkv~~~C~~CG~~~ 62 (148)
T PRK05978 21 KRPVGRAMWRGFRGRCPACGEGKLFRAFLKPVDHCAACGEDF 62 (148)
T ss_pred cCchHHHHHHHHcCcCCCCCCCcccccccccCCCccccCCcc
Confidence 3555654 358999974 554 566678899999866
No 204
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=30.35 E-value=57 Score=19.70 Aligned_cols=31 Identities=23% Similarity=0.599 Sum_probs=18.8
Q ss_pred CccccCccccccccccccccc-cceecCCCCCC
Q psy509 31 TCHRCRTTFSLVQRKHHCRAC-GQVFCQLCSSK 62 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~C-G~vfC~~Cs~~ 62 (158)
.|..|.+... ...|.+|-.| ...+|..|-..
T Consensus 2 ~Cd~C~~~~~-~g~r~~C~~C~d~dLC~~Cf~~ 33 (49)
T cd02335 2 HCDYCSKDIT-GTIRIKCAECPDFDLCLECFSA 33 (49)
T ss_pred CCCCcCCCCC-CCcEEECCCCCCcchhHHhhhC
Confidence 4778887553 2267888888 33355555443
No 205
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=30.27 E-value=11 Score=30.42 Aligned_cols=29 Identities=28% Similarity=0.889 Sum_probs=22.2
Q ss_pred CccccCccccccccccccccccceecCCCCCCc
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKS 63 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~ 63 (158)
.|.+|.+.|- ...=-.||+.||+.|.-..
T Consensus 198 ~C~iCKkdy~----spvvt~CGH~FC~~Cai~~ 226 (259)
T COG5152 198 LCGICKKDYE----SPVVTECGHSFCSLCAIRK 226 (259)
T ss_pred eehhchhhcc----chhhhhcchhHHHHHHHHH
Confidence 7999998773 2333589999999997654
No 206
>PRK07591 threonine synthase; Validated
Probab=30.02 E-value=29 Score=30.37 Aligned_cols=25 Identities=24% Similarity=0.595 Sum_probs=19.8
Q ss_pred CCccccCcccccccccccccccccee
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVF 55 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vf 55 (158)
-.|..|++.|..-.. ..|..||..+
T Consensus 19 l~C~~Cg~~~~~~~~-~~C~~cg~~l 43 (421)
T PRK07591 19 LKCRECGAEYPLGPI-HVCEECFGPL 43 (421)
T ss_pred EEeCCCCCcCCCCCC-ccCCCCCCeE
Confidence 479999999986545 8898898765
No 207
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=29.99 E-value=26 Score=26.25 Aligned_cols=24 Identities=25% Similarity=0.654 Sum_probs=17.6
Q ss_pred CccccCcccccccc-----ccccccccce
Q psy509 31 TCHRCRTTFSLVQR-----KHHCRACGQV 54 (158)
Q Consensus 31 ~C~~C~~~F~~~~R-----khhCr~CG~v 54 (158)
.|..|+.+-+.+.+ -.+|..||..
T Consensus 104 lC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 104 ICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred ECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 69999998886655 2567777763
No 208
>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=29.98 E-value=22 Score=21.84 Aligned_cols=12 Identities=17% Similarity=0.279 Sum_probs=5.7
Q ss_pred cccceecCCCCC
Q psy509 50 ACGQVFCQLCSS 61 (158)
Q Consensus 50 ~CG~vfC~~Cs~ 61 (158)
.||++||..|..
T Consensus 18 ~~G~v~~~~~i~ 29 (63)
T smart00504 18 PSGQTYERRAIE 29 (63)
T ss_pred CCCCEEeHHHHH
Confidence 445555444443
No 209
>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=29.94 E-value=18 Score=25.81 Aligned_cols=55 Identities=27% Similarity=0.551 Sum_probs=33.1
Q ss_pred CCCccccCcccccccccccc------ccc---cceecCCCCCCcccc-CCCCCCCceeeChhhHHHH
Q psy509 29 GDTCHRCRTTFSLVQRKHHC------RAC---GQVFCQLCSSKSTSL-PKFGIEKEVRVCEDCHEKF 85 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhC------r~C---G~vfC~~Cs~~~~~l-p~~~~~~~~RVC~~C~~~l 85 (158)
+..|..|..+-. ..+..| ..| ...||..|...+-.. +.-....+..+|..|..+-
T Consensus 7 g~~CHqCrqKt~--~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiC 71 (105)
T PF10497_consen 7 GKTCHQCRQKTL--DFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGIC 71 (105)
T ss_pred CCCchhhcCCCC--CCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCee
Confidence 467999987433 222334 556 889999998875321 1001134567788777653
No 210
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.69 E-value=8.6 Score=23.98 Aligned_cols=18 Identities=22% Similarity=0.632 Sum_probs=14.3
Q ss_pred ccCCCccccCcccccccc
Q psy509 27 MDGDTCHRCRTTFSLVQR 44 (158)
Q Consensus 27 ~~~~~C~~C~~~F~~~~R 44 (158)
.++..|..|+++|++-++
T Consensus 10 lp~KICpvCqRPFsWRkK 27 (54)
T COG4338 10 LPDKICPVCQRPFSWRKK 27 (54)
T ss_pred cchhhhhhhcCchHHHHH
Confidence 456789999999987644
No 211
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=28.96 E-value=33 Score=22.17 Aligned_cols=25 Identities=28% Similarity=0.699 Sum_probs=18.6
Q ss_pred CCccccCccccccc--cccccccccce
Q psy509 30 DTCHRCRTTFSLVQ--RKHHCRACGQV 54 (158)
Q Consensus 30 ~~C~~C~~~F~~~~--RkhhCr~CG~v 54 (158)
..|..|+....-.. -+..|.+||.+
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGEV 34 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCCe
Confidence 46888988765333 47889999987
No 212
>KOG4323|consensus
Probab=28.15 E-value=27 Score=31.36 Aligned_cols=58 Identities=19% Similarity=0.275 Sum_probs=38.8
Q ss_pred CCccccC-ccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 30 DTCHRCR-TTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 30 ~~C~~C~-~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
.+|..|+ -.++.++|-..|+.|+..|=..|..-.+.--.+|-..-+-.|..|......
T Consensus 169 ~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~ 227 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKK 227 (464)
T ss_pred ceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchhh
Confidence 4688888 678889999999999998744444332222223334556788888766543
No 213
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=28.04 E-value=30 Score=24.95 Aligned_cols=23 Identities=26% Similarity=0.667 Sum_probs=17.4
Q ss_pred CccccCcccccccc-----ccccccccc
Q psy509 31 TCHRCRTTFSLVQR-----KHHCRACGQ 53 (158)
Q Consensus 31 ~C~~C~~~F~~~~R-----khhCr~CG~ 53 (158)
.|..|+.+-+.+.+ -.+|..||.
T Consensus 82 lC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 82 LCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred ECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 69999998886665 356888874
No 214
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=28.03 E-value=22 Score=25.58 Aligned_cols=11 Identities=55% Similarity=1.437 Sum_probs=9.6
Q ss_pred cccccccccee
Q psy509 45 KHHCRACGQVF 55 (158)
Q Consensus 45 khhCr~CG~vf 55 (158)
-|.|-+||.+|
T Consensus 2 pH~CtrCG~vf 12 (112)
T COG3364 2 PHQCTRCGEVF 12 (112)
T ss_pred Cceeccccccc
Confidence 38899999998
No 215
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=27.96 E-value=27 Score=24.33 Aligned_cols=15 Identities=27% Similarity=0.425 Sum_probs=11.2
Q ss_pred cccccccceecCCCC
Q psy509 46 HHCRACGQVFCQLCS 60 (158)
Q Consensus 46 hhCr~CG~vfC~~Cs 60 (158)
-.|+.||++++-.+.
T Consensus 74 ~~C~~Cg~i~~~~~~ 88 (116)
T cd07153 74 LICTKCGKVIDFEDC 88 (116)
T ss_pred eEeCCCCCEEEecCc
Confidence 358899999886554
No 216
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=27.92 E-value=44 Score=20.66 Aligned_cols=12 Identities=33% Similarity=1.016 Sum_probs=9.9
Q ss_pred eeChhhHHHHhc
Q psy509 76 RVCEDCHEKFTN 87 (158)
Q Consensus 76 RVC~~C~~~l~~ 87 (158)
-||..|+.++..
T Consensus 21 ~iC~~C~~Kl~~ 32 (51)
T PF14471_consen 21 YICKDCLKKLSG 32 (51)
T ss_pred cchHHHHHHhcC
Confidence 599999999843
No 217
>PRK08359 transcription factor; Validated
Probab=27.91 E-value=2.2e+02 Score=22.24 Aligned_cols=15 Identities=40% Similarity=0.899 Sum_probs=11.5
Q ss_pred CceeeChhhHHHHhc
Q psy509 73 KEVRVCEDCHEKFTN 87 (158)
Q Consensus 73 ~~~RVC~~C~~~l~~ 87 (158)
.-+.||+.|+..+-.
T Consensus 28 ael~VC~~Ca~k~G~ 42 (176)
T PRK08359 28 AELLVCDRCYEKYGR 42 (176)
T ss_pred eEEehHHHHHHHhCC
Confidence 458999999976643
No 218
>KOG1734|consensus
Probab=27.62 E-value=21 Score=30.07 Aligned_cols=54 Identities=19% Similarity=0.433 Sum_probs=41.5
Q ss_pred cCCCccccCccccccc------cccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 28 DGDTCHRCRTTFSLVQ------RKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 28 ~~~~C~~C~~~F~~~~------RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
++..|+.|+++|.... -+-|=-.|+++|=..|-+.+..+- ....|.-|.+++..
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivG------KkqtCPYCKekVdl 282 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVG------KKQTCPYCKEKVDL 282 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeec------CCCCCchHHHHhhH
Confidence 4679999999986443 355667899999999998887653 34579999998754
No 219
>TIGR01195 oadG_fam sodium pump decarboxylases, gamma subunit. Most sequences scoring between the noise and trusted cutoffs are eukaryotic sodium channel proteins.
Probab=27.08 E-value=91 Score=21.13 Aligned_cols=20 Identities=35% Similarity=0.363 Sum_probs=15.7
Q ss_pred cchHHHHHHHHhcHHHHhhc
Q psy509 135 KEEEELQLALALSQSEAESN 154 (158)
Q Consensus 135 ~eeedl~~aia~Sl~e~e~~ 154 (158)
.+|+++-+||.+++.+...+
T Consensus 61 ~~~~elvAaIsAAI~~~r~~ 80 (82)
T TIGR01195 61 DEDEELVAAIAAAVHEHLRK 80 (82)
T ss_pred CCChhHHHHHHHHHHHHHHc
Confidence 34567889999999988655
No 220
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=26.98 E-value=61 Score=19.64 Aligned_cols=20 Identities=30% Similarity=0.903 Sum_probs=11.8
Q ss_pred CccccC-cccccccccccccccc
Q psy509 31 TCHRCR-TTFSLVQRKHHCRACG 52 (158)
Q Consensus 31 ~C~~C~-~~F~~~~RkhhCr~CG 52 (158)
.|..|+ ..+. ..|.+|..|.
T Consensus 2 ~C~~C~~~~i~--g~R~~C~~C~ 22 (49)
T cd02338 2 SCDGCGKSNFT--GRRYKCLICY 22 (49)
T ss_pred CCCCCcCCCcE--EeeEEeCCCC
Confidence 467777 3433 4666666663
No 221
>KOG0006|consensus
Probab=26.98 E-value=17 Score=31.48 Aligned_cols=33 Identities=33% Similarity=0.755 Sum_probs=24.7
Q ss_pred CCcc--ccCcccc--cccccccccc-ccceecCCCCCC
Q psy509 30 DTCH--RCRTTFS--LVQRKHHCRA-CGQVFCQLCSSK 62 (158)
Q Consensus 30 ~~C~--~C~~~F~--~~~RkhhCr~-CG~vfC~~Cs~~ 62 (158)
-.|. +|+..|- -=-||..|.. ||.+||.+|...
T Consensus 316 VlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~C~e~ 353 (446)
T KOG0006|consen 316 VLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCRECKEA 353 (446)
T ss_pred EecCCCCCCcccccCCCCCcccCCCCchhHhHHHHHhh
Confidence 3565 6777553 2368999998 999999998763
No 222
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=26.87 E-value=29 Score=21.00 Aligned_cols=10 Identities=20% Similarity=0.803 Sum_probs=7.2
Q ss_pred eeeChhhHHH
Q psy509 75 VRVCEDCHEK 84 (158)
Q Consensus 75 ~RVC~~C~~~ 84 (158)
.-+|..||..
T Consensus 23 ~dLC~~CF~~ 32 (45)
T cd02336 23 YDLCPSCYQE 32 (45)
T ss_pred cccChHHHhC
Confidence 5678888864
No 223
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=26.77 E-value=37 Score=24.69 Aligned_cols=27 Identities=26% Similarity=0.572 Sum_probs=20.3
Q ss_pred ccccCccccccccccccccccceecCCCC
Q psy509 32 CHRCRTTFSLVQRKHHCRACGQVFCQLCS 60 (158)
Q Consensus 32 C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs 60 (158)
|..|+.. +...+.+|.+||-.+-+.-.
T Consensus 1 CPvCg~~--l~vt~l~C~~C~t~i~G~F~ 27 (113)
T PF09862_consen 1 CPVCGGE--LVVTRLKCPSCGTEIEGEFE 27 (113)
T ss_pred CCCCCCc--eEEEEEEcCCCCCEEEeeec
Confidence 7788875 45668899999988766543
No 224
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=26.62 E-value=32 Score=25.78 Aligned_cols=57 Identities=11% Similarity=0.212 Sum_probs=33.9
Q ss_pred CCccccCccccccc-cccccccccceecCCCCCCc---cccCCCCCCCceeeChhhHHHHhc
Q psy509 30 DTCHRCRTTFSLVQ-RKHHCRACGQVFCQLCSSKS---TSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 30 ~~C~~C~~~F~~~~-RkhhCr~CG~vfC~~Cs~~~---~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
..|..|+++..... ....|..|+..+ ..+.... +.+-.......+.+-+.+.+.|..
T Consensus 35 ~aC~~C~kkv~~~~~~~~~C~~C~~~~-~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~l~G 95 (166)
T cd04476 35 PACPGCNKKVVEEGNGTYRCEKCNKSV-PNPEYRYILSLNVADHTGEAWLTLFDEVAEQIFG 95 (166)
T ss_pred ccccccCcccEeCCCCcEECCCCCCcC-CCccEEEEEEEEEEeCCCCEEEEEehHHHHHHhC
Confidence 46999999876555 778888888765 3332221 112222224556666677776655
No 225
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=26.61 E-value=29 Score=20.14 Aligned_cols=11 Identities=27% Similarity=0.854 Sum_probs=6.2
Q ss_pred cccccccccee
Q psy509 45 KHHCRACGQVF 55 (158)
Q Consensus 45 khhCr~CG~vf 55 (158)
-+.|..||.|+
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 46799999886
No 226
>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=26.53 E-value=40 Score=18.70 Aligned_cols=10 Identities=30% Similarity=1.035 Sum_probs=5.7
Q ss_pred ccccccccee
Q psy509 46 HHCRACGQVF 55 (158)
Q Consensus 46 hhCr~CG~vf 55 (158)
+.|..||.++
T Consensus 2 ~~C~~CGy~y 11 (33)
T cd00350 2 YVCPVCGYIY 11 (33)
T ss_pred EECCCCCCEE
Confidence 4466666654
No 227
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=26.23 E-value=60 Score=20.87 Aligned_cols=15 Identities=33% Similarity=0.855 Sum_probs=11.7
Q ss_pred CceeeChhhHHHHhc
Q psy509 73 KEVRVCEDCHEKFTN 87 (158)
Q Consensus 73 ~~~RVC~~C~~~l~~ 87 (158)
.+.-||..|.++...
T Consensus 42 ~~~PVCP~Ck~iye~ 56 (58)
T PF11238_consen 42 KPFPVCPECKEIYES 56 (58)
T ss_pred CCCCCCcCHHHHHHh
Confidence 447899999987654
No 228
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=26.16 E-value=54 Score=19.58 Aligned_cols=33 Identities=30% Similarity=0.591 Sum_probs=24.4
Q ss_pred CCccccCccc-cccccccccccccceecCCCCCC
Q psy509 30 DTCHRCRTTF-SLVQRKHHCRACGQVFCQLCSSK 62 (158)
Q Consensus 30 ~~C~~C~~~F-~~~~RkhhCr~CG~vfC~~Cs~~ 62 (158)
..|..|++.. ++...-..|..|+.++=.+|...
T Consensus 12 ~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 12 TYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp EB-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 5789998866 56677889999999887777765
No 229
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=26.13 E-value=34 Score=25.14 Aligned_cols=24 Identities=25% Similarity=0.719 Sum_probs=18.0
Q ss_pred CccccCccccccccc-----cccccccce
Q psy509 31 TCHRCRTTFSLVQRK-----HHCRACGQV 54 (158)
Q Consensus 31 ~C~~C~~~F~~~~Rk-----hhCr~CG~v 54 (158)
.|..|+.+-+.+.++ .+|..||..
T Consensus 95 lC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 95 LCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp SCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred EcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 699999988866543 677788753
No 230
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=26.05 E-value=27 Score=30.88 Aligned_cols=26 Identities=27% Similarity=0.632 Sum_probs=22.4
Q ss_pred CCccccCcccccccccccccccccee
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVF 55 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vf 55 (158)
..|..|++.|.--...+.|+.||..+
T Consensus 6 ~rc~~cg~~f~~a~~~~~c~~cGl~l 31 (411)
T COG0498 6 LRCLKCGREFSQALLQGLCPDCGLFL 31 (411)
T ss_pred eecCCCCcchhhHHhhCcCCcCCccc
Confidence 47999999998777799999999865
No 231
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=25.88 E-value=30 Score=25.43 Aligned_cols=10 Identities=30% Similarity=0.840 Sum_probs=6.5
Q ss_pred CccccCcccc
Q psy509 31 TCHRCRTTFS 40 (158)
Q Consensus 31 ~C~~C~~~F~ 40 (158)
+|..|++.++
T Consensus 28 hCs~Crk~~G 37 (133)
T COG3791 28 HCSDCRKASG 37 (133)
T ss_pred CchHhhhhhC
Confidence 5667777643
No 232
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=25.84 E-value=40 Score=21.72 Aligned_cols=15 Identities=27% Similarity=0.831 Sum_probs=8.3
Q ss_pred cccccccccccccee
Q psy509 41 LVQRKHHCRACGQVF 55 (158)
Q Consensus 41 ~~~RkhhCr~CG~vf 55 (158)
.....-.|..||++|
T Consensus 49 i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 49 IVEGELICPECGREY 63 (68)
T ss_dssp TTTTEEEETTTTEEE
T ss_pred ccCCEEEcCCCCCEE
Confidence 344555566666654
No 233
>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=25.79 E-value=34 Score=21.17 Aligned_cols=12 Identities=42% Similarity=1.060 Sum_probs=9.3
Q ss_pred ccccccccceec
Q psy509 45 KHHCRACGQVFC 56 (158)
Q Consensus 45 khhCr~CG~vfC 56 (158)
++.|+.||.|+=
T Consensus 1 ~y~C~~CgyiYd 12 (50)
T cd00730 1 KYECRICGYIYD 12 (50)
T ss_pred CcCCCCCCeEEC
Confidence 467889998874
No 234
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=25.67 E-value=28 Score=24.73 Aligned_cols=14 Identities=36% Similarity=1.001 Sum_probs=11.7
Q ss_pred ccccccccccccee
Q psy509 42 VQRKHHCRACGQVF 55 (158)
Q Consensus 42 ~~RkhhCr~CG~vf 55 (158)
..|+..|.+||..|
T Consensus 85 ~~r~~rC~nCG~~f 98 (98)
T PF10164_consen 85 AMRERRCSNCGATF 98 (98)
T ss_pred hcCccccCCCCccC
Confidence 47889999999876
No 235
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=25.66 E-value=46 Score=22.26 Aligned_cols=14 Identities=36% Similarity=0.980 Sum_probs=8.1
Q ss_pred cccccccc--ccccee
Q psy509 42 VQRKHHCR--ACGQVF 55 (158)
Q Consensus 42 ~~RkhhCr--~CG~vf 55 (158)
..|.+.|. .||..|
T Consensus 24 ~~~Y~qC~N~eCg~tF 39 (72)
T PRK09678 24 KERYHQCQNVNCSATF 39 (72)
T ss_pred heeeeecCCCCCCCEE
Confidence 34556666 666655
No 236
>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=25.65 E-value=34 Score=16.30 Aligned_cols=9 Identities=44% Similarity=1.353 Sum_probs=3.7
Q ss_pred cccccccee
Q psy509 47 HCRACGQVF 55 (158)
Q Consensus 47 hCr~CG~vf 55 (158)
.|..||..|
T Consensus 2 ~C~~C~~~~ 10 (24)
T PF13894_consen 2 QCPICGKSF 10 (24)
T ss_dssp E-SSTS-EE
T ss_pred CCcCCCCcC
Confidence 355565554
No 237
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=25.57 E-value=39 Score=25.75 Aligned_cols=14 Identities=29% Similarity=0.930 Sum_probs=7.6
Q ss_pred ccccccccccccee
Q psy509 42 VQRKHHCRACGQVF 55 (158)
Q Consensus 42 ~~RkhhCr~CG~vf 55 (158)
++||..|..||+-|
T Consensus 25 IRRRReC~~C~~RF 38 (147)
T TIGR00244 25 IRRRRECLECHERF 38 (147)
T ss_pred eeecccCCccCCcc
Confidence 45555555555544
No 238
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=25.57 E-value=26 Score=19.39 Aligned_cols=18 Identities=17% Similarity=0.482 Sum_probs=14.3
Q ss_pred ccccccccceecCCCCCC
Q psy509 45 KHHCRACGQVFCQLCSSK 62 (158)
Q Consensus 45 khhCr~CG~vfC~~Cs~~ 62 (158)
+..|..|+..+|..|...
T Consensus 12 ~~fC~~~~~~iC~~C~~~ 29 (39)
T cd00021 12 SLFCETDRALLCVDCDLS 29 (39)
T ss_pred EEEeCccChhhhhhcChh
Confidence 456889999999999744
No 239
>PRK08197 threonine synthase; Validated
Probab=25.13 E-value=41 Score=29.06 Aligned_cols=24 Identities=29% Similarity=0.747 Sum_probs=18.2
Q ss_pred CCccccCccccccccccccccccce
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQV 54 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~v 54 (158)
-.|..|++.|..-.....| .||..
T Consensus 8 ~~C~~Cg~~~~~~~~~~~C-~cg~~ 31 (394)
T PRK08197 8 LECSKCGETYDADQVHNLC-KCGKP 31 (394)
T ss_pred EEECCCCCCCCCCCcceec-CCCCe
Confidence 3699999999866566678 78755
No 240
>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=25.12 E-value=43 Score=21.28 Aligned_cols=27 Identities=37% Similarity=0.775 Sum_probs=12.3
Q ss_pred CccccCc---cccccccccccccccceecC
Q psy509 31 TCHRCRT---TFSLVQRKHHCRACGQVFCQ 57 (158)
Q Consensus 31 ~C~~C~~---~F~~~~RkhhCr~CG~vfC~ 57 (158)
.|..|.. .|+--.....|..||.++|.
T Consensus 9 kCp~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 9 KCPGCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp E-TTT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred ECCCCCCeeEEEecCCeEEEcccCCCEecC
Confidence 4555643 45544555566666666653
No 241
>PLN02400 cellulose synthase
Probab=24.88 E-value=42 Score=33.32 Aligned_cols=53 Identities=17% Similarity=0.589 Sum_probs=38.0
Q ss_pred CCCccccCccccccc---cccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhcc
Q psy509 29 GDTCHRCRTTFSLVQ---RKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTNY 88 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~---RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~~ 88 (158)
+..|.+|+-.-++.. =-.-|..||.-+|..|-.+.. .....+|..|.....+.
T Consensus 36 gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYER-------keGnq~CPQCkTrYkR~ 91 (1085)
T PLN02400 36 GQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYER-------KDGTQCCPQCKTRYRRH 91 (1085)
T ss_pred CceeeecccccCcCCCCCEEEEEccCCCccccchhheec-------ccCCccCcccCCccccc
Confidence 568999998665321 116799999999999987752 23456888887766653
No 242
>PRK12495 hypothetical protein; Provisional
Probab=24.87 E-value=39 Score=27.48 Aligned_cols=11 Identities=18% Similarity=0.622 Sum_probs=6.1
Q ss_pred CCccccCcccc
Q psy509 30 DTCHRCRTTFS 40 (158)
Q Consensus 30 ~~C~~C~~~F~ 40 (158)
..|..|+.+.-
T Consensus 43 ~hC~~CG~PIp 53 (226)
T PRK12495 43 AHCDECGDPIF 53 (226)
T ss_pred hhcccccCccc
Confidence 45666666443
No 243
>PF12251 zf-SNAP50_C: snRNA-activating protein of 50kDa MW C terminal; InterPro: IPR022042 This domain family is found in eukaryotes, and is typically between 196 and 207 amino acids in length. There is a conserved CEH sequence motif. SNAP50 is part of the snRNA-activating protein complex which activates RNA polymerases II and III. There is a cysteine-histidine cluster which contains two possible zinc finger motifs.
Probab=24.76 E-value=36 Score=26.88 Aligned_cols=39 Identities=21% Similarity=0.507 Sum_probs=23.4
Q ss_pred cccccccccceecCCCCCCccccC-CCCCCCceeeChhhHHHHhc
Q psy509 44 RKHHCRACGQVFCQLCSSKSTSLP-KFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 44 RkhhCr~CG~vfC~~Cs~~~~~lp-~~~~~~~~RVC~~C~~~l~~ 87 (158)
|+..|..||... ..++..- ......|.-.|+.||..+.-
T Consensus 138 ~~~~C~vC~~~~-----A~~v~~~d~~~p~~P~~~C~~Cf~~lhy 177 (196)
T PF12251_consen 138 RRRKCSVCGIYP-----AKWVTYNDELAPEDPCFFCDSCFRLLHY 177 (196)
T ss_pred ccccCCCCCCCC-----CEEEEECCccCCCCCchhHHHHHHHhCC
Confidence 455666665543 2222221 12236789999999998875
No 244
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=24.73 E-value=26 Score=29.61 Aligned_cols=23 Identities=30% Similarity=0.826 Sum_probs=17.0
Q ss_pred CCccccCccccccccccccccccce
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQV 54 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~v 54 (158)
.-|..|.. =.--|-|||+.|++.
T Consensus 110 ~~C~~C~~--~KP~RS~HC~~Cn~C 132 (309)
T COG5273 110 NFCSTCNI--YKPPRSHHCSICNRC 132 (309)
T ss_pred eecccccc--ccCCCCccchhhcch
Confidence 46777764 234688999999986
No 245
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=24.65 E-value=36 Score=26.92 Aligned_cols=25 Identities=24% Similarity=0.558 Sum_probs=18.6
Q ss_pred CccccCcccccccc-----cccccccccee
Q psy509 31 TCHRCRTTFSLVQR-----KHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~~~R-----khhCr~CG~vf 55 (158)
.|..|+.+-+.+.+ -.+|..||..-
T Consensus 100 ~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 100 ICSECGLPDTRLVKEDRVLMLRCDACGAHR 129 (201)
T ss_pred ECCCCCCCCcEEEEcCCeEEEEcccCCCCc
Confidence 69999998887665 24777777754
No 246
>PRK08329 threonine synthase; Validated
Probab=24.59 E-value=45 Score=28.32 Aligned_cols=23 Identities=26% Similarity=0.817 Sum_probs=16.5
Q ss_pred CccccCcccccccccccccccccee
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~vf 55 (158)
.|..|++.|..-.. +.| .||..+
T Consensus 3 ~C~~Cg~~~~~~~~-~~C-~c~~~l 25 (347)
T PRK08329 3 RCTKCGRTYEEKFK-LRC-DCGGTL 25 (347)
T ss_pred CcCCCCCCcCCCCc-eec-CCCCcE
Confidence 69999999974333 788 687653
No 247
>KOG2272|consensus
Probab=24.15 E-value=35 Score=28.60 Aligned_cols=33 Identities=21% Similarity=0.631 Sum_probs=21.2
Q ss_pred Ccc-cCCCccccCcccc---cccc--------------ccccccccceecC
Q psy509 25 EWM-DGDTCHRCRTTFS---LVQR--------------KHHCRACGQVFCQ 57 (158)
Q Consensus 25 ~W~-~~~~C~~C~~~F~---~~~R--------------khhCr~CG~vfC~ 57 (158)
.|- +--+|..|.++|- -..| -++|=.|++++++
T Consensus 216 hWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G 266 (332)
T KOG2272|consen 216 HWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGG 266 (332)
T ss_pred ccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCc
Confidence 564 4558999999983 1111 2688888887543
No 248
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=24.14 E-value=41 Score=17.43 Aligned_cols=10 Identities=40% Similarity=1.009 Sum_probs=5.0
Q ss_pred ccccccccee
Q psy509 46 HHCRACGQVF 55 (158)
Q Consensus 46 hhCr~CG~vf 55 (158)
+.|..|+..|
T Consensus 2 ~~C~~C~k~f 11 (27)
T PF12171_consen 2 FYCDACDKYF 11 (27)
T ss_dssp CBBTTTTBBB
T ss_pred CCcccCCCCc
Confidence 3455555544
No 249
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=24.13 E-value=32 Score=29.84 Aligned_cols=30 Identities=30% Similarity=0.556 Sum_probs=18.1
Q ss_pred eecCCCCCCccccCCCCCCCceeeChhhHH
Q psy509 54 VFCQLCSSKSTSLPKFGIEKEVRVCEDCHE 83 (158)
Q Consensus 54 vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~ 83 (158)
.+|..|--...++-..+..-.+++|..|-.
T Consensus 22 ~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga 51 (355)
T COG1499 22 GLCGDCYVETTPLIEIPDEVNVEVCRHCGA 51 (355)
T ss_pred cccHHHHhccCccccCCCceEEEECCcCCC
Confidence 357777655444444444456788888873
No 250
>KOG1315|consensus
Probab=24.05 E-value=25 Score=29.90 Aligned_cols=22 Identities=32% Similarity=0.949 Sum_probs=15.1
Q ss_pred CccccCccccccccccccccccce
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQV 54 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~v 54 (158)
-|..|.. -.--|-|||+.|++.
T Consensus 111 ~C~kC~~--iKPdRaHHCsvC~rC 132 (307)
T KOG1315|consen 111 YCDKCKC--IKPDRAHHCSVCNRC 132 (307)
T ss_pred eeccccc--ccCCccccchhhhhh
Confidence 4666654 133589999999765
No 251
>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=24.04 E-value=45 Score=18.73 Aligned_cols=10 Identities=30% Similarity=0.909 Sum_probs=7.0
Q ss_pred ccccccccee
Q psy509 46 HHCRACGQVF 55 (158)
Q Consensus 46 hhCr~CG~vf 55 (158)
+-|+.||.++
T Consensus 3 ~~C~~CG~i~ 12 (34)
T cd00729 3 WVCPVCGYIH 12 (34)
T ss_pred EECCCCCCEe
Confidence 5677777775
No 252
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=23.99 E-value=26 Score=33.87 Aligned_cols=7 Identities=29% Similarity=1.118 Sum_probs=0.0
Q ss_pred CccccCc
Q psy509 31 TCHRCRT 37 (158)
Q Consensus 31 ~C~~C~~ 37 (158)
.|..|++
T Consensus 657 ~Cp~Cg~ 663 (900)
T PF03833_consen 657 RCPKCGK 663 (900)
T ss_dssp -------
T ss_pred cCcccCC
Confidence 4555544
No 253
>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=23.69 E-value=34 Score=20.09 Aligned_cols=15 Identities=20% Similarity=0.625 Sum_probs=11.8
Q ss_pred ceeeChhhHHHHhcc
Q psy509 74 EVRVCEDCHEKFTNY 88 (158)
Q Consensus 74 ~~RVC~~C~~~l~~~ 88 (158)
.+-+|+.|.......
T Consensus 23 ~~~IC~~Cv~~~~~i 37 (41)
T PF06689_consen 23 GAYICDECVEQAYEI 37 (41)
T ss_dssp SEEEEHHHHHHHHHH
T ss_pred CcEECHHHHHHHHHH
Confidence 489999999876543
No 254
>KOG2177|consensus
Probab=23.69 E-value=16 Score=28.36 Aligned_cols=34 Identities=29% Similarity=0.598 Sum_probs=25.8
Q ss_pred cCCCccccCccccccccccccccccceecCCCCCCccc
Q psy509 28 DGDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTS 65 (158)
Q Consensus 28 ~~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~ 65 (158)
+--.|.+|-..|..- ..-.||+.||..|......
T Consensus 12 ~~~~C~iC~~~~~~p----~~l~C~H~~c~~C~~~~~~ 45 (386)
T KOG2177|consen 12 EELTCPICLEYFREP----VLLPCGHNFCRACLTRSWE 45 (386)
T ss_pred ccccChhhHHHhhcC----ccccccchHhHHHHHHhcC
Confidence 345799998877654 6667999999999876543
No 255
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.55 E-value=41 Score=24.61 Aligned_cols=26 Identities=12% Similarity=0.080 Sum_probs=18.5
Q ss_pred CCccccCcccccccc-cccccccccee
Q psy509 30 DTCHRCRTTFSLVQR-KHHCRACGQVF 55 (158)
Q Consensus 30 ~~C~~C~~~F~~~~R-khhCr~CG~vf 55 (158)
..|..|+++|--+|| ...|..||..|
T Consensus 10 ridPetg~KFYDLNrdPiVsPytG~s~ 36 (129)
T COG4530 10 RIDPETGKKFYDLNRDPIVSPYTGKSY 36 (129)
T ss_pred ccCccccchhhccCCCccccCcccccc
Confidence 368889999976665 45677777654
No 256
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=23.53 E-value=46 Score=21.06 Aligned_cols=25 Identities=24% Similarity=0.494 Sum_probs=13.3
Q ss_pred CCccccCccccccccccccccccce
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQV 54 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~v 54 (158)
..|..|+.+|..-.=...|..||..
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAP 30 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCc
Confidence 4677777777433333344444443
No 257
>KOG4317|consensus
Probab=23.42 E-value=39 Score=29.11 Aligned_cols=23 Identities=26% Similarity=0.837 Sum_probs=19.8
Q ss_pred CccccCccccccccccccccccceecC
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQVFCQ 57 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~vfC~ 57 (158)
.|.+|++.| |++.|..|...+|+
T Consensus 9 ~C~ic~vq~----~~YtCPRCn~~YCs 31 (383)
T KOG4317|consen 9 ACGICGVQK----REYTCPRCNLLYCS 31 (383)
T ss_pred ecccccccc----ccccCCCCCcccee
Confidence 588888877 56999999999998
No 258
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.39 E-value=40 Score=24.60 Aligned_cols=11 Identities=18% Similarity=0.368 Sum_probs=8.0
Q ss_pred CCccccCccccc
Q psy509 30 DTCHRCRTTFSL 41 (158)
Q Consensus 30 ~~C~~C~~~F~~ 41 (158)
-.| .|+..|..
T Consensus 71 ~~C-~Cg~~~~~ 81 (124)
T PRK00762 71 IEC-ECGYEGVV 81 (124)
T ss_pred EEe-eCcCcccc
Confidence 368 88888764
No 259
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=23.14 E-value=15 Score=23.19 Aligned_cols=45 Identities=20% Similarity=0.661 Sum_probs=31.4
Q ss_pred CCccccCccccccccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHh
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFT 86 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~ 86 (158)
-+|-.|...|..- .-..|-.||+--|+.|-... --.|+.|-..+.
T Consensus 8 y~CDLCn~~~p~~-~LRQCvlCGRWaC~sCW~de-----------YY~CksC~Gii~ 52 (57)
T PF14445_consen 8 YSCDLCNSSHPIS-ELRQCVLCGRWACNSCWQDE-----------YYTCKSCNGIIN 52 (57)
T ss_pred HhHHhhcccCcHH-HHHHHhhhchhhhhhhhhhh-----------HhHHHhhhchhh
Confidence 3688888888643 33579999999999886542 345777766553
No 260
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=23.03 E-value=48 Score=23.30 Aligned_cols=24 Identities=33% Similarity=0.668 Sum_probs=15.4
Q ss_pred CCccccCccccc----cccccccccccc
Q psy509 30 DTCHRCRTTFSL----VQRKHHCRACGQ 53 (158)
Q Consensus 30 ~~C~~C~~~F~~----~~RkhhCr~CG~ 53 (158)
-.|..|+..... ...+.||.+|=.
T Consensus 5 F~C~~CG~~V~p~~~g~~~RNHCP~CL~ 32 (92)
T PF12647_consen 5 FTCVHCGLTVSPLAAGSAHRNHCPSCLS 32 (92)
T ss_pred cCccccCCCcccCCCCCCccCcCccccc
Confidence 367888876643 236778877743
No 261
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=22.89 E-value=27 Score=22.41 Aligned_cols=11 Identities=36% Similarity=1.060 Sum_probs=8.6
Q ss_pred cccccccccee
Q psy509 45 KHHCRACGQVF 55 (158)
Q Consensus 45 khhCr~CG~vf 55 (158)
..+||.||+.+
T Consensus 10 ~t~CrRCGk~i 20 (60)
T PF10892_consen 10 ETPCRRCGKSI 20 (60)
T ss_pred eehhhhhCccH
Confidence 46899999864
No 262
>KOG0804|consensus
Probab=22.86 E-value=30 Score=31.04 Aligned_cols=28 Identities=32% Similarity=0.630 Sum_probs=20.8
Q ss_pred cCCCccccCccccccccccccccccceecCCC
Q psy509 28 DGDTCHRCRTTFSLVQRKHHCRACGQVFCQLC 59 (158)
Q Consensus 28 ~~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~C 59 (158)
+...|..|+..|+++ -|-.||.|.|+.=
T Consensus 227 e~~~c~~c~~~~~Lw----icliCg~vgcgrY 254 (493)
T KOG0804|consen 227 ESSLCLACGCTEDLW----ICLICGNVGCGRY 254 (493)
T ss_pred hhhhhhhhcccccEE----EEEEccceecccc
Confidence 345677788777765 5889999998753
No 263
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.56 E-value=60 Score=22.99 Aligned_cols=14 Identities=14% Similarity=0.354 Sum_probs=7.6
Q ss_pred cccceecCCCCCCc
Q psy509 50 ACGQVFCQLCSSKS 63 (158)
Q Consensus 50 ~CG~vfC~~Cs~~~ 63 (158)
+=+++.|..|..+.
T Consensus 39 ~~~h~~C~~CG~y~ 52 (99)
T PRK14892 39 NIAIITCGNCGLYT 52 (99)
T ss_pred CcceEECCCCCCcc
Confidence 34555666665543
No 264
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=22.48 E-value=19 Score=20.56 Aligned_cols=28 Identities=18% Similarity=0.603 Sum_probs=17.8
Q ss_pred CccccCccccccccccccccccceecCCCCCC
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQVFCQLCSSK 62 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~ 62 (158)
.|..+... .-...|..|+..+|..|...
T Consensus 5 ~C~~H~~~----~~~~~C~~C~~~~C~~C~~~ 32 (42)
T PF00643_consen 5 KCPEHPEE----PLSLFCEDCNEPLCSECTVS 32 (42)
T ss_dssp B-SSTTTS----BEEEEETTTTEEEEHHHHHT
T ss_pred cCccCCcc----ceEEEecCCCCccCccCCCC
Confidence 45555543 13456888999999888654
No 265
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=22.45 E-value=42 Score=21.79 Aligned_cols=9 Identities=33% Similarity=0.884 Sum_probs=4.2
Q ss_pred cccccccee
Q psy509 47 HCRACGQVF 55 (158)
Q Consensus 47 hCr~CG~vf 55 (158)
-||+|+.+.
T Consensus 5 AC~~C~~i~ 13 (61)
T PRK08351 5 ACRHCHYIT 13 (61)
T ss_pred hhhhCCccc
Confidence 344554443
No 266
>PRK06450 threonine synthase; Validated
Probab=22.26 E-value=51 Score=28.03 Aligned_cols=23 Identities=22% Similarity=0.628 Sum_probs=17.6
Q ss_pred CccccCccccccccccccccccce
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQV 54 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~v 54 (158)
.|..|++.|.. ...+.|..||..
T Consensus 5 ~C~~Cg~~~~~-~~~~~C~~cg~~ 27 (338)
T PRK06450 5 VCMKCGKERES-IYEIRCKKCGGP 27 (338)
T ss_pred EECCcCCcCCC-cccccCCcCCCE
Confidence 69999999876 434778888764
No 267
>KOG2463|consensus
Probab=22.02 E-value=35 Score=29.52 Aligned_cols=23 Identities=35% Similarity=0.814 Sum_probs=13.7
Q ss_pred CccccCccccccccccccccccce
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQV 54 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~v 54 (158)
.|.+|-+.|+-+ -|+.|..||.-
T Consensus 244 RCh~Cfsit~~m-~k~FCp~CG~~ 266 (376)
T KOG2463|consen 244 RCHGCFSITSEM-PKDFCPSCGHK 266 (376)
T ss_pred EeeeeeEecCcc-chhcccccCCC
Confidence 577777666544 34566666653
No 268
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=22.00 E-value=56 Score=26.13 Aligned_cols=21 Identities=38% Similarity=1.070 Sum_probs=16.0
Q ss_pred ccccccccccce----ecCCCCCCc
Q psy509 43 QRKHHCRACGQV----FCQLCSSKS 63 (158)
Q Consensus 43 ~RkhhCr~CG~v----fC~~Cs~~~ 63 (158)
..-.||..||.+ .|.-|+..+
T Consensus 52 ~~i~~C~~C~~~te~d~C~ICsd~~ 76 (198)
T COG0353 52 ENIKHCSVCGNLTESDPCDICSDES 76 (198)
T ss_pred hcCccccccCCcCCCCcCcCcCCcc
Confidence 455889999987 788888653
No 269
>KOG1074|consensus
Probab=21.88 E-value=55 Score=31.75 Aligned_cols=52 Identities=23% Similarity=0.478 Sum_probs=32.7
Q ss_pred CCccccCcccc------------ccccccccccccceecCCCCCCccccCCCCCCCceeeChhhH
Q psy509 30 DTCHRCRTTFS------------LVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCH 82 (158)
Q Consensus 30 ~~C~~C~~~F~------------~~~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~ 82 (158)
..|.+|.+..+ .-.|-..|..||+.|-.+---+ ..+.......+.||+..|=
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLk-aH~~vHka~p~~R~q~ScP 669 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLK-AHMSVHKAKPPARVQFSCP 669 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchh-hcccccccCccccccccCC
Confidence 57999988775 2356678999999995543222 1111122345678887775
No 270
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=21.79 E-value=57 Score=19.23 Aligned_cols=24 Identities=38% Similarity=0.703 Sum_probs=15.3
Q ss_pred ccccCccccccccccccccccceecCCC
Q psy509 32 CHRCRTTFSLVQRKHHCRACGQVFCQLC 59 (158)
Q Consensus 32 C~~C~~~F~~~~RkhhCr~CG~vfC~~C 59 (158)
|..|+..=+ ..-|-.||+++|..-
T Consensus 2 C~~C~~~~~----l~~CL~C~~~~c~~~ 25 (50)
T smart00290 2 CSVCGTIEN----LWLCLTCGQVGCGRY 25 (50)
T ss_pred cccCCCcCC----eEEecCCCCcccCCC
Confidence 556664322 457888888888653
No 271
>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=21.77 E-value=35 Score=25.63 Aligned_cols=26 Identities=31% Similarity=0.801 Sum_probs=15.5
Q ss_pred cccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHh
Q psy509 46 HHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFT 86 (158)
Q Consensus 46 hhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~ 86 (158)
.+|+.||++|=. ....+|..|+....
T Consensus 4 ~nC~~CgklF~~---------------~~~~iCp~C~~~~e 29 (137)
T TIGR03826 4 ANCPKCGRLFVK---------------TGRDVCPSCYEEEE 29 (137)
T ss_pred ccccccchhhhh---------------cCCccCHHHhHHHH
Confidence 367777777610 12257888876543
No 272
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=21.76 E-value=41 Score=22.04 Aligned_cols=16 Identities=19% Similarity=0.800 Sum_probs=9.9
Q ss_pred cccccccee----cCCCCCC
Q psy509 47 HCRACGQVF----CQLCSSK 62 (158)
Q Consensus 47 hCr~CG~vf----C~~Cs~~ 62 (158)
-||.|+.++ |..|.+.
T Consensus 7 AC~~C~~i~~~~~Cp~Cgs~ 26 (64)
T PRK06393 7 ACKKCKRLTPEKTCPVHGDE 26 (64)
T ss_pred hHhhCCcccCCCcCCCCCCC
Confidence 477777765 6666543
No 273
>PF14279 HNH_5: HNH endonuclease
Probab=21.66 E-value=83 Score=20.76 Aligned_cols=11 Identities=45% Similarity=1.262 Sum_probs=9.7
Q ss_pred eChhhHHHHhc
Q psy509 77 VCEDCHEKFTN 87 (158)
Q Consensus 77 VC~~C~~~l~~ 87 (158)
||+.|...+..
T Consensus 32 vC~~CN~~~g~ 42 (71)
T PF14279_consen 32 VCDKCNNKFGS 42 (71)
T ss_pred hhHHHhHHHhH
Confidence 99999998765
No 274
>KOG2879|consensus
Probab=21.44 E-value=50 Score=27.89 Aligned_cols=32 Identities=25% Similarity=0.682 Sum_probs=24.7
Q ss_pred CCCccccCccccccccccccccccceecCCCCCCc
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKS 63 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vfC~~Cs~~~ 63 (158)
+.+|..|+..=+ =-|+=-.||+++|-.|....
T Consensus 239 ~~~C~~Cg~~Pt---iP~~~~~C~HiyCY~Ci~ts 270 (298)
T KOG2879|consen 239 DTECPVCGEPPT---IPHVIGKCGHIYCYYCIATS 270 (298)
T ss_pred CceeeccCCCCC---CCeeeccccceeehhhhhhh
Confidence 568999998433 24677789999999998764
No 275
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=21.39 E-value=71 Score=18.98 Aligned_cols=9 Identities=56% Similarity=0.730 Sum_probs=8.0
Q ss_pred hHHHHHHHH
Q psy509 137 EEELQLALA 145 (158)
Q Consensus 137 eedl~~aia 145 (158)
||+|++||+
T Consensus 2 ee~l~~Ai~ 10 (45)
T PF05225_consen 2 EEDLQKAIE 10 (45)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 689999997
No 276
>KOG1812|consensus
Probab=21.36 E-value=42 Score=29.27 Aligned_cols=32 Identities=31% Similarity=0.849 Sum_probs=21.2
Q ss_pred CccccCccc--cccccccccccccceecCCCCCCc
Q psy509 31 TCHRCRTTF--SLVQRKHHCRACGQVFCQLCSSKS 63 (158)
Q Consensus 31 ~C~~C~~~F--~~~~RkhhCr~CG~vfC~~Cs~~~ 63 (158)
.|..|+... +-.--.-+|| ||+-||..|...+
T Consensus 308 ~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~ 341 (384)
T KOG1812|consen 308 QCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDW 341 (384)
T ss_pred cCcccceeeeecCCcceEEee-ccccchhhcCcch
Confidence 455555432 2223457899 9999999998554
No 277
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.29 E-value=57 Score=33.01 Aligned_cols=48 Identities=23% Similarity=0.596 Sum_probs=25.9
Q ss_pred CCccccCccccccccccccccccce-----ecCCCCCCccccCCCCCCCceeeChhhHHHHh
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQV-----FCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFT 86 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~v-----fC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~ 86 (158)
..|..|+.. +.. ..|..||.. +|..|-..... -. .. ...|..|-..+.
T Consensus 668 rkCPkCG~~-t~~---~fCP~CGs~te~vy~CPsCGaev~~---de-s~-a~~CP~CGtplv 720 (1337)
T PRK14714 668 RRCPSCGTE-TYE---NRCPDCGTHTEPVYVCPDCGAEVPP---DE-SG-RVECPRCDVELT 720 (1337)
T ss_pred EECCCCCCc-ccc---ccCcccCCcCCCceeCccCCCccCC---Cc-cc-cccCCCCCCccc
Confidence 468888873 111 277777755 37777654211 10 11 345777765443
No 278
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=21.13 E-value=66 Score=23.93 Aligned_cols=46 Identities=20% Similarity=0.349 Sum_probs=23.9
Q ss_pred CCcCCCCCccc------ccccCCCCCCcccCCCccccCccccccccccccccccc
Q psy509 5 GFQFPVLKESD------AMFSADTAPEWMDGDTCHRCRTTFSLVQRKHHCRACGQ 53 (158)
Q Consensus 5 g~~fp~~~~s~------~~~~~~~~p~W~~~~~C~~C~~~F~~~~RkhhCr~CG~ 53 (158)
.|.-|+.++.+ .|+....+..-+-.=.|..|+.-|. .+.+|..||-
T Consensus 67 ~yl~pe~k~~~ri~~L~~~i~~~~pv~~~~~W~Cv~C~~~Y~---GeK~C~~C~t 118 (128)
T PF11682_consen 67 PYLDPEEKERRRIKRLRRMIADLDPVPRKTDWHCVMCGNHYH---GEKYCPKCGT 118 (128)
T ss_pred ceECcccchHHHHHHHHHhccccCCCCcCceEEEecCCCccC---cCEecCCCCC
Confidence 46667766552 3344332322222336777877543 3566666664
No 279
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=20.98 E-value=51 Score=19.93 Aligned_cols=31 Identities=29% Similarity=0.865 Sum_probs=18.0
Q ss_pred CccccCccccccccccccccccce-ecCCCCCC
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQV-FCQLCSSK 62 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~v-fC~~Cs~~ 62 (158)
.|..|+.. .+...|++|..|... +|..|-..
T Consensus 2 ~Cd~C~~~-pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 2 TCDGCQMF-PINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCC-CCccCeEECCCCCCccchHHhhCC
Confidence 46667652 344577788877633 55555443
No 280
>PLN02569 threonine synthase
Probab=20.90 E-value=55 Score=29.44 Aligned_cols=26 Identities=15% Similarity=0.148 Sum_probs=19.9
Q ss_pred CCCccccCcccccccccccccccccee
Q psy509 29 GDTCHRCRTTFSLVQRKHHCRACGQVF 55 (158)
Q Consensus 29 ~~~C~~C~~~F~~~~RkhhCr~CG~vf 55 (158)
.-.|..|++.|..-.....| .||..+
T Consensus 49 ~l~C~~Cg~~y~~~~~~~~C-~cgg~l 74 (484)
T PLN02569 49 FLECPLTGEKYSLDEVVYRS-KSGGLL 74 (484)
T ss_pred ccEeCCCCCcCCCccccccC-CCCCeE
Confidence 35799999988877677778 688665
No 281
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=20.81 E-value=74 Score=20.24 Aligned_cols=22 Identities=32% Similarity=0.792 Sum_probs=14.3
Q ss_pred CCccccCcccccccccccccccccee
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACGQVF 55 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG~vf 55 (158)
..|..|+.- ++ +..|..||...
T Consensus 6 r~C~~CgvY-TL---k~~CP~CG~~t 27 (56)
T PRK13130 6 RKCPKCGVY-TL---KEICPVCGGKT 27 (56)
T ss_pred eECCCCCCE-Ec---cccCcCCCCCC
Confidence 357777762 22 77888888754
No 282
>PLN02189 cellulose synthase
Probab=20.79 E-value=57 Score=32.27 Aligned_cols=53 Identities=23% Similarity=0.669 Sum_probs=37.5
Q ss_pred cCCCccccCcccccc---ccccccccccceecCCCCCCccccCCCCCCCceeeChhhHHHHhc
Q psy509 28 DGDTCHRCRTTFSLV---QRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKFTN 87 (158)
Q Consensus 28 ~~~~C~~C~~~F~~~---~RkhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~ 87 (158)
....|.+|+-.-++. .--.-|..||.-+|..|-.+.. ......|..|.....+
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer-------~eg~q~CpqCkt~Y~r 88 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYER-------REGTQNCPQCKTRYKR 88 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchhhhhh-------hcCCccCcccCCchhh
Confidence 356899999876521 1127899999999999987752 2345678888766654
No 283
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=20.67 E-value=54 Score=20.82 Aligned_cols=20 Identities=25% Similarity=0.677 Sum_probs=10.1
Q ss_pred CCccccCcccccccccccccccc
Q psy509 30 DTCHRCRTTFSLVQRKHHCRACG 52 (158)
Q Consensus 30 ~~C~~C~~~F~~~~RkhhCr~CG 52 (158)
..|..|+. +....|-|.+||
T Consensus 28 ~~C~~CG~---~~~~H~vC~~CG 47 (57)
T PRK12286 28 VECPNCGE---PKLPHRVCPSCG 47 (57)
T ss_pred eECCCCCC---ccCCeEECCCCC
Confidence 35666665 233344455555
No 284
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=20.53 E-value=37 Score=19.98 Aligned_cols=28 Identities=32% Similarity=1.007 Sum_probs=15.9
Q ss_pred CccccCccccccccccccccccce-ecCCCCC
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQV-FCQLCSS 61 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~v-fC~~Cs~ 61 (158)
.|..|... ...+.||..|... .|..|-.
T Consensus 2 ~C~~C~~~---~~~r~~C~~C~dfDLC~~C~~ 30 (41)
T cd02337 2 TCNECKHH---VETRWHCTVCEDYDLCITCYN 30 (41)
T ss_pred cCCCCCCc---CCCceECCCCcchhhHHHHhC
Confidence 36677662 2377777777433 4555543
No 285
>PRK05638 threonine synthase; Validated
Probab=20.51 E-value=55 Score=28.77 Aligned_cols=23 Identities=22% Similarity=0.816 Sum_probs=16.3
Q ss_pred CccccCcccccccccccccccccee
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQVF 55 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~vf 55 (158)
.|..|++.|..- ....| .||..+
T Consensus 3 ~C~~Cg~~~~~~-~~~~C-~c~~~l 25 (442)
T PRK05638 3 KCPKCGREYNSY-IPPFC-ICGELL 25 (442)
T ss_pred EeCCCCCCCCCC-Cceec-CCCCcE
Confidence 588999988733 33778 788654
No 286
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=20.32 E-value=41 Score=29.62 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=6.0
Q ss_pred cceecCCCCC
Q psy509 52 GQVFCQLCSS 61 (158)
Q Consensus 52 G~vfC~~Cs~ 61 (158)
|..+|..|..
T Consensus 59 ~~~YCr~Cl~ 68 (441)
T COG4098 59 GCLYCRNCLM 68 (441)
T ss_pred ceEeehhhhh
Confidence 3557777754
No 287
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=20.29 E-value=17 Score=21.25 Aligned_cols=12 Identities=25% Similarity=0.874 Sum_probs=5.7
Q ss_pred ccccccccccce
Q psy509 43 QRKHHCRACGQV 54 (158)
Q Consensus 43 ~RkhhCr~CG~v 54 (158)
.+-++|..||.+
T Consensus 15 ~~i~~C~~C~nl 26 (41)
T PF02132_consen 15 ENIKFCSICGNL 26 (41)
T ss_dssp HH-EE-SSS--E
T ss_pred HcCCccCCCCCc
Confidence 345788888876
No 288
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=20.26 E-value=50 Score=23.13 Aligned_cols=22 Identities=36% Similarity=0.922 Sum_probs=10.7
Q ss_pred CccccCccccccccccccccccc
Q psy509 31 TCHRCRTTFSLVQRKHHCRACGQ 53 (158)
Q Consensus 31 ~C~~C~~~F~~~~RkhhCr~CG~ 53 (158)
.|..|++. ++-..|..|..||.
T Consensus 18 lCrRCG~~-syH~qK~~CasCGy 39 (91)
T PTZ00073 18 LCRRCGKR-SFHVQKKRCASCGY 39 (91)
T ss_pred hhcccCcc-ccccccccchhcCC
Confidence 45555542 23344555555554
Done!