Query psy8222
Match_columns 198
No_of_seqs 198 out of 1227
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 21:47:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8222.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8222hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1729|consensus 100.0 7E-29 1.5E-33 216.2 7.5 119 2-120 105-226 (288)
2 PF01363 FYVE: FYVE zinc finge 99.8 5.2E-21 1.1E-25 133.4 1.4 65 54-119 1-68 (69)
3 smart00064 FYVE Protein presen 99.8 5.6E-19 1.2E-23 122.8 4.0 65 54-119 2-67 (68)
4 KOG1818|consensus 99.6 8.7E-16 1.9E-20 144.9 2.7 72 50-125 156-228 (634)
5 KOG4424|consensus 99.6 8.3E-15 1.8E-19 136.2 8.3 122 1-125 333-478 (623)
6 cd00065 FYVE FYVE domain; Zinc 99.5 4E-15 8.7E-20 99.7 2.5 54 62-116 2-56 (57)
7 PTZ00303 phosphatidylinositol 99.5 6.1E-15 1.3E-19 140.8 3.6 69 51-120 448-531 (1374)
8 KOG1819|consensus 99.5 3.4E-15 7.3E-20 137.6 1.7 65 52-117 891-961 (990)
9 KOG1841|consensus 99.2 1.1E-11 2.5E-16 122.0 2.9 64 50-114 545-608 (1287)
10 KOG1842|consensus 99.1 9.4E-12 2E-16 113.1 1.0 71 50-121 168-261 (505)
11 cd01218 PH_phafin2 Phafin2 Pl 99.1 3.2E-10 6.9E-15 85.7 5.9 41 2-42 63-103 (104)
12 cd01220 PH_CDEP Chondrocyte-de 98.8 7.2E-09 1.6E-13 77.5 5.6 37 2-38 62-98 (99)
13 cd01219 PH_FGD FGD (faciogenit 98.7 1.9E-08 4.1E-13 75.0 5.1 37 2-38 64-100 (101)
14 KOG1843|consensus 98.5 4.1E-08 8.9E-13 89.0 2.9 69 51-120 149-220 (473)
15 KOG1409|consensus 98.4 6.2E-08 1.3E-12 86.4 0.9 69 51-123 274-354 (404)
16 cd01226 PH_exo84 Exocyst compl 98.4 5.8E-07 1.2E-11 67.5 5.1 37 2-38 63-99 (100)
17 cd01261 PH_SOS Son of Sevenles 98.4 5.8E-07 1.3E-11 68.8 5.0 37 2-38 73-110 (112)
18 KOG1811|consensus 98.1 2E-07 4.4E-12 88.5 -3.1 66 54-119 314-384 (1141)
19 cd01264 PH_melted Melted pleck 98.1 6.1E-06 1.3E-10 62.1 4.7 35 3-37 67-101 (101)
20 cd01251 PH_centaurin_alpha Cen 97.9 1.8E-05 3.9E-10 59.2 4.9 34 5-38 68-101 (103)
21 cd01228 PH_BCR-related BCR (br 97.9 1.6E-05 3.5E-10 59.0 3.7 27 10-36 67-93 (96)
22 cd01265 PH_PARIS-1 PARIS-1 ple 97.7 5.8E-05 1.3E-09 55.6 4.8 33 4-36 61-93 (95)
23 cd01233 Unc104 Unc-104 pleckst 97.6 0.00011 2.3E-09 54.5 5.0 35 3-37 64-98 (100)
24 cd01244 PH_RasGAP_CG9209 RAS_G 97.5 0.00014 3E-09 54.4 4.3 32 4-35 66-97 (98)
25 cd01222 PH_clg Clg (common-sit 97.5 0.00027 5.9E-09 52.7 5.3 34 4-37 59-95 (97)
26 cd01257 PH_IRS Insulin recepto 97.4 0.00024 5.3E-09 53.3 4.8 32 4-35 69-100 (101)
27 cd01236 PH_outspread Outspread 97.4 0.00026 5.6E-09 53.4 4.8 31 4-34 71-101 (104)
28 cd01235 PH_SETbf Set binding f 97.3 0.00032 6.9E-09 51.2 4.4 33 5-37 69-101 (101)
29 PF00169 PH: PH domain; Inter 97.3 0.00073 1.6E-08 47.7 5.7 36 2-37 67-103 (104)
30 cd01238 PH_Tec Tec pleckstrin 97.3 0.0004 8.7E-09 52.1 4.5 32 4-35 74-105 (106)
31 cd01246 PH_oxysterol_bp Oxyste 97.2 0.00051 1.1E-08 48.6 4.4 33 4-36 58-91 (91)
32 KOG0230|consensus 97.2 0.00041 9E-09 71.5 4.9 54 62-126 5-58 (1598)
33 cd01260 PH_CNK Connector enhan 97.2 0.00052 1.1E-08 49.9 4.2 33 4-36 63-96 (96)
34 cd01247 PH_GPBP Goodpasture an 97.2 0.00077 1.7E-08 49.4 5.0 32 4-35 58-90 (91)
35 PF02318 FYVE_2: FYVE-type zin 97.1 0.0004 8.8E-09 53.3 2.7 52 61-119 53-105 (118)
36 cd01266 PH_Gab Gab (Grb2-assoc 97.0 0.0011 2.4E-08 49.7 4.8 32 4-35 75-106 (108)
37 cd01250 PH_centaurin Centaurin 97.0 0.001 2.2E-08 47.3 4.1 32 4-35 62-93 (94)
38 cd01223 PH_Vav Vav pleckstrin 97.0 0.0012 2.6E-08 50.9 4.5 39 2-40 74-114 (116)
39 cd01224 PH_Collybistin Collybi 96.9 0.0015 3.2E-08 49.8 4.8 33 3-35 71-105 (109)
40 cd01232 PH_TRIO Trio pleckstri 96.8 0.0025 5.5E-08 48.8 5.2 36 3-38 75-113 (114)
41 smart00233 PH Pleckstrin homol 96.7 0.0038 8.1E-08 43.0 5.3 35 3-37 66-101 (102)
42 cd01245 PH_RasGAP_CG5898 RAS G 96.6 0.0027 5.8E-08 47.5 3.9 31 4-35 65-97 (98)
43 cd00821 PH Pleckstrin homology 96.5 0.0053 1.2E-07 41.9 4.5 33 3-35 62-95 (96)
44 cd01241 PH_Akt Akt pleckstrin 96.4 0.0052 1.1E-07 45.7 4.2 31 4-36 65-101 (102)
45 cd01252 PH_cytohesin Cytohesin 96.2 0.011 2.3E-07 45.3 5.3 26 14-39 90-115 (125)
46 KOG0230|consensus 96.1 0.0022 4.8E-08 66.3 1.1 34 57-93 92-125 (1598)
47 KOG1841|consensus 96.0 0.011 2.4E-07 59.9 5.5 57 51-120 646-702 (1287)
48 cd00900 PH-like Pleckstrin hom 95.8 0.018 3.9E-07 39.5 4.3 33 3-35 63-98 (99)
49 cd01253 PH_beta_spectrin Beta- 95.6 0.019 4.1E-07 42.2 4.0 32 4-35 71-103 (104)
50 cd01230 PH_EFA6 EFA6 Pleckstri 95.4 0.037 8.1E-07 42.5 5.3 37 3-39 76-113 (117)
51 cd01225 PH_Cool_Pix Cool (clon 94.5 0.068 1.5E-06 40.9 4.5 34 3-36 74-108 (111)
52 cd01249 PH_oligophrenin Oligop 94.1 0.068 1.5E-06 40.5 3.8 30 5-34 71-102 (104)
53 KOG1729|consensus 92.8 0.022 4.9E-07 50.3 -0.9 64 53-117 11-81 (288)
54 KOG0690|consensus 91.9 0.28 6.1E-06 44.8 4.9 40 4-43 79-122 (516)
55 KOG0521|consensus 91.7 0.28 6E-06 49.0 5.1 39 4-42 335-373 (785)
56 cd01237 Unc112 Unc-112 pleckst 91.4 0.46 1E-05 36.1 4.9 33 4-36 66-102 (106)
57 cd01227 PH_Dbs Dbs (DBL's big 91.3 0.7 1.5E-05 36.4 6.1 36 6-41 82-119 (133)
58 KOG0705|consensus 90.2 0.32 6.9E-06 46.9 3.8 37 6-42 447-484 (749)
59 KOG1117|consensus 90.0 0.18 4E-06 50.4 2.0 99 5-114 247-347 (1186)
60 cd01231 PH_Lnk LNK-family Plec 87.6 0.91 2E-05 34.3 3.9 33 4-36 74-107 (107)
61 cd01242 PH_ROK Rok (Rho- assoc 86.9 1.4 3.1E-05 33.7 4.7 36 2-37 73-110 (112)
62 KOG0932|consensus 86.8 0.94 2E-05 43.7 4.4 35 4-38 583-618 (774)
63 PRK00464 nrdR transcriptional 86.5 0.39 8.5E-06 38.7 1.6 25 64-89 2-38 (154)
64 PF08458 PH_2: Plant pleckstri 85.9 2 4.3E-05 32.8 5.1 34 6-39 72-105 (110)
65 PF15409 PH_8: Pleckstrin homo 85.4 2 4.4E-05 31.5 4.8 33 4-36 56-88 (89)
66 smart00154 ZnF_AN1 AN1-like Zi 84.0 0.67 1.5E-05 28.8 1.5 26 65-93 1-26 (39)
67 PF07975 C1_4: TFIIH C1-like d 83.1 0.21 4.6E-06 33.0 -1.2 29 64-93 1-35 (51)
68 KOG0320|consensus 82.5 0.098 2.1E-06 43.2 -3.5 49 62-120 131-179 (187)
69 KOG2164|consensus 81.4 0.42 9.2E-06 45.1 -0.3 52 62-120 186-237 (513)
70 TIGR00622 ssl1 transcription f 80.9 2 4.2E-05 33.0 3.2 40 55-95 48-97 (112)
71 KOG3520|consensus 80.0 2.9 6.2E-05 43.3 5.0 36 7-42 688-726 (1167)
72 PF14593 PH_3: PH domain; PDB: 79.8 4.5 9.8E-05 30.4 4.9 34 5-39 68-101 (104)
73 KOG2996|consensus 78.2 1.3 2.9E-05 42.9 1.9 90 4-96 476-568 (865)
74 PF13717 zinc_ribbon_4: zinc-r 78.1 1.3 2.7E-05 27.0 1.2 25 64-89 4-35 (36)
75 KOG4275|consensus 77.7 0.38 8.2E-06 42.7 -1.7 52 57-117 39-90 (350)
76 PF14634 zf-RING_5: zinc-RING 77.3 0.39 8.5E-06 30.1 -1.3 33 64-98 1-33 (44)
77 KOG0993|consensus 77.3 0.054 1.2E-06 50.0 -7.3 66 54-122 460-528 (542)
78 KOG1314|consensus 75.5 0.83 1.8E-05 41.6 -0.2 37 50-89 74-115 (414)
79 KOG3799|consensus 74.8 1.4 3.1E-05 35.0 1.0 54 61-118 64-117 (169)
80 KOG3531|consensus 74.7 2.9 6.3E-05 42.0 3.2 41 3-43 810-850 (1036)
81 PF07282 OrfB_Zn_ribbon: Putat 74.2 4.5 9.7E-05 27.4 3.3 28 61-89 27-56 (69)
82 PF13719 zinc_ribbon_5: zinc-r 74.0 1.9 4.2E-05 26.2 1.2 25 64-89 4-35 (37)
83 cd01262 PH_PDK1 3-Phosphoinosi 70.1 8.1 0.00018 28.4 4.0 32 5-37 57-88 (89)
84 PF13923 zf-C3HC4_2: Zinc fing 68.3 1.4 3E-05 26.7 -0.3 29 65-97 1-29 (39)
85 PRK00420 hypothetical protein; 68.0 3.8 8.2E-05 31.4 1.9 26 62-88 23-49 (112)
86 PLN02638 cellulose synthase A 67.8 3.7 8E-05 42.4 2.3 56 57-119 12-70 (1079)
87 PF07191 zinc-ribbons_6: zinc- 67.8 2.3 5E-05 30.0 0.6 56 64-121 3-63 (70)
88 KOG0317|consensus 66.7 1.4 3.1E-05 38.9 -0.7 46 62-119 239-284 (293)
89 KOG3576|consensus 66.4 1.2 2.7E-05 37.8 -1.1 61 58-120 113-185 (267)
90 PF09538 FYDLN_acid: Protein o 66.1 3.6 7.8E-05 31.2 1.4 28 61-89 8-36 (108)
91 PF10571 UPF0547: Uncharacteri 65.4 4.1 8.9E-05 23.1 1.3 23 64-89 2-24 (26)
92 PF01485 IBR: IBR domain; Int 64.6 5.9 0.00013 25.8 2.2 34 62-96 18-57 (64)
93 PF13639 zf-RING_2: Ring finge 63.9 1.3 2.8E-05 27.5 -1.2 33 64-98 2-34 (44)
94 PLN02400 cellulose synthase 63.6 5.4 0.00012 41.2 2.6 57 57-120 31-90 (1085)
95 TIGR00570 cdk7 CDK-activating 63.5 1.6 3.6E-05 39.0 -1.0 49 63-120 4-55 (309)
96 KOG2059|consensus 63.5 15 0.00032 36.5 5.4 38 2-39 629-666 (800)
97 PF01529 zf-DHHC: DHHC palmito 63.2 3.9 8.5E-05 32.2 1.3 27 60-89 46-72 (174)
98 KOG3173|consensus 63.1 3.8 8.3E-05 33.4 1.2 29 61-93 104-132 (167)
99 PF03107 C1_2: C1 domain; Int 62.9 7.6 0.00017 22.4 2.1 29 64-94 2-30 (30)
100 KOG1814|consensus 62.8 2.9 6.3E-05 38.8 0.5 42 54-97 361-404 (445)
101 PLN03208 E3 ubiquitin-protein 62.8 1.5 3.3E-05 36.6 -1.2 60 56-120 12-80 (193)
102 PF12773 DZR: Double zinc ribb 62.8 5.7 0.00012 25.2 1.8 27 61-88 11-38 (50)
103 TIGR02300 FYDLN_acid conserved 62.8 5.3 0.00011 31.3 1.8 28 61-89 8-36 (129)
104 PLN02436 cellulose synthase A 60.5 7.4 0.00016 40.2 2.9 56 57-119 31-89 (1094)
105 PF14569 zf-UDP: Zinc-binding 60.4 1.1 2.4E-05 32.2 -2.1 50 59-115 6-58 (80)
106 KOG0823|consensus 59.7 2.1 4.6E-05 36.7 -0.9 51 61-120 46-96 (230)
107 KOG4305|consensus 59.4 11 0.00023 38.9 3.8 38 8-45 657-694 (1029)
108 PRK04136 rpl40e 50S ribosomal 59.3 6.2 0.00013 25.8 1.4 23 62-87 14-36 (48)
109 KOG1117|consensus 58.8 7.7 0.00017 39.4 2.6 37 4-40 144-180 (1186)
110 PLN02189 cellulose synthase 58.2 6.4 0.00014 40.5 2.0 55 58-119 30-87 (1040)
111 KOG1315|consensus 57.6 4.3 9.4E-05 36.3 0.7 27 59-88 106-132 (307)
112 PRK00398 rpoP DNA-directed RNA 57.0 6 0.00013 24.9 1.1 24 64-88 5-30 (46)
113 KOG1311|consensus 56.4 5 0.00011 35.0 0.8 25 62-89 113-137 (299)
114 KOG4739|consensus 55.6 4.7 0.0001 34.7 0.5 43 64-118 5-47 (233)
115 cd01258 PH_syntrophin Syntroph 55.0 28 0.0006 26.4 4.6 33 3-35 73-107 (108)
116 TIGR01562 FdhE formate dehydro 55.0 12 0.00025 33.5 2.9 61 61-121 183-265 (305)
117 KOG1818|consensus 54.9 1.4 3E-05 42.9 -3.1 72 39-115 34-107 (634)
118 COG0675 Transposase and inacti 54.8 16 0.00036 31.1 3.8 26 60-89 307-332 (364)
119 smart00647 IBR In Between Ring 54.1 13 0.00028 24.2 2.4 34 62-96 18-57 (64)
120 PF09297 zf-NADH-PPase: NADH p 52.6 11 0.00023 22.0 1.6 24 89-115 5-28 (32)
121 COG5574 PEX10 RING-finger-cont 52.5 3.5 7.5E-05 36.1 -0.8 46 63-118 216-261 (271)
122 PF14835 zf-RING_6: zf-RING of 52.1 8.9 0.00019 26.6 1.4 29 63-96 8-37 (65)
123 cd00162 RING RING-finger (Real 50.5 3.9 8.4E-05 24.1 -0.6 30 64-97 1-30 (45)
124 TIGR02098 MJ0042_CXXC MJ0042 f 50.5 8.8 0.00019 23.0 1.0 12 64-76 4-15 (38)
125 cd01256 PH_dynamin Dynamin ple 49.5 30 0.00065 26.3 3.9 32 4-35 64-103 (110)
126 PHA02768 hypothetical protein; 49.0 8.6 0.00019 25.8 0.9 25 64-89 7-41 (55)
127 PF06221 zf-C2HC5: Putative zi 49.0 9 0.00019 25.9 1.0 17 75-91 14-30 (57)
128 COG5273 Uncharacterized protei 48.4 8 0.00017 34.4 0.9 26 60-88 107-132 (309)
129 cd02341 ZZ_ZZZ3 Zinc finger, Z 48.3 7.6 0.00016 25.2 0.5 31 64-96 2-35 (48)
130 COG4888 Uncharacterized Zn rib 48.3 4.5 9.7E-05 30.5 -0.7 56 74-134 17-72 (104)
131 COG1996 RPC10 DNA-directed RNA 47.8 8.5 0.00018 25.2 0.7 23 64-87 8-32 (49)
132 PLN02400 cellulose synthase 47.6 21 0.00046 37.1 3.7 25 80-117 37-72 (1085)
133 PLN02866 phospholipase D 47.6 37 0.00081 35.3 5.5 36 3-38 273-308 (1068)
134 PF08271 TF_Zn_Ribbon: TFIIB z 47.4 10 0.00022 23.6 1.0 7 64-70 2-8 (43)
135 PRK05462 S-adenosylmethionine 46.3 24 0.00053 30.9 3.4 33 5-37 9-45 (266)
136 TIGR03331 SAM_DCase_Eco S-aden 45.5 26 0.00056 30.6 3.5 33 5-37 5-41 (259)
137 PF10367 Vps39_2: Vacuolar sor 45.4 20 0.00044 25.7 2.5 32 61-95 77-108 (109)
138 PF06750 DiS_P_DiS: Bacterial 44.9 16 0.00036 26.7 1.9 26 62-88 33-67 (92)
139 PRK14559 putative protein seri 44.8 14 0.0003 36.3 1.9 23 61-88 14-36 (645)
140 PF03604 DNA_RNApol_7kD: DNA d 44.7 16 0.00034 21.7 1.5 23 64-87 2-25 (32)
141 TIGR00100 hypA hydrogenase nic 44.7 11 0.00023 28.7 0.9 26 61-87 69-94 (115)
142 PF10170 C6_DPF: Cysteine-rich 44.6 13 0.00027 27.9 1.3 34 76-118 46-81 (97)
143 PRK00432 30S ribosomal protein 43.8 18 0.00038 23.6 1.7 27 62-89 20-47 (50)
144 PRK03564 formate dehydrogenase 43.6 24 0.00053 31.6 3.1 61 61-121 186-265 (309)
145 KOG1356|consensus 43.5 10 0.00022 38.2 0.8 36 60-98 227-262 (889)
146 TIGR02605 CxxC_CxxC_SSSS putat 43.1 11 0.00024 24.0 0.7 14 64-78 7-20 (52)
147 PF00097 zf-C3HC4: Zinc finger 42.9 7.7 0.00017 23.3 -0.1 29 65-97 1-29 (41)
148 PF01428 zf-AN1: AN1-like Zinc 42.2 17 0.00038 22.6 1.5 15 79-93 13-27 (43)
149 PF11238 DUF3039: Protein of u 42.2 22 0.00048 24.1 2.0 20 101-120 37-56 (58)
150 PF15135 UPF0515: Uncharacteri 42.0 17 0.00036 31.8 1.8 34 57-91 127-167 (278)
151 KOG0978|consensus 41.5 2.5 5.3E-05 41.7 -3.7 45 61-116 642-686 (698)
152 PF14803 Nudix_N_2: Nudix N-te 40.1 22 0.00049 21.4 1.6 18 98-115 12-29 (34)
153 COG1773 Rubredoxin [Energy pro 40.0 13 0.00029 24.9 0.7 13 78-90 2-14 (55)
154 PF09947 DUF2180: Uncharacteri 39.8 7.4 0.00016 27.2 -0.6 40 80-119 17-67 (68)
155 PF15451 DUF4632: Domain of un 39.3 26 0.00056 24.1 2.0 11 183-193 55-65 (71)
156 PF01927 Mut7-C: Mut7-C RNAse 39.2 46 0.001 26.1 3.8 12 61-73 90-101 (147)
157 PF11781 RRN7: RNA polymerase 39.0 13 0.00028 22.6 0.5 26 63-88 9-34 (36)
158 PF13901 DUF4206: Domain of un 38.6 15 0.00032 30.6 0.9 43 81-123 2-50 (202)
159 PF07754 DUF1610: Domain of un 38.0 24 0.00051 19.7 1.4 9 79-87 16-24 (24)
160 PHA02926 zinc finger-like prot 38.0 6.4 0.00014 33.9 -1.3 56 61-120 169-231 (242)
161 PRK00564 hypA hydrogenase nick 37.5 18 0.0004 27.5 1.2 26 61-87 70-96 (117)
162 PLN02915 cellulose synthase A 36.5 20 0.00042 37.2 1.6 52 61-119 14-68 (1044)
163 KOG1170|consensus 36.5 27 0.0006 35.4 2.5 88 3-93 60-150 (1099)
164 PF01155 HypA: Hydrogenase exp 36.2 9.8 0.00021 28.7 -0.4 26 61-87 69-94 (113)
165 cd02342 ZZ_UBA_plant Zinc fing 35.6 15 0.00033 23.4 0.4 30 64-95 2-32 (43)
166 PLN02436 cellulose synthase A 35.6 40 0.00087 35.1 3.6 26 80-118 37-73 (1094)
167 smart00659 RPOLCX RNA polymera 35.2 25 0.00054 22.3 1.4 23 64-87 4-27 (44)
168 PF13590 DUF4136: Domain of un 35.2 64 0.0014 24.4 4.0 47 11-57 15-64 (151)
169 PF13248 zf-ribbon_3: zinc-rib 35.1 26 0.00057 19.4 1.3 7 64-70 4-10 (26)
170 PF15227 zf-C3HC4_4: zinc fing 35.0 12 0.00026 23.3 -0.2 15 83-97 14-28 (42)
171 PHA02942 putative transposase; 34.7 33 0.00072 31.4 2.6 29 61-89 324-352 (383)
172 PF09862 DUF2089: Protein of u 34.5 25 0.00054 27.0 1.5 30 65-97 1-30 (113)
173 KOG2462|consensus 34.4 12 0.00025 33.1 -0.3 38 80-118 216-253 (279)
174 PRK12380 hydrogenase nickel in 34.3 19 0.00042 27.2 0.9 25 62-87 70-94 (113)
175 PF00643 zf-B_box: B-box zinc 34.3 15 0.00033 22.2 0.2 29 62-95 3-31 (42)
176 KOG0689|consensus 33.7 65 0.0014 30.4 4.4 28 13-40 336-363 (448)
177 COG1998 RPS31 Ribosomal protei 33.3 27 0.00058 23.1 1.3 26 62-87 19-45 (51)
178 PF15616 TerY-C: TerY-C metal 33.2 30 0.00066 27.2 1.8 40 62-119 77-116 (131)
179 KOG3518|consensus 32.9 24 0.00052 32.4 1.4 35 5-39 397-434 (521)
180 PTZ00255 60S ribosomal protein 32.5 30 0.00065 25.5 1.6 30 61-93 35-68 (90)
181 PF01780 Ribosomal_L37ae: Ribo 32.5 23 0.00051 26.1 1.0 29 61-92 34-66 (90)
182 COG1327 Predicted transcriptio 32.5 24 0.00052 28.5 1.2 15 106-120 26-40 (156)
183 smart00834 CxxC_CXXC_SSSS Puta 32.3 21 0.00046 21.3 0.7 13 64-77 7-19 (41)
184 PF04216 FdhE: Protein involve 32.3 15 0.00033 32.0 0.0 61 62-122 172-252 (290)
185 PRK14892 putative transcriptio 31.9 42 0.0009 25.1 2.3 12 85-96 40-51 (99)
186 TIGR00373 conserved hypothetic 31.8 23 0.00051 28.3 1.1 25 63-88 110-137 (158)
187 PF14851 FAM176: FAM176 family 31.8 89 0.0019 25.2 4.4 22 167-189 94-116 (153)
188 COG5151 SSL1 RNA polymerase II 31.5 19 0.00042 32.5 0.6 38 56-94 356-403 (421)
189 smart00291 ZnF_ZZ Zinc-binding 30.7 28 0.0006 21.7 1.0 30 62-94 4-34 (44)
190 PRK03824 hypA hydrogenase nick 30.5 24 0.00053 27.5 0.9 13 63-76 71-83 (135)
191 PRK11595 DNA utilization prote 30.4 12 0.00026 31.5 -0.9 30 63-95 21-56 (227)
192 KOG3551|consensus 30.3 1.1E+02 0.0024 28.7 5.1 37 6-42 238-276 (506)
193 PRK03681 hypA hydrogenase nick 29.8 26 0.00056 26.6 0.9 25 62-87 70-95 (114)
194 smart00661 RPOL9 RNA polymeras 29.8 40 0.00086 21.2 1.7 7 108-114 20-26 (52)
195 PF04438 zf-HIT: HIT zinc fing 29.8 33 0.00072 19.9 1.2 23 63-91 3-25 (30)
196 PRK12496 hypothetical protein; 29.4 35 0.00075 27.6 1.7 23 64-87 129-151 (164)
197 PF02148 zf-UBP: Zn-finger in 28.9 33 0.00071 22.9 1.2 24 65-92 1-24 (63)
198 PF06524 NOA36: NOA36 protein; 28.9 1.2E+02 0.0026 26.9 4.9 35 79-115 182-216 (314)
199 PF00569 ZZ: Zinc finger, ZZ t 28.9 20 0.00044 22.6 0.2 23 62-86 4-26 (46)
200 PF13445 zf-RING_UBOX: RING-ty 28.9 13 0.00027 23.5 -0.8 14 83-96 17-30 (43)
201 cd02340 ZZ_NBR1_like Zinc fing 28.7 26 0.00056 21.9 0.7 30 64-96 2-32 (43)
202 TIGR00244 transcriptional regu 28.7 38 0.00082 27.2 1.7 12 76-87 25-36 (147)
203 smart00109 C1 Protein kinase C 28.4 34 0.00073 20.7 1.2 32 62-94 11-42 (49)
204 PF13240 zinc_ribbon_2: zinc-r 28.4 29 0.00064 18.9 0.8 6 65-70 2-7 (23)
205 TIGR00357 methionine-R-sulfoxi 28.2 89 0.0019 24.7 3.7 47 26-73 4-51 (134)
206 PF09845 DUF2072: Zn-ribbon co 28.2 32 0.00069 27.1 1.2 10 80-89 2-11 (131)
207 PF09723 Zn-ribbon_8: Zinc rib 28.0 26 0.00056 21.7 0.5 11 65-76 8-18 (42)
208 PRK03976 rpl37ae 50S ribosomal 28.0 39 0.00085 24.9 1.6 30 61-93 35-68 (90)
209 TIGR01384 TFS_arch transcripti 27.9 36 0.00079 24.8 1.5 24 64-88 2-25 (104)
210 cd02249 ZZ Zinc finger, ZZ typ 27.8 23 0.00051 22.2 0.3 29 64-95 2-31 (46)
211 PF14445 Prok-RING_2: Prokaryo 27.7 10 0.00022 25.2 -1.4 31 64-96 9-39 (57)
212 KOG1829|consensus 27.6 19 0.00042 34.9 -0.1 58 63-121 341-406 (580)
213 PF09332 Mcm10: Mcm10 replicat 27.6 21 0.00046 32.4 0.2 45 61-116 251-311 (344)
214 TIGR00280 L37a ribosomal prote 27.6 40 0.00088 24.9 1.6 30 61-93 34-67 (91)
215 PF04981 NMD3: NMD3 family ; 27.4 27 0.00058 29.6 0.7 31 89-119 15-46 (236)
216 PF10497 zf-4CXXC_R1: Zinc-fin 27.3 15 0.00033 27.6 -0.7 55 61-118 6-71 (105)
217 TIGR00595 priA primosomal prot 27.2 45 0.00098 31.6 2.3 36 63-99 223-265 (505)
218 PRK03988 translation initiatio 27.1 34 0.00074 27.0 1.2 26 62-88 102-132 (138)
219 smart00184 RING Ring finger. E 26.8 13 0.00028 20.8 -1.0 15 83-97 14-28 (39)
220 PRK14559 putative protein seri 26.4 56 0.0012 32.2 2.8 48 63-120 2-53 (645)
221 COG1997 RPL43A Ribosomal prote 26.1 47 0.001 24.4 1.7 29 61-92 34-66 (89)
222 smart00531 TFIIE Transcription 26.0 32 0.0007 27.0 0.9 27 62-89 99-133 (147)
223 PF14353 CpXC: CpXC protein 26.0 33 0.00072 26.0 1.0 11 79-89 38-48 (128)
224 PF01907 Ribosomal_L37e: Ribos 25.5 47 0.001 22.3 1.5 7 82-88 18-24 (55)
225 PF00301 Rubredoxin: Rubredoxi 25.2 33 0.00072 22.1 0.7 12 79-90 1-12 (47)
226 KOG2845|consensus 25.2 40 0.00087 32.2 1.5 11 81-91 172-182 (505)
227 PF13920 zf-C3HC4_3: Zinc fing 25.0 25 0.00054 22.2 0.1 30 63-97 3-33 (50)
228 PRK06266 transcription initiat 24.7 30 0.00066 28.3 0.6 25 63-88 118-145 (178)
229 TIGR00311 aIF-2beta translatio 24.5 40 0.00088 26.4 1.2 25 63-88 98-127 (133)
230 cd02335 ZZ_ADA2 Zinc finger, Z 24.4 34 0.00074 21.9 0.6 31 64-96 2-33 (49)
231 PRK04023 DNA polymerase II lar 24.3 56 0.0012 34.0 2.4 45 61-119 625-674 (1121)
232 smart00504 Ubox Modified RING 24.3 33 0.00071 22.2 0.6 29 64-97 3-31 (63)
233 TIGR01031 rpmF_bact ribosomal 24.2 51 0.0011 21.8 1.5 23 60-86 24-46 (55)
234 PF15277 Sec3-PIP2_bind: Exocy 24.1 2.4E+02 0.0053 20.3 5.2 32 6-38 58-89 (91)
235 PF02150 RNA_POL_M_15KD: RNA p 24.1 40 0.00087 20.2 0.9 26 88-115 2-27 (35)
236 KOG0153|consensus 24.0 40 0.00088 30.8 1.2 22 56-78 35-56 (377)
237 KOG3795|consensus 23.9 39 0.00085 28.2 1.0 23 72-94 8-33 (230)
238 KOG0931|consensus 23.9 1.6E+02 0.0034 28.3 5.1 40 1-40 483-528 (627)
239 PF06397 Desulfoferrod_N: Desu 23.9 36 0.00077 20.8 0.6 11 79-89 6-16 (36)
240 TIGR02159 PA_CoA_Oxy4 phenylac 23.8 42 0.00091 26.7 1.2 30 88-117 106-139 (146)
241 PF13465 zf-H2C2_2: Zinc-finge 23.7 38 0.00083 18.6 0.7 12 78-89 13-24 (26)
242 PRK14873 primosome assembly pr 23.7 44 0.00096 32.9 1.5 35 63-98 393-433 (665)
243 PF12760 Zn_Tnp_IS1595: Transp 23.7 42 0.00091 21.0 0.9 25 63-87 19-45 (46)
244 cd02345 ZZ_dah Zinc finger, ZZ 23.5 38 0.00081 21.8 0.7 28 64-93 2-30 (49)
245 TIGR00599 rad18 DNA repair pro 23.3 28 0.00061 32.3 0.1 32 61-97 25-56 (397)
246 COG1439 Predicted nucleic acid 22.8 41 0.0009 27.8 1.0 21 64-87 141-161 (177)
247 PF13453 zf-TFIIB: Transcripti 22.7 60 0.0013 19.8 1.5 9 107-115 18-26 (41)
248 PRK14890 putative Zn-ribbon RN 22.7 80 0.0017 21.5 2.2 28 61-89 6-35 (59)
249 PRK08665 ribonucleotide-diphos 22.5 1.4E+02 0.0031 29.9 4.8 62 28-90 686-751 (752)
250 PLN00188 enhanced disease resi 22.4 1E+02 0.0023 30.8 3.8 30 11-40 83-112 (719)
251 KOG2593|consensus 22.4 39 0.00084 31.7 0.8 34 62-96 128-170 (436)
252 PRK09678 DNA-binding transcrip 22.1 70 0.0015 22.5 1.9 13 77-89 25-39 (72)
253 KOG1311|consensus 22.1 53 0.0012 28.5 1.6 26 60-88 125-150 (299)
254 cd02336 ZZ_RSC8 Zinc finger, Z 21.9 39 0.00084 21.6 0.5 9 108-116 23-31 (45)
255 PF14599 zinc_ribbon_6: Zinc-r 21.7 33 0.00071 23.4 0.1 21 64-86 32-55 (61)
256 PF01873 eIF-5_eIF-2B: Domain 21.7 46 0.00099 25.8 1.0 25 63-88 94-123 (125)
257 KOG1813|consensus 21.4 69 0.0015 28.7 2.1 29 64-97 243-271 (313)
258 cd00350 rubredoxin_like Rubred 21.2 53 0.0012 19.2 1.0 10 80-89 2-11 (33)
259 KOG3362|consensus 21.0 92 0.002 25.1 2.6 25 61-91 117-141 (156)
260 COG3364 Zn-ribbon containing p 20.9 36 0.00078 25.8 0.3 10 80-89 3-12 (112)
261 COG0266 Nei Formamidopyrimidin 20.8 2.4E+02 0.0052 24.9 5.4 25 22-46 195-219 (273)
262 PRK10445 endonuclease VIII; Pr 20.7 2.8E+02 0.0062 23.8 5.8 25 22-46 191-215 (263)
263 PF00096 zf-C2H2: Zinc finger, 20.6 45 0.00098 17.1 0.5 9 81-89 2-10 (23)
264 COG2888 Predicted Zn-ribbon RN 20.6 81 0.0018 21.6 1.9 31 62-93 9-41 (61)
265 CHL00112 rpl28 ribosomal prote 20.3 1.1E+02 0.0025 20.8 2.6 15 106-120 47-61 (63)
266 KOG3521|consensus 20.1 1.5E+02 0.0032 29.7 4.2 38 4-41 487-530 (846)
267 KOG4323|consensus 20.1 50 0.0011 31.3 1.0 27 63-89 169-195 (464)
268 PF12172 DUF35_N: Rubredoxin-l 20.0 38 0.00082 20.1 0.2 8 81-88 13-20 (37)
No 1
>KOG1729|consensus
Probab=99.95 E-value=7e-29 Score=216.20 Aligned_cols=119 Identities=57% Similarity=1.135 Sum_probs=114.8
Q ss_pred CCcceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHHHHHHh---cCCCCCCCCCCccccCCCCCccccCCccCCCcccc
Q psy8222 2 ELRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIEDLLRK---SGKKPAATHAAVWIPDNEAAVCMHCKRTQFTVLSR 78 (198)
Q Consensus 2 ~~~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~~---~g~~~~~~~~~~Wv~d~~~~~C~~C~~~~Fs~~~R 78 (198)
.++|.|+|.+..|||.++|++..||.+|+.+|.+++.++|+. .+..|...++++|+||+++.+||.|+++.|+++.|
T Consensus 105 ~~~~~~~~~S~~ks~~~~~as~~ek~e~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~W~PD~ea~~C~~C~~~~Ftl~~R 184 (288)
T KOG1729|consen 105 RVRNGWQILSALKSFTVLAASQTEKNEWQNHITECVEDLLSKNEEDGKSPSNNSAAVWLPDSEATECMVCGCTEFTLSER 184 (288)
T ss_pred ccccchhhhcccchhhhhcchhhhhHHHHHHHHHHHHHHHHHhhhccCCCCCCcCCcccCcccceecccCCCccccHHHH
Confidence 578899999999999999999999999999999999999998 88899999999999999999999999999999999
Q ss_pred ccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhcc
Q psy8222 79 RHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 79 rhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~ 120 (198)
|||||+||.|||..|+..++.||....+++|||+.||+.|..
T Consensus 185 RHHCR~CG~ivC~~Cs~n~~~l~~~~~k~~rvC~~CF~el~~ 226 (288)
T KOG1729|consen 185 RHHCRNCGDIVCAPCSRNRFLLPNLSTKPIRVCDICFEELEK 226 (288)
T ss_pred HHHHHhcchHhhhhhhcCcccccccCCCCceecHHHHHHHhc
Confidence 999999999999999999999999999999999999999975
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=99.81 E-value=5.2e-21 Score=133.43 Aligned_cols=65 Identities=52% Similarity=1.210 Sum_probs=47.6
Q ss_pred CccccCCCCCccccCCccCCCccccccccccCCceEeCCCCCCeeecC--CC-CCCCeeeccchHHhhc
Q psy8222 54 AVWIPDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLP--SQ-SAKPLRVCLTCYDVLS 119 (198)
Q Consensus 54 ~~Wv~d~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp--~~-~~~~~RVC~~C~~~l~ 119 (198)
|.|+||.++..|+.|++ +|++++||||||.||.+||+.|+.++..++ .. ..+++|||+.||..|+
T Consensus 1 ~~W~~d~~~~~C~~C~~-~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~~~~~~RvC~~C~~~~~ 68 (69)
T PF01363_consen 1 PHWVPDSEASNCMICGK-KFSLFRRRHHCRNCGRVVCSSCSSQRIPLPTPSSGSGEPVRVCDSCYSKLQ 68 (69)
T ss_dssp --SSSGGG-SB-TTT---B-BSSS-EEE-TTT--EEECCCS-EEEEET--GGTESEEEEE-HHHHHHHH
T ss_pred CCcCCCCCCCcCcCcCC-cCCCceeeEccCCCCCEECCchhCCEEcccccccCCCCcCEECHHHHHHhc
Confidence 57999999999999999 999999999999999999999999999887 32 4499999999999875
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 KOG1818|consensus
Probab=99.56 E-value=8.7e-16 Score=144.89 Aligned_cols=72 Identities=42% Similarity=1.000 Sum_probs=65.3
Q ss_pred CCCCCccccCCCCCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCC-CCeeeccchHHhhcccccCC
Q psy8222 50 ATHAAVWIPDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSA-KPLRVCLTCYDVLSRDKTVS 125 (198)
Q Consensus 50 ~~~~~~Wv~d~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~-~~~RVC~~C~~~l~~~~~~~ 125 (198)
.+.++.|+ +...|+.|.. .|++++|+||||+||.|||..|+.+...||..|. ++||||+.||+.+...+...
T Consensus 156 ~~~~pdW~---D~~~C~rCr~-~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l~~~s~~~ 228 (634)
T KOG1818|consen 156 AETAPDWI---DSEECLRCRV-KFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELLTRASVGE 228 (634)
T ss_pred ccCCcccc---cccccceeee-eeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHhhhcccch
Confidence 34578898 4678999999 9999999999999999999999999999999998 99999999999998876653
No 5
>KOG4424|consensus
Probab=99.56 E-value=8.3e-15 Score=136.22 Aligned_cols=122 Identities=26% Similarity=0.517 Sum_probs=99.5
Q ss_pred CCCcceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHHHHHHh------cCCCC-----------------CCCCCCccc
Q psy8222 1 MELRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIEDLLRK------SGKKP-----------------AATHAAVWI 57 (198)
Q Consensus 1 ~~~~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~~------~g~~~-----------------~~~~~~~Wv 57 (198)
+.++|+|.|.+++++.+|.|.|.+||.+|++.|+.+|+.+.+. .++.+ .....+.|
T Consensus 333 ~~~~~tF~~~G~~r~vel~a~t~~ek~eWv~~I~~~Id~~kq~~eTfr~~s~t~~~~~d~~s~~~~~~l~~r~~~~~r~- 411 (623)
T KOG4424|consen 333 EELPHTFILTGKKRGVELQARTEQEKKEWVQAIQDAIDKHKQCRETFRKDSRTPISDNDMKSFSSDYVLGKRKRKAPRR- 411 (623)
T ss_pred ccCCceEEEecccceEEeecCchhhHHHHHHHHHHHHHHHHHHHHHHHhccCCchhhccccccccccccccccccCccc-
Confidence 3579999999999999999999999999999999999876432 12111 01124456
Q ss_pred cCCCCCccccCCccCCCcc-ccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhcccccCC
Q psy8222 58 PDNEAAVCMHCKRTQFTVL-SRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSRDKTVS 125 (198)
Q Consensus 58 ~d~~~~~C~~C~~~~Fs~~-~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~~~~~~ 125 (198)
++....|+.|.. +|+-. .|||||+.||.|+|+.|+..+..+...+....|||..||..........
T Consensus 412 -~~k~~~c~~c~e-~~~s~t~~R~~~k~~~~vlc~~cs~~~~~l~~~~s~ssrv~~~~~~~~~~a~~s~ 478 (623)
T KOG4424|consen 412 -DNKVTSCDSCEE-TFNSITFRRHRCKAKGAVLCDKCSDFMAKLSYDNSRSSRVCMDRYLTPSGAPGSP 478 (623)
T ss_pred -ccccccchhhcC-chhhHHHhhhhhhhccceeeccccchhhhhcccccchhhhhhhhccCCCCCCCCc
Confidence 778999999999 89754 6899999999999999999998887777799999999999876554433
No 6
>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=99.53 E-value=4e-15 Score=99.74 Aligned_cols=54 Identities=52% Similarity=1.204 Sum_probs=50.0
Q ss_pred CCccccCCccCCCccccccccccCCceEeCCCCCCeeecCC-CCCCCeeeccchHH
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPS-QSAKPLRVCLTCYD 116 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~-~~~~~~RVC~~C~~ 116 (198)
+..|+.|.+ .|+++.|+|||+.||.+||..|+..+..++. .+.+++|||..||.
T Consensus 2 ~~~C~~C~~-~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~~~~~~~~~~rvC~~C~~ 56 (57)
T cd00065 2 ASSCMGCGK-PFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSCYE 56 (57)
T ss_pred cCcCcccCc-cccCCccccccCcCcCCcChHHcCCeeecCcccCCCccEeChHHhC
Confidence 568999999 9999999999999999999999999998887 46699999999985
No 7
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=99.51 E-value=6.1e-15 Score=140.76 Aligned_cols=69 Identities=38% Similarity=0.785 Sum_probs=55.1
Q ss_pred CCCCccccCCC-CCccccCCccCCCcc-----ccccccccCCceEeCCCCCCeee-----cCCCC--C--CCeeeccchH
Q psy8222 51 THAAVWIPDNE-AAVCMHCKRTQFTVL-----SRRHHCRKCGSVVCAPCSNKRFL-----LPSQS--A--KPLRVCLTCY 115 (198)
Q Consensus 51 ~~~~~Wv~d~~-~~~C~~C~~~~Fs~~-----~RrhhCr~CG~vvC~~Cs~~~~~-----lp~~~--~--~~~RVC~~C~ 115 (198)
.+.+.|++|++ ++.|+.|++ .|+++ .||||||+||.|||..||.++.. ++..+ . .+.|||+.||
T Consensus 448 LhAPvWqpDDEaSdtC~~C~k-kFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs~yp~aKLpKPgsseE~ppRRVCD~CY 526 (1374)
T PTZ00303 448 LHNPSWQKDDESSDSCPSCGR-AFISLSRPLGTRAHHCRSCGIRLCVFCITKRAHYSFAKLAKPGSSDEAEERLVCDTCY 526 (1374)
T ss_pred ccCCCCCCCcccCCcccCcCC-cccccccccccccccccCCccccCccccCCcccCcccccCCCCCcccccccchhHHHH
Confidence 46899999998 488999999 99754 69999999999999999998753 22222 1 4678999999
Q ss_pred Hhhcc
Q psy8222 116 DVLSR 120 (198)
Q Consensus 116 ~~l~~ 120 (198)
+.+..
T Consensus 527 dq~En 531 (1374)
T PTZ00303 527 KEYET 531 (1374)
T ss_pred HHHHh
Confidence 76653
No 8
>KOG1819|consensus
Probab=99.51 E-value=3.4e-15 Score=137.56 Aligned_cols=65 Identities=40% Similarity=0.965 Sum_probs=60.8
Q ss_pred CCCccccCCCCCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCC-CCeeecc-----chHHh
Q psy8222 52 HAAVWIPDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSA-KPLRVCL-----TCYDV 117 (198)
Q Consensus 52 ~~~~Wv~d~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~-~~~RVC~-----~C~~~ 117 (198)
.+|.|+||.++..||.|.. +|++|+||||||+||.|||+.|+...++||..|. +.+|||. .||..
T Consensus 891 sppawipd~~a~~cmacq~-pf~afrrrhhcrncggifcg~cs~asapip~~gl~ka~rvcrpqsnldc~~r 961 (990)
T KOG1819|consen 891 SPPAWIPDEDAEQCMACQM-PFNAFRRRHHCRNCGGIFCGKCSCASAPIPEHGLDKAPRVCRPQSNLDCLTR 961 (990)
T ss_pred CCcccCCCCcchhhhhccC-cHHHHHHhhhhcccCceeecccccCCCCCcccccccCceecCCcccccceee
Confidence 3678999999999999998 9999999999999999999999999999999987 9999999 78754
No 9
>KOG1841|consensus
Probab=99.17 E-value=1.1e-11 Score=122.01 Aligned_cols=64 Identities=41% Similarity=0.831 Sum_probs=58.1
Q ss_pred CCCCCccccCCCCCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccch
Q psy8222 50 ATHAAVWIPDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTC 114 (198)
Q Consensus 50 ~~~~~~Wv~d~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C 114 (198)
....|.|+||.++..||.|.. .|++++||||||.||+|+|+.|+..++.+........|||..|
T Consensus 545 gkkqP~wvpdse~pncm~clq-kft~ikrrhhcRacgkVlcgvccnek~~leyl~e~~~rv~nV~ 608 (1287)
T KOG1841|consen 545 GKKQPSWVPDSEAPNCMDCLQ-KFTPIKRRHHCRACGKVLCGVCCNEKSALEYLSESEGRVSNVD 608 (1287)
T ss_pred CCCCCccCccccCchHHHHHh-hcccccccccchhccceeehhhcchhhhhhhcCcccccccccc
Confidence 345789999999999999999 9999999999999999999999999998888777777888777
No 10
>KOG1842|consensus
Probab=99.14 E-value=9.4e-12 Score=113.10 Aligned_cols=71 Identities=37% Similarity=0.847 Sum_probs=56.9
Q ss_pred CCCCCccccCCCCCccccCCccCCCccccccccccCCceEeCCCCCCee----------e------cCC-------CCCC
Q psy8222 50 ATHAAVWIPDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRF----------L------LPS-------QSAK 106 (198)
Q Consensus 50 ~~~~~~Wv~d~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~----------~------lp~-------~~~~ 106 (198)
+.....|+.|..+..|..|.. +|++++||||||.||.|+|.+|+..-- . .|. ....
T Consensus 168 EqsvVpW~DDs~V~~CP~Ca~-~F~l~rRrHHCRLCG~VmC~~C~k~iSle~a~~ltsss~~dt~~e~~qq~~~lH~~~~ 246 (505)
T KOG1842|consen 168 EQSVVPWLDDSSVQFCPECAN-SFGLTRRRHHCRLCGRVMCRDCSKFISLEIAIGLTSSSASDTHFEPNQQKDDLHQHPQ 246 (505)
T ss_pred HhccccccCCCcccccccccc-hhhhHHHhhhhhhcchHHHHHHHHhcChHHHHHHhhccCCCCCcCcccCcccccCChh
Confidence 445678999999999999999 999999999999999999999987521 0 000 1225
Q ss_pred CeeeccchHHhhccc
Q psy8222 107 PLRVCLTCYDVLSRD 121 (198)
Q Consensus 107 ~~RVC~~C~~~l~~~ 121 (198)
+.|+|..|...|...
T Consensus 247 ~iRlC~hCl~~L~~R 261 (505)
T KOG1842|consen 247 PIRLCMHCLDNLFRR 261 (505)
T ss_pred HhHHHHHHHHHHHHH
Confidence 689999999887653
No 11
>cd01218 PH_phafin2 Phafin2 Pleckstrin Homology (PH) domain. Phafin2 Pleckstrin Homology (PH) domain. Phafin contains a PH domain and a FYVE domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=99.06 E-value=3.2e-10 Score=85.67 Aligned_cols=41 Identities=68% Similarity=1.107 Sum_probs=39.0
Q ss_pred CCcceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHHHHHH
Q psy8222 2 ELRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIEDLLR 42 (198)
Q Consensus 2 ~~~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~ 42 (198)
.++|+|+|.+++|||+|+|+|++||++||++|++||+++|.
T Consensus 63 ~~~n~f~I~~~~kSf~v~A~s~~eK~eWl~~i~~ai~~~l~ 103 (104)
T cd01218 63 IERNGWIIKTPTKSFAVYAATETEKREWMLHINKCVTDLLE 103 (104)
T ss_pred cccceEEEecCCeEEEEEcCCHHHHHHHHHHHHHHHHHHhc
Confidence 47899999999999999999999999999999999999875
No 12
>cd01220 PH_CDEP Chondrocyte-derived ezrin-like domain containing protein (CDEP) Pleckstrin homology (PH) domain. Chondrocyte-derived ezrin-like domain containing protein (CDEP) Pleckstrin homology (PH) domain. CDEP consists of a Ferm domain, a rhoGEF (DH) domain followed by two PH domains. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=98.82 E-value=7.2e-09 Score=77.51 Aligned_cols=37 Identities=27% Similarity=0.472 Sum_probs=35.5
Q ss_pred CCcceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHH
Q psy8222 2 ELRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIE 38 (198)
Q Consensus 2 ~~~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~ 38 (198)
.++|.|+|.+++|||.|+|+|++||++||++|++||+
T Consensus 62 ~~~~~F~I~~~~ks~~l~A~s~~Ek~~Wi~~i~~aI~ 98 (99)
T cd01220 62 GVPHCFTIFGGQCAITVAASTRAEKEKWLADLSKAIA 98 (99)
T ss_pred CCceeEEEEcCCeEEEEECCCHHHHHHHHHHHHHHhh
Confidence 4789999999999999999999999999999999986
No 13
>cd01219 PH_FGD FGD (faciogenital dysplasia protein) pleckstrin homology (PH) domain. FGD (faciogenital dysplasia protein) pleckstrin homology (PH) domain. FGD has a RhoGEF (DH) domain, followed by a PH domain, a FYVE domain and a C-terminal PH domain. FGD is a guanine nucleotide exchange factor that activates the Rho GTPase Cdc42. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=98.72 E-value=1.9e-08 Score=75.04 Aligned_cols=37 Identities=24% Similarity=0.507 Sum_probs=35.4
Q ss_pred CCcceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHH
Q psy8222 2 ELRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIE 38 (198)
Q Consensus 2 ~~~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~ 38 (198)
.++|+|.|.+++++|+|+|.|++||++||++|+.+|+
T Consensus 64 ~~~~~F~I~~~~rsf~l~A~s~eEk~~W~~ai~~~i~ 100 (101)
T cd01219 64 ERPHSFLVSGKQRCLELQARTQKEKNDWVQAIFSIID 100 (101)
T ss_pred CcCceEEEecCCcEEEEEcCCHHHHHHHHHHHHHHhh
Confidence 4789999999999999999999999999999999986
No 14
>KOG1843|consensus
Probab=98.54 E-value=4.1e-08 Score=88.96 Aligned_cols=69 Identities=20% Similarity=0.204 Sum_probs=59.5
Q ss_pred CCCCccccCCCCCccccCCccCCCcc-ccccccccCCceEeCCCCCCeeecCCC--CCCCeeeccchHHhhcc
Q psy8222 51 THAAVWIPDNEAAVCMHCKRTQFTVL-SRRHHCRKCGSVVCAPCSNKRFLLPSQ--SAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 51 ~~~~~Wv~d~~~~~C~~C~~~~Fs~~-~RrhhCr~CG~vvC~~Cs~~~~~lp~~--~~~~~RVC~~C~~~l~~ 120 (198)
-.+|.|.+++....||.|.. +|+.+ -||||||.|+.++|..|+..+..+|.. -..+.|||+.|+..+..
T Consensus 149 ~~ap~f~yskskglfagvSv-egsaI~erR~anR~~yg~~cra~~ilsg~vp~p~a~d~l~RVldS~~~nl~~ 220 (473)
T KOG1843|consen 149 GEAPVFLYSKSKGLFAGVSV-EGSAIIERREANRKFYGIFCRAKSILSGLVPVPFAADPLQRVLDSCAFNLES 220 (473)
T ss_pred CcCccccccccccceeeeec-ccceeeecchhhhhhcCccchhhhhhccCCCCCcccCCHHHHHhhHhhccCC
Confidence 34889999999999999999 99976 599999999999999999887555443 45899999999999843
No 15
>KOG1409|consensus
Probab=98.42 E-value=6.2e-08 Score=86.40 Aligned_cols=69 Identities=33% Similarity=0.816 Sum_probs=57.4
Q ss_pred CCCCccccCCCCCccccCCccCCCc-----------cccccccccCCceEeCCCCCCeeecCCCCC-CCeeeccchHHhh
Q psy8222 51 THAAVWIPDNEAAVCMHCKRTQFTV-----------LSRRHHCRKCGSVVCAPCSNKRFLLPSQSA-KPLRVCLTCYDVL 118 (198)
Q Consensus 51 ~~~~~Wv~d~~~~~C~~C~~~~Fs~-----------~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~-~~~RVC~~C~~~l 118 (198)
...|.|+. ...|..|.. +|.. -.|.||||.||..||..|+.++...|..|. -.+|+|+.||..+
T Consensus 274 ~etpewl~---s~~cQ~c~q-pffwn~~~m~~~k~~glr~h~crkcg~avc~~c~s~~~~~p~mg~e~~vR~~~~c~~~i 349 (404)
T KOG1409|consen 274 VETPEWLD---SDSCQKCNQ-PFFWNFRQMWDRKQLGLRQHHCRKCGKAVCGKCSSNRSSYPTMGFEFSVRVCDSCYPTI 349 (404)
T ss_pred ecCccccc---cchhhhhCc-hHHHHHHHHHhhhhhhhhhhhhhhhhhhcCcccccCccccccccceeEEEEecccchhh
Confidence 34688985 568999998 7743 136799999999999999999999998877 7899999999998
Q ss_pred ccccc
Q psy8222 119 SRDKT 123 (198)
Q Consensus 119 ~~~~~ 123 (198)
....+
T Consensus 350 ~~~~~ 354 (404)
T KOG1409|consen 350 KDEER 354 (404)
T ss_pred hcCCC
Confidence 76544
No 16
>cd01226 PH_exo84 Exocyst complex 84-kDa subunit Pleckstrin Homology (PH) domain. Exocyst complex 84-kDa subunit Pleckstrin Homology (PH) domain. Exo84 is a subunit of the exocyt complex, which is important in intracellular trafficking. In metazoa, Exo84 has a PH domain towards its N-terminus. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=98.38 E-value=5.8e-07 Score=67.48 Aligned_cols=37 Identities=11% Similarity=0.200 Sum_probs=35.0
Q ss_pred CCcceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHH
Q psy8222 2 ELRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIE 38 (198)
Q Consensus 2 ~~~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~ 38 (198)
.++|+|.|.++.+||.++|+|+++|.+||++|++|++
T Consensus 63 ~~kNafki~t~~~s~i~qaes~~~K~eWl~~le~a~~ 99 (100)
T cd01226 63 NAKKVLKLLIFPESRIYQCESARIKTEWFEELEQAKR 99 (100)
T ss_pred CcCceEEEEeCCccEEEEeCCHHHHHHHHHHHHHHhc
Confidence 5799999999999999999999999999999999863
No 17
>cd01261 PH_SOS Son of Sevenless (SOS) Pleckstrin homology (PH) domain. Son of Sevenless (SOS) Pleckstrin homology (PH) domain. SOS is a Ras guanine nucleotide exchange factor. It has a RhoGEF (DbH) domain, a PH domain, and a RasGEF domain. The SOS PH domain can bind to inositol 1,4,5-triphosphate. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=98.37 E-value=5.8e-07 Score=68.80 Aligned_cols=37 Identities=27% Similarity=0.407 Sum_probs=33.9
Q ss_pred CCcceEEEecC-CeEEEEEeCChHHHHHHHHHHHHHHH
Q psy8222 2 ELRNGWLIQTS-SKSFAVHAATSTEKQEWMAHINKCIE 38 (198)
Q Consensus 2 ~~~n~f~i~t~-~KSf~v~A~s~~Ek~~Wi~~i~~~i~ 38 (198)
.++|+|+|.+. ++||+|+|.|++||++||++|..++.
T Consensus 73 ~~knaF~I~~~~~~s~~l~Akt~eeK~~Wm~~l~~~~~ 110 (112)
T cd01261 73 EYKNAFEIILKDGNSVIFSAKNAEEKNNWMAALISVQT 110 (112)
T ss_pred ccCceEEEEcCCCCEEEEEECCHHHHHHHHHHHHHHhc
Confidence 47999999985 79999999999999999999998875
No 18
>KOG1811|consensus
Probab=98.10 E-value=2e-07 Score=88.49 Aligned_cols=66 Identities=35% Similarity=0.766 Sum_probs=56.7
Q ss_pred CccccCC----CCCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCC-CCCeeeccchHHhhc
Q psy8222 54 AVWIPDN----EAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQS-AKPLRVCLTCYDVLS 119 (198)
Q Consensus 54 ~~Wv~d~----~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~-~~~~RVC~~C~~~l~ 119 (198)
.+|+||. .-..||.|.++.|..|+||||||.||..+|+.|...+......+ ..|.++|+.|+.+..
T Consensus 314 ~nfq~darrafs~a~~~a~~R~~~kd~~Rk~~~~g~Ga~e~aa~ea~kgiqEd~gse~~Adg~Dq~psvsi 384 (1141)
T KOG1811|consen 314 HNFQPDARRAFSEAICMACCREHFKDFNRKHHCRGCGALECAACEAKKGIQEDCGSENPADGCDQCPSVSI 384 (1141)
T ss_pred hhcChhhhhhhhhhHHHHHHHHHHHHHHHhhhccccchHHHhHHHHhhhhhhcccccCcccccccccchhh
Confidence 4789887 55679987776999999999999999999999999988777776 499999999997544
No 19
>cd01264 PH_melted Melted pleckstrin homology (PH) domain. Melted pleckstrin homology (PH) domain. The melted protein has a C-terminal PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=98.06 E-value=6.1e-06 Score=62.08 Aligned_cols=35 Identities=23% Similarity=0.513 Sum_probs=32.5
Q ss_pred CcceEEEecCCeEEEEEeCChHHHHHHHHHHHHHH
Q psy8222 3 LRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCI 37 (198)
Q Consensus 3 ~~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i 37 (198)
.+|.|.|.+|.|+|+|+|.|++|+++||++|+.|+
T Consensus 67 ~~~~Fei~tp~rt~~l~A~se~e~e~WI~~i~~a~ 101 (101)
T cd01264 67 LPKAFEIFTADKTYILKAKDEKNAEEWLQCLNIAV 101 (101)
T ss_pred cCcEEEEEcCCceEEEEeCCHHHHHHHHHHHHhhC
Confidence 46999999999999999999999999999998763
No 20
>cd01251 PH_centaurin_alpha Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha is a phophatidlyinositide binding protein consisting of an N-terminal ArfGAP domain and two PH domains. In response to growth factor activation, PI3K phosphorylates phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 1 is recruited to the plasma membrane following growth factor stimulation by specific binding of its PH domain to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 2 is constitutively bound to the plasma membrane since it binds phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate with equal affinity. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specifici
Probab=97.91 E-value=1.8e-05 Score=59.17 Aligned_cols=34 Identities=21% Similarity=0.502 Sum_probs=32.4
Q ss_pred ceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHH
Q psy8222 5 NGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIE 38 (198)
Q Consensus 5 n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~ 38 (198)
+.|.|.++.+.|.+.|.|++|+++||++|+.++.
T Consensus 68 ~~F~i~t~~Rty~l~a~s~~e~~~Wi~ai~~v~~ 101 (103)
T cd01251 68 YGVTLVTPERKFLFACETEQDRREWIAAFQNVLS 101 (103)
T ss_pred ceEEEEeCCeEEEEECCCHHHHHHHHHHHHHHhc
Confidence 4899999999999999999999999999999876
No 21
>cd01228 PH_BCR-related BCR (breakpoint cluster region)-related pleckstrin homology (PH) domain. BCR (breakpoint cluster region)-related pleckstrin homology (PH) domain. The BCR-related protein has a RhoGEF(DH) domain followed by a PH domain, a C2 domain and a RhoGAP domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinases, tyrosine kinases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=97.85 E-value=1.6e-05 Score=58.98 Aligned_cols=27 Identities=26% Similarity=0.497 Sum_probs=24.8
Q ss_pred ecCCeEEEEEeCChHHHHHHHHHHHHH
Q psy8222 10 QTSSKSFAVHAATSTEKQEWMAHINKC 36 (198)
Q Consensus 10 ~t~~KSf~v~A~s~~Ek~~Wi~~i~~~ 36 (198)
.++.|||.|+|+|..||.+||+||++.
T Consensus 67 ~~~~KSf~~~asS~~Er~eW~~hI~~~ 93 (96)
T cd01228 67 NKNGKSYTFLLSSDYERSEWRESIQKL 93 (96)
T ss_pred ccCCceEEEEecCHHHHHHHHHHHHHH
Confidence 468999999999999999999999864
No 22
>cd01265 PH_PARIS-1 PARIS-1 pleckstrin homology (PH) domain. PARIS-1 pleckstrin homology (PH) domain. PARIS-1 contains a PH domain and a TBC-type GTPase catalytic domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=97.71 E-value=5.8e-05 Score=55.57 Aligned_cols=33 Identities=12% Similarity=0.386 Sum_probs=31.3
Q ss_pred cceEEEecCCeEEEEEeCChHHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSSKSFAVHAATSTEKQEWMAHINKC 36 (198)
Q Consensus 4 ~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~ 36 (198)
+|.|.|.++++.|.+.|.|++|+++||++|+.+
T Consensus 61 ~~~F~i~t~~r~y~l~A~s~~e~~~Wi~al~~~ 93 (95)
T cd01265 61 KGRFEIHSNNEVIALKASSDKQMNYWLQALQSK 93 (95)
T ss_pred CCEEEEEcCCcEEEEECCCHHHHHHHHHHHHhh
Confidence 689999999999999999999999999999875
No 23
>cd01233 Unc104 Unc-104 pleckstrin homology (PH) domain. Unc-104 pleckstrin homology (PH) domain. Unc-104 is a kinesin-like protein containing an N-terminal kinesin catalytic domain, followed by a forkhead associated domain with a C-terminal PH domain. These proteins are responsible for the transport of membrane vesicles along microtubules. The mechanism involves the binding of the PH domain to phosphatidiylinositol (4,5) P2-containing liposomes.
Probab=97.61 E-value=0.00011 Score=54.53 Aligned_cols=35 Identities=17% Similarity=0.338 Sum_probs=32.1
Q ss_pred CcceEEEecCCeEEEEEeCChHHHHHHHHHHHHHH
Q psy8222 3 LRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCI 37 (198)
Q Consensus 3 ~~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i 37 (198)
-+|.|.|.++.++|.+.|.|++|+++||++|+..+
T Consensus 64 ~~~~F~I~t~~rt~~~~A~s~~e~~~Wi~ai~~~~ 98 (100)
T cd01233 64 GPNTFAVCTKHRGYLFQALSDKEMIDWLYALNPLY 98 (100)
T ss_pred CCcEEEEECCCCEEEEEcCCHHHHHHHHHHhhhhh
Confidence 36899999999999999999999999999997654
No 24
>cd01244 PH_RasGAP_CG9209 RAS_GTPase activating protein (GAP)_CG9209 pleckstrin homology (PH) domain. RAS_GTPase activating protein (GAP)_CG9209 pleckstrin homology (PH) domain. This protein consists of two C2 domains, followed by a RasGAP domain, a PH domain and a BTK domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=97.50 E-value=0.00014 Score=54.35 Aligned_cols=32 Identities=13% Similarity=0.305 Sum_probs=30.3
Q ss_pred cceEEEecCCeEEEEEeCChHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSSKSFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 4 ~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
+|.|+|.++.+.|+|.|.+++|+++||.+|++
T Consensus 66 ~~~fqivt~~r~~yi~a~s~~E~~~Wi~al~k 97 (98)
T cd01244 66 VDIITIVCEDDTMQLQFEAPVEATDWLNALEK 97 (98)
T ss_pred CceEEEEeCCCeEEEECCCHHHHHHHHHHHhc
Confidence 58999999999999999999999999999975
No 25
>cd01222 PH_clg Clg (common-site lymphoma/leukemia guanine nucleotide exchange factor) pleckstrin homology (PH) domain. Clg (common-site lymphoma/leukemia guanine nucleotide exchange factor) pleckstrin homology (PH) domain. Clg contains a RhoGEF (DH) domain and a PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=97.45 E-value=0.00027 Score=52.74 Aligned_cols=34 Identities=12% Similarity=0.289 Sum_probs=30.6
Q ss_pred cceEEEecCC---eEEEEEeCChHHHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSS---KSFAVHAATSTEKQEWMAHINKCI 37 (198)
Q Consensus 4 ~n~f~i~t~~---KSf~v~A~s~~Ek~~Wi~~i~~~i 37 (198)
+++|.|.+.. .++.++|.|.++|+.||++|+.+|
T Consensus 59 ~~~F~v~~~~~p~~~~~l~A~s~e~K~~W~~~i~~~i 95 (97)
T cd01222 59 PLCFRVIPFDDPKGALQLTARNREEKRIWTQQLKRAM 95 (97)
T ss_pred CcEEEEEecCCCceEEEEEecCHHHHHHHHHHHHHHh
Confidence 7899997654 699999999999999999999876
No 26
>cd01257 PH_IRS Insulin receptor substrate (IRS) pleckstrin homology (PH) domain. Insulin receptor substrate (IRS) pleckstrin homology (PH) domain. PH domains are only found in eukaryotes, and are often involved in targeting proteins to the plasma membrane via lipid binding. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes. The IRS PH domain targets IRS molecules to the plasma membrane, usually in response to insulin stimulation.
Probab=97.43 E-value=0.00024 Score=53.29 Aligned_cols=32 Identities=25% Similarity=0.393 Sum_probs=30.1
Q ss_pred cceEEEecCCeEEEEEeCChHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSSKSFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 4 ~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
+|.|.|.|+.++|.|.|.|++|+++|+++|.+
T Consensus 69 ~~~f~i~t~dr~f~l~aese~E~~~Wi~~i~~ 100 (101)
T cd01257 69 RHLIALYTRDEYFAVAAENEAEQDSWYQALLE 100 (101)
T ss_pred CeEEEEEeCCceEEEEeCCHHHHHHHHHHHhh
Confidence 58999999999999999999999999999864
No 27
>cd01236 PH_outspread Outspread Pleckstrin homology (PH) domain. Outspread Pleckstrin homology (PH) domain. Outspread contains two PH domains and a C-terminal coiled-coil region. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=97.41 E-value=0.00026 Score=53.45 Aligned_cols=31 Identities=23% Similarity=0.276 Sum_probs=29.4
Q ss_pred cceEEEecCCeEEEEEeCChHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSSKSFAVHAATSTEKQEWMAHIN 34 (198)
Q Consensus 4 ~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~ 34 (198)
+|.|.|.++.+.|+|.|.|++|+++||..|.
T Consensus 71 ~~~f~I~tp~R~f~l~Aete~E~~~Wi~~l~ 101 (104)
T cd01236 71 KFSICILTPDKEHFIKAETKEEISWWLNMLM 101 (104)
T ss_pred ccEEEEECCCceEEEEeCCHHHHHHHHHHHH
Confidence 4799999999999999999999999999986
No 28
>cd01235 PH_SETbf Set binding factor Pleckstrin Homology (PH) domain. Set binding factor Pleckstrin Homology (PH) domain. Set binding factor is a myotubularin-related pseudo-phosphatase consisting of a Denn domain, a Gram domain, an inactive phosphatase domain, a SID motif and a C-terminal PH domain. Its PH domain is predicted to bind lipids based upon its ability to respond to phosphatidylinositol 3-kinase .
Probab=97.33 E-value=0.00032 Score=51.16 Aligned_cols=33 Identities=27% Similarity=0.547 Sum_probs=30.2
Q ss_pred ceEEEecCCeEEEEEeCChHHHHHHHHHHHHHH
Q psy8222 5 NGWLIQTSSKSFAVHAATSTEKQEWMAHINKCI 37 (198)
Q Consensus 5 n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i 37 (198)
+.|.|.++.+.|.|+|.+++|+++||.+|+.+|
T Consensus 69 ~~f~i~t~~r~~~~~a~s~~e~~~Wi~ai~~~i 101 (101)
T cd01235 69 GFFDLKTSKRTYNFLAENINEAQRWKEKIQQCI 101 (101)
T ss_pred eEEEEEeCCceEEEECCCHHHHHHHHHHHHhhC
Confidence 458888999999999999999999999998875
No 29
>PF00169 PH: PH domain; InterPro: IPR001849 The pleckstrin homology (PH) domain is a domain of about 100 residues that occurs in a wide range of proteins involved in intracellular signalling or as constituents of the cytoskeleton [, , , , , , ]. The pleckstrin homology domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids. The 3D structure of several PH domains has been determined []. All known cases have a common structure consisting of two perpendicular anti-parallel beta sheets, followed by a C-terminal amphipathic helix. The loops connecting the beta-strands differ greatly in length, making the PH domain relatively difficult to detect. There are no totally invariant residues within the PH domain. Proteins reported to contain one more PH domains belong to the following families: Pleckstrin, the protein where this domain was first detected, is the major substrate of protein kinase C in platelets. Pleckstrin is one of the rare proteins to contains two PH domains. Ser/Thr protein kinases such as the Akt/Rac family, the beta-adrenergic receptor kinases, the mu isoform of PKC and the trypanosomal NrkA family. Tyrosine protein kinases belonging to the Btk/Itk/Tec subfamily. Insulin Receptor Substrate 1 (IRS-1). Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and Saccharomyces cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr. Cytoskeletal proteins such as dynamin (see IPR001401 from INTERPRO), Caenorhabditis elegans kinesin-like protein unc-104 (see IPR001752 from INTERPRO), spectrin beta-chain, syntrophin (2 PH domains) and S. cerevisiae nuclear migration protein NUM1. Mammalian phosphatidylinositol-specific phospholipase C (PI-PLC) (see IPR000909 from INTERPRO) isoforms gamma and delta. Isoform gamma contains two PH domains, the second one is split into two parts separated by about 400 residues. Oxysterol binding proteins OSBP, S. cerevisiae OSH1 and YHR073w. Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac. Several S. cerevisiae proteins involved in cell cycle regulation and bud formation like BEM2, BEM3, BUD4 and the BEM1-binding proteins BOI2 (BEB1) and BOI1 (BOB1). C. elegans protein MIG-10. C. elegans hypothetical proteins C04D8.1, K06H7.4 and ZK632.12. S. cerevisiae hypothetical proteins YBR129c and YHR155w. ; GO: 0005515 protein binding; PDB: 1DYN_B 2DYN_B 3SNH_A 3ZYS_C 1X05_A 2I5F_A 1ZM0_B 1XX0_A 2I5C_C 3A8P_D ....
Probab=97.28 E-value=0.00073 Score=47.72 Aligned_cols=36 Identities=28% Similarity=0.531 Sum_probs=33.2
Q ss_pred CCcceEEEecCCe-EEEEEeCChHHHHHHHHHHHHHH
Q psy8222 2 ELRNGWLIQTSSK-SFAVHAATSTEKQEWMAHINKCI 37 (198)
Q Consensus 2 ~~~n~f~i~t~~K-Sf~v~A~s~~Ek~~Wi~~i~~~i 37 (198)
..+|.|.|.++.. +|.|.|.|+++++.|+++|+.++
T Consensus 67 ~~~~~f~i~~~~~~~~~~~~~s~~~~~~W~~~i~~~~ 103 (104)
T PF00169_consen 67 KRKNCFEITTPNGKSYLFSAESEEERKRWIQAIQKAI 103 (104)
T ss_dssp SSSSEEEEEETTSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred CCCcEEEEEeCCCcEEEEEcCCHHHHHHHHHHHHHHh
Confidence 4679999999996 99999999999999999999886
No 30
>cd01238 PH_Tec Tec pleckstrin homology (PH) domain. Tec pleckstrin homology (PH) domain. Proteins in the Tec family of cytoplasmic protein tyrosine kinases that includes Bruton's tyrosine kinase (BTK), BMX, IL2-inducible T-cell kinase (Itk) and Tec. These proteins generally have an N-terminal PH domain, followed by a Tek homology (TH) domain, a SH3 domain, a SH2 domain and a kinase domain. Tec PH domains tether these proteins to membranes following the activation of PI3K and its subsequent phosphorylation of phosphoinositides. The importance of PH domain membrane anchoring is confirmed by the discovery of a mutation of a critical arginine residue in the BTK PH domain, which causes X-linked agammaglobulinemia (XLA) in humans and a related disorder is mice. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few dis
Probab=97.27 E-value=0.0004 Score=52.11 Aligned_cols=32 Identities=13% Similarity=0.365 Sum_probs=30.0
Q ss_pred cceEEEecCCeEEEEEeCChHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSSKSFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 4 ~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
++.|.|.++.+.|++.|.+++|+++||++|+.
T Consensus 74 ~~~F~i~t~~r~~yl~A~s~~er~~WI~ai~~ 105 (106)
T cd01238 74 KYPFQVVHDEGTLYVFAPTEELRKRWIKALKQ 105 (106)
T ss_pred CccEEEEeCCCeEEEEcCCHHHHHHHHHHHHh
Confidence 67899999999999999999999999999975
No 31
>cd01246 PH_oxysterol_bp Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=97.22 E-value=0.00051 Score=48.59 Aligned_cols=33 Identities=21% Similarity=0.478 Sum_probs=30.6
Q ss_pred cceEEEecCC-eEEEEEeCChHHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSS-KSFAVHAATSTEKQEWMAHINKC 36 (198)
Q Consensus 4 ~n~f~i~t~~-KSf~v~A~s~~Ek~~Wi~~i~~~ 36 (198)
+|.|.|.+++ +.|.+.|.+.+|+.+||.+|+.|
T Consensus 58 ~~~F~i~~~~~~~~~~~a~s~~e~~~Wi~al~~a 91 (91)
T cd01246 58 DKCFTIDTGGDKTLHLRANSEEERQRWVDALELA 91 (91)
T ss_pred CcEEEEEcCCCCEEEEECCCHHHHHHHHHHHHhC
Confidence 6899999998 99999999999999999999764
No 32
>KOG0230|consensus
Probab=97.19 E-value=0.00041 Score=71.46 Aligned_cols=54 Identities=35% Similarity=0.905 Sum_probs=41.7
Q ss_pred CCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhcccccCCC
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSRDKTVSG 126 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~~~~~~~ 126 (198)
...|..|. +.++|+|||+.||++||+.|... .....|||..|+...........
T Consensus 5 ~~~~~~~~----t~~~~~~~~~~~g~~~~~~~~~~-------~~~~i~~~~~~~~~~~~~~~~~~ 58 (1598)
T KOG0230|consen 5 SNVCYDCD----TSVNRRHHCRVCGRVFCSKCQDS-------PETSIRVCNECRGQWEQGNVAPS 58 (1598)
T ss_pred ccchhccc----cccccCCCCcccCceeccccCCC-------CccceeehhhhhhhccccCCCCc
Confidence 45566666 57899999999999999999832 22489999999998776554443
No 33
>cd01260 PH_CNK Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. CNK is believed to regulate the activity and the subcellular localization of RAS activated RAF. CNK is composed of N-terminal SAM and PDZ domains along with a central or C-terminal PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskelet
Probab=97.19 E-value=0.00052 Score=49.93 Aligned_cols=33 Identities=21% Similarity=0.405 Sum_probs=30.5
Q ss_pred cceEEEecCC-eEEEEEeCChHHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSS-KSFAVHAATSTEKQEWMAHINKC 36 (198)
Q Consensus 4 ~n~f~i~t~~-KSf~v~A~s~~Ek~~Wi~~i~~~ 36 (198)
+|.|.|.++. +.|.|.|.+++|.++||.+|+.|
T Consensus 63 ~~~F~I~~~~~~~~~f~a~s~~e~~~Wi~ai~~~ 96 (96)
T cd01260 63 KYAFKVCHPVYKSFYFAAETLDDLSQWVNHLITA 96 (96)
T ss_pred ceEEEECCCCCcEEEEEeCCHHHHHHHHHHHHhC
Confidence 5789999999 99999999999999999999764
No 34
>cd01247 PH_GPBP Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. The GPBP protein is a kinase that phosphorylates an N-terminal region of the alpha 3 chain of type IV collagen , which is commonly known as the goodpasture antigen. It has has an N-terminal PH domain and a C-terminal START domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cyt
Probab=97.18 E-value=0.00077 Score=49.36 Aligned_cols=32 Identities=19% Similarity=0.360 Sum_probs=28.6
Q ss_pred cceEEEecCC-eEEEEEeCChHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSS-KSFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 4 ~n~f~i~t~~-KSf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
++.|.|.++. +.|.|.|.+++|+++||++|+.
T Consensus 58 ~~~F~i~~~~~r~~~L~A~s~~e~~~Wi~al~~ 90 (91)
T cd01247 58 ENRFDISVNENVVWYLRAENSQSRLLWMDSVVR 90 (91)
T ss_pred CCEEEEEeCCCeEEEEEeCCHHHHHHHHHHHhh
Confidence 4789997666 9999999999999999999974
No 35
>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=97.07 E-value=0.0004 Score=53.25 Aligned_cols=52 Identities=25% Similarity=0.652 Sum_probs=41.5
Q ss_pred CCCccccCCccCCCcc-ccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhc
Q psy8222 61 EAAVCMHCKRTQFTVL-SRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLS 119 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~-~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~ 119 (198)
....|..|.+ +|+++ ++.+.|..|++.||..|... ....+.-+|..|+....
T Consensus 53 ~~~~C~~C~~-~fg~l~~~~~~C~~C~~~VC~~C~~~------~~~~~~WlC~vC~k~re 105 (118)
T PF02318_consen 53 GERHCARCGK-PFGFLFNRGRVCVDCKHRVCKKCGVY------SKKEPIWLCKVCQKQRE 105 (118)
T ss_dssp CCSB-TTTS--BCSCTSTTCEEETTTTEEEETTSEEE------TSSSCCEEEHHHHHHHH
T ss_pred CCcchhhhCC-cccccCCCCCcCCcCCccccCccCCc------CCCCCCEEChhhHHHHH
Confidence 3468999999 99988 58999999999999999765 23478899999997543
No 36
>cd01266 PH_Gab Gab (Grb2-associated binder) pleckstrin homology (PH) domain. Gab (Grb2-associated binder) pleckstrin homology (PH) domain. The Gab subfamily includes several Gab proteins, Drosophila DOS and C. elegans SOC-1. They are scaffolding adaptor proteins, which possess N-terminal PH domains and a C-terminus with proline-rich regions and multiple phosphorylation sites. Following activation of growth factor receptors, Gab proteins are tyrosine phosphorylated and activate PI3K, which generates 3-phosphoinositide lipids. By binding to these lipids via the PH domain, Gab proteins remain in proximity to the receptor, leading to further signaling. While not all Gab proteins depend on the PH domain for recruitment, it is required for Gab activity. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display str
Probab=97.05 E-value=0.0011 Score=49.70 Aligned_cols=32 Identities=25% Similarity=0.351 Sum_probs=29.2
Q ss_pred cceEEEecCCeEEEEEeCChHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSSKSFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 4 ~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
...|.|.++.++|.|.|.|++|+++||.+|.+
T Consensus 75 ~~~f~i~t~~r~y~l~A~s~ee~~~Wi~~I~~ 106 (108)
T cd01266 75 GYGFDIETIVRDLYLVAKNEEEMTLWVNCICK 106 (108)
T ss_pred ceEEEEEeCCccEEEEECCHHHHHHHHHHHHh
Confidence 34699999999999999999999999999965
No 37
>cd01250 PH_centaurin Centaurin Pleckstrin homology (PH) domain. Centaurin Pleckstrin homology (PH) domain. Centaurin beta and gamma consist of a PH domain, an ArfGAP domain and three ankyrin repeats. Centaurain gamma also has an N-terminal Ras homology domain. Centaurin alpha has a different domain architecture and its PH domain is in a different subfamily. Centaurin can bind to phosphatidlyinositol (3,4,5)P3. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=96.99 E-value=0.001 Score=47.30 Aligned_cols=32 Identities=19% Similarity=0.525 Sum_probs=30.1
Q ss_pred cceEEEecCCeEEEEEeCChHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSSKSFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 4 ~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
++.|.|.++.+.|.|.|.+.++.++|+.+|+.
T Consensus 62 ~~~f~i~~~~~~~~f~a~s~~~~~~Wi~al~~ 93 (94)
T cd01250 62 RFCFEVISPTKTWHFQADSEEERDDWISAIQE 93 (94)
T ss_pred ceEEEEEcCCcEEEEECCCHHHHHHHHHHHhc
Confidence 67899999999999999999999999999975
No 38
>cd01223 PH_Vav Vav pleckstrin homology (PH) domain. Vav pleckstrin homology (PH) domain. Vav acts as a guanosine nucleotide exchange factor(GEF) for Rho/Rac proteins. Mammalian Vav proteins consist of a calponin homology (CH) domain, an acidic region, a rho-GEF (DH)domain, a PH domain, a Zinc finger region and an SH2 domain, flanked by two SH3 domains. In invertebrates such as Drosophila and C.elegans, Vav is missing the N-terminal SH3 domain . PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=96.97 E-value=0.0012 Score=50.86 Aligned_cols=39 Identities=10% Similarity=0.415 Sum_probs=34.5
Q ss_pred CCcceEEEecCC--eEEEEEeCChHHHHHHHHHHHHHHHHH
Q psy8222 2 ELRNGWLIQTSS--KSFAVHAATSTEKQEWMAHINKCIEDL 40 (198)
Q Consensus 2 ~~~n~f~i~t~~--KSf~v~A~s~~Ek~~Wi~~i~~~i~~l 40 (198)
.++|+|.|...+ .+|.++|.|+++|+.||++|..|++.+
T Consensus 74 ~~~~~f~L~~~~~~~~~~f~~Ktee~K~kWm~al~~a~sni 114 (116)
T cd01223 74 RWKYGFYLAHKQGKTGFTFYFKTEHLRKKWLKALEMAMSNI 114 (116)
T ss_pred ceEEEEEEEecCCCccEEEEeCCHHHHHHHHHHHHHHHhcC
Confidence 478899998776 789999999999999999999998753
No 39
>cd01224 PH_Collybistin Collybistin pleckstrin homology (PH) domain. Collybistin pleckstrin homology (PH) domain. Collybistin is GEF which induces submembrane clustering of the receptor-associated peripheral membrane protein gephyrin. It consists of an SH3 domain, followed by a RhoGEF(dbH) and PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=96.95 E-value=0.0015 Score=49.83 Aligned_cols=33 Identities=15% Similarity=0.362 Sum_probs=29.7
Q ss_pred CcceEEEecCC--eEEEEEeCChHHHHHHHHHHHH
Q psy8222 3 LRNGWLIQTSS--KSFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 3 ~~n~f~i~t~~--KSf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
.+|+|.|...+ ++|.++|.|+++|..||++|..
T Consensus 71 ~knafkl~~~~~~~~~~f~~Kt~e~K~~Wm~a~~~ 105 (109)
T cd01224 71 IKNSLKIYSESTDEWYLFSFKSAERKHRWLSAFAL 105 (109)
T ss_pred eEEEEEEEEcCCCeEEEEEECCHHHHHHHHHHHHH
Confidence 58999999665 9999999999999999999864
No 40
>cd01232 PH_TRIO Trio pleckstrin homology (PH) domain. Trio pleckstrin homology (PH) domain. Trio is a multidomain signaling protein that contains two RhoGEF(DH)-PH domains in tandem. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=96.81 E-value=0.0025 Score=48.85 Aligned_cols=36 Identities=19% Similarity=0.357 Sum_probs=29.5
Q ss_pred CcceEEEecCC---eEEEEEeCChHHHHHHHHHHHHHHH
Q psy8222 3 LRNGWLIQTSS---KSFAVHAATSTEKQEWMAHINKCIE 38 (198)
Q Consensus 3 ~~n~f~i~t~~---KSf~v~A~s~~Ek~~Wi~~i~~~i~ 38 (198)
++.++.+.++. ++|.|+|+|.++|++|+.+|+++++
T Consensus 75 ~kF~i~~~~~~~~~~~~ilqA~s~e~K~~W~~~I~~il~ 113 (114)
T cd01232 75 CRFALWSGDPPISDNRIILKANSQETKQEWVKKIREILQ 113 (114)
T ss_pred ceEEEEeCCCCCCceEEEEECCCHHHHHHHHHHHHHHhh
Confidence 34455556665 8999999999999999999998765
No 41
>smart00233 PH Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
Probab=96.75 E-value=0.0038 Score=43.04 Aligned_cols=35 Identities=26% Similarity=0.567 Sum_probs=32.3
Q ss_pred CcceEEEecCCe-EEEEEeCChHHHHHHHHHHHHHH
Q psy8222 3 LRNGWLIQTSSK-SFAVHAATSTEKQEWMAHINKCI 37 (198)
Q Consensus 3 ~~n~f~i~t~~K-Sf~v~A~s~~Ek~~Wi~~i~~~i 37 (198)
..+.|.|..+++ .|.+.|.|++|+..|+.+|+.++
T Consensus 66 ~~~~f~l~~~~~~~~~f~~~s~~~~~~W~~~i~~~~ 101 (102)
T smart00233 66 KPHCFEIKTADRRSYLLQAESEEEREEWVDALRKAI 101 (102)
T ss_pred CceEEEEEecCCceEEEEcCCHHHHHHHHHHHHHhh
Confidence 578999998888 99999999999999999998775
No 42
>cd01245 PH_RasGAP_CG5898 RAS GTPase-activating protein (GAP) CG5898 Pleckstrin homology (PH) domain. RAS GTPase-activating protein (GAP) CG5898 Pleckstrin homology (PH) domain. This protein has a domain architecture of SH2-SH3-SH2-PH-C2-Ras_GAP. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=96.62 E-value=0.0027 Score=47.48 Aligned_cols=31 Identities=13% Similarity=0.363 Sum_probs=27.7
Q ss_pred cceEEEecCCe--EEEEEeCChHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSSK--SFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 4 ~n~f~i~t~~K--Sf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
+|-|+|.++.+ .|.+.|++ +|+++||+.|++
T Consensus 65 ~~cFel~~~~~~~~y~~~a~~-~er~~Wi~~l~~ 97 (98)
T cd01245 65 PNCFQIVERALPTVYYSCRSS-EERDKWIESLQA 97 (98)
T ss_pred CeEEEEecCCCCeEEEEeCCH-HHHHHHHHHHhc
Confidence 59999999987 88888888 999999999874
No 43
>cd00821 PH Pleckstrin homology (PH) domain. Pleckstrin homology (PH) domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=96.47 E-value=0.0053 Score=41.88 Aligned_cols=33 Identities=24% Similarity=0.596 Sum_probs=30.5
Q ss_pred CcceEEEecCC-eEEEEEeCChHHHHHHHHHHHH
Q psy8222 3 LRNGWLIQTSS-KSFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 3 ~~n~f~i~t~~-KSf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
.++.|.|.+.. +++.+.|.|.+|++.|+.+|+.
T Consensus 62 ~~~~f~i~~~~~~~~~~~~~s~~~~~~W~~~l~~ 95 (96)
T cd00821 62 RKNCFEIRTPDGRSYLLQAESEEEREEWIEALQS 95 (96)
T ss_pred CCcEEEEecCCCcEEEEEeCCHHHHHHHHHHHhc
Confidence 47899999888 9999999999999999999975
No 44
>cd01241 PH_Akt Akt pleckstrin homology (PH) domain. Akt pleckstrin homology (PH) domain. Akt (Protein Kinase B (PKB)) is a phosphatidylinositol 3'-kinase (PI3K)-dependent Ser/Thr kinase. The PH domain recruits Akt to the plasma membrane by binding to phosphoinositides (PtdIns-3,4-P2) and is required for activation. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=96.37 E-value=0.0052 Score=45.66 Aligned_cols=31 Identities=26% Similarity=0.675 Sum_probs=25.5
Q ss_pred cceEEEe------cCCeEEEEEeCChHHHHHHHHHHHHH
Q psy8222 4 RNGWLIQ------TSSKSFAVHAATSTEKQEWMAHINKC 36 (198)
Q Consensus 4 ~n~f~i~------t~~KSf~v~A~s~~Ek~~Wi~~i~~~ 36 (198)
+|.|.|. ++.+.| +|.|++|+++||++|+.+
T Consensus 65 ~~~F~i~~~~~~~~~~r~f--~a~s~ee~~eWi~ai~~v 101 (102)
T cd01241 65 PNTFIIRCLQWTTVIERTF--HVESPEEREEWIHAIQTV 101 (102)
T ss_pred cceEEEEeccCCcccCEEE--EeCCHHHHHHHHHHHHhh
Confidence 5789997 345666 589999999999999865
No 45
>cd01252 PH_cytohesin Cytohesin Pleckstrin homology (PH) domain. Cytohesin Pleckstrin homology (PH) domain. Cytohesin is an ARF-Guanine nucleotide Exchange Factor (GEF), which has a Sec7-type Arf-GEFdomain and a pleckstrin homology domain. It specifically binds phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4, 5)P3) via its PH domain and it acts as a PI 3-kinase effector mediating biological responses such as cell adhesion and membrane trafficking. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=96.21 E-value=0.011 Score=45.33 Aligned_cols=26 Identities=27% Similarity=0.552 Sum_probs=23.6
Q ss_pred eEEEEEeCChHHHHHHHHHHHHHHHH
Q psy8222 14 KSFAVHAATSTEKQEWMAHINKCIED 39 (198)
Q Consensus 14 KSf~v~A~s~~Ek~~Wi~~i~~~i~~ 39 (198)
+.|.|.|.+.+|+++||++|+.++..
T Consensus 90 ~~~~~~A~s~~e~~~Wi~al~~~~~~ 115 (125)
T cd01252 90 SVYRISAANDEEMDEWIKSIKASISP 115 (125)
T ss_pred eEEEEECCCHHHHHHHHHHHHHHHhc
Confidence 58889999999999999999998863
No 46
>KOG0230|consensus
Probab=96.07 E-value=0.0022 Score=66.32 Aligned_cols=34 Identities=38% Similarity=1.250 Sum_probs=33.0
Q ss_pred ccCCCCCccccCCccCCCccccccccccCCceEeCCC
Q psy8222 57 IPDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPC 93 (198)
Q Consensus 57 v~d~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~C 93 (198)
+||.....|..|.+ .|+-|+|+||| ||+++|..|
T Consensus 92 m~d~s~~ec~~~~~-~~~t~Rr~~~~--~gqi~~ss~ 125 (1598)
T KOG0230|consen 92 MPDSSSKECYDCEQ-KFETFRRKHHC--CGQIFCSSC 125 (1598)
T ss_pred CCccccchhhhhcc-chhhhhccccc--CccccCCcc
Confidence 78889999999999 99999999999 999999999
No 47
>KOG1841|consensus
Probab=95.99 E-value=0.011 Score=59.91 Aligned_cols=57 Identities=32% Similarity=0.438 Sum_probs=49.9
Q ss_pred CCCCccccCCCCCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhcc
Q psy8222 51 THAAVWIPDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 51 ~~~~~Wv~d~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~ 120 (198)
+.+++|++|+.+..|+.|.+ .|.+..++|||| |.++ +-+.+.+..|+|..|...+.+
T Consensus 646 e~ksVw~aDg~aPng~la~t-~~~~~~e~~hsr--~~ls----------~~~~s~~~~~~~n~t~s~~rn 702 (1287)
T KOG1841|consen 646 EVKSVWFADGIAPNGELAET-RFTFTGERHHSR--GKLS----------LLYSSRKEARPCNITHSVLRN 702 (1287)
T ss_pred eecceeccCCcCCCceeccc-ceeeeccccccc--cccc----------ccccccccCCCCcccCccchh
Confidence 56889999999999999998 999999999999 7776 344466889999999998776
No 48
>cd00900 PH-like Pleckstrin homology-like domain. Pleckstrin homology-like domain. This family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. The PH domain is commonly found in eukaryotic signaling proteins. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins.
Probab=95.75 E-value=0.018 Score=39.53 Aligned_cols=33 Identities=27% Similarity=0.481 Sum_probs=30.4
Q ss_pred CcceEEEecC---CeEEEEEeCChHHHHHHHHHHHH
Q psy8222 3 LRNGWLIQTS---SKSFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 3 ~~n~f~i~t~---~KSf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
.++.|.|... .+.+.+.|.+.+|++.|+.+|+.
T Consensus 63 ~~~~F~i~~~~~~~~~~~~~~~~~~~~~~W~~al~~ 98 (99)
T cd00900 63 DPNCFAIVTKDRGRRVFVFQADSEEEAQEWVEALQQ 98 (99)
T ss_pred CCceEEEECCCCCcEEEEEEcCCHHHHHHHHHHHhc
Confidence 4689999988 79999999999999999999975
No 49
>cd01253 PH_beta_spectrin Beta-spectrin pleckstrin homology (PH) domain. Beta-spectrin pleckstrin homology (PH) domain. Beta spectrin binds actin and functions as a major component of the cytoskeleton underlying cellular membranes. Beta spectrin consists of multiple spectrin repeats followed by a PH domain, which binds to Inositol-1,4,5-Trisphosphate. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. PH domains are often involved in targeting proteins to the plasma membrane via lipid binding. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=95.55 E-value=0.019 Score=42.21 Aligned_cols=32 Identities=13% Similarity=0.379 Sum_probs=28.2
Q ss_pred cceEEEecCC-eEEEEEeCChHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSS-KSFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 4 ~n~f~i~t~~-KSf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
+|.|.|.++. +.|.+.|.+.++..+|+.+|+.
T Consensus 71 ~~~F~l~~~~~~~~~f~a~s~e~~~~Wi~aL~~ 103 (104)
T cd01253 71 KHVFRLRLPDGAEFLFQAPDEEEMSSWVRALKS 103 (104)
T ss_pred ceEEEEEecCCCEEEEECCCHHHHHHHHHHHhc
Confidence 5889997555 9999999999999999999974
No 50
>cd01230 PH_EFA6 EFA6 Pleckstrin Homology (PH) domain. EFA6 Pleckstrin Homology (PH) domain. EFA6 is an guanine nucleotide exchange factor for ARF6, which is involved in membrane recycling. It consists of a SEC7 domain followed by a PH domain. The EFA6 PH domain regulates its association with the plasma membrane. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=95.40 E-value=0.037 Score=42.55 Aligned_cols=37 Identities=19% Similarity=0.385 Sum_probs=32.9
Q ss_pred CcceEEEecCC-eEEEEEeCChHHHHHHHHHHHHHHHH
Q psy8222 3 LRNGWLIQTSS-KSFAVHAATSTEKQEWMAHINKCIED 39 (198)
Q Consensus 3 ~~n~f~i~t~~-KSf~v~A~s~~Ek~~Wi~~i~~~i~~ 39 (198)
-+|.|.|.++. +.|.++|.+.+|.+.|+.+|+.+...
T Consensus 76 r~~VF~L~~~~g~~~lfqA~~~ee~~~Wi~~I~~~~~~ 113 (117)
T cd01230 76 KPHVFRLRTADWREFLFQTSSLKELQSWIERINVVAAA 113 (117)
T ss_pred CCcEEEEEcCCCCEEEEECCCHHHHHHHHHHHHHHHHh
Confidence 36899999986 99999999999999999999987653
No 51
>cd01225 PH_Cool_Pix Cool (cloned out of library)/Pix (PAK-interactive exchange factor) pleckstrin homology (PH) domain. Cool (cloned out of library)/Pix (PAK-interactive exchange factor) pleckstrin homology (PH) domain. Cool/Pix contains an N-terminal SH3 domain followed by a RhoGEF (DH) and PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=94.51 E-value=0.068 Score=40.88 Aligned_cols=34 Identities=24% Similarity=0.439 Sum_probs=30.7
Q ss_pred CcceEEEecCC-eEEEEEeCChHHHHHHHHHHHHH
Q psy8222 3 LRNGWLIQTSS-KSFAVHAATSTEKQEWMAHINKC 36 (198)
Q Consensus 3 ~~n~f~i~t~~-KSf~v~A~s~~Ek~~Wi~~i~~~ 36 (198)
-+|+|+|.++- -...|++++.+|.++|+.++++.
T Consensus 74 ~~~aFeI~G~li~~i~v~C~~~~e~~~Wl~hL~~~ 108 (111)
T cd01225 74 LKNAFEISGPLIERIVVVCNNPQDAQEWVELLNAN 108 (111)
T ss_pred ccceEEEeccCcCcEEEEeCCHHHHHHHHHHHHhh
Confidence 36999999888 88999999999999999999864
No 52
>cd01249 PH_oligophrenin Oligophrenin Pleckstrin homology (PH) domain. Oligophrenin Pleckstrin homology (PH) domain. Oligophrenin is composed of a PH domain, a rhoGAP domain and a proline rich region. Closely related proteins have a C-terminal SH3 domain. PH domains a share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=94.14 E-value=0.068 Score=40.45 Aligned_cols=30 Identities=10% Similarity=0.379 Sum_probs=26.7
Q ss_pred ceEEEecCCe--EEEEEeCChHHHHHHHHHHH
Q psy8222 5 NGWLIQTSSK--SFAVHAATSTEKQEWMAHIN 34 (198)
Q Consensus 5 n~f~i~t~~K--Sf~v~A~s~~Ek~~Wi~~i~ 34 (198)
.=|.|.++.+ ++.|+|.|+.++.+||++|.
T Consensus 71 FCFei~~~~~~~~~~lQA~Se~~~~~Wi~A~d 102 (104)
T cd01249 71 FCFDVEVEEKPGVITMQALSEKDRRLWIEAMD 102 (104)
T ss_pred eeEeeeecCCCCeEEEEecCHHHHHHHHHhhc
Confidence 4588988887 99999999999999999985
No 53
>KOG1729|consensus
Probab=92.76 E-value=0.022 Score=50.26 Aligned_cols=64 Identities=28% Similarity=0.479 Sum_probs=49.1
Q ss_pred CCccccCCCCCccccCCccCCCccccccccccCCceEeCCCCCCe----eecCCC---CCCCeeeccchHHh
Q psy8222 53 AAVWIPDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKR----FLLPSQ---SAKPLRVCLTCYDV 117 (198)
Q Consensus 53 ~~~Wv~d~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~----~~lp~~---~~~~~RVC~~C~~~ 117 (198)
.+.|+-+.++..|..|.. .|.+..|+|||+.||+|+|..|+..+ .+-+.. -......|..|+..
T Consensus 11 ~~~~~~~~e~~s~~~~~~-e~~~~~r~~~~~~~grv~~~q~~~~k~~rk~~q~r~~~l~~D~~~~~~~~~~~ 81 (288)
T KOG1729|consen 11 MVDWQANSEANSCRNCKV-EFCFGRRGHPCRECGRVLCRQGTLVKRCRKKLQSRSFFLFNDILVYGNIVSDN 81 (288)
T ss_pred hHHHHHhccchhhhhhcc-cchhhhccCcccccchhhhhhhhhHHHHhcccccccccccccchhhcccccCH
Confidence 456888889999999998 99999999999999999999998721 111111 12566777777765
No 54
>KOG0690|consensus
Probab=91.90 E-value=0.28 Score=44.80 Aligned_cols=40 Identities=20% Similarity=0.364 Sum_probs=31.1
Q ss_pred cceEEEecCC----eEEEEEeCChHHHHHHHHHHHHHHHHHHHh
Q psy8222 4 RNGWLIQTSS----KSFAVHAATSTEKQEWMAHINKCIEDLLRK 43 (198)
Q Consensus 4 ~n~f~i~t~~----KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~~ 43 (198)
||.|.|+--+ -.-.+++.|++||++|+.+|+..-+.+.+.
T Consensus 79 PntFiiRcLQWTTVIERTF~ves~~eRq~W~~AIq~vsn~l~q~ 122 (516)
T KOG0690|consen 79 PNTFIIRCLQWTTVIERTFYVESAEERQEWIEAIQAVSNRLKQE 122 (516)
T ss_pred CceEEEEeeeeeeeeeeeeecCCHHHHHHHHHHHHHHhhhhhhh
Confidence 7999999544 233467899999999999999877766543
No 55
>KOG0521|consensus
Probab=91.68 E-value=0.28 Score=48.96 Aligned_cols=39 Identities=23% Similarity=0.462 Sum_probs=35.9
Q ss_pred cceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIEDLLR 42 (198)
Q Consensus 4 ~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~ 42 (198)
+--|+|.+++|++.++|.+..+..+||..|++.|..++.
T Consensus 335 r~CF~iiS~tks~~lQAes~~d~~~Wi~~i~nsi~s~l~ 373 (785)
T KOG0521|consen 335 RFCFEIISPTKSYLLQAESEKDCQDWISALQNSILSALN 373 (785)
T ss_pred eeeEEEecCCcceEEecCchhHHHHHHHHHHHHHHHHHh
Confidence 456999999999999999999999999999999988765
No 56
>cd01237 Unc112 Unc-112 pleckstrin homology (PH) domain. Unc-112 pleckstrin homology (PH) domain. Unc-112 and related proteins contain two FERM domains with a PH domain between them. Both the PH and FERM domains have a PH-like fold. The FERM domains are likely responsible for the role of Unc-112 in organizing beta-integrin. The specific role of the Unc-112 PH domain is not known, but it is predicted to be involved in mediating membrane interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=91.39 E-value=0.46 Score=36.08 Aligned_cols=33 Identities=9% Similarity=0.164 Sum_probs=27.8
Q ss_pred cceEEEecCC----eEEEEEeCChHHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSS----KSFAVHAATSTEKQEWMAHINKC 36 (198)
Q Consensus 4 ~n~f~i~t~~----KSf~v~A~s~~Ek~~Wi~~i~~~ 36 (198)
.+.|.|.+|. +.|.|.|.|+++.+.||++.+-|
T Consensus 66 kf~I~l~~ps~~~~r~y~l~cdsEeqya~Wmaa~rla 102 (106)
T cd01237 66 KFHIKLLIPTAEGMNEVWLRCDNEKQYAKWMAACRLA 102 (106)
T ss_pred ceEEEEecCCccCCeEEEEECCCHHHHHHHHHHHHHh
Confidence 3566666887 99999999999999999998654
No 57
>cd01227 PH_Dbs Dbs (DBL's big sister) pleckstrin homology (PH) domain. Dbs (DBL's big sister) pleckstrin homology (PH) domain. Dbs is a guanine nucleotide exchange factor (GEF), which contains spectrin repeats, a rhoGEF (DH) domain and a PH domain. The Dbs PH domain participates in binding to both the Cdc42 and RhoA GTPases. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=91.34 E-value=0.7 Score=36.39 Aligned_cols=36 Identities=22% Similarity=0.408 Sum_probs=28.5
Q ss_pred eEEEe--cCCeEEEEEeCChHHHHHHHHHHHHHHHHHH
Q psy8222 6 GWLIQ--TSSKSFAVHAATSTEKQEWMAHINKCIEDLL 41 (198)
Q Consensus 6 ~f~i~--t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll 41 (198)
.|.|- .....|.|+|.|.+.|+.|+..|.+.+...+
T Consensus 82 kFeiw~~~~~~~yilqA~t~e~K~~Wv~~I~~iL~~Q~ 119 (133)
T cd01227 82 KFEIWYNAREEVYILQAPTPEIKAAWVNEIRKVLTSQL 119 (133)
T ss_pred EEEEEeCCCCcEEEEEcCCHHHHHHHHHHHHHHHHHHH
Confidence 45444 3346899999999999999999998887643
No 58
>KOG0705|consensus
Probab=90.24 E-value=0.32 Score=46.86 Aligned_cols=37 Identities=22% Similarity=0.391 Sum_probs=29.0
Q ss_pred eEEEec-CCeEEEEEeCChHHHHHHHHHHHHHHHHHHH
Q psy8222 6 GWLIQT-SSKSFAVHAATSTEKQEWMAHINKCIEDLLR 42 (198)
Q Consensus 6 ~f~i~t-~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~ 42 (198)
-|+|.+ ......+.|.+.|||++|+++|+..|..-|+
T Consensus 447 ~F~IVs~tgqtWhFeAtt~EERdaWvQai~sqIlaSlq 484 (749)
T KOG0705|consen 447 CFEIVSNTGQTWHFEATTYEERDAWVQAIQSQILASLQ 484 (749)
T ss_pred eEEEeccccchhhhhhcchhhHHHHHHHHHHHHHHHHh
Confidence 455553 3467778899999999999999998876544
No 59
>KOG1117|consensus
Probab=89.96 E-value=0.18 Score=50.39 Aligned_cols=99 Identities=20% Similarity=0.398 Sum_probs=65.0
Q ss_pred ceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCccccCCCCCccccCCccCCCcccccccccc
Q psy8222 5 NGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIEDLLRKSGKKPAATHAAVWIPDNEAAVCMHCKRTQFTVLSRRHHCRK 84 (198)
Q Consensus 5 n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~~~g~~~~~~~~~~Wv~d~~~~~C~~C~~~~Fs~~~RrhhCr~ 84 (198)
-.|.|.||-++|.++|.+..||+.|+.+++.+|...|.. -...-..|.... ...|..|+. +=-= ----+
T Consensus 247 ~sfdl~Tp~r~fsftaese~erq~w~ea~q~siAeTlSd-----~evaeriW~ne~-nr~cadC~s-srPd----wasiN 315 (1186)
T KOG1117|consen 247 RSFDLNTPYREFSFTAESETERQIWGEAPQPSIAETLSD-----YEVAERIWLNEE-NRECADCGS-SRPD----WASIN 315 (1186)
T ss_pred ceeccCCceeeeeeeeccchhhhhhhhccCcccccccCh-----HHHHHHHHhccc-cccccccCC-CCCc----ccccc
Confidence 478999999999999999999999999999887654321 111224576532 347899987 3210 01113
Q ss_pred CCceEeCCCCCCeeecCCC-CC-CCeeeccch
Q psy8222 85 CGSVVCAPCSNKRFLLPSQ-SA-KPLRVCLTC 114 (198)
Q Consensus 85 CG~vvC~~Cs~~~~~lp~~-~~-~~~RVC~~C 114 (198)
=+-|+|..|....-.++.. +. ++...|..=
T Consensus 316 L~vvIck~caGqhrslgs~dSkvrslkmd~sv 347 (1186)
T KOG1117|consen 316 LCVVICKPCAGQHRSLGSGDSKVRSLKMDPSV 347 (1186)
T ss_pred cceEEcccCCCccccCCCccccccccccCccc
Confidence 3578999998876554442 22 555555543
No 60
>cd01231 PH_Lnk LNK-family Pleckstrin homology (PH) domain. LNK-family Pleckstrin homology (PH) domain. The Lnk family of proteins consists of Lnk, APS and SH2B. They are adaptor proteins consisting of a PH domain and an SH2 domain, which mediates signaling through growth factor receptors. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. The lnk family PH domain is likely involved in targeting of the adaptor proteins to the plasma membrane.
Probab=87.59 E-value=0.91 Score=34.33 Aligned_cols=33 Identities=9% Similarity=0.418 Sum_probs=28.2
Q ss_pred cceEEEec-CCeEEEEEeCChHHHHHHHHHHHHH
Q psy8222 4 RNGWLIQT-SSKSFAVHAATSTEKQEWMAHINKC 36 (198)
Q Consensus 4 ~n~f~i~t-~~KSf~v~A~s~~Ek~~Wi~~i~~~ 36 (198)
.|+|.|.. .+-.|.+.|.++++.+.|+..|+.|
T Consensus 74 ~nTFvLK~~~~~eyI~Ea~d~~q~~SWla~Ir~C 107 (107)
T cd01231 74 LYTFVLKVDDNTDIIFEVGDEQQLNSWLAELRYC 107 (107)
T ss_pred ccEEEEEecCCceEEEEcCCHHHHHHHHHHHhcC
Confidence 58999995 3468889999999999999999764
No 61
>cd01242 PH_ROK Rok (Rho- associated kinase) pleckstrin homology (PH) domain. Rok (Rho- associated kinase) pleckstrin homology (PH) domain. Rok is a serine/threonine kinase that binds GTP-rho. It consists of a kinase domain, a coiled coil region and a PH domain. The Rok PH domain is interrupted by a C1 domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=86.87 E-value=1.4 Score=33.72 Aligned_cols=36 Identities=19% Similarity=0.408 Sum_probs=29.4
Q ss_pred CCcceEEEecCC--eEEEEEeCChHHHHHHHHHHHHHH
Q psy8222 2 ELRNGWLIQTSS--KSFAVHAATSTEKQEWMAHINKCI 37 (198)
Q Consensus 2 ~~~n~f~i~t~~--KSf~v~A~s~~Ek~~Wi~~i~~~i 37 (198)
++|-=|.|.... ++..+.|.+..||+.|+.++.+-|
T Consensus 73 DiP~IF~I~~~~~~~~lllLA~s~~ek~kWV~~L~~~~ 110 (112)
T cd01242 73 EIPKIFQILYANEARDLLLLAPQTDEQNKWVSRLVKKI 110 (112)
T ss_pred cCCeEEEEEeCCccceEEEEeCCchHHHHHHHHHHHhc
Confidence 355667887555 899999999999999999987655
No 62
>KOG0932|consensus
Probab=86.77 E-value=0.94 Score=43.67 Aligned_cols=35 Identities=23% Similarity=0.452 Sum_probs=31.2
Q ss_pred cceEEEecCC-eEEEEEeCChHHHHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSS-KSFAVHAATSTEKQEWMAHINKCIE 38 (198)
Q Consensus 4 ~n~f~i~t~~-KSf~v~A~s~~Ek~~Wi~~i~~~i~ 38 (198)
+|-|++++.. +.|.++|.+.+|.+.||..|+=+..
T Consensus 583 p~Vf~lrtAdwrv~LFQaps~eEmqsWi~rIN~vAA 618 (774)
T KOG0932|consen 583 PHVFKLRTADWRVFLFQAPSQEEMQSWIERINLVAA 618 (774)
T ss_pred CceEEEEeccceeEEEeCCCHHHHHHHHHHHHHHHH
Confidence 6889999888 9999999999999999999975543
No 63
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=86.46 E-value=0.39 Score=38.72 Aligned_cols=25 Identities=32% Similarity=0.721 Sum_probs=18.9
Q ss_pred ccccCCccCCC------------ccccccccccCCceE
Q psy8222 64 VCMHCKRTQFT------------VLSRRHHCRKCGSVV 89 (198)
Q Consensus 64 ~C~~C~~~~Fs------------~~~RrhhCr~CG~vv 89 (198)
.|+.|+. +++ +++|+++|++||..|
T Consensus 2 ~cp~c~~-~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGH-PDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCC-CCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 5888887 771 456679999998876
No 64
>PF08458 PH_2: Plant pleckstrin homology-like region; InterPro: IPR013666 This domain describes a pleckstrin homology (PH)-like region found in several plant proteins of unknown function.
Probab=85.85 E-value=2 Score=32.83 Aligned_cols=34 Identities=12% Similarity=0.290 Sum_probs=31.3
Q ss_pred eEEEecCCeEEEEEeCChHHHHHHHHHHHHHHHH
Q psy8222 6 GWLIQTSSKSFAVHAATSTEKQEWMAHINKCIED 39 (198)
Q Consensus 6 ~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ 39 (198)
-|-|.|.+..+++.+.+..+++.|.+.|+.++..
T Consensus 72 yfgL~T~~G~vEfec~~~~~~k~W~~gI~~mL~~ 105 (110)
T PF08458_consen 72 YFGLKTAQGVVEFECDSQREYKRWVQGIQHMLSQ 105 (110)
T ss_pred EEEEEecCcEEEEEeCChhhHHHHHHHHHHHHHH
Confidence 4889999999999999999999999999988775
No 65
>PF15409 PH_8: Pleckstrin homology domain
Probab=85.43 E-value=2 Score=31.53 Aligned_cols=33 Identities=15% Similarity=0.351 Sum_probs=29.1
Q ss_pred cceEEEecCCeEEEEEeCChHHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSSKSFAVHAATSTEKQEWMAHINKC 36 (198)
Q Consensus 4 ~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~ 36 (198)
...|.|.+....+.|-|.++++.+.|+.+|+.+
T Consensus 56 ~~~I~idsg~~i~hLKa~s~~~f~~Wv~aL~~a 88 (89)
T PF15409_consen 56 SRRIDIDSGDEIWHLKAKSQEDFQRWVSALQKA 88 (89)
T ss_pred CCEEEEEcCCeEEEEEcCCHHHHHHHHHHHHhc
Confidence 346788888899999999999999999999865
No 66
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=84.05 E-value=0.67 Score=28.76 Aligned_cols=26 Identities=27% Similarity=0.966 Sum_probs=19.0
Q ss_pred cccCCccCCCccccccccccCCceEeCCC
Q psy8222 65 CMHCKRTQFTVLSRRHHCRKCGSVVCAPC 93 (198)
Q Consensus 65 C~~C~~~~Fs~~~RrhhCr~CG~vvC~~C 93 (198)
|..|++ .-.++ ...|+.||.+||...
T Consensus 1 C~~C~~-~~~l~--~f~C~~C~~~FC~~H 26 (39)
T smart00154 1 CHFCRK-KVGLT--GFKCRHCGNLFCGEH 26 (39)
T ss_pred CcccCC-ccccc--CeECCccCCcccccc
Confidence 566877 44333 678999999998765
No 67
>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=83.08 E-value=0.21 Score=33.04 Aligned_cols=29 Identities=34% Similarity=0.870 Sum_probs=18.5
Q ss_pred ccccCCccCCCcc------ccccccccCCceEeCCC
Q psy8222 64 VCMHCKRTQFTVL------SRRHHCRKCGSVVCAPC 93 (198)
Q Consensus 64 ~C~~C~~~~Fs~~------~RrhhCr~CG~vvC~~C 93 (198)
.|..|.+ +|... ..++.|..|+.+||-.|
T Consensus 1 ~CfgC~~-~~~~~~~~~~~~~~y~C~~C~~~FC~dC 35 (51)
T PF07975_consen 1 YCFGCQK-PFPDGPEKKADSSRYRCPKCKNHFCIDC 35 (51)
T ss_dssp EETTTTE-E-TTS-------EEE--TTTT--B-HHH
T ss_pred CCccCCC-CCCCcccccccCCeEECCCCCCccccCc
Confidence 3788998 88875 35799999999999988
No 68
>KOG0320|consensus
Probab=82.54 E-value=0.098 Score=43.19 Aligned_cols=49 Identities=24% Similarity=0.566 Sum_probs=33.7
Q ss_pred CCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhcc
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~ 120 (198)
.-.|.+|-. .|+ .+--.--+||+|||..|.... .+..++|..|..+|..
T Consensus 131 ~~~CPiCl~-~~s--ek~~vsTkCGHvFC~~Cik~a-------lk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 131 TYKCPICLD-SVS--EKVPVSTKCGHVFCSQCIKDA-------LKNTNKCPTCRKKITH 179 (187)
T ss_pred ccCCCceec-chh--hccccccccchhHHHHHHHHH-------HHhCCCCCCcccccch
Confidence 356778876 443 222245689999999997552 2567889999876654
No 69
>KOG2164|consensus
Probab=81.44 E-value=0.42 Score=45.14 Aligned_cols=52 Identities=23% Similarity=0.529 Sum_probs=39.5
Q ss_pred CCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhcc
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~ 120 (198)
-..|.+|-. ++.+-.|- .||+|||..|.-+....+ ..+..+-|.-|+..+..
T Consensus 186 ~~~CPICL~-~~~~p~~t----~CGHiFC~~CiLqy~~~s--~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLE-PPSVPVRT----NCGHIFCGPCILQYWNYS--AIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccC-CCCccccc----ccCceeeHHHHHHHHhhh--cccCCccCCchhhhccc
Confidence 468999998 77765553 399999999976544333 34778899999998765
No 70
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.88 E-value=2 Score=32.99 Aligned_cols=40 Identities=28% Similarity=0.581 Sum_probs=29.7
Q ss_pred ccccCCCCCccccCCccCCCcc----------ccccccccCCceEeCCCCC
Q psy8222 55 VWIPDNEAAVCMHCKRTQFTVL----------SRRHHCRKCGSVVCAPCSN 95 (198)
Q Consensus 55 ~Wv~d~~~~~C~~C~~~~Fs~~----------~RrhhCr~CG~vvC~~Cs~ 95 (198)
.|........|..|.+ +|.-. .-++.|..|..+||-+|=-
T Consensus 48 ~~~~~~~~~~C~~C~~-~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~ 97 (112)
T TIGR00622 48 PLEEYNGSRFCFGCQG-PFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDV 97 (112)
T ss_pred cccccCCCCcccCcCC-CCCCcccccccccccccceeCCCCCCccccccch
Confidence 3443434567999999 99742 3478899999999999953
No 71
>KOG3520|consensus
Probab=80.01 E-value=2.9 Score=43.33 Aligned_cols=36 Identities=22% Similarity=0.515 Sum_probs=28.7
Q ss_pred EEEecC---CeEEEEEeCChHHHHHHHHHHHHHHHHHHH
Q psy8222 7 WLIQTS---SKSFAVHAATSTEKQEWMAHINKCIEDLLR 42 (198)
Q Consensus 7 f~i~t~---~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~ 42 (198)
|+|.+. --=++|.|.|.+||..||++|+++|....+
T Consensus 688 FlIs~s~~~pqmYEL~a~T~serntW~~li~~~v~s~~~ 726 (1167)
T KOG3520|consen 688 FLISMSDQGPEMYELVAQSKSERNTWIQLIQDAVASCPR 726 (1167)
T ss_pred EEEecCCCCCeeEEEecCCHHHHHHHHHHHHHHHHhCCc
Confidence 445543 256889999999999999999999987543
No 72
>PF14593 PH_3: PH domain; PDB: 1W1H_D 1W1D_A 1W1G_A 2VKI_A.
Probab=79.76 E-value=4.5 Score=30.45 Aligned_cols=34 Identities=15% Similarity=0.468 Sum_probs=26.7
Q ss_pred ceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHHH
Q psy8222 5 NGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIED 39 (198)
Q Consensus 5 n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ 39 (198)
..|.|.||.|+|.|...+ ..=..|.++|++++..
T Consensus 68 ~~F~I~tp~RtY~l~d~~-~~A~~W~~~I~~~~~~ 101 (104)
T PF14593_consen 68 KTFFIHTPKRTYYLEDPE-GNAQQWVEAIEEVKKQ 101 (104)
T ss_dssp SEEEEEETTEEEEEE-TT-S-HHHHHHHHHHHHHH
T ss_pred CEEEEECCCcEEEEECCC-CCHHHHHHHHHHHHHH
Confidence 589999999999998744 4456699999998764
No 73
>KOG2996|consensus
Probab=78.23 E-value=1.3 Score=42.86 Aligned_cols=90 Identities=16% Similarity=0.347 Sum_probs=58.7
Q ss_pred cceEEEecC--CeEEEEEeCChHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCccccCCCCCccccCCccCC-Ccccccc
Q psy8222 4 RNGWLIQTS--SKSFAVHAATSTEKQEWMAHINKCIEDLLRKSGKKPAATHAAVWIPDNEAAVCMHCKRTQF-TVLSRRH 80 (198)
Q Consensus 4 ~n~f~i~t~--~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~~~g~~~~~~~~~~Wv~d~~~~~C~~C~~~~F-s~~~Rrh 80 (198)
.++|.|.-. ..-|.+++.+.+-|+.||++++-+++.+.. .......|.-....-+....|..|.. -. +.|---+
T Consensus 476 s~~f~lI~tqg~ngl~fy~Kte~~kkkWmeqfema~SNi~P--dya~an~H~fqmhtF~~~tsCkvC~m-llrGtfYQGY 552 (865)
T KOG2996|consen 476 SYGFYLIHTQGRNGLEFYCKTEDLKKKWMEQFEMAKSNISP--DYARANNHDFQMHTFKNTTSCKVCQM-LLRGTFYQGY 552 (865)
T ss_pred eeeEEEEEEcCCcceEEEEecHHHHHHHHHHHHHHHhcCCc--ccccccCcceEEEeccCCcchHHHHH-Hhhhhhhcce
Confidence 467777633 368999999999999999999988775421 00011223333444467889999987 21 2333457
Q ss_pred ccccCCceEeCCCCCC
Q psy8222 81 HCRKCGSVVCAPCSNK 96 (198)
Q Consensus 81 hCr~CG~vvC~~Cs~~ 96 (198)
.|-.||.-.=..|+..
T Consensus 553 ~C~~c~~~ahkecl~~ 568 (865)
T KOG2996|consen 553 KCEKCGADAHKECLGR 568 (865)
T ss_pred eeeeccccHHHHhccC
Confidence 8888887665556543
No 74
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=78.11 E-value=1.3 Score=26.99 Aligned_cols=25 Identities=32% Similarity=0.941 Sum_probs=17.7
Q ss_pred ccccCCccCCCcc-------ccccccccCCceE
Q psy8222 64 VCMHCKRTQFTVL-------SRRHHCRKCGSVV 89 (198)
Q Consensus 64 ~C~~C~~~~Fs~~-------~RrhhCr~CG~vv 89 (198)
.|..|++ .|.+- .++..|.+||++|
T Consensus 4 ~Cp~C~~-~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQA-KYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCC-EEeCCHHHCCCCCcEEECCCCCCEe
Confidence 5788887 88763 3457788888765
No 75
>KOG4275|consensus
Probab=77.73 E-value=0.38 Score=42.74 Aligned_cols=52 Identities=29% Similarity=0.696 Sum_probs=42.9
Q ss_pred ccCCCCCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHh
Q psy8222 57 IPDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDV 117 (198)
Q Consensus 57 v~d~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~ 117 (198)
-+...+..|..|+. .|..+.+||-|--|-+-||.-||... ...|.|..|...
T Consensus 39 s~~~~~p~ckacg~-~f~~~~~k~~c~dckk~fc~tcs~v~--------~~lr~c~~c~r~ 90 (350)
T KOG4275|consen 39 SSSSQAPHCKACGE-EFEDAQSKSDCEDCKKEFCATCSRVS--------ISLRTCTSCRRV 90 (350)
T ss_pred Ccccccchhhhhch-hHhhhhhhhhhhhhhHHHHHHHHHhc--------ccchhhhHHHHH
Confidence 45567779999999 99999999999999999999998332 346778888764
No 76
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=77.32 E-value=0.39 Score=30.11 Aligned_cols=33 Identities=27% Similarity=0.671 Sum_probs=23.0
Q ss_pred ccccCCccCCCccccccccccCCceEeCCCCCCee
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRF 98 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~ 98 (198)
.|.+|.. .|+ -.++..=-.||++||..|.....
T Consensus 1 ~C~~C~~-~~~-~~~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 1 HCNICFE-KYS-EERRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CCcCcCc-ccc-CCCCeEEcccCCHHHHHHHHhhc
Confidence 4778888 772 23344555799999999987644
No 77
>KOG0993|consensus
Probab=77.27 E-value=0.054 Score=49.97 Aligned_cols=66 Identities=23% Similarity=0.602 Sum_probs=54.3
Q ss_pred CccccCCCCCccccCCccCCCcccccccccc--CCceEeCCCCCCeeecCCC-CCCCeeeccchHHhhcccc
Q psy8222 54 AVWIPDNEAAVCMHCKRTQFTVLSRRHHCRK--CGSVVCAPCSNKRFLLPSQ-SAKPLRVCLTCYDVLSRDK 122 (198)
Q Consensus 54 ~~Wv~d~~~~~C~~C~~~~Fs~~~RrhhCr~--CG~vvC~~Cs~~~~~lp~~-~~~~~RVC~~C~~~l~~~~ 122 (198)
..|.-+.+...|..|-. +|.-++-.-||-+ |+.+||-.|+... +|.. ...+..||.-|+..+.+-.
T Consensus 460 le~ql~~~ve~c~~~~a-S~~slk~e~erl~qq~eqi~~~~~~Kat--vp~l~~e~~akv~rlq~eL~~seq 528 (542)
T KOG0993|consen 460 LEWQLDDDVEQCSNCDA-SFASLKVEPERLHQQCEQIFCMNCLKAT--VPSLPNERPAKVCRLQHELLNSEQ 528 (542)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHhccHHHHHHHHHHHHHHhHHHhh--cccccccchHHHHHHHHHHhhhcc
Confidence 35777778899999999 9999998888887 9999999998665 4554 3489999999999877644
No 78
>KOG1314|consensus
Probab=75.48 E-value=0.83 Score=41.60 Aligned_cols=37 Identities=35% Similarity=0.859 Sum_probs=25.1
Q ss_pred CCCCCccccCCCC-----CccccCCccCCCccccccccccCCceE
Q psy8222 50 ATHAAVWIPDNEA-----AVCMHCKRTQFTVLSRRHHCRKCGSVV 89 (198)
Q Consensus 50 ~~~~~~Wv~d~~~-----~~C~~C~~~~Fs~~~RrhhCr~CG~vv 89 (198)
+..+..|.|.... ..|..|+. |- --|-||||.|.+.|
T Consensus 74 G~vp~~wkPe~~~D~~~lqfCk~Cqg--YK-apRSHHCrkCnrCv 115 (414)
T KOG1314|consen 74 GFVPLGWKPENPKDEMFLQFCKKCQG--YK-APRSHHCRKCNRCV 115 (414)
T ss_pred CCCCCCCCCCCChhHHHHHHHhhccC--cC-CCccccchHHHHHH
Confidence 4445678775443 46888876 21 35889999998863
No 79
>KOG3799|consensus
Probab=74.80 E-value=1.4 Score=34.99 Aligned_cols=54 Identities=31% Similarity=0.674 Sum_probs=40.0
Q ss_pred CCCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhh
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVL 118 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l 118 (198)
+...|.+|.+|+|.- .=-|.|..|.--+|+.|-.. +.+. +++-.-||..|-...
T Consensus 64 ddatC~IC~KTKFAD-G~GH~C~YCq~r~CARCGGr-v~lr--sNKv~wvcnlc~k~q 117 (169)
T KOG3799|consen 64 DDATCGICHKTKFAD-GCGHNCSYCQTRFCARCGGR-VSLR--SNKVMWVCNLCRKQQ 117 (169)
T ss_pred cCcchhhhhhccccc-ccCcccchhhhhHHHhcCCe-eeec--cCceEEeccCCcHHH
Confidence 345799999988742 23499999999999999765 3222 457788999997543
No 80
>KOG3531|consensus
Probab=74.65 E-value=2.9 Score=42.05 Aligned_cols=41 Identities=24% Similarity=0.336 Sum_probs=37.0
Q ss_pred CcceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHHHHHHh
Q psy8222 3 LRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIEDLLRK 43 (198)
Q Consensus 3 ~~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~~ 43 (198)
.+|.|.|.+.+|.++|.|.+-++++.|+..++.+|...+++
T Consensus 810 ~p~~~ti~~~qk~i~vsast~~~sk~~~~~r~~~i~~~~k~ 850 (1036)
T KOG3531|consen 810 VPHCFTISGAQKQIYVSASTRRESKKWEFDRRKAIDLAPKK 850 (1036)
T ss_pred CCceEEEeccceEEEEeccchhhhhhhhhccchhhhhcccc
Confidence 58999999999999999999999999999999999665544
No 81
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=74.25 E-value=4.5 Score=27.42 Aligned_cols=28 Identities=21% Similarity=0.536 Sum_probs=21.5
Q ss_pred CCCccccCCccCCC--ccccccccccCCceE
Q psy8222 61 EAAVCMHCKRTQFT--VLSRRHHCRKCGSVV 89 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs--~~~RrhhCr~CG~vv 89 (198)
....|..|+. .-. .-.|.+.|..||..+
T Consensus 27 TSq~C~~CG~-~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGH-RNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCccc-ccccccccceEEcCCCCCEE
Confidence 5678999998 433 356789999999874
No 82
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=73.96 E-value=1.9 Score=26.24 Aligned_cols=25 Identities=40% Similarity=0.987 Sum_probs=18.1
Q ss_pred ccccCCccCCCcc-------ccccccccCCceE
Q psy8222 64 VCMHCKRTQFTVL-------SRRHHCRKCGSVV 89 (198)
Q Consensus 64 ~C~~C~~~~Fs~~-------~RrhhCr~CG~vv 89 (198)
.|..|+. .|.+- .++..|..||++|
T Consensus 4 ~CP~C~~-~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQT-RFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCc-eEEcCHHHcccCCcEEECCCCCcEe
Confidence 5888887 88663 3467788887775
No 83
>cd01262 PH_PDK1 3-Phosphoinositide dependent protein kinase 1 (PDK1) pleckstrin homology (PH) domain. 3-Phosphoinositide dependent protein kinase 1 (PDK1) pleckstrin homology (PH) domain. PDK1 contains an N-terminal serine/threonine kinase domain followed by a PH domain. Following binding of the PH domain to PtdIns(3,4,5)P3 and PtdIns(3,4)P2, PDK1 activates kinases such as Akt (PKB). PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=70.14 E-value=8.1 Score=28.43 Aligned_cols=32 Identities=13% Similarity=0.382 Sum_probs=25.9
Q ss_pred ceEEEecCCeEEEEEeCChHHHHHHHHHHHHHH
Q psy8222 5 NGWLIQTSSKSFAVHAATSTEKQEWMAHINKCI 37 (198)
Q Consensus 5 n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i 37 (198)
++|.|.||.|++.|.-.. ..=+.|+++|+++.
T Consensus 57 ~~F~I~Tp~rty~leD~~-~~a~~W~~~I~~~~ 88 (89)
T cd01262 57 SHFFVHTPNKVYSFEDPK-GRASQWKKAIEDLQ 88 (89)
T ss_pred ccEEEECCCceEEEECCC-CCHHHHHHHHHHHh
Confidence 589999999999997543 55667999998763
No 84
>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=68.35 E-value=1.4 Score=26.72 Aligned_cols=29 Identities=28% Similarity=0.592 Sum_probs=19.4
Q ss_pred cccCCccCCCccccccccccCCceEeCCCCCCe
Q psy8222 65 CMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKR 97 (198)
Q Consensus 65 C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~ 97 (198)
|.+|.. .+......-.||++||..|....
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 556765 23334567789999999986553
No 85
>PRK00420 hypothetical protein; Validated
Probab=68.02 E-value=3.8 Score=31.40 Aligned_cols=26 Identities=19% Similarity=0.299 Sum_probs=15.1
Q ss_pred CCccccCCccCCCc-cccccccccCCce
Q psy8222 62 AAVCMHCKRTQFTV-LSRRHHCRKCGSV 88 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~-~~RrhhCr~CG~v 88 (198)
...|..|+. +|.- -..+..|..||.+
T Consensus 23 ~~~CP~Cg~-pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGL-PLFELKDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCC-cceecCCCceECCCCCCe
Confidence 468999998 5533 2334445555443
No 86
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=67.77 E-value=3.7 Score=42.36 Aligned_cols=56 Identities=20% Similarity=0.419 Sum_probs=37.8
Q ss_pred ccCCCCCccccCCccCCCccc---cccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhc
Q psy8222 57 IPDNEAAVCMHCKRTQFTVLS---RRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLS 119 (198)
Q Consensus 57 v~d~~~~~C~~C~~~~Fs~~~---RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~ 119 (198)
+..-....|.+|+. .-++.. --.-|.-||.-||..|-.+-. ..-...|..|-....
T Consensus 12 ~~~~~~qiCqICGD-~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr------~eG~q~CPqCktrYk 70 (1079)
T PLN02638 12 MKHGGGQVCQICGD-NVGKTVDGEPFVACDVCAFPVCRPCYEYER------KDGNQSCPQCKTKYK 70 (1079)
T ss_pred ccccCCceeeeccc-ccCcCCCCCEEEEeccCCCccccchhhhhh------hcCCccCCccCCchh
Confidence 44456779999998 655432 127899999999999976531 134567777765544
No 87
>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=67.76 E-value=2.3 Score=29.96 Aligned_cols=56 Identities=20% Similarity=0.538 Sum_probs=26.6
Q ss_pred ccccCCccCCCccccccccccCCce-----EeCCCCCCeeecCCCCCCCeeeccchHHhhccc
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSV-----VCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSRD 121 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~v-----vC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~~ 121 (198)
.|..|+. +......+.||..|+.- +|..|-..-..|.. -.-..-.|..|...+++.
T Consensus 3 ~CP~C~~-~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkA-CGAvdYFC~~c~gLiSKk 63 (70)
T PF07191_consen 3 TCPKCQQ-ELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKA-CGAVDYFCNHCHGLISKK 63 (70)
T ss_dssp B-SSS-S-BEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEE-TTEEEEE-TTTT-EE-TT
T ss_pred cCCCCCC-ccEEeCCEEECccccccceecccCCCcccHHHHHHH-hcccceeeccCCceeecc
Confidence 5888988 76666667888888764 56666544332222 112345566666655543
No 88
>KOG0317|consensus
Probab=66.72 E-value=1.4 Score=38.87 Aligned_cols=46 Identities=20% Similarity=0.458 Sum_probs=31.4
Q ss_pred CCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhc
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLS 119 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~ 119 (198)
...|..|-. .+.---|-.||++||+.|-..+..- ++. |.-|-+..+
T Consensus 239 ~~kC~LCLe-----~~~~pSaTpCGHiFCWsCI~~w~~e-----k~e--CPlCR~~~~ 284 (293)
T KOG0317|consen 239 TRKCSLCLE-----NRSNPSATPCGHIFCWSCILEWCSE-----KAE--CPLCREKFQ 284 (293)
T ss_pred CCceEEEec-----CCCCCCcCcCcchHHHHHHHHHHcc-----ccC--CCcccccCC
Confidence 467888876 4445679999999999997665421 222 777755443
No 89
>KOG3576|consensus
Probab=66.42 E-value=1.2 Score=37.82 Aligned_cols=61 Identities=26% Similarity=0.598 Sum_probs=36.1
Q ss_pred cCCCCCccccCCccCCCc---ccc---------ccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhcc
Q psy8222 58 PDNEAAVCMHCKRTQFTV---LSR---------RHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 58 ~d~~~~~C~~C~~~~Fs~---~~R---------rhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~ 120 (198)
+|.+.-.|.+|++ .|++ ++| ||-|+.||+-|=+.---++-.-.+.|.+|- -|..|-...+.
T Consensus 113 sd~d~ftCrvCgK-~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpy-kc~~c~kaftq 185 (267)
T KOG3576|consen 113 SDQDSFTCRVCGK-KFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPY-KCSLCEKAFTQ 185 (267)
T ss_pred CCCCeeeeehhhh-hhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCcccc-chhhhhHHHHh
Confidence 4566778999999 9986 333 788999998764322111111122233443 37777665543
No 90
>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=66.07 E-value=3.6 Score=31.25 Aligned_cols=28 Identities=29% Similarity=0.667 Sum_probs=21.4
Q ss_pred CCCccccCCccCCCccccc-cccccCCceE
Q psy8222 61 EAAVCMHCKRTQFTVLSRR-HHCRKCGSVV 89 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~Rr-hhCr~CG~vv 89 (198)
.-..|..|++ +|==|+|. -+|..||.+|
T Consensus 8 tKR~Cp~CG~-kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 8 TKRTCPSCGA-KFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred CcccCCCCcc-hhccCCCCCccCCCCCCcc
Confidence 4568999999 88777664 5688888875
No 91
>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=65.44 E-value=4.1 Score=23.10 Aligned_cols=23 Identities=22% Similarity=0.605 Sum_probs=12.4
Q ss_pred ccccCCccCCCccccccccccCCceE
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSVV 89 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~vv 89 (198)
.|..|++ ..... -.-|.+||..|
T Consensus 2 ~CP~C~~-~V~~~--~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGA-EVPES--AKFCPHCGYDF 24 (26)
T ss_pred cCCCCcC-Cchhh--cCcCCCCCCCC
Confidence 4666666 33322 33566777654
No 92
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=64.57 E-value=5.9 Score=25.79 Aligned_cols=34 Identities=21% Similarity=0.536 Sum_probs=20.3
Q ss_pred CCcccc--CCccCCCcccc----ccccccCCceEeCCCCCC
Q psy8222 62 AAVCMH--CKRTQFTVLSR----RHHCRKCGSVVCAPCSNK 96 (198)
Q Consensus 62 ~~~C~~--C~~~~Fs~~~R----rhhCr~CG~vvC~~Cs~~ 96 (198)
...|.. |.. .|..-.. ...|..||..||..|...
T Consensus 18 ~~~Cp~~~C~~-~~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 57 (64)
T PF01485_consen 18 IRWCPNPDCEY-IIEKDDGCNSPIVTCPSCGTEFCFKCGEP 57 (64)
T ss_dssp CC--TTSST----ECS-SSTTS--CCTTSCCSEECSSSTSE
T ss_pred ccCCCCCCCcc-cEEecCCCCCCeeECCCCCCcCccccCcc
Confidence 347865 887 6554432 268999999999999754
No 93
>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=63.90 E-value=1.3 Score=27.49 Aligned_cols=33 Identities=21% Similarity=0.461 Sum_probs=23.2
Q ss_pred ccccCCccCCCccccccccccCCceEeCCCCCCee
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRF 98 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~ 98 (198)
.|.+|.. .|..-..-.-. .||++||..|...++
T Consensus 2 ~C~IC~~-~~~~~~~~~~l-~C~H~fh~~Ci~~~~ 34 (44)
T PF13639_consen 2 ECPICLE-EFEDGEKVVKL-PCGHVFHRSCIKEWL 34 (44)
T ss_dssp CETTTTC-BHHTTSCEEEE-TTSEEEEHHHHHHHH
T ss_pred CCcCCCh-hhcCCCeEEEc-cCCCeeCHHHHHHHH
Confidence 6899998 77543333333 499999999976654
No 94
>PLN02400 cellulose synthase
Probab=63.63 E-value=5.4 Score=41.24 Aligned_cols=57 Identities=21% Similarity=0.504 Sum_probs=39.1
Q ss_pred ccCCCCCccccCCccCCCccc---cccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhcc
Q psy8222 57 IPDNEAAVCMHCKRTQFTVLS---RRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 57 v~d~~~~~C~~C~~~~Fs~~~---RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~ 120 (198)
+..-....|.+|+. .-++.. --.-|..||.-||..|-.+-. ..-..+|..|-.....
T Consensus 31 ~~~~~gqiCqICGD-~VG~t~dGe~FVAC~eCaFPVCRpCYEYER------keGnq~CPQCkTrYkR 90 (1085)
T PLN02400 31 LKNLNGQICQICGD-DVGVTETGDVFVACNECAFPVCRPCYEYER------KDGTQCCPQCKTRYRR 90 (1085)
T ss_pred ccccCCceeeeccc-ccCcCCCCCEEEEEccCCCccccchhheec------ccCCccCcccCCcccc
Confidence 44456679999998 655432 127899999999999986632 2345678888655543
No 95
>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=63.54 E-value=1.6 Score=38.97 Aligned_cols=49 Identities=22% Similarity=0.476 Sum_probs=30.4
Q ss_pred CccccCCccCCCcccc---ccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhcc
Q psy8222 63 AVCMHCKRTQFTVLSR---RHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~~R---rhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~ 120 (198)
..|.+|.. .--+-.+ -.+ .||+.||..|...-+..+ ...|..|...+..
T Consensus 4 ~~CP~Ck~-~~y~np~~kl~i~--~CGH~~C~sCv~~l~~~~------~~~CP~C~~~lrk 55 (309)
T TIGR00570 4 QGCPRCKT-TKYRNPSLKLMVN--VCGHTLCESCVDLLFVRG------SGSCPECDTPLRK 55 (309)
T ss_pred CCCCcCCC-CCccCcccccccC--CCCCcccHHHHHHHhcCC------CCCCCCCCCccch
Confidence 47999987 3222221 233 799999999987754221 1268888665544
No 96
>KOG2059|consensus
Probab=63.53 E-value=15 Score=36.52 Aligned_cols=38 Identities=16% Similarity=0.392 Sum_probs=33.8
Q ss_pred CCcceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHHH
Q psy8222 2 ELRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIED 39 (198)
Q Consensus 2 ~~~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ 39 (198)
.++|-|+|..+.++.+|+|.+--|-.+|++.|.+....
T Consensus 629 ~~knv~qVV~~drtly~Q~~n~vEandWldaL~kvs~~ 666 (800)
T KOG2059|consen 629 KMKNVFQVVHTDRTLYVQAKNCVEANDWLDALRKVSCC 666 (800)
T ss_pred CCCceEEEEecCcceeEecCCchHHHHHHHHHHHHhcc
Confidence 36899999999999999999999999999999876543
No 97
>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=63.19 E-value=3.9 Score=32.20 Aligned_cols=27 Identities=41% Similarity=0.806 Sum_probs=19.2
Q ss_pred CCCCccccCCccCCCccccccccccCCceE
Q psy8222 60 NEAAVCMHCKRTQFTVLSRRHHCRKCGSVV 89 (198)
Q Consensus 60 ~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vv 89 (198)
.....|..|.. -.-.|-|||+.||+.|
T Consensus 46 ~~~~~C~~C~~---~kp~Rs~HC~~C~~CV 72 (174)
T PF01529_consen 46 GELKYCSTCKI---IKPPRSHHCRVCNRCV 72 (174)
T ss_pred CCCEECcccCC---cCCCcceecccccccc
Confidence 45667888875 2345789999988764
No 98
>KOG3173|consensus
Probab=63.13 E-value=3.8 Score=33.41 Aligned_cols=29 Identities=24% Similarity=0.885 Sum_probs=23.5
Q ss_pred CCCccccCCccCCCccccccccccCCceEeCCC
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPC 93 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~C 93 (198)
....|..|.+ .-.+.. +||| ||.+||+.+
T Consensus 104 ~~~rC~~C~k-k~gltg--f~Cr-CG~~fC~~H 132 (167)
T KOG3173|consen 104 KKKRCFKCRK-KVGLTG--FKCR-CGNTFCGTH 132 (167)
T ss_pred cchhhhhhhh-hhcccc--cccc-cCCcccccc
Confidence 3456999998 888887 8887 899999865
No 99
>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=62.93 E-value=7.6 Score=22.38 Aligned_cols=29 Identities=24% Similarity=0.623 Sum_probs=22.9
Q ss_pred ccccCCccCCCccccccccccCCceEeCCCC
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSVVCAPCS 94 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs 94 (198)
.|.+|.+ ..+-+. -++|..|+..+-..|.
T Consensus 2 ~C~~C~~-~~~~~~-~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRR-KIDGFY-FYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCC-CcCCCE-eEEeCCCCCeEcCccC
Confidence 5888998 776666 8999999988877663
No 100
>KOG1814|consensus
Probab=62.82 E-value=2.9 Score=38.80 Aligned_cols=42 Identities=26% Similarity=0.699 Sum_probs=31.0
Q ss_pred CccccCCCCCccccCCccCCCccc--cccccccCCceEeCCCCCCe
Q psy8222 54 AVWIPDNEAAVCMHCKRTQFTVLS--RRHHCRKCGSVVCAPCSNKR 97 (198)
Q Consensus 54 ~~Wv~d~~~~~C~~C~~~~Fs~~~--RrhhCr~CG~vvC~~Cs~~~ 97 (198)
..|+.. ..+.|..|.. ...-.. -|+||-.||..||.-|+..-
T Consensus 361 ekwl~~-N~krCP~C~v-~IEr~eGCnKM~C~~c~~~fc~~c~~~l 404 (445)
T KOG1814|consen 361 EKWLES-NSKRCPKCKV-VIERSEGCNKMHCTKCGTYFCWICAELL 404 (445)
T ss_pred HHHHHh-cCCCCCcccc-eeecCCCccceeeccccccceeehhhhc
Confidence 468764 5789999988 333222 27999999999999997653
No 101
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=62.81 E-value=1.5 Score=36.62 Aligned_cols=60 Identities=20% Similarity=0.394 Sum_probs=38.6
Q ss_pred cccCCCCCccccCCccCCCccccccccccCCceEeCCCCCCeeecCC---------CCCCCeeeccchHHhhcc
Q psy8222 56 WIPDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPS---------QSAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 56 Wv~d~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~---------~~~~~~RVC~~C~~~l~~ 120 (198)
-+.....-.|.+|.. .|.- -.--.||++||..|...+..... ...+....|..|...+..
T Consensus 12 ~~~~~~~~~CpICld-~~~d----PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 12 LVDSGGDFDCNICLD-QVRD----PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred eccCCCccCCccCCC-cCCC----cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 344445678999998 6532 22357999999999876532111 012345689999887754
No 102
>PF12773 DZR: Double zinc ribbon
Probab=62.81 E-value=5.7 Score=25.17 Aligned_cols=27 Identities=26% Similarity=0.691 Sum_probs=16.5
Q ss_pred CCCccccCCccCCC-ccccccccccCCce
Q psy8222 61 EAAVCMHCKRTQFT-VLSRRHHCRKCGSV 88 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs-~~~RrhhCr~CG~v 88 (198)
++..|..|+. ++. .......|..||..
T Consensus 11 ~~~fC~~CG~-~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 11 DAKFCPHCGT-PLPPPDQSKKICPNCGAE 38 (50)
T ss_pred cccCChhhcC-ChhhccCCCCCCcCCcCC
Confidence 4677888887 554 12334567777663
No 103
>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=62.76 E-value=5.3 Score=31.34 Aligned_cols=28 Identities=18% Similarity=0.265 Sum_probs=21.9
Q ss_pred CCCccccCCccCCCccc-cccccccCCceE
Q psy8222 61 EAAVCMHCKRTQFTVLS-RRHHCRKCGSVV 89 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~-RrhhCr~CG~vv 89 (198)
.-..|+.|++ +|==|+ +-.+|..||.++
T Consensus 8 tKr~Cp~cg~-kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICPNTGS-KFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred ccccCCCcCc-cccccCCCCccCCCcCCcc
Confidence 4568999999 887665 458888888875
No 104
>PLN02436 cellulose synthase A
Probab=60.48 E-value=7.4 Score=40.23 Aligned_cols=56 Identities=18% Similarity=0.471 Sum_probs=37.6
Q ss_pred ccCCCCCccccCCccCCCccc---cccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhc
Q psy8222 57 IPDNEAAVCMHCKRTQFTVLS---RRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLS 119 (198)
Q Consensus 57 v~d~~~~~C~~C~~~~Fs~~~---RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~ 119 (198)
+.......|.+|+. .-++.. --.-|.-||.-||..|-.+-. ..-...|..|-....
T Consensus 31 ~~~~~~~iCqICGD-~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer------~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 31 VQELSGQTCQICGD-EIELTVDGEPFVACNECAFPVCRPCYEYER------REGNQACPQCKTRYK 89 (1094)
T ss_pred ccccCCcccccccc-ccCcCCCCCEEEeeccCCCccccchhhhhh------hcCCccCcccCCchh
Confidence 34445679999998 654432 127799999999999976531 234567888865544
No 105
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=60.35 E-value=1.1 Score=32.17 Aligned_cols=50 Identities=22% Similarity=0.565 Sum_probs=17.0
Q ss_pred CCCCCccccCCccCCCcccc---ccccccCCceEeCCCCCCeeecCCCCCCCeeeccchH
Q psy8222 59 DNEAAVCMHCKRTQFTVLSR---RHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCY 115 (198)
Q Consensus 59 d~~~~~C~~C~~~~Fs~~~R---rhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~ 115 (198)
+-....|.+|+. ...+..- =.-|..|+..+|..|-.+.. ..-..+|..|-
T Consensus 6 ~~~~qiCqiCGD-~VGl~~~Ge~FVAC~eC~fPvCr~CyEYEr------keg~q~CpqCk 58 (80)
T PF14569_consen 6 NLNGQICQICGD-DVGLTENGEVFVACHECAFPVCRPCYEYER------KEGNQVCPQCK 58 (80)
T ss_dssp --SS-B-SSS---B--B-SSSSB--S-SSS-----HHHHHHHH------HTS-SB-TTT-
T ss_pred hcCCcccccccC-ccccCCCCCEEEEEcccCCccchhHHHHHh------hcCcccccccC
Confidence 345678999988 6655422 24566777777766654421 12345666664
No 106
>KOG0823|consensus
Probab=59.72 E-value=2.1 Score=36.68 Aligned_cols=51 Identities=22% Similarity=0.443 Sum_probs=31.7
Q ss_pred CCCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhcc
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~ 120 (198)
.-=.|.+|-. +.+---=-.||+.||+.|.-++..+.. ....|..|...++.
T Consensus 46 ~~FdCNICLd-----~akdPVvTlCGHLFCWpClyqWl~~~~----~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 46 GFFDCNICLD-----LAKDPVVTLCGHLFCWPCLYQWLQTRP----NSKECPVCKAEVSI 96 (230)
T ss_pred Cceeeeeecc-----ccCCCEEeecccceehHHHHHHHhhcC----CCeeCCcccccccc
Confidence 3445777765 222233347999999999988754332 34556677666653
No 107
>KOG4305|consensus
Probab=59.42 E-value=11 Score=38.95 Aligned_cols=38 Identities=18% Similarity=0.381 Sum_probs=31.9
Q ss_pred EEecCCeEEEEEeCChHHHHHHHHHHHHHHHHHHHhcC
Q psy8222 8 LIQTSSKSFAVHAATSTEKQEWMAHINKCIEDLLRKSG 45 (198)
Q Consensus 8 ~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~~~g 45 (198)
.+..-+.+|.++|.+..+++.|+++|..+.+..+++..
T Consensus 657 ~~ga~~~~ftly~~s~~~r~~w~ekI~~aq~~~le~~~ 694 (1029)
T KOG4305|consen 657 LGGARGASFTLYAESLNGRDQWVEKIKQAQKRSLERND 694 (1029)
T ss_pred eccccceEEEeeccchHHhhhHHhhhhHHHHhhhhhhc
Confidence 34466689999999999999999999999888776543
No 108
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=59.34 E-value=6.2 Score=25.79 Aligned_cols=23 Identities=39% Similarity=0.928 Sum_probs=16.7
Q ss_pred CCccccCCccCCCccccccccccCCc
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCGS 87 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG~ 87 (198)
...|+.|.. . .-.|-..||.||.
T Consensus 14 k~ICrkC~A-R--np~~A~~CRKCg~ 36 (48)
T PRK04136 14 KKICMRCNA-R--NPWRATKCRKCGY 36 (48)
T ss_pred ccchhcccC-C--CCccccccccCCC
Confidence 457888987 2 2346788999886
No 109
>KOG1117|consensus
Probab=58.84 E-value=7.7 Score=39.41 Aligned_cols=37 Identities=14% Similarity=0.419 Sum_probs=33.9
Q ss_pred cceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIEDL 40 (198)
Q Consensus 4 ~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~l 40 (198)
.|.|.|.+.++.|++.+.++.++..|++.++.|....
T Consensus 144 d~kfevitn~r~fvfr~e~~~~r~~w~s~l~s~~~~Q 180 (1186)
T KOG1117|consen 144 DNKFEVITNQRTFVFRQESEGERFIWVSPLQSALKEQ 180 (1186)
T ss_pred CceEEEEecceEEEEecCCcccceeeechhhhcchhh
Confidence 4789999999999999999999999999999887654
No 110
>PLN02189 cellulose synthase
Probab=58.23 E-value=6.4 Score=40.54 Aligned_cols=55 Identities=22% Similarity=0.502 Sum_probs=36.9
Q ss_pred cCCCCCccccCCccCCCccc---cccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhc
Q psy8222 58 PDNEAAVCMHCKRTQFTVLS---RRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLS 119 (198)
Q Consensus 58 ~d~~~~~C~~C~~~~Fs~~~---RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~ 119 (198)
.......|.+|+. ..++.. --.-|.-||.-||..|-.+-. ..-...|..|-....
T Consensus 30 ~~~~~~~C~iCgd-~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer------~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 30 RNLDGQVCEICGD-EIGLTVDGDLFVACNECGFPVCRPCYEYER------REGTQNCPQCKTRYK 87 (1040)
T ss_pred ccccCcccccccc-ccCcCCCCCEEEeeccCCCccccchhhhhh------hcCCccCcccCCchh
Confidence 3445678999998 655321 127899999999999976531 134567777765544
No 111
>KOG1315|consensus
Probab=57.62 E-value=4.3 Score=36.28 Aligned_cols=27 Identities=33% Similarity=0.721 Sum_probs=15.3
Q ss_pred CCCCCccccCCccCCCccccccccccCCce
Q psy8222 59 DNEAAVCMHCKRTQFTVLSRRHHCRKCGSV 88 (198)
Q Consensus 59 d~~~~~C~~C~~~~Fs~~~RrhhCr~CG~v 88 (198)
+.....|..|+. -.=-|-|||+.|++.
T Consensus 106 ~g~~R~C~kC~~---iKPdRaHHCsvC~rC 132 (307)
T KOG1315|consen 106 DGAVRYCDKCKC---IKPDRAHHCSVCNRC 132 (307)
T ss_pred CCCceeeccccc---ccCCccccchhhhhh
Confidence 345566666665 112366777777654
No 112
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=57.04 E-value=6 Score=24.94 Aligned_cols=24 Identities=25% Similarity=0.598 Sum_probs=15.6
Q ss_pred ccccCCccCCCcccc--ccccccCCce
Q psy8222 64 VCMHCKRTQFTVLSR--RHHCRKCGSV 88 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~R--rhhCr~CG~v 88 (198)
.|..|+. .|.+-.. ..+|..||.-
T Consensus 5 ~C~~CG~-~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 5 KCARCGR-EVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred ECCCCCC-EEEECCCCCceECCCCCCe
Confidence 5778887 7765543 4667777653
No 113
>KOG1311|consensus
Probab=56.36 E-value=5 Score=34.99 Aligned_cols=25 Identities=28% Similarity=0.590 Sum_probs=19.4
Q ss_pred CCccccCCccCCCccccccccccCCceE
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCGSVV 89 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG~vv 89 (198)
...|..|.. -.-.|-|||+.|+..|
T Consensus 113 ~~~C~~C~~---~rPpRs~HCsvC~~CV 137 (299)
T KOG1311|consen 113 WKYCDTCQL---YRPPRSSHCSVCNNCV 137 (299)
T ss_pred eEEcCcCcc---cCCCCcccchhhcccc
Confidence 578999987 2445789999998865
No 114
>KOG4739|consensus
Probab=55.65 E-value=4.7 Score=34.72 Aligned_cols=43 Identities=28% Similarity=0.649 Sum_probs=28.3
Q ss_pred ccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhh
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVL 118 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l 118 (198)
+|-.|+. |.- ....+=-.|++|||..|...-. .++|..|-..+
T Consensus 5 hCn~C~~--~~~-~~~f~LTaC~HvfC~~C~k~~~---------~~~C~lCkk~i 47 (233)
T KOG4739|consen 5 HCNKCFR--FPS-QDPFFLTACRHVFCEPCLKASS---------PDVCPLCKKSI 47 (233)
T ss_pred Eeccccc--cCC-CCceeeeechhhhhhhhcccCC---------cccccccccee
Confidence 4767765 222 4455556899999999986532 12888886654
No 115
>cd01258 PH_syntrophin Syntrophin pleckstrin homology (PH) domain. Syntrophin pleckstrin homology (PH) domain. Syntrophins are peripheral membrane proteins, which associate with the Duchenne muscular dystrophy protein dystrophin and other proteins to form the dystrophin glycoprotein complex (DGC). There are five syntrophin isoforms, alpha1, beta1, beta2, gamma1, and gamma2. They all contain two PH domains, with the N-teminal PH domain interupted by a PDZ domain. The N-terminal PH domain of alpha1syntrophin binds phosphatidylinositol 4,5-bisphosphate. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=55.03 E-value=28 Score=26.44 Aligned_cols=33 Identities=18% Similarity=0.364 Sum_probs=28.5
Q ss_pred CcceEEEecCC--eEEEEEeCChHHHHHHHHHHHH
Q psy8222 3 LRNGWLIQTSS--KSFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 3 ~~n~f~i~t~~--KSf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
-++.|.|++.. .+..+...+..|...|..+|+.
T Consensus 73 ~~~~F~irtg~~vesh~fsVEt~~dL~~W~raiv~ 107 (108)
T cd01258 73 RDNCFLIRTGTQVENHYLRVETHRDLASWERALVR 107 (108)
T ss_pred CceEEEEEcCCceeeEEEEecCHHHHHHHHHHHhc
Confidence 35789999776 6888999999999999999864
No 116
>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=54.97 E-value=12 Score=33.52 Aligned_cols=61 Identities=21% Similarity=0.543 Sum_probs=37.5
Q ss_pred CCCccccCCccCC-Ccc--------ccccccccCCc------eEeCCCCCCe----eecCCC-CCCCee--eccchHHhh
Q psy8222 61 EAAVCMHCKRTQF-TVL--------SRRHHCRKCGS------VVCAPCSNKR----FLLPSQ-SAKPLR--VCLTCYDVL 118 (198)
Q Consensus 61 ~~~~C~~C~~~~F-s~~--------~RrhhCr~CG~------vvC~~Cs~~~----~~lp~~-~~~~~R--VC~~C~~~l 118 (198)
....|.+|+..+. +++ .|..||-.|+. +-|..|-+.+ ..+... +...+| +|..|...+
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~Yl 262 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYL 262 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeEeecCCCCCcceEEeeccccccch
Confidence 3568999997332 322 25689999984 5788886643 112211 122345 999998776
Q ss_pred ccc
Q psy8222 119 SRD 121 (198)
Q Consensus 119 ~~~ 121 (198)
...
T Consensus 263 K~~ 265 (305)
T TIGR01562 263 KIL 265 (305)
T ss_pred hhh
Confidence 654
No 117
>KOG1818|consensus
Probab=54.94 E-value=1.4 Score=42.92 Aligned_cols=72 Identities=19% Similarity=0.236 Sum_probs=48.3
Q ss_pred HHHHhcCCCCCC-CCCCccccCCCCCccccCCccCCCccccccccccCC-ceEeCCCCCCeeecCCCCCCCeeeccchH
Q psy8222 39 DLLRKSGKKPAA-THAAVWIPDNEAAVCMHCKRTQFTVLSRRHHCRKCG-SVVCAPCSNKRFLLPSQSAKPLRVCLTCY 115 (198)
Q Consensus 39 ~ll~~~g~~~~~-~~~~~Wv~d~~~~~C~~C~~~~Fs~~~RrhhCr~CG-~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~ 115 (198)
++++..+.++.. .+.-.|.-+ .|..|-+ .|++..+.|+|++|| .|+|.-|+....-+-......+|+|..=-
T Consensus 34 d~ir~~~~~~k~slr~~~~~i~----h~np~~~-~~~~~~~d~cvkn~G~gv~~ei~tre~m~~~~~~l~~~~~~e~v~ 107 (634)
T KOG1818|consen 34 DMIRSGGVPPKPSLRGIKKRID----HENPNVQ-LFTLKLTDHCVKNCGHGVHCEIATREFMDLLKSLLESQRIHEEVK 107 (634)
T ss_pred HHHHhcCCCCchhHHHHHHHHh----ccCCCcc-cchhhhHHHHHhcCCcchhHHHHHHHHHHHHHhhhccccccchHH
Confidence 344555555543 234456544 7888998 999999999999999 88888888766544443445555555543
No 118
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=54.83 E-value=16 Score=31.08 Aligned_cols=26 Identities=27% Similarity=0.655 Sum_probs=19.8
Q ss_pred CCCCccccCCccCCCccccccccccCCceE
Q psy8222 60 NEAAVCMHCKRTQFTVLSRRHHCRKCGSVV 89 (198)
Q Consensus 60 ~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vv 89 (198)
.....|..|+. +..|.+.|..||.++
T Consensus 307 ~tS~~C~~cg~----~~~r~~~C~~cg~~~ 332 (364)
T COG0675 307 YTSKTCPCCGH----LSGRLFKCPRCGFVH 332 (364)
T ss_pred CCcccccccCC----ccceeEECCCCCCee
Confidence 35688999985 446778888888864
No 119
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=54.08 E-value=13 Score=24.16 Aligned_cols=34 Identities=29% Similarity=0.624 Sum_probs=23.4
Q ss_pred CCccc--cCCccCCCc----cccccccccCCceEeCCCCCC
Q psy8222 62 AAVCM--HCKRTQFTV----LSRRHHCRKCGSVVCAPCSNK 96 (198)
Q Consensus 62 ~~~C~--~C~~~~Fs~----~~RrhhCr~CG~vvC~~Cs~~ 96 (198)
...|. .|.. .+.. ......|..||..||..|...
T Consensus 18 ~~~CP~~~C~~-~~~~~~~~~~~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 18 LKWCPAPDCSA-AIIVTEEEGCNRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred ccCCCCCCCcc-eEEecCCCCCCeeECCCCCCeECCCCCCc
Confidence 33466 6665 3322 345788999999999999754
No 120
>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=52.65 E-value=11 Score=21.96 Aligned_cols=24 Identities=25% Similarity=0.512 Sum_probs=12.6
Q ss_pred EeCCCCCCeeecCCCCCCCeeeccchH
Q psy8222 89 VCAPCSNKRFLLPSQSAKPLRVCLTCY 115 (198)
Q Consensus 89 vC~~Cs~~~~~lp~~~~~~~RVC~~C~ 115 (198)
||+.|-....+.+. ...|+|..|-
T Consensus 5 fC~~CG~~t~~~~~---g~~r~C~~Cg 28 (32)
T PF09297_consen 5 FCGRCGAPTKPAPG---GWARRCPSCG 28 (32)
T ss_dssp B-TTT--BEEE-SS---SS-EEESSSS
T ss_pred ccCcCCccccCCCC---cCEeECCCCc
Confidence 56666655554443 5789998884
No 121
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.45 E-value=3.5 Score=36.12 Aligned_cols=46 Identities=22% Similarity=0.551 Sum_probs=28.3
Q ss_pred CccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhh
Q psy8222 63 AVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVL 118 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l 118 (198)
-.|.+|.. .--.--|..||+|||..|.-.. ...+..-.|.-|-...
T Consensus 216 ~kC~lC~e-----~~~~ps~t~CgHlFC~~Cl~~~-----~t~~k~~~CplCRak~ 261 (271)
T COG5574 216 YKCFLCLE-----EPEVPSCTPCGHLFCLSCLLIS-----WTKKKYEFCPLCRAKV 261 (271)
T ss_pred cceeeeec-----ccCCcccccccchhhHHHHHHH-----HHhhccccCchhhhhc
Confidence 45777776 2223568899999999996441 1123444566665543
No 122
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=52.12 E-value=8.9 Score=26.61 Aligned_cols=29 Identities=24% Similarity=0.762 Sum_probs=13.5
Q ss_pred CccccCCccCCCcccccccc-ccCCceEeCCCCCC
Q psy8222 63 AVCMHCKRTQFTVLSRRHHC-RKCGSVVCAPCSNK 96 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~~RrhhC-r~CG~vvC~~Cs~~ 96 (198)
-.|..|.. ++ |.-+| -.|.++||+.|.+.
T Consensus 8 LrCs~C~~----~l-~~pv~l~~CeH~fCs~Ci~~ 37 (65)
T PF14835_consen 8 LRCSICFD----IL-KEPVCLGGCEHIFCSSCIRD 37 (65)
T ss_dssp TS-SSS-S-------SS-B---SSS--B-TTTGGG
T ss_pred cCCcHHHH----Hh-cCCceeccCccHHHHHHhHH
Confidence 34666665 33 44555 78999999999755
No 123
>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=50.52 E-value=3.9 Score=24.11 Aligned_cols=30 Identities=30% Similarity=0.675 Sum_probs=20.3
Q ss_pred ccccCCccCCCccccccccccCCceEeCCCCCCe
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKR 97 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~ 97 (198)
.|.+|.. .| .....-..||+.||..|....
T Consensus 1 ~C~iC~~-~~---~~~~~~~~C~H~~c~~C~~~~ 30 (45)
T cd00162 1 ECPICLE-EF---REPVVLLPCGHVFCRSCIDKW 30 (45)
T ss_pred CCCcCch-hh---hCceEecCCCChhcHHHHHHH
Confidence 3777877 55 333444559999999997654
No 124
>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=50.51 E-value=8.8 Score=22.97 Aligned_cols=12 Identities=42% Similarity=0.985 Sum_probs=7.4
Q ss_pred ccccCCccCCCcc
Q psy8222 64 VCMHCKRTQFTVL 76 (198)
Q Consensus 64 ~C~~C~~~~Fs~~ 76 (198)
.|..|+. .|.+-
T Consensus 4 ~CP~C~~-~~~v~ 15 (38)
T TIGR02098 4 QCPNCKT-SFRVV 15 (38)
T ss_pred ECCCCCC-EEEeC
Confidence 4667776 66553
No 125
>cd01256 PH_dynamin Dynamin pleckstrin homology (PH) domain. Dynamin pleckstrin homology (PH) domain. Dynamin is a GTPase that regulates endocytic vesicle formation. It has an N-terminal GTPase domain, followed by a PH domain, a GTPase effector domain and a C-terminal proline arginine rich domain. Dynamin-like proteins, which are found in metazoa, plants and yeast have the same domain architecture as dynamin, but lack the PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=49.48 E-value=30 Score=26.28 Aligned_cols=32 Identities=16% Similarity=0.286 Sum_probs=25.7
Q ss_pred cceEEEecCC--------eEEEEEeCChHHHHHHHHHHHH
Q psy8222 4 RNGWLIQTSS--------KSFAVHAATSTEKQEWMAHINK 35 (198)
Q Consensus 4 ~n~f~i~t~~--------KSf~v~A~s~~Ek~~Wi~~i~~ 35 (198)
+|.|.|..|. |.++|.|.|.+|-+.|.+.+-+
T Consensus 64 ~~~FeLfnpd~rnvykd~k~lel~~~~~e~vdswkasflr 103 (110)
T cd01256 64 NHKFALFYPDGRNVYKDYKQLELGCETLEEVDSWKASFLR 103 (110)
T ss_pred CcEEEEEcCcccccccchheeeecCCCHHHHHHHHHHHHh
Confidence 5677777553 6788999999999999988754
No 126
>PHA02768 hypothetical protein; Provisional
Probab=49.03 E-value=8.6 Score=25.81 Aligned_cols=25 Identities=16% Similarity=0.400 Sum_probs=16.5
Q ss_pred ccccCCccCCCcc------ccc----cccccCCceE
Q psy8222 64 VCMHCKRTQFTVL------SRR----HHCRKCGSVV 89 (198)
Q Consensus 64 ~C~~C~~~~Fs~~------~Rr----hhCr~CG~vv 89 (198)
.|..|++ .|+.. .|+ +.|-.||++|
T Consensus 7 ~C~~CGK-~Fs~~~~L~~H~r~H~k~~kc~~C~k~f 41 (55)
T PHA02768 7 ECPICGE-IYIKRKSMITHLRKHNTNLKLSNCKRIS 41 (55)
T ss_pred CcchhCC-eeccHHHHHHHHHhcCCcccCCccccee
Confidence 6999999 89752 123 4466676655
No 127
>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=48.96 E-value=9 Score=25.88 Aligned_cols=17 Identities=24% Similarity=0.938 Sum_probs=12.5
Q ss_pred ccccccccccCCceEeC
Q psy8222 75 VLSRRHHCRKCGSVVCA 91 (198)
Q Consensus 75 ~~~RrhhCr~CG~vvC~ 91 (198)
++.---+|-.||+|+|.
T Consensus 14 L~~~~~NCl~CGkIiC~ 30 (57)
T PF06221_consen 14 LFPYAPNCLNCGKIICE 30 (57)
T ss_pred CccccccccccChhhcc
Confidence 33335689999999886
No 128
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=48.39 E-value=8 Score=34.44 Aligned_cols=26 Identities=27% Similarity=0.663 Sum_probs=15.1
Q ss_pred CCCCccccCCccCCCccccccccccCCce
Q psy8222 60 NEAAVCMHCKRTQFTVLSRRHHCRKCGSV 88 (198)
Q Consensus 60 ~~~~~C~~C~~~~Fs~~~RrhhCr~CG~v 88 (198)
.....|..|+. =---|-|||+.|++.
T Consensus 107 ~~~~~C~~C~~---~KP~RS~HC~~Cn~C 132 (309)
T COG5273 107 GTENFCSTCNI---YKPPRSHHCSICNRC 132 (309)
T ss_pred ccceecccccc---ccCCCCccchhhcch
Confidence 34556666654 112366777777765
No 129
>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=48.29 E-value=7.6 Score=25.18 Aligned_cols=31 Identities=29% Similarity=0.673 Sum_probs=22.1
Q ss_pred ccccCCccCCCccccccccccCC---ceEeCCCCCC
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCG---SVVCAPCSNK 96 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG---~vvC~~Cs~~ 96 (198)
.|..|+. ..+...|+||..|. .-+|..|-..
T Consensus 2 ~Cd~C~~--~pI~G~R~~C~~C~~~d~DlC~~C~~~ 35 (48)
T cd02341 2 KCDSCGI--EPIPGTRYHCSECDDGDFDLCQDCVVK 35 (48)
T ss_pred CCCCCCC--CccccceEECCCCCCCCCccCHHHHhC
Confidence 4778875 34568899999998 4567776443
No 130
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=48.26 E-value=4.5 Score=30.50 Aligned_cols=56 Identities=21% Similarity=0.397 Sum_probs=34.5
Q ss_pred CccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhcccccCCCCCCCCCCC
Q psy8222 74 TVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSRDKTVSGKPMAGNTA 134 (198)
Q Consensus 74 s~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~~~~~~~~~~~~~~~ 134 (198)
..|.+++.|..||+.--..|+-. .......-+|..|-.............+..++.
T Consensus 17 ~~L~k~FtCp~Cghe~vs~ctvk-----k~~~~g~~~Cg~CGls~e~ev~~l~~~vDvYs~ 72 (104)
T COG4888 17 QVLPKTFTCPRCGHEKVSSCTVK-----KTVNIGTAVCGNCGLSFECEVPELSEPVDVYSA 72 (104)
T ss_pred ccCCceEecCccCCeeeeEEEEE-----ecCceeEEEcccCcceEEEeccccccchhHHHH
Confidence 34667788999998877777622 223466788888876655544444444433333
No 131
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=47.82 E-value=8.5 Score=25.24 Aligned_cols=23 Identities=35% Similarity=0.803 Sum_probs=15.4
Q ss_pred ccccCCccCCCccc--cccccccCCc
Q psy8222 64 VCMHCKRTQFTVLS--RRHHCRKCGS 87 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~--RrhhCr~CG~ 87 (198)
.|+.|++ .|.++. +-.-|..||.
T Consensus 8 ~C~~Cg~-~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 8 KCARCGR-EVELDQETRGIRCPYCGS 32 (49)
T ss_pred EhhhcCC-eeehhhccCceeCCCCCc
Confidence 5899999 997553 3455555554
No 132
>PLN02400 cellulose synthase
Probab=47.64 E-value=21 Score=37.08 Aligned_cols=25 Identities=40% Similarity=1.200 Sum_probs=17.8
Q ss_pred cccccCCc-----------eEeCCCCCCeeecCCCCCCCeeeccchHHh
Q psy8222 80 HHCRKCGS-----------VVCAPCSNKRFLLPSQSAKPLRVCLTCYDV 117 (198)
Q Consensus 80 hhCr~CG~-----------vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~ 117 (198)
+-|+.||. |.|..|. --||..||+.
T Consensus 37 qiCqICGD~VG~t~dGe~FVAC~eCa-------------FPVCRpCYEY 72 (1085)
T PLN02400 37 QICQICGDDVGVTETGDVFVACNECA-------------FPVCRPCYEY 72 (1085)
T ss_pred ceeeecccccCcCCCCCEEEEEccCC-------------Cccccchhhe
Confidence 57888886 3566663 4589999963
No 133
>PLN02866 phospholipase D
Probab=47.63 E-value=37 Score=35.28 Aligned_cols=36 Identities=25% Similarity=0.486 Sum_probs=33.9
Q ss_pred CcceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHH
Q psy8222 3 LRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIE 38 (198)
Q Consensus 3 ~~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~ 38 (198)
++|+|.|.+.++++.|.+.|..+-..|+.+|+.+..
T Consensus 273 ~~~~~~i~~~~r~l~l~~~s~~~~~~w~~ai~~~~~ 308 (1068)
T PLN02866 273 LRFGFKVTCGNRSIRLRTKSSAKVKDWVAAINDAGL 308 (1068)
T ss_pred CcceEEEecCceEEEEEECCHHHHHHHHHHHHHHHh
Confidence 578999999999999999999999999999999874
No 134
>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=47.44 E-value=10 Score=23.58 Aligned_cols=7 Identities=29% Similarity=0.894 Sum_probs=4.0
Q ss_pred ccccCCc
Q psy8222 64 VCMHCKR 70 (198)
Q Consensus 64 ~C~~C~~ 70 (198)
.|..|+.
T Consensus 2 ~Cp~Cg~ 8 (43)
T PF08271_consen 2 KCPNCGS 8 (43)
T ss_dssp SBTTTSS
T ss_pred CCcCCcC
Confidence 3566665
No 135
>PRK05462 S-adenosylmethionine decarboxylase; Provisional
Probab=46.34 E-value=24 Score=30.86 Aligned_cols=33 Identities=30% Similarity=0.391 Sum_probs=27.9
Q ss_pred ceEEEecCCeEEEE----EeCChHHHHHHHHHHHHHH
Q psy8222 5 NGWLIQTSSKSFAV----HAATSTEKQEWMAHINKCI 37 (198)
Q Consensus 5 n~f~i~t~~KSf~v----~A~s~~Ek~~Wi~~i~~~i 37 (198)
++|.-.|+.-||.+ ||.++++|+++++.|.+..
T Consensus 9 ~gfnnltkslsFniydicya~t~~~~~~Yi~Yide~y 45 (266)
T PRK05462 9 HGFNNLTKSLSFNIYDICYAKTEEERDGYIAYIDEQY 45 (266)
T ss_pred eccccccceeeeeeeeeEeeCCHHHHHHHHHHHHHhc
Confidence 57888899999986 4999999999999996543
No 136
>TIGR03331 SAM_DCase_Eco S-adenosylmethionine decarboxylase proenzyme, Escherichia coli form. Members of this protein family are the single chain precursor of the S-adenosylmethionine decarboxylase as found in Escherichia coli. This form shows a substantially different architecture from the form shared by the Archaea, Bacillus, and many other species (TIGR03330). It shows little or no similarity to the form found in eukaryotes (TIGR00535).
Probab=45.48 E-value=26 Score=30.55 Aligned_cols=33 Identities=27% Similarity=0.383 Sum_probs=28.2
Q ss_pred ceEEEecCCeEEEE----EeCChHHHHHHHHHHHHHH
Q psy8222 5 NGWLIQTSSKSFAV----HAATSTEKQEWMAHINKCI 37 (198)
Q Consensus 5 n~f~i~t~~KSf~v----~A~s~~Ek~~Wi~~i~~~i 37 (198)
++|.-.|+.-||.+ ||.++++|+++++.|.+..
T Consensus 5 ~gfnnltkslsfniydicya~t~~~~~~yi~yide~y 41 (259)
T TIGR03331 5 HGFNNLTKSLSFNIYDICYAKTEEEREAYIEYIDEQY 41 (259)
T ss_pred cccccccceeeeeeeeeEEeCCHHHHHHHHHHHHHhc
Confidence 67888899999986 4999999999999996543
No 137
>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=45.38 E-value=20 Score=25.69 Aligned_cols=32 Identities=25% Similarity=0.494 Sum_probs=23.1
Q ss_pred CCCccccCCccCCCccccccccccCCceEeCCCCC
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSN 95 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~ 95 (198)
....|..|++ +|.- ....--.||.+|-..|..
T Consensus 77 ~~~~C~vC~k-~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGK-PLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCC-cCCC--ceEEEeCCCeEEeccccc
Confidence 4567999999 6643 444455788999888864
No 138
>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=44.91 E-value=16 Score=26.66 Aligned_cols=26 Identities=35% Similarity=0.793 Sum_probs=18.4
Q ss_pred CCccccCCccCCC---------ccccccccccCCce
Q psy8222 62 AAVCMHCKRTQFT---------VLSRRHHCRKCGSV 88 (198)
Q Consensus 62 ~~~C~~C~~~~Fs---------~~~RrhhCr~CG~v 88 (198)
...|..|++ +.. .+.-|.+||.|+.-
T Consensus 33 rS~C~~C~~-~L~~~~lIPi~S~l~lrGrCr~C~~~ 67 (92)
T PF06750_consen 33 RSHCPHCGH-PLSWWDLIPILSYLLLRGRCRYCGAP 67 (92)
T ss_pred CCcCcCCCC-cCcccccchHHHHHHhCCCCcccCCC
Confidence 467888888 543 34558889988763
No 139
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=44.81 E-value=14 Score=36.35 Aligned_cols=23 Identities=26% Similarity=0.774 Sum_probs=14.0
Q ss_pred CCCccccCCccCCCccccccccccCCce
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHCRKCGSV 88 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhCr~CG~v 88 (198)
.+..|..|+. ++.. ..|..||..
T Consensus 14 ~akFC~~CG~-~l~~----~~Cp~CG~~ 36 (645)
T PRK14559 14 NNRFCQKCGT-SLTH----KPCPQCGTE 36 (645)
T ss_pred CCccccccCC-CCCC----CcCCCCCCC
Confidence 4566777776 5542 256667665
No 140
>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=44.71 E-value=16 Score=21.72 Aligned_cols=23 Identities=22% Similarity=0.725 Sum_probs=14.4
Q ss_pred ccccCCccCCCccc-cccccccCCc
Q psy8222 64 VCMHCKRTQFTVLS-RRHHCRKCGS 87 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~-RrhhCr~CG~ 87 (198)
.|..|+. .|.+-. -...|+.||.
T Consensus 2 ~C~~Cg~-~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGA-EVELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSS-SE-BSTSSTSSBSSSS-
T ss_pred CCCcCCC-eeEcCCCCcEECCcCCC
Confidence 4778888 777543 2467888875
No 141
>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=44.71 E-value=11 Score=28.73 Aligned_cols=26 Identities=19% Similarity=0.459 Sum_probs=16.9
Q ss_pred CCCccccCCccCCCccccccccccCCc
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHCRKCGS 87 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhCr~CG~ 87 (198)
..-.|..|+. .|.+......|..||.
T Consensus 69 ~~~~C~~Cg~-~~~~~~~~~~CP~Cgs 94 (115)
T TIGR00100 69 VECECEDCSE-EVSPEIDLYRCPKCHG 94 (115)
T ss_pred cEEEcccCCC-EEecCCcCccCcCCcC
Confidence 3456888887 7776655555666654
No 142
>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=44.59 E-value=13 Score=27.87 Aligned_cols=34 Identities=35% Similarity=0.655 Sum_probs=25.7
Q ss_pred cccccccccCCceEeCC--CCCCeeecCCCCCCCeeeccchHHhh
Q psy8222 76 LSRRHHCRKCGSVVCAP--CSNKRFLLPSQSAKPLRVCLTCYDVL 118 (198)
Q Consensus 76 ~~RrhhCr~CG~vvC~~--Cs~~~~~lp~~~~~~~RVC~~C~~~l 118 (198)
+.---+|-.||++||.. ||-+. ..|.|..|...-
T Consensus 46 LvLGa~CS~C~~~VC~~~~CSlFY---------tkrFC~pC~~~~ 81 (97)
T PF10170_consen 46 LVLGAPCSICGKPVCVGQDCSLFY---------TKRFCLPCVKRN 81 (97)
T ss_pred EEECccccccCCceEcCCCccEEe---------eCceeHHHHHHH
Confidence 33457999999999964 87543 579999998653
No 143
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=43.77 E-value=18 Score=23.61 Aligned_cols=27 Identities=33% Similarity=0.710 Sum_probs=18.2
Q ss_pred CCccccCCccCCCcc-ccccccccCCceE
Q psy8222 62 AAVCMHCKRTQFTVL-SRRHHCRKCGSVV 89 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~-~RrhhCr~CG~vv 89 (198)
...|..|+. .|-.. ..+++|..||...
T Consensus 20 ~~fCP~Cg~-~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGS-GFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCc-chheccCCcEECCCcCCEE
Confidence 457999987 44332 2478888888764
No 144
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=43.62 E-value=24 Score=31.58 Aligned_cols=61 Identities=28% Similarity=0.472 Sum_probs=39.3
Q ss_pred CCCccccCCccC-CCcc-------ccccccccCCc------eEeCCCCCCee----ecCCC-CCCCeeeccchHHhhccc
Q psy8222 61 EAAVCMHCKRTQ-FTVL-------SRRHHCRKCGS------VVCAPCSNKRF----LLPSQ-SAKPLRVCLTCYDVLSRD 121 (198)
Q Consensus 61 ~~~~C~~C~~~~-Fs~~-------~RrhhCr~CG~------vvC~~Cs~~~~----~lp~~-~~~~~RVC~~C~~~l~~~ 121 (198)
....|.+|+..+ .+++ .|.-||-.|+. +-|..|-..+. .+... ....+-+|..|...+...
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~ 265 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKIL 265 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeeeecCCCcceEeeecccccccceec
Confidence 357899999732 3432 36789999985 57888876431 12221 124667899998876654
No 145
>KOG1356|consensus
Probab=43.50 E-value=10 Score=38.25 Aligned_cols=36 Identities=31% Similarity=0.756 Sum_probs=28.6
Q ss_pred CCCCccccCCccCCCccccccccccCCceEeCCCCCCee
Q psy8222 60 NEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRF 98 (198)
Q Consensus 60 ~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~ 98 (198)
.....|..|.+|.|+ -.--|+.||..||-.|...+.
T Consensus 227 g~~~mC~~C~~tlfn---~hw~C~~C~~~~Cl~C~r~~~ 262 (889)
T KOG1356|consen 227 GIREMCDRCETTLFN---IHWRCPRCGFGVCLDCYRKWY 262 (889)
T ss_pred Ccchhhhhhcccccc---eeEEccccCCeeeecchhhcc
Confidence 355789999995554 345699999999999998875
No 146
>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=43.13 E-value=11 Score=24.03 Aligned_cols=14 Identities=36% Similarity=0.899 Sum_probs=8.8
Q ss_pred ccccCCccCCCcccc
Q psy8222 64 VCMHCKRTQFTVLSR 78 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~R 78 (198)
.|..|+. .|.++..
T Consensus 7 ~C~~Cg~-~fe~~~~ 20 (52)
T TIGR02605 7 RCTACGH-RFEVLQK 20 (52)
T ss_pred EeCCCCC-EeEEEEe
Confidence 4667776 6776643
No 147
>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=42.86 E-value=7.7 Score=23.25 Aligned_cols=29 Identities=28% Similarity=0.566 Sum_probs=18.1
Q ss_pred cccCCccCCCccccccccccCCceEeCCCCCCe
Q psy8222 65 CMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKR 97 (198)
Q Consensus 65 C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~ 97 (198)
|.+|.. .|..-. .=..||+.||..|....
T Consensus 1 C~iC~~-~~~~~~---~~~~C~H~fC~~C~~~~ 29 (41)
T PF00097_consen 1 CPICLE-PFEDPV---ILLPCGHSFCRDCLRKW 29 (41)
T ss_dssp ETTTSS-BCSSEE---EETTTSEEEEHHHHHHH
T ss_pred CCcCCc-cccCCC---EEecCCCcchHHHHHHH
Confidence 556666 444332 34578888888886554
No 148
>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=42.24 E-value=17 Score=22.57 Aligned_cols=15 Identities=27% Similarity=0.891 Sum_probs=9.8
Q ss_pred ccccccCCceEeCCC
Q psy8222 79 RHHCRKCGSVVCAPC 93 (198)
Q Consensus 79 rhhCr~CG~vvC~~C 93 (198)
...|+.||..||..+
T Consensus 13 ~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKH 27 (43)
T ss_dssp HEE-TTTS-EE-TTT
T ss_pred CeECCCCCcccCccc
Confidence 467999999999865
No 149
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=42.21 E-value=22 Score=24.10 Aligned_cols=20 Identities=30% Similarity=0.850 Sum_probs=14.4
Q ss_pred CCCCCCCeeeccchHHhhcc
Q psy8222 101 PSQSAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 101 p~~~~~~~RVC~~C~~~l~~ 120 (198)
|....++..||..|-++...
T Consensus 37 p~rdp~~~PVCP~Ck~iye~ 56 (58)
T PF11238_consen 37 PTRDPKPFPVCPECKEIYES 56 (58)
T ss_pred CCCCCCCCCCCcCHHHHHHh
Confidence 44345669999999887654
No 150
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=41.98 E-value=17 Score=31.82 Aligned_cols=34 Identities=21% Similarity=0.581 Sum_probs=26.7
Q ss_pred ccCCCCCccccCCccCCCcccc-------ccccccCCceEeC
Q psy8222 57 IPDNEAAVCMHCKRTQFTVLSR-------RHHCRKCGSVVCA 91 (198)
Q Consensus 57 v~d~~~~~C~~C~~~~Fs~~~R-------rhhCr~CG~vvC~ 91 (198)
-..+++..|..|.+ .|..+-. .+||..||+.|=+
T Consensus 127 p~rKeVSRCr~C~~-rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 127 PQRKEVSRCRKCRK-RYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred Cccccccccccccc-ccCCCccccccceeeeecccccccchh
Confidence 45578899999999 8876532 5999999998743
No 151
>KOG0978|consensus
Probab=41.54 E-value=2.5 Score=41.72 Aligned_cols=45 Identities=29% Similarity=0.718 Sum_probs=31.7
Q ss_pred CCCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHH
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYD 116 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~ 116 (198)
..-.|..|.. .+- ---=-.||++||..|...+. ....|-|..|-.
T Consensus 642 ~~LkCs~Cn~-R~K----d~vI~kC~H~FC~~Cvq~r~------etRqRKCP~Cn~ 686 (698)
T KOG0978|consen 642 ELLKCSVCNT-RWK----DAVITKCGHVFCEECVQTRY------ETRQRKCPKCNA 686 (698)
T ss_pred hceeCCCccC-chh----hHHHHhcchHHHHHHHHHHH------HHhcCCCCCCCC
Confidence 5568999986 542 11113699999999987653 256889999954
No 152
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=40.12 E-value=22 Score=21.35 Aligned_cols=18 Identities=22% Similarity=0.425 Sum_probs=10.0
Q ss_pred eecCCCCCCCeeeccchH
Q psy8222 98 FLLPSQSAKPLRVCLTCY 115 (198)
Q Consensus 98 ~~lp~~~~~~~RVC~~C~ 115 (198)
..+|....++-.||..|-
T Consensus 12 ~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 12 RRIPEGDDRERLVCPACG 29 (34)
T ss_dssp EE--TT-SS-EEEETTTT
T ss_pred hhcCCCCCccceECCCCC
Confidence 345554558888999984
No 153
>COG1773 Rubredoxin [Energy production and conversion]
Probab=39.96 E-value=13 Score=24.90 Aligned_cols=13 Identities=38% Similarity=0.823 Sum_probs=10.8
Q ss_pred cccccccCCceEe
Q psy8222 78 RRHHCRKCGSVVC 90 (198)
Q Consensus 78 RrhhCr~CG~vvC 90 (198)
+++.|+.||.|+=
T Consensus 2 ~~~~C~~CG~vYd 14 (55)
T COG1773 2 KRWRCSVCGYVYD 14 (55)
T ss_pred CceEecCCceEec
Confidence 4789999999973
No 154
>PF09947 DUF2180: Uncharacterized protein conserved in archaea (DUF2180); InterPro: IPR017211 This group represents a predicted zinc finger protein, AF1427 type.
Probab=39.84 E-value=7.4 Score=27.24 Aligned_cols=40 Identities=28% Similarity=0.556 Sum_probs=24.6
Q ss_pred cccccCCceEeCCCCCCee--------ecCC--C-CCCCeeeccchHHhhc
Q psy8222 80 HHCRKCGSVVCAPCSNKRF--------LLPS--Q-SAKPLRVCLTCYDVLS 119 (198)
Q Consensus 80 hhCr~CG~vvC~~Cs~~~~--------~lp~--~-~~~~~RVC~~C~~~l~ 119 (198)
--|..||.-+|..++.... ++|. . ..-+.-+|..|+..+.
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 3578899999998876421 1111 0 1134568999988653
No 155
>PF15451 DUF4632: Domain of unknown function (DUF4632)
Probab=39.28 E-value=26 Score=24.14 Aligned_cols=11 Identities=55% Similarity=1.102 Sum_probs=8.6
Q ss_pred ccccccccccc
Q psy8222 183 CNGYYCPEIEG 193 (198)
Q Consensus 183 ~~~~~~~~~~~ 193 (198)
.++.|||||..
T Consensus 55 snvlycpeikd 65 (71)
T PF15451_consen 55 SNVLYCPEIKD 65 (71)
T ss_pred ccceechhHhH
Confidence 45899999964
No 156
>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=39.22 E-value=46 Score=26.06 Aligned_cols=12 Identities=17% Similarity=0.470 Sum_probs=8.4
Q ss_pred CCCccccCCccCC
Q psy8222 61 EAAVCMHCKRTQF 73 (198)
Q Consensus 61 ~~~~C~~C~~~~F 73 (198)
.-+.|..|+. .+
T Consensus 90 ~~sRC~~CN~-~L 101 (147)
T PF01927_consen 90 IFSRCPKCNG-PL 101 (147)
T ss_pred CCCccCCCCc-Ee
Confidence 4567888887 44
No 157
>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=39.04 E-value=13 Score=22.59 Aligned_cols=26 Identities=23% Similarity=0.448 Sum_probs=16.0
Q ss_pred CccccCCccCCCccccccccccCCce
Q psy8222 63 AVCMHCKRTQFTVLSRRHHCRKCGSV 88 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~~RrhhCr~CG~v 88 (198)
..|..|+...|..-.-++.|..||.+
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 34888887322233456777777765
No 158
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=38.65 E-value=15 Score=30.62 Aligned_cols=43 Identities=19% Similarity=0.409 Sum_probs=34.6
Q ss_pred ccccCCceEeCCCCCC-eeecCCC-----CCCCeeeccchHHhhccccc
Q psy8222 81 HCRKCGSVVCAPCSNK-RFLLPSQ-----SAKPLRVCLTCYDVLSRDKT 123 (198)
Q Consensus 81 hCr~CG~vvC~~Cs~~-~~~lp~~-----~~~~~RVC~~C~~~l~~~~~ 123 (198)
.|...|+.+|..|-.. ..+||.. ..++..||...++.|.....
T Consensus 2 ~C~Y~G~yyC~~CH~~~~~vIParil~~WDf~~~pVs~~a~~~L~~~~~ 50 (202)
T PF13901_consen 2 FCDYTGKYYCSSCHWNDTSVIPARILHNWDFRPYPVSRFAKQFLDQIWS 50 (202)
T ss_pred ccCCCCCcCCCCCCCCCceeccHHHHHhcCCCccHHHHHHHHHHHHhcc
Confidence 5888999999999776 5677774 34899999999999876543
No 159
>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=38.04 E-value=24 Score=19.72 Aligned_cols=9 Identities=33% Similarity=0.911 Sum_probs=6.3
Q ss_pred ccccccCCc
Q psy8222 79 RHHCRKCGS 87 (198)
Q Consensus 79 rhhCr~CG~ 87 (198)
++.|.+||.
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 467888874
No 160
>PHA02926 zinc finger-like protein; Provisional
Probab=38.01 E-value=6.4 Score=33.87 Aligned_cols=56 Identities=18% Similarity=0.370 Sum_probs=33.8
Q ss_pred CCCccccCCccCCCcccc-cccc------ccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhcc
Q psy8222 61 EAAVCMHCKRTQFTVLSR-RHHC------RKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~R-rhhC------r~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~ 120 (198)
....|.+|-. . ++.+ .-.+ ..|+++||-.|-..+..... +....+.|..|-..+..
T Consensus 169 kE~eCgICmE-~--I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~-~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 169 KEKECGICYE-V--VYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRR-ETGASDNCPICRTRFRN 231 (242)
T ss_pred CCCCCccCcc-c--cccccccccccccccCCCCchHHHHHHHHHHHhcc-ccCcCCcCCCCcceeee
Confidence 4577888876 2 1111 1222 38999999999887654221 33456777777655443
No 161
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.48 E-value=18 Score=27.53 Aligned_cols=26 Identities=27% Similarity=0.517 Sum_probs=16.4
Q ss_pred CCCccccCCccCCCcccccc-ccccCCc
Q psy8222 61 EAAVCMHCKRTQFTVLSRRH-HCRKCGS 87 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~Rrh-hCr~CG~ 87 (198)
..-.|..|+. .|.+-...+ +|..||.
T Consensus 70 ~~~~C~~Cg~-~~~~~~~~~~~CP~Cgs 96 (117)
T PRK00564 70 VELECKDCSH-VFKPNALDYGVCEKCHS 96 (117)
T ss_pred CEEEhhhCCC-ccccCCccCCcCcCCCC
Confidence 3456888887 777654433 3666664
No 162
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=36.53 E-value=20 Score=37.18 Aligned_cols=52 Identities=25% Similarity=0.553 Sum_probs=34.6
Q ss_pred CCCccccCCccCCCccc---cccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhc
Q psy8222 61 EAAVCMHCKRTQFTVLS---RRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLS 119 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~---RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~ 119 (198)
....|.+|+. .-++.. --.-|.-||.-||..|-.+-. ..-..+|..|-....
T Consensus 14 ~~~~c~iCGd-~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~------~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 14 DAKTCRVCGD-EVGVKEDGQPFVACHVCGFPVCKPCYEYER------SEGNQCCPQCNTRYK 68 (1044)
T ss_pred Ccchhhcccc-ccCcCCCCCEEEEeccCCCccccchhhhhh------hcCCccCCccCCchh
Confidence 4678999998 544331 127799999999999976532 134567777755444
No 163
>KOG1170|consensus
Probab=36.46 E-value=27 Score=35.41 Aligned_cols=88 Identities=19% Similarity=0.375 Sum_probs=57.5
Q ss_pred CcceEEEecCCeEEEEEeCChHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCccccCC--CCCccccCCccCCCccc-cc
Q psy8222 3 LRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIEDLLRKSGKKPAATHAAVWIPDN--EAAVCMHCKRTQFTVLS-RR 79 (198)
Q Consensus 3 ~~n~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~~~g~~~~~~~~~~Wv~d~--~~~~C~~C~~~~Fs~~~-Rr 79 (198)
.+|.|-|.++.+...+.|.+..|...|+.++...... +... .+....+-.|+..+ ....|..|.++--+.++ --
T Consensus 60 ~~~sf~vi~~~rk~r~~adn~ke~e~wi~~~kt~q~~--e~~s-~~~a~mphqw~Egnlpvsskc~vc~k~cgs~~rlqd 136 (1099)
T KOG1170|consen 60 PRPSFCVITPVRKHRLCADNRKEMEKWINQSKTPQHL--EFIS-PENAIMPHQWMEGNLPVSSKCSVCEKPCGSVLRLQD 136 (1099)
T ss_pred CCCCeeEecccHHhhhhccchhHHHHhhccccchhhc--cccC-CCcccCchhhhhcCCCccccccccccccccccccCC
Confidence 5789999999999999999999999999887543321 1111 11122344687654 34678888873223332 23
Q ss_pred cccccCCceEeCCC
Q psy8222 80 HHCRKCGSVVCAPC 93 (198)
Q Consensus 80 hhCr~CG~vvC~~C 93 (198)
..|-.||-+|=..|
T Consensus 137 ~rclwc~~~vh~~c 150 (1099)
T KOG1170|consen 137 YRCLWCGCCVHDTC 150 (1099)
T ss_pred cceEeeccEeehhh
Confidence 66777777765555
No 164
>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=36.20 E-value=9.8 Score=28.74 Aligned_cols=26 Identities=31% Similarity=0.690 Sum_probs=17.3
Q ss_pred CCCccccCCccCCCccccccccccCCc
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHCRKCGS 87 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhCr~CG~ 87 (198)
..-.|..|+. .|.+-.....|..||.
T Consensus 69 ~~~~C~~Cg~-~~~~~~~~~~CP~Cgs 94 (113)
T PF01155_consen 69 ARARCRDCGH-EFEPDEFDFSCPRCGS 94 (113)
T ss_dssp -EEEETTTS--EEECHHCCHH-SSSSS
T ss_pred CcEECCCCCC-EEecCCCCCCCcCCcC
Confidence 4567888998 8887766677777765
No 165
>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=35.62 E-value=15 Score=23.40 Aligned_cols=30 Identities=17% Similarity=0.427 Sum_probs=20.3
Q ss_pred ccccCCccCCCccccccccccCCce-EeCCCCC
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSV-VCAPCSN 95 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~v-vC~~Cs~ 95 (198)
.|-.|+. +.+...|++|..|... +|..|-.
T Consensus 2 ~CDgCg~--~PI~G~RykC~~C~dyDLC~~C~~ 32 (43)
T cd02342 2 QCDGCGV--LPITGPRYKSKVKEDYDLCTICFS 32 (43)
T ss_pred CCCCCCC--CcccccceEeCCCCCCccHHHHhh
Confidence 4777885 5567788998887554 5555543
No 166
>PLN02436 cellulose synthase A
Probab=35.59 E-value=40 Score=35.11 Aligned_cols=26 Identities=35% Similarity=1.074 Sum_probs=17.8
Q ss_pred cccccCCce-----------EeCCCCCCeeecCCCCCCCeeeccchHHhh
Q psy8222 80 HHCRKCGSV-----------VCAPCSNKRFLLPSQSAKPLRVCLTCYDVL 118 (198)
Q Consensus 80 hhCr~CG~v-----------vC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l 118 (198)
+-|+.||.- .|..|. -.||..||+.-
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~-------------fpvCr~Cyeye 73 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECA-------------FPVCRPCYEYE 73 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCC-------------Cccccchhhhh
Confidence 578888864 455553 45899999643
No 167
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=35.21 E-value=25 Score=22.31 Aligned_cols=23 Identities=35% Similarity=0.843 Sum_probs=13.9
Q ss_pred ccccCCccCCCccc-cccccccCCc
Q psy8222 64 VCMHCKRTQFTVLS-RRHHCRKCGS 87 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~-RrhhCr~CG~ 87 (198)
.|..|+. .|.+-. -.-.|+.||.
T Consensus 4 ~C~~Cg~-~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGR-ENEIKSKDVVRCRECGY 27 (44)
T ss_pred ECCCCCC-EeecCCCCceECCCCCc
Confidence 4788888 787652 2344555554
No 168
>PF13590 DUF4136: Domain of unknown function (DUF4136)
Probab=35.16 E-value=64 Score=24.40 Aligned_cols=47 Identities=15% Similarity=0.219 Sum_probs=34.5
Q ss_pred cCCeEEEEEeC---ChHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCccc
Q psy8222 11 TSSKSFAVHAA---TSTEKQEWMAHINKCIEDLLRKSGKKPAATHAAVWI 57 (198)
Q Consensus 11 t~~KSf~v~A~---s~~Ek~~Wi~~i~~~i~~ll~~~g~~~~~~~~~~Wv 57 (198)
+.-|+|.+... .......-.+.|+.+|+..|.+.|.......+..++
T Consensus 15 ~~ykTy~~~~~~~~~~~~~~~~~~~i~~~v~~~L~~~G~~~~~~~aDl~V 64 (151)
T PF13590_consen 15 SQYKTYAFVPSSSDPAQSNPLDDQRIQDAVEQELAAKGYRRVPENADLLV 64 (151)
T ss_pred CCCCeEEEecCCcCccccCcHHHHHHHHHHHHHHHHCCCeecccCCCEEE
Confidence 46688888877 455556666789999999999999887644444443
No 169
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=35.12 E-value=26 Score=19.41 Aligned_cols=7 Identities=29% Similarity=0.961 Sum_probs=3.5
Q ss_pred ccccCCc
Q psy8222 64 VCMHCKR 70 (198)
Q Consensus 64 ~C~~C~~ 70 (198)
.|..|++
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4555554
No 170
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=34.99 E-value=12 Score=23.26 Aligned_cols=15 Identities=27% Similarity=0.806 Sum_probs=11.5
Q ss_pred ccCCceEeCCCCCCe
Q psy8222 83 RKCGSVVCAPCSNKR 97 (198)
Q Consensus 83 r~CG~vvC~~Cs~~~ 97 (198)
-.||++||..|....
T Consensus 14 l~CGH~FC~~Cl~~~ 28 (42)
T PF15227_consen 14 LPCGHSFCRSCLERL 28 (42)
T ss_dssp -SSSSEEEHHHHHHH
T ss_pred cCCcCHHHHHHHHHH
Confidence 369999999997654
No 171
>PHA02942 putative transposase; Provisional
Probab=34.65 E-value=33 Score=31.41 Aligned_cols=29 Identities=24% Similarity=0.615 Sum_probs=19.8
Q ss_pred CCCccccCCccCCCccccccccccCCceE
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHCRKCGSVV 89 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhCr~CG~vv 89 (198)
....|..|+...-.+-.|.+.|..||...
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCCEe
Confidence 45779999862223335778999998864
No 172
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=34.47 E-value=25 Score=26.97 Aligned_cols=30 Identities=20% Similarity=0.500 Sum_probs=23.2
Q ss_pred cccCCccCCCccccccccccCCceEeCCCCCCe
Q psy8222 65 CMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKR 97 (198)
Q Consensus 65 C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~ 97 (198)
|..|+. .+...+.+|..||-.+-+.-...+
T Consensus 1 CPvCg~---~l~vt~l~C~~C~t~i~G~F~l~~ 30 (113)
T PF09862_consen 1 CPVCGG---ELVVTRLKCPSCGTEIEGEFELPW 30 (113)
T ss_pred CCCCCC---ceEEEEEEcCCCCCEEEeeeccch
Confidence 889998 456678999999999877655433
No 173
>KOG2462|consensus
Probab=34.45 E-value=12 Score=33.06 Aligned_cols=38 Identities=24% Similarity=0.465 Sum_probs=19.0
Q ss_pred cccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhh
Q psy8222 80 HHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVL 118 (198)
Q Consensus 80 hhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l 118 (198)
+.|..||+.|=++ |+.|+-+.-.+....--|..|.+..
T Consensus 216 F~C~hC~kAFADR-SNLRAHmQTHS~~K~~qC~~C~KsF 253 (279)
T KOG2462|consen 216 FSCPHCGKAFADR-SNLRAHMQTHSDVKKHQCPRCGKSF 253 (279)
T ss_pred ccCCcccchhcch-HHHHHHHHhhcCCccccCcchhhHH
Confidence 4455555555221 3333333333444466777776543
No 174
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=34.28 E-value=19 Score=27.21 Aligned_cols=25 Identities=20% Similarity=0.612 Sum_probs=15.7
Q ss_pred CCccccCCccCCCccccccccccCCc
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCGS 87 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG~ 87 (198)
.-.|..|+. .|.+-....-|..||.
T Consensus 70 ~~~C~~Cg~-~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQ-VVEIHQHDAQCPHCHG 94 (113)
T ss_pred EEEcccCCC-EEecCCcCccCcCCCC
Confidence 456777777 7766554445666663
No 175
>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=34.28 E-value=15 Score=22.20 Aligned_cols=29 Identities=17% Similarity=0.595 Sum_probs=19.1
Q ss_pred CCccccCCccCCCccccccccccCCceEeCCCCC
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSN 95 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~ 95 (198)
...|..+.. . .-...|..|+..+|..|..
T Consensus 3 ~~~C~~H~~-~----~~~~~C~~C~~~~C~~C~~ 31 (42)
T PF00643_consen 3 EPKCPEHPE-E----PLSLFCEDCNEPLCSECTV 31 (42)
T ss_dssp SSB-SSTTT-S----BEEEEETTTTEEEEHHHHH
T ss_pred CccCccCCc-c----ceEEEecCCCCccCccCCC
Confidence 455666665 2 2346788899999988854
No 176
>KOG0689|consensus
Probab=33.73 E-value=65 Score=30.42 Aligned_cols=28 Identities=14% Similarity=0.323 Sum_probs=23.7
Q ss_pred CeEEEEEeCChHHHHHHHHHHHHHHHHH
Q psy8222 13 SKSFAVHAATSTEKQEWMAHINKCIEDL 40 (198)
Q Consensus 13 ~KSf~v~A~s~~Ek~~Wi~~i~~~i~~l 40 (198)
.-.|.++|.+.++|++|+++|...+.+.
T Consensus 336 ~~~~vlqa~s~~~k~~W~~~i~~~l~~Q 363 (448)
T KOG0689|consen 336 REAYVLQAGSKEIKYAWTRAISSLLWQQ 363 (448)
T ss_pred cceeEEeeCCHHHHHHHHHHHHHHHHHH
Confidence 3579999999999999999998766553
No 177
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=33.35 E-value=27 Score=23.06 Aligned_cols=26 Identities=31% Similarity=0.655 Sum_probs=12.9
Q ss_pred CCccccCCccCCCcc-ccccccccCCc
Q psy8222 62 AAVCMHCKRTQFTVL-SRRHHCRKCGS 87 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~-~RrhhCr~CG~ 87 (198)
...|..|+.-.|-.. .-|.+|-.||.
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred cccCCCCCCcchhhhcCceeEeccccc
Confidence 356777763123221 23566666664
No 178
>PF15616 TerY-C: TerY-C metal binding domain
Probab=33.18 E-value=30 Score=27.20 Aligned_cols=40 Identities=30% Similarity=0.626 Sum_probs=27.8
Q ss_pred CCccccCCccCCCccccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHHhhc
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLS 119 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~ 119 (198)
...|..|+. .|.|. -| .||+++|-.= ...-+|..|-....
T Consensus 77 ~PgCP~CGn-~~~fa----~C-~CGkl~Ci~g------------~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 77 APGCPHCGN-QYAFA----VC-GCGKLFCIDG------------EGEVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCCcC-hhcEE----Ee-cCCCEEEeCC------------CCCEECCCCCCeee
Confidence 478999999 87765 35 7999998632 22567777765443
No 179
>KOG3518|consensus
Probab=32.88 E-value=24 Score=32.40 Aligned_cols=35 Identities=17% Similarity=0.335 Sum_probs=27.7
Q ss_pred ceEEEe---cCCeEEEEEeCChHHHHHHHHHHHHHHHH
Q psy8222 5 NGWLIQ---TSSKSFAVHAATSTEKQEWMAHINKCIED 39 (198)
Q Consensus 5 n~f~i~---t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ 39 (198)
-+|+|. .|.--..+.|.+-++|+.||.++.++|-+
T Consensus 397 lsfqv~~fdnpkaq~~fma~sme~kr~wm~elkrlild 434 (521)
T KOG3518|consen 397 LSFQVFHFDNPKAQHTFMAKSMEDKRLWMLELKRLILD 434 (521)
T ss_pred ceeEEEecCCcchhhhhhhhhhHHHHHHHHHHHHHHHh
Confidence 345554 66667788999999999999999987754
No 180
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=32.51 E-value=30 Score=25.51 Aligned_cols=30 Identities=20% Similarity=0.559 Sum_probs=20.9
Q ss_pred CCCccccCCccCCCcccc----ccccccCCceEeCCC
Q psy8222 61 EAAVCMHCKRTQFTVLSR----RHHCRKCGSVVCAPC 93 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~R----rhhCr~CG~vvC~~C 93 (198)
....|..|+++ -+.| --+|+.||..|-+..
T Consensus 35 a~y~CpfCgk~---~vkR~a~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 35 AKYFCPFCGKH---AVKRQAVGIWRCKGCKKTVAGGA 68 (90)
T ss_pred CCccCCCCCCC---ceeeeeeEEEEcCCCCCEEeCCc
Confidence 45679999872 2333 368999999886644
No 181
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=32.49 E-value=23 Score=26.09 Aligned_cols=29 Identities=28% Similarity=0.676 Sum_probs=18.8
Q ss_pred CCCccccCCccCCCccccc----cccccCCceEeCC
Q psy8222 61 EAAVCMHCKRTQFTVLSRR----HHCRKCGSVVCAP 92 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~Rr----hhCr~CG~vvC~~ 92 (198)
....|..|++ ..+.|. -+|+.||..|-+.
T Consensus 34 ~ky~Cp~Cgk---~~vkR~a~GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 34 AKYTCPFCGK---TSVKRVATGIWKCKKCGKKFAGG 66 (90)
T ss_dssp S-BEESSSSS---SEEEEEETTEEEETTTTEEEE-B
T ss_pred CCCcCCCCCC---ceeEEeeeEEeecCCCCCEEeCC
Confidence 3457999998 234443 6888888887654
No 182
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=32.47 E-value=24 Score=28.53 Aligned_cols=15 Identities=27% Similarity=0.651 Sum_probs=7.1
Q ss_pred CCeeeccchHHhhcc
Q psy8222 106 KPLRVCLTCYDVLSR 120 (198)
Q Consensus 106 ~~~RVC~~C~~~l~~ 120 (198)
+.-|.|..|....++
T Consensus 26 RRRReC~~C~~RFTT 40 (156)
T COG1327 26 RRRRECLECGERFTT 40 (156)
T ss_pred hhhhcccccccccch
Confidence 444555555444433
No 183
>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=32.29 E-value=21 Score=21.30 Aligned_cols=13 Identities=38% Similarity=0.856 Sum_probs=7.5
Q ss_pred ccccCCccCCCccc
Q psy8222 64 VCMHCKRTQFTVLS 77 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~ 77 (198)
.|..|+. .|.++.
T Consensus 7 ~C~~Cg~-~fe~~~ 19 (41)
T smart00834 7 RCEDCGH-TFEVLQ 19 (41)
T ss_pred EcCCCCC-EEEEEE
Confidence 4666666 665543
No 184
>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=32.28 E-value=15 Score=32.03 Aligned_cols=61 Identities=28% Similarity=0.594 Sum_probs=31.1
Q ss_pred CCccccCCccC-CCcc-------ccccccccCCce------EeCCCCCCee-e-----cCCCCCCCeeeccchHHhhccc
Q psy8222 62 AAVCMHCKRTQ-FTVL-------SRRHHCRKCGSV------VCAPCSNKRF-L-----LPSQSAKPLRVCLTCYDVLSRD 121 (198)
Q Consensus 62 ~~~C~~C~~~~-Fs~~-------~RrhhCr~CG~v------vC~~Cs~~~~-~-----lp~~~~~~~RVC~~C~~~l~~~ 121 (198)
...|.+|+..+ .+++ .|..||-.||.- -|..|-+... . ........+-||..|...+...
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~v 251 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTV 251 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEE
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHH
Confidence 36899999731 2222 367899999964 7888876431 1 1222336788999998877655
Q ss_pred c
Q psy8222 122 K 122 (198)
Q Consensus 122 ~ 122 (198)
.
T Consensus 252 d 252 (290)
T PF04216_consen 252 D 252 (290)
T ss_dssp E
T ss_pred h
Confidence 4
No 185
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=31.90 E-value=42 Score=25.10 Aligned_cols=12 Identities=17% Similarity=0.517 Sum_probs=5.8
Q ss_pred CCceEeCCCCCC
Q psy8222 85 CGSVVCAPCSNK 96 (198)
Q Consensus 85 CG~vvC~~Cs~~ 96 (198)
=++++|..|-.+
T Consensus 40 ~~h~~C~~CG~y 51 (99)
T PRK14892 40 IAIITCGNCGLY 51 (99)
T ss_pred cceEECCCCCCc
Confidence 344555555444
No 186
>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=31.84 E-value=23 Score=28.31 Aligned_cols=25 Identities=24% Similarity=0.607 Sum_probs=20.1
Q ss_pred CccccCCccCCCcc---ccccccccCCce
Q psy8222 63 AVCMHCKRTQFTVL---SRRHHCRKCGSV 88 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~---~RrhhCr~CG~v 88 (198)
=.|..|+. .|++. .--.+|..||.+
T Consensus 110 Y~Cp~c~~-r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 110 FICPNMCV-RFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred EECCCCCc-EeeHHHHHHcCCcCCCCCCE
Confidence 35999998 99874 456899999986
No 187
>PF14851 FAM176: FAM176 family
Probab=31.76 E-value=89 Score=25.20 Aligned_cols=22 Identities=14% Similarity=0.176 Sum_probs=13.8
Q ss_pred CCCCcccchhccccc-cccccccc
Q psy8222 167 NIMPADQLSFKVDGL-NCNGYYCP 189 (198)
Q Consensus 167 ~~~p~~~~~~~~~~~-~~~~~~~~ 189 (198)
...|... ....+|. +.++|...
T Consensus 94 t~~p~~~-~~~~~~~ls~nvf~sa 116 (153)
T PF14851_consen 94 TESPMSE-HSQFDRTLSVNVFTSA 116 (153)
T ss_pred ccCCCCC-CCCCCCCCccCCcccH
Confidence 3456555 4555666 88888763
No 188
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=31.55 E-value=19 Score=32.54 Aligned_cols=38 Identities=26% Similarity=0.623 Sum_probs=29.5
Q ss_pred cccCCCCCccccCCccCCCc----------cccccccccCCceEeCCCC
Q psy8222 56 WIPDNEAAVCMHCKRTQFTV----------LSRRHHCRKCGSVVCAPCS 94 (198)
Q Consensus 56 Wv~d~~~~~C~~C~~~~Fs~----------~~RrhhCr~CG~vvC~~Cs 94 (198)
|-..-....|..|+. +|-. ..-|+.|..|-.-||..|-
T Consensus 356 ~~~~~ks~~Cf~CQ~-~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCd 403 (421)
T COG5151 356 EGTNPKSTHCFVCQG-PFPKPPVSPFDESTSSGRYQCELCKSTFCSDCD 403 (421)
T ss_pred CCCCCCCccceeccC-CCCCCCCCcccccccccceechhhhhhhhhhhH
Confidence 444445678999998 8843 2458999999999999994
No 189
>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=30.69 E-value=28 Score=21.71 Aligned_cols=30 Identities=27% Similarity=0.757 Sum_probs=19.5
Q ss_pred CCccccCCccCCCccccccccccCCc-eEeCCCC
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCGS-VVCAPCS 94 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG~-vvC~~Cs 94 (198)
...|..|++ . +...|++|..|.. -+|..|-
T Consensus 4 ~~~C~~C~~-~--i~g~ry~C~~C~d~dlC~~Cf 34 (44)
T smart00291 4 SYSCDTCGK-P--IVGVRYHCLVCPDYDLCQSCF 34 (44)
T ss_pred CcCCCCCCC-C--CcCCEEECCCCCCccchHHHH
Confidence 346888987 4 4566788888843 3555553
No 190
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=30.50 E-value=24 Score=27.52 Aligned_cols=13 Identities=15% Similarity=0.649 Sum_probs=7.5
Q ss_pred CccccCCccCCCcc
Q psy8222 63 AVCMHCKRTQFTVL 76 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~ 76 (198)
-.|..|+. .|.+-
T Consensus 71 ~~C~~CG~-~~~~~ 83 (135)
T PRK03824 71 LKCRNCGN-EWSLK 83 (135)
T ss_pred EECCCCCC-EEecc
Confidence 34666666 55554
No 191
>PRK11595 DNA utilization protein GntX; Provisional
Probab=30.37 E-value=12 Score=31.47 Aligned_cols=30 Identities=30% Similarity=0.893 Sum_probs=21.1
Q ss_pred CccccCCccCCCccccccccccCCce------EeCCCCC
Q psy8222 63 AVCMHCKRTQFTVLSRRHHCRKCGSV------VCAPCSN 95 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~~RrhhCr~CG~v------vC~~Cs~ 95 (198)
..|..|.. .|.++ .++|..||.. +|..|..
T Consensus 21 ~lC~~C~~-~l~~~--~~~C~~Cg~~~~~~~~~C~~C~~ 56 (227)
T PRK11595 21 GICSVCSR-ALRTL--KTCCPQCGLPATHPHLPCGRCLQ 56 (227)
T ss_pred cccHHHHh-hCCcc--cCcCccCCCcCCCCCCCcHHHHc
Confidence 36888877 77665 4789999974 3666644
No 192
>KOG3551|consensus
Probab=30.27 E-value=1.1e+02 Score=28.72 Aligned_cols=37 Identities=22% Similarity=0.431 Sum_probs=30.8
Q ss_pred eEEEecCC--eEEEEEeCChHHHHHHHHHHHHHHHHHHH
Q psy8222 6 GWLIQTSS--KSFAVHAATSTEKQEWMAHINKCIEDLLR 42 (198)
Q Consensus 6 ~f~i~t~~--KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll~ 42 (198)
.|.|.+|. -+..+-|++.++-+.|..+|..++..++.
T Consensus 238 ~lEihSpdg~~tliLR~kdsa~A~~Wf~AiHa~v~~ll~ 276 (506)
T KOG3551|consen 238 QLEIHSPDGRHTLILRAKDSAEADSWFEAIHANVNTLLT 276 (506)
T ss_pred eeeeeCCCCcceEEEEccCcHHHHHHHHHHHHHHhhHHH
Confidence 47788776 67888899999999999999988876543
No 193
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=29.81 E-value=26 Score=26.57 Aligned_cols=25 Identities=28% Similarity=0.797 Sum_probs=14.3
Q ss_pred CCccccCCccCCCccccc-cccccCCc
Q psy8222 62 AAVCMHCKRTQFTVLSRR-HHCRKCGS 87 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~Rr-hhCr~CG~ 87 (198)
.-.|..|+. .|....+. ..|..||.
T Consensus 70 ~~~C~~Cg~-~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 70 ECWCETCQQ-YVTLLTQRVRRCPQCHG 95 (114)
T ss_pred EEEcccCCC-eeecCCccCCcCcCcCC
Confidence 456777776 66654332 34666653
No 194
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=29.79 E-value=40 Score=21.19 Aligned_cols=7 Identities=43% Similarity=0.899 Sum_probs=3.5
Q ss_pred eeeccch
Q psy8222 108 LRVCLTC 114 (198)
Q Consensus 108 ~RVC~~C 114 (198)
..||..|
T Consensus 20 ~~vC~~C 26 (52)
T smart00661 20 RFVCRKC 26 (52)
T ss_pred EEECCcC
Confidence 4455555
No 195
>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=29.75 E-value=33 Score=19.92 Aligned_cols=23 Identities=26% Similarity=0.914 Sum_probs=14.5
Q ss_pred CccccCCccCCCccccccccccCCceEeC
Q psy8222 63 AVCMHCKRTQFTVLSRRHHCRKCGSVVCA 91 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~ 91 (198)
..|.+|+. ..++.|..||..+|+
T Consensus 3 ~~C~vC~~------~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 3 KLCSVCGN------PAKYRCPRCGARYCS 25 (30)
T ss_dssp EEETSSSS------EESEE-TTT--EESS
T ss_pred CCCccCcC------CCEEECCCcCCceeC
Confidence 35777763 457889999999886
No 196
>PRK12496 hypothetical protein; Provisional
Probab=29.39 E-value=35 Score=27.56 Aligned_cols=23 Identities=35% Similarity=0.807 Sum_probs=12.3
Q ss_pred ccccCCccCCCccccccccccCCc
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGS 87 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~ 87 (198)
.|..|++ .|..-.-.-.|..||.
T Consensus 129 ~C~gC~~-~~~~~~~~~~C~~CG~ 151 (164)
T PRK12496 129 VCKGCKK-KYPEDYPDDVCEICGS 151 (164)
T ss_pred ECCCCCc-cccCCCCCCcCCCCCC
Confidence 4666666 5544333345666654
No 197
>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=28.94 E-value=33 Score=22.92 Aligned_cols=24 Identities=33% Similarity=0.690 Sum_probs=15.3
Q ss_pred cccCCccCCCccccccccccCCceEeCC
Q psy8222 65 CMHCKRTQFTVLSRRHHCRKCGSVVCAP 92 (198)
Q Consensus 65 C~~C~~~~Fs~~~RrhhCr~CG~vvC~~ 92 (198)
|..|.. . ..+..-|-.||.+.|..
T Consensus 1 C~~C~~-~---~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGS-T---NSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHT-C---SSSEEEETTTS-EEETT
T ss_pred CCCCCC-c---CCceEEeCCCCcccccC
Confidence 455654 1 34556799999999986
No 198
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=28.90 E-value=1.2e+02 Score=26.91 Aligned_cols=35 Identities=14% Similarity=0.340 Sum_probs=23.5
Q ss_pred ccccccCCceEeCCCCCCeeecCCCCCCCeeeccchH
Q psy8222 79 RHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCY 115 (198)
Q Consensus 79 rhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~ 115 (198)
.|.|-+|--.||..+...+...-.. ...-.|..|-
T Consensus 182 q~sCLRCK~cfCddHvrrKg~ky~k--~k~~PCPKCg 216 (314)
T PF06524_consen 182 QYSCLRCKICFCDDHVRRKGFKYEK--GKPIPCPKCG 216 (314)
T ss_pred chhhhheeeeehhhhhhhccccccc--CCCCCCCCCC
Confidence 5888899999999998776432221 2444577774
No 199
>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=28.89 E-value=20 Score=22.60 Aligned_cols=23 Identities=26% Similarity=0.680 Sum_probs=14.4
Q ss_pred CCccccCCccCCCccccccccccCC
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCG 86 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG 86 (198)
.-.|..|+. . .+...|++|..|.
T Consensus 4 ~~~C~~C~~-~-~i~g~Ry~C~~C~ 26 (46)
T PF00569_consen 4 GYTCDGCGT-D-PIIGVRYHCLVCP 26 (46)
T ss_dssp SCE-SSS-S-S-SEESSEEEESSSS
T ss_pred CeECcCCCC-C-cCcCCeEECCCCC
Confidence 346888886 3 4556788888874
No 200
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=28.87 E-value=13 Score=23.49 Aligned_cols=14 Identities=43% Similarity=1.006 Sum_probs=9.8
Q ss_pred ccCCceEeCCCCCC
Q psy8222 83 RKCGSVVCAPCSNK 96 (198)
Q Consensus 83 r~CG~vvC~~Cs~~ 96 (198)
-.||++||..|...
T Consensus 17 L~CGH~~c~~cl~~ 30 (43)
T PF13445_consen 17 LPCGHVFCKDCLQK 30 (43)
T ss_dssp -SSS-EEEHHHHHH
T ss_pred EeCccHHHHHHHHH
Confidence 35999999988654
No 201
>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=28.71 E-value=26 Score=21.95 Aligned_cols=30 Identities=27% Similarity=0.793 Sum_probs=22.2
Q ss_pred ccccCCccCCCccccccccccC-CceEeCCCCCC
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKC-GSVVCAPCSNK 96 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~C-G~vvC~~Cs~~ 96 (198)
.|..|++ .+...|++|..| ..-+|..|-..
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 4788886 356678999999 46678888554
No 202
>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=28.67 E-value=38 Score=27.20 Aligned_cols=12 Identities=33% Similarity=0.938 Sum_probs=5.3
Q ss_pred cccccccccCCc
Q psy8222 76 LSRRHHCRKCGS 87 (198)
Q Consensus 76 ~~RrhhCr~CG~ 87 (198)
++||-.|..||+
T Consensus 25 IRRRReC~~C~~ 36 (147)
T TIGR00244 25 IRRRRECLECHE 36 (147)
T ss_pred eeecccCCccCC
Confidence 344444444444
No 203
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=28.43 E-value=34 Score=20.72 Aligned_cols=32 Identities=16% Similarity=0.410 Sum_probs=20.1
Q ss_pred CCccccCCccCCCccccccccccCCceEeCCCC
Q psy8222 62 AAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCS 94 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs 94 (198)
...|..|++ .+..+..-..|+.|+.++=.+|.
T Consensus 11 ~~~C~~C~~-~i~~~~~~~~C~~C~~~~H~~C~ 42 (49)
T smart00109 11 PTKCCVCRK-SIWGSFQGLRCSWCKVKCHKKCA 42 (49)
T ss_pred CCCcccccc-ccCcCCCCcCCCCCCchHHHHHH
Confidence 567899988 65543335678888765444443
No 204
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=28.40 E-value=29 Score=18.87 Aligned_cols=6 Identities=33% Similarity=1.115 Sum_probs=2.7
Q ss_pred cccCCc
Q psy8222 65 CMHCKR 70 (198)
Q Consensus 65 C~~C~~ 70 (198)
|..|+.
T Consensus 2 Cp~CG~ 7 (23)
T PF13240_consen 2 CPNCGA 7 (23)
T ss_pred CcccCC
Confidence 444444
No 205
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=28.22 E-value=89 Score=24.66 Aligned_cols=47 Identities=17% Similarity=0.338 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCCCCccccC-CCCCccccCCccCC
Q psy8222 26 KQEWMAHINKCIEDLLRKSGKKPAATHAAVWIPD-NEAAVCMHCKRTQF 73 (198)
Q Consensus 26 k~~Wi~~i~~~i~~ll~~~g~~~~~~~~~~Wv~d-~~~~~C~~C~~~~F 73 (198)
..+|.+.|....-.+++..|..++.. -.-|... .-.=.|..|+.+.|
T Consensus 4 ~~ewr~~Lt~~qy~V~r~~gTE~pft-g~y~~~~~~G~Y~C~~Cg~pLF 51 (134)
T TIGR00357 4 DEELKKKLTPLQYEVTQNAGTEPPFT-NEYWDNKEEGIYVDITCGEPLF 51 (134)
T ss_pred HHHHHHhCCHHHHHHHHHhCCCCCCC-CCCCCCCCCeEEEccCCCCccc
Confidence 47888877766666777666544321 1123222 22345777877433
No 206
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=28.17 E-value=32 Score=27.10 Aligned_cols=10 Identities=60% Similarity=1.434 Sum_probs=5.4
Q ss_pred cccccCCceE
Q psy8222 80 HHCRKCGSVV 89 (198)
Q Consensus 80 hhCr~CG~vv 89 (198)
|.|-+||++|
T Consensus 2 H~Ct~Cg~~f 11 (131)
T PF09845_consen 2 HQCTKCGRVF 11 (131)
T ss_pred cccCcCCCCc
Confidence 5555555554
No 207
>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=28.00 E-value=26 Score=21.73 Aligned_cols=11 Identities=45% Similarity=1.117 Sum_probs=5.0
Q ss_pred cccCCccCCCcc
Q psy8222 65 CMHCKRTQFTVL 76 (198)
Q Consensus 65 C~~C~~~~Fs~~ 76 (198)
|..|+. .|.++
T Consensus 8 C~~Cg~-~fe~~ 18 (42)
T PF09723_consen 8 CEECGH-EFEVL 18 (42)
T ss_pred eCCCCC-EEEEE
Confidence 444444 44443
No 208
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=27.99 E-value=39 Score=24.90 Aligned_cols=30 Identities=33% Similarity=0.706 Sum_probs=20.9
Q ss_pred CCCccccCCccCCCcccc----ccccccCCceEeCCC
Q psy8222 61 EAAVCMHCKRTQFTVLSR----RHHCRKCGSVVCAPC 93 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~R----rhhCr~CG~vvC~~C 93 (198)
....|..|++ .-+.| --+|+.||..|-+..
T Consensus 35 a~y~CpfCgk---~~vkR~a~GIW~C~~C~~~~AGGA 68 (90)
T PRK03976 35 AKHVCPVCGR---PKVKRVGTGIWECRKCGAKFAGGA 68 (90)
T ss_pred cCccCCCCCC---CceEEEEEEEEEcCCCCCEEeCCc
Confidence 4567999976 22333 378999999986654
No 209
>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=27.95 E-value=36 Score=24.82 Aligned_cols=24 Identities=25% Similarity=0.519 Sum_probs=11.8
Q ss_pred ccccCCccCCCccccccccccCCce
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSV 88 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~v 88 (198)
.|..|+. .+....-...|+.||..
T Consensus 2 fC~~Cg~-~l~~~~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGS-LMTPKNGVYVCPSCGYE 25 (104)
T ss_pred CCcccCc-ccccCCCeEECcCCCCc
Confidence 4667776 44332233445555443
No 210
>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=27.81 E-value=23 Score=22.20 Aligned_cols=29 Identities=28% Similarity=0.764 Sum_probs=19.7
Q ss_pred ccccCCccCCCccccccccccCC-ceEeCCCCC
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCG-SVVCAPCSN 95 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG-~vvC~~Cs~ 95 (198)
.|..|++ . +...|.+|..|. .-+|..|-.
T Consensus 2 ~C~~C~~-~--i~g~r~~C~~C~d~dLC~~Cf~ 31 (46)
T cd02249 2 SCDGCLK-P--IVGVRYHCLVCEDFDLCSSCYA 31 (46)
T ss_pred CCcCCCC-C--CcCCEEECCCCCCCcCHHHHHC
Confidence 4788887 4 345788888886 445666644
No 211
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=27.66 E-value=10 Score=25.21 Aligned_cols=31 Identities=23% Similarity=0.674 Sum_probs=23.7
Q ss_pred ccccCCccCCCccccccccccCCceEeCCCCCC
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNK 96 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~ 96 (198)
.|-.|+. .|.+- --..|-.||+--|+.|-..
T Consensus 9 ~CDLCn~-~~p~~-~LRQCvlCGRWaC~sCW~d 39 (57)
T PF14445_consen 9 SCDLCNS-SHPIS-ELRQCVLCGRWACNSCWQD 39 (57)
T ss_pred hHHhhcc-cCcHH-HHHHHhhhchhhhhhhhhh
Confidence 5788887 77654 3357999999999999643
No 212
>KOG1829|consensus
Probab=27.63 E-value=19 Score=34.95 Aligned_cols=58 Identities=19% Similarity=0.367 Sum_probs=41.5
Q ss_pred CccccCCccCCC--ccccccccccCCceEeCCCCCCee-ecCCC-----CCCCeeeccchHHhhccc
Q psy8222 63 AVCMHCKRTQFT--VLSRRHHCRKCGSVVCAPCSNKRF-LLPSQ-----SAKPLRVCLTCYDVLSRD 121 (198)
Q Consensus 63 ~~C~~C~~~~Fs--~~~RrhhCr~CG~vvC~~Cs~~~~-~lp~~-----~~~~~RVC~~C~~~l~~~ 121 (198)
-.|..|+. .+. ++.+-.-|+.+|+.||..|-..-. +||.- ..++-.||+.=...|...
T Consensus 341 ~~CAgC~~-~i~~~~~~~~R~C~y~G~y~C~~Ch~~~~svIPARVl~~WDf~~y~Vs~~a~~~L~~i 406 (580)
T KOG1829|consen 341 FRCAGCGH-TIGPDLEQRPRLCRYLGKYFCDCCHQNDKSVIPARVLHNWDFTKYPVSNFAKQFLDEI 406 (580)
T ss_pred ceecccCC-CcccccccchhHhhhhhhhhCchhcccCcccccccceecccCcccccchhHHHHHHHH
Confidence 47999999 887 446778999999999999977643 34553 236677776665555443
No 213
>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=27.63 E-value=21 Score=32.42 Aligned_cols=45 Identities=31% Similarity=0.706 Sum_probs=18.2
Q ss_pred CCCccccCCccCCCc----------------cccccccccCCceEeCCCCCCeeecCCCCCCCeeeccchHH
Q psy8222 61 EAAVCMHCKRTQFTV----------------LSRRHHCRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYD 116 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~----------------~~RrhhCr~CG~vvC~~Cs~~~~~lp~~~~~~~RVC~~C~~ 116 (198)
.+-.|..|.-|.|.. +.|=..|..||.-. +.+.. -|...|..|-.
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt--------~sl~r---~P~~~C~~Cg~ 311 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRT--------ISLER---LPKKHCSNCGS 311 (344)
T ss_dssp EEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EE--------EESSS---S--S--TTT-S
T ss_pred EEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCee--------eeccc---CCCCCCCcCCc
Confidence 355688887655543 23346788887741 22211 35567888854
No 214
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=27.61 E-value=40 Score=24.89 Aligned_cols=30 Identities=30% Similarity=0.700 Sum_probs=21.1
Q ss_pred CCCccccCCccCCCcccc----ccccccCCceEeCCC
Q psy8222 61 EAAVCMHCKRTQFTVLSR----RHHCRKCGSVVCAPC 93 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~R----rhhCr~CG~vvC~~C 93 (198)
....|..|+++ -+.| --+|+.||..|-+..
T Consensus 34 a~y~CpfCgk~---~vkR~a~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 34 AKYVCPFCGKK---TVKRGSTGIWTCRKCGAKFAGGA 67 (91)
T ss_pred cCccCCCCCCC---ceEEEeeEEEEcCCCCCEEeCCc
Confidence 45679999872 2444 378999999886644
No 215
>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=27.37 E-value=27 Score=29.64 Aligned_cols=31 Identities=23% Similarity=0.458 Sum_probs=14.1
Q ss_pred EeCCCCCCeeecCCCCC-CCeeeccchHHhhc
Q psy8222 89 VCAPCSNKRFLLPSQSA-KPLRVCLTCYDVLS 119 (198)
Q Consensus 89 vC~~Cs~~~~~lp~~~~-~~~RVC~~C~~~l~ 119 (198)
.|..|.-....+-.... -.+.+|..|-....
T Consensus 15 lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~ 46 (236)
T PF04981_consen 15 LCPDCYLKRFDIIEIPDRIEVTICPKCGRYRI 46 (236)
T ss_pred cChHHhcccCCeeecCCccCceECCCCCCEEC
Confidence 55555544433322211 34555666644433
No 216
>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=27.28 E-value=15 Score=27.58 Aligned_cols=55 Identities=18% Similarity=0.515 Sum_probs=34.1
Q ss_pred CCCccccCCccCCCcccccccc------ccC---CceEeCCCCCCeeecCC--CCCCCeeeccchHHhh
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHC------RKC---GSVVCAPCSNKRFLLPS--QSAKPLRVCLTCYDVL 118 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhC------r~C---G~vvC~~Cs~~~~~lp~--~~~~~~RVC~~C~~~l 118 (198)
....|..|.+ +-. ..+..| ..| ...||..|...+..... ....+.-+|..|..+-
T Consensus 6 ~g~~CHqCrq-Kt~--~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiC 71 (105)
T PF10497_consen 6 NGKTCHQCRQ-KTL--DFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGIC 71 (105)
T ss_pred CCCCchhhcC-CCC--CCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCee
Confidence 4567888876 322 222334 556 88999999887653211 1235678888887643
No 217
>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=27.21 E-value=45 Score=31.59 Aligned_cols=36 Identities=22% Similarity=0.696 Sum_probs=23.0
Q ss_pred CccccCCccCCCcc--ccccccccCCce-----EeCCCCCCeee
Q psy8222 63 AVCMHCKRTQFTVL--SRRHHCRKCGSV-----VCAPCSNKRFL 99 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~--~RrhhCr~CG~v-----vC~~Cs~~~~~ 99 (198)
-.|..|.. ..++- ..+-.|..||.. .|..|.+..+.
T Consensus 223 ~~C~~C~~-~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~ 265 (505)
T TIGR00595 223 LCCPNCDV-SLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLV 265 (505)
T ss_pred cCCCCCCC-ceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeE
Confidence 35677776 44432 345678888877 68888775543
No 218
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=27.15 E-value=34 Score=27.02 Aligned_cols=26 Identities=27% Similarity=0.606 Sum_probs=18.6
Q ss_pred CCccccCCccCCCcccc-----ccccccCCce
Q psy8222 62 AAVCMHCKRTQFTVLSR-----RHHCRKCGSV 88 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~R-----rhhCr~CG~v 88 (198)
--.|..|+. +-+.+.+ -.+|..||..
T Consensus 102 yVlC~~C~s-pdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGS-PDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCC-CCcEEEEcCCeEEEEcccCCCC
Confidence 357999999 8777765 2577777764
No 219
>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=26.79 E-value=13 Score=20.78 Aligned_cols=15 Identities=33% Similarity=0.846 Sum_probs=10.6
Q ss_pred ccCCceEeCCCCCCe
Q psy8222 83 RKCGSVVCAPCSNKR 97 (198)
Q Consensus 83 r~CG~vvC~~Cs~~~ 97 (198)
..||++||..|....
T Consensus 14 ~~C~H~~c~~C~~~~ 28 (39)
T smart00184 14 LPCGHTFCRSCIRKW 28 (39)
T ss_pred ecCCChHHHHHHHHH
Confidence 358888888886543
No 220
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=26.41 E-value=56 Score=32.21 Aligned_cols=48 Identities=23% Similarity=0.659 Sum_probs=31.1
Q ss_pred CccccCCccCCCccccccccccCCce----EeCCCCCCeeecCCCCCCCeeeccchHHhhcc
Q psy8222 63 AVCMHCKRTQFTVLSRRHHCRKCGSV----VCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSR 120 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~~RrhhCr~CG~v----vC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~ 120 (198)
..|..|+. . .-..-..|..||.. +|..|... +| ...+.|..|-..+..
T Consensus 2 ~~Cp~Cg~-~--n~~~akFC~~CG~~l~~~~Cp~CG~~---~~----~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 2 LICPQCQF-E--NPNNNRFCQKCGTSLTHKPCPQCGTE---VP----VDEAHCPNCGAETGT 53 (645)
T ss_pred CcCCCCCC-c--CCCCCccccccCCCCCCCcCCCCCCC---CC----cccccccccCCcccc
Confidence 36888987 3 23344578888876 47777543 12 457789999766544
No 221
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.10 E-value=47 Score=24.41 Aligned_cols=29 Identities=34% Similarity=0.767 Sum_probs=19.4
Q ss_pred CCCccccCCccCCCcccc----ccccccCCceEeCC
Q psy8222 61 EAAVCMHCKRTQFTVLSR----RHHCRKCGSVVCAP 92 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~R----rhhCr~CG~vvC~~ 92 (198)
....|..|++ . ...| --.|+.||..|=+.
T Consensus 34 ~~~~Cp~C~~-~--~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGR-T--TVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCC-c--ceeeeccCeEEcCCCCCeeccc
Confidence 3467999998 4 3333 36788888877443
No 222
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=25.97 E-value=32 Score=26.99 Aligned_cols=27 Identities=26% Similarity=0.744 Sum_probs=16.7
Q ss_pred CCccccCCccCCCccc--------cccccccCCceE
Q psy8222 62 AAVCMHCKRTQFTVLS--------RRHHCRKCGSVV 89 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~--------RrhhCr~CG~vv 89 (198)
.=.|..|+. .|++.. +...|..||..+
T Consensus 99 ~Y~Cp~C~~-~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 99 YYKCPNCQS-KYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred EEECcCCCC-EeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 345889998 888642 125566665543
No 223
>PF14353 CpXC: CpXC protein
Probab=25.96 E-value=33 Score=25.98 Aligned_cols=11 Identities=27% Similarity=0.800 Sum_probs=8.1
Q ss_pred ccccccCCceE
Q psy8222 79 RHHCRKCGSVV 89 (198)
Q Consensus 79 rhhCr~CG~vv 89 (198)
.+.|..||..+
T Consensus 38 ~~~CP~Cg~~~ 48 (128)
T PF14353_consen 38 SFTCPSCGHKF 48 (128)
T ss_pred EEECCCCCCce
Confidence 47788888764
No 224
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=25.45 E-value=47 Score=22.31 Aligned_cols=7 Identities=57% Similarity=1.654 Sum_probs=2.9
Q ss_pred cccCCce
Q psy8222 82 CRKCGSV 88 (198)
Q Consensus 82 Cr~CG~v 88 (198)
||.||..
T Consensus 18 CrRCG~~ 24 (55)
T PF01907_consen 18 CRRCGRR 24 (55)
T ss_dssp -TTTSSE
T ss_pred ecccCCe
Confidence 4455543
No 225
>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=25.25 E-value=33 Score=22.11 Aligned_cols=12 Identities=33% Similarity=0.719 Sum_probs=8.8
Q ss_pred ccccccCCceEe
Q psy8222 79 RHHCRKCGSVVC 90 (198)
Q Consensus 79 rhhCr~CG~vvC 90 (198)
|+.|+.||.|+=
T Consensus 1 ky~C~~CgyvYd 12 (47)
T PF00301_consen 1 KYQCPVCGYVYD 12 (47)
T ss_dssp EEEETTTSBEEE
T ss_pred CcCCCCCCEEEc
Confidence 567888888763
No 226
>KOG2845|consensus
Probab=25.19 E-value=40 Score=32.15 Aligned_cols=11 Identities=45% Similarity=1.380 Sum_probs=10.0
Q ss_pred ccccCCceEeC
Q psy8222 81 HCRKCGSVVCA 91 (198)
Q Consensus 81 hCr~CG~vvC~ 91 (198)
+|-.||+|||-
T Consensus 172 NCL~CGkIVCe 182 (505)
T KOG2845|consen 172 NCLGCGKIVCE 182 (505)
T ss_pred cccccceeEEE
Confidence 89999999995
No 227
>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=24.99 E-value=25 Score=22.17 Aligned_cols=30 Identities=20% Similarity=0.517 Sum_probs=20.2
Q ss_pred CccccCCccCCCccccccccccCCce-EeCCCCCCe
Q psy8222 63 AVCMHCKRTQFTVLSRRHHCRKCGSV-VCAPCSNKR 97 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~~RrhhCr~CG~v-vC~~Cs~~~ 97 (198)
..|.+|.. .+. ...-..||++ ||..|....
T Consensus 3 ~~C~iC~~-~~~----~~~~~pCgH~~~C~~C~~~~ 33 (50)
T PF13920_consen 3 EECPICFE-NPR----DVVLLPCGHLCFCEECAERL 33 (50)
T ss_dssp SB-TTTSS-SBS----SEEEETTCEEEEEHHHHHHH
T ss_pred CCCccCCc-cCC----ceEEeCCCChHHHHHHhHHh
Confidence 46888887 433 3445579999 999997654
No 228
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=24.71 E-value=30 Score=28.29 Aligned_cols=25 Identities=28% Similarity=0.731 Sum_probs=19.4
Q ss_pred CccccCCccCCCcc---ccccccccCCce
Q psy8222 63 AVCMHCKRTQFTVL---SRRHHCRKCGSV 88 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~---~RrhhCr~CG~v 88 (198)
=.|..|+. .|++. .--.+|..||..
T Consensus 118 Y~Cp~C~~-rytf~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 118 FFCPNCHI-RFTFDEAMEYGFRCPQCGEM 145 (178)
T ss_pred EECCCCCc-EEeHHHHhhcCCcCCCCCCC
Confidence 35999998 99875 456888888875
No 229
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=24.50 E-value=40 Score=26.43 Aligned_cols=25 Identities=32% Similarity=0.830 Sum_probs=18.2
Q ss_pred CccccCCccCCCcccc--c---cccccCCce
Q psy8222 63 AVCMHCKRTQFTVLSR--R---HHCRKCGSV 88 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~~R--r---hhCr~CG~v 88 (198)
-.|..|+. +-+-+.+ | .+|..||..
T Consensus 98 VlC~~C~s-PdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNR-PDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred EECCCCCC-CCcEEEEeCCeEEEecccCCCC
Confidence 57999999 7777655 2 477777764
No 230
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=24.36 E-value=34 Score=21.85 Aligned_cols=31 Identities=26% Similarity=0.641 Sum_probs=19.6
Q ss_pred ccccCCccCCCccccccccccC-CceEeCCCCCC
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKC-GSVVCAPCSNK 96 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~C-G~vvC~~Cs~~ 96 (198)
.|..|.+ ... -..|.+|..| ..-+|..|-..
T Consensus 2 ~Cd~C~~-~~~-~g~r~~C~~C~d~dLC~~Cf~~ 33 (49)
T cd02335 2 HCDYCSK-DIT-GTIRIKCAECPDFDLCLECFSA 33 (49)
T ss_pred CCCCcCC-CCC-CCcEEECCCCCCcchhHHhhhC
Confidence 4888887 442 2277888888 44466666443
No 231
>PRK04023 DNA polymerase II large subunit; Validated
Probab=24.32 E-value=56 Score=34.00 Aligned_cols=45 Identities=20% Similarity=0.449 Sum_probs=29.4
Q ss_pred CCCccccCCccCCCccccccccccCCce-----EeCCCCCCeeecCCCCCCCeeeccchHHhhc
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHCRKCGSV-----VCAPCSNKRFLLPSQSAKPLRVCLTCYDVLS 119 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhCr~CG~v-----vC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~ 119 (198)
....|..|+. .. -...|..||.. +|..|-.... .-.|..|-..+.
T Consensus 625 g~RfCpsCG~-~t----~~frCP~CG~~Te~i~fCP~CG~~~~---------~y~CPKCG~El~ 674 (1121)
T PRK04023 625 GRRKCPSCGK-ET----FYRRCPFCGTHTEPVYRCPRCGIEVE---------EDECEKCGREPT 674 (1121)
T ss_pred cCccCCCCCC-cC----CcccCCCCCCCCCcceeCccccCcCC---------CCcCCCCCCCCC
Confidence 4578999998 53 23689999964 8999933211 133777755544
No 232
>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=24.31 E-value=33 Score=22.20 Aligned_cols=29 Identities=10% Similarity=0.001 Sum_probs=17.9
Q ss_pred ccccCCccCCCccccccccccCCceEeCCCCCCe
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKR 97 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~ 97 (198)
.|.+|.. .|.- -....||++||..|....
T Consensus 3 ~Cpi~~~-~~~~----Pv~~~~G~v~~~~~i~~~ 31 (63)
T smart00504 3 LCPISLE-VMKD----PVILPSGQTYERRAIEKW 31 (63)
T ss_pred CCcCCCC-cCCC----CEECCCCCEEeHHHHHHH
Confidence 4677776 4322 244578888888776554
No 233
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=24.18 E-value=51 Score=21.85 Aligned_cols=23 Identities=26% Similarity=0.658 Sum_probs=12.2
Q ss_pred CCCCccccCCccCCCccccccccccCC
Q psy8222 60 NEAAVCMHCKRTQFTVLSRRHHCRKCG 86 (198)
Q Consensus 60 ~~~~~C~~C~~~~Fs~~~RrhhCr~CG 86 (198)
.....|..|+. +....|-|..||
T Consensus 24 p~l~~C~~cG~----~~~~H~vc~~cG 46 (55)
T TIGR01031 24 PTLVVCPNCGE----FKLPHRVCPSCG 46 (55)
T ss_pred CcceECCCCCC----cccCeeECCccC
Confidence 34456777776 223334455555
No 234
>PF15277 Sec3-PIP2_bind: Exocyst complex component SEC3 N-terminal PIP2 binding PH; PDB: 3HIE_D 3A58_E.
Probab=24.08 E-value=2.4e+02 Score=20.33 Aligned_cols=32 Identities=16% Similarity=0.256 Sum_probs=25.3
Q ss_pred eEEEecCCeEEEEEeCChHHHHHHHHHHHHHHH
Q psy8222 6 GWLIQTSSKSFAVHAATSTEKQEWMAHINKCIE 38 (198)
Q Consensus 6 ~f~i~t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~ 38 (198)
+|.|. -.|.+...|.|.+||..++..|-+...
T Consensus 58 ~F~l~-~~k~y~W~a~s~~Ek~~Fi~~L~k~~~ 89 (91)
T PF15277_consen 58 EFDLT-FDKPYYWEASSAKEKNTFIRSLWKLYQ 89 (91)
T ss_dssp EEEEE-SSSEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred CEEEE-ECCCcEEEeCCHHHHHHHHHHHHHHhc
Confidence 45544 467999999999999999998876543
No 235
>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=24.07 E-value=40 Score=20.19 Aligned_cols=26 Identities=27% Similarity=0.579 Sum_probs=13.4
Q ss_pred eEeCCCCCCeeecCCCCCCCeeeccchH
Q psy8222 88 VVCAPCSNKRFLLPSQSAKPLRVCLTCY 115 (198)
Q Consensus 88 vvC~~Cs~~~~~lp~~~~~~~RVC~~C~ 115 (198)
.||..|.+.-.+... ....+ +|..|-
T Consensus 2 ~FCp~C~nlL~p~~~-~~~~~-~C~~C~ 27 (35)
T PF02150_consen 2 RFCPECGNLLYPKED-KEKRV-ACRTCG 27 (35)
T ss_dssp -BETTTTSBEEEEEE-TTTTE-EESSSS
T ss_pred eeCCCCCccceEcCC-CccCc-CCCCCC
Confidence 467777665443222 12223 788873
No 236
>KOG0153|consensus
Probab=23.96 E-value=40 Score=30.81 Aligned_cols=22 Identities=23% Similarity=0.484 Sum_probs=17.4
Q ss_pred cccCCCCCccccCCccCCCcccc
Q psy8222 56 WIPDNEAAVCMHCKRTQFTVLSR 78 (198)
Q Consensus 56 Wv~d~~~~~C~~C~~~~Fs~~~R 78 (198)
........+|.+|.+ +|++|+.
T Consensus 35 MtK~~~gkECKICtr-PfT~Frw 56 (377)
T KOG0153|consen 35 MTKEPYGKECKICTR-PFTIFRW 56 (377)
T ss_pred eeccccCCccceecC-cceEEEe
Confidence 334456789999999 9999965
No 237
>KOG3795|consensus
Probab=23.90 E-value=39 Score=28.18 Aligned_cols=23 Identities=30% Similarity=0.780 Sum_probs=18.1
Q ss_pred CCCccccccccccCCc---eEeCCCC
Q psy8222 72 QFTVLSRRHHCRKCGS---VVCAPCS 94 (198)
Q Consensus 72 ~Fs~~~RrhhCr~CG~---vvC~~Cs 94 (198)
.|.-...||.|+.||. .||-.|.
T Consensus 8 ~~d~ieGRs~C~~C~~SRkFfCY~C~ 33 (230)
T KOG3795|consen 8 SFDPIEGRSTCPGCKSSRKFFCYDCR 33 (230)
T ss_pred ccCcccccccCCCCCCcceEEEEeec
Confidence 5666778899999986 4888885
No 238
>KOG0931|consensus
Probab=23.88 E-value=1.6e+02 Score=28.31 Aligned_cols=40 Identities=10% Similarity=0.211 Sum_probs=33.7
Q ss_pred CCCcceEEEecCCeE------EEEEeCChHHHHHHHHHHHHHHHHH
Q psy8222 1 MELRNGWLIQTSSKS------FAVHAATSTEKQEWMAHINKCIEDL 40 (198)
Q Consensus 1 ~~~~n~f~i~t~~KS------f~v~A~s~~Ek~~Wi~~i~~~i~~l 40 (198)
++|++++.|.++-+- +.+.|.+.++|..+++.+.+.|.+.
T Consensus 483 ~yY~fGitltsp~~g~e~k~~ihFnA~n~~dr~kFv~Dl~ESIaEv 528 (627)
T KOG0931|consen 483 GYYEFGITLTSPVPGSEKKVLIHFNAPNFQDRCKFVADLRESIAEV 528 (627)
T ss_pred ccccCceEEeccCCCCceeEEEEecCCCHHHHHHHHHHHHHHHHHH
Confidence 578999999977653 6688999999999999999888754
No 239
>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=23.87 E-value=36 Score=20.85 Aligned_cols=11 Identities=36% Similarity=1.005 Sum_probs=6.2
Q ss_pred ccccccCCceE
Q psy8222 79 RHHCRKCGSVV 89 (198)
Q Consensus 79 rhhCr~CG~vv 89 (198)
-+.|..||.+|
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 36899999986
No 240
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=23.82 E-value=42 Score=26.67 Aligned_cols=30 Identities=23% Similarity=0.500 Sum_probs=17.1
Q ss_pred eEeCCCCCC-eeecCCCCC---CCeeeccchHHh
Q psy8222 88 VVCAPCSNK-RFLLPSQSA---KPLRVCLTCYDV 117 (198)
Q Consensus 88 vvC~~Cs~~-~~~lp~~~~---~~~RVC~~C~~~ 117 (198)
|-|..|-+. ...+...|. |....|..|.+-
T Consensus 106 ~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~ep 139 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFGPTACKALYRCRACKEP 139 (146)
T ss_pred CcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCc
Confidence 444445333 334444454 778888888653
No 241
>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=23.75 E-value=38 Score=18.59 Aligned_cols=12 Identities=25% Similarity=0.722 Sum_probs=7.1
Q ss_pred cccccccCCceE
Q psy8222 78 RRHHCRKCGSVV 89 (198)
Q Consensus 78 RrhhCr~CG~vv 89 (198)
+.+.|..||+.|
T Consensus 13 k~~~C~~C~k~F 24 (26)
T PF13465_consen 13 KPYKCPYCGKSF 24 (26)
T ss_dssp SSEEESSSSEEE
T ss_pred CCCCCCCCcCee
Confidence 446666666654
No 242
>PRK14873 primosome assembly protein PriA; Provisional
Probab=23.67 E-value=44 Score=32.94 Aligned_cols=35 Identities=34% Similarity=0.829 Sum_probs=21.4
Q ss_pred CccccCCccCCCccc--cccccccCCce----EeCCCCCCee
Q psy8222 63 AVCMHCKRTQFTVLS--RRHHCRKCGSV----VCAPCSNKRF 98 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~~--RrhhCr~CG~v----vC~~Cs~~~~ 98 (198)
-.|..|.. +.++-+ ++-.|+.||.. .|..|.+..+
T Consensus 393 ~~C~~C~~-~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~~l 433 (665)
T PRK14873 393 ARCRHCTG-PLGLPSAGGTPRCRWCGRAAPDWRCPRCGSDRL 433 (665)
T ss_pred eECCCCCC-ceeEecCCCeeECCCCcCCCcCccCCCCcCCcc
Confidence 45677776 665532 34668888764 5777766543
No 243
>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=23.66 E-value=42 Score=21.04 Aligned_cols=25 Identities=36% Similarity=0.778 Sum_probs=15.7
Q ss_pred CccccCCccCCCcc-c-cccccccCCc
Q psy8222 63 AVCMHCKRTQFTVL-S-RRHHCRKCGS 87 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~-~-RrhhCr~CG~ 87 (198)
-.|+.|+.+....+ . .++.|+.|++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 56999986322222 2 4678888864
No 244
>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=23.54 E-value=38 Score=21.78 Aligned_cols=28 Identities=25% Similarity=0.844 Sum_probs=16.9
Q ss_pred ccccCCccCCCccccccccccCCce-EeCCC
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSV-VCAPC 93 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~v-vC~~C 93 (198)
.|..|.+. .+...|.+|-.|..+ .|..|
T Consensus 2 ~C~~C~~~--~i~g~R~~C~~C~dydLC~~C 30 (49)
T cd02345 2 SCSACRKQ--DISGIRFPCQVCRDYSLCLGC 30 (49)
T ss_pred cCCCCCCC--CceEeeEECCCCCCcCchHHH
Confidence 47778762 444677788887543 34433
No 245
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.32 E-value=28 Score=32.28 Aligned_cols=32 Identities=25% Similarity=0.583 Sum_probs=23.2
Q ss_pred CCCccccCCccCCCccccccccccCCceEeCCCCCCe
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKR 97 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~ 97 (198)
..-.|.+|.. .|.- ..--.||+.||..|....
T Consensus 25 ~~l~C~IC~d-~~~~----PvitpCgH~FCs~CI~~~ 56 (397)
T TIGR00599 25 TSLRCHICKD-FFDV----PVLTSCSHTFCSLCIRRC 56 (397)
T ss_pred cccCCCcCch-hhhC----ccCCCCCCchhHHHHHHH
Confidence 4568999998 6632 223589999999997653
No 246
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=22.76 E-value=41 Score=27.80 Aligned_cols=21 Identities=43% Similarity=0.991 Sum_probs=11.0
Q ss_pred ccccCCccCCCccccccccccCCc
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGS 87 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~ 87 (198)
.|..|.+ .|. .-.+.|..||.
T Consensus 141 rC~GC~~-~f~--~~~~~Cp~CG~ 161 (177)
T COG1439 141 RCHGCKR-IFP--EPKDFCPICGS 161 (177)
T ss_pred EEecCce-ecC--CCCCcCCCCCC
Confidence 4555655 554 34455555554
No 247
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=22.69 E-value=60 Score=19.78 Aligned_cols=9 Identities=33% Similarity=0.873 Sum_probs=3.8
Q ss_pred CeeeccchH
Q psy8222 107 PLRVCLTCY 115 (198)
Q Consensus 107 ~~RVC~~C~ 115 (198)
++-+|..|.
T Consensus 18 ~id~C~~C~ 26 (41)
T PF13453_consen 18 EIDVCPSCG 26 (41)
T ss_pred EEEECCCCC
Confidence 344444443
No 248
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=22.69 E-value=80 Score=21.49 Aligned_cols=28 Identities=25% Similarity=0.662 Sum_probs=20.1
Q ss_pred CCCccccCCccCCCccc--cccccccCCceE
Q psy8222 61 EAAVCMHCKRTQFTVLS--RRHHCRKCGSVV 89 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~--RrhhCr~CG~vv 89 (198)
....|..|+. ...... -++.|.+||.++
T Consensus 6 ~~~~CtSCg~-~i~~~~~~~~F~CPnCG~~~ 35 (59)
T PRK14890 6 EPPKCTSCGI-EIAPREKAVKFLCPNCGEVI 35 (59)
T ss_pred cCccccCCCC-cccCCCccCEeeCCCCCCee
Confidence 3457999998 555443 368999999883
No 249
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=22.52 E-value=1.4e+02 Score=29.91 Aligned_cols=62 Identities=23% Similarity=0.351 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCCCccc----cCCCCCccccCCccCCCccccccccccCCceEe
Q psy8222 28 EWMAHINKCIEDLLRKSGKKPAATHAAVWI----PDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVC 90 (198)
Q Consensus 28 ~Wi~~i~~~i~~ll~~~g~~~~~~~~~~Wv----~d~~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC 90 (198)
.+.++|-++|+.++...+..........+. +......|..|+. ..-+-.-=.-|+.||..-|
T Consensus 686 ScpDaI~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~-~l~~~~GC~~C~~CG~skC 751 (752)
T PRK08665 686 SCPDAIAKVLEKHYLGGGKDVGAGNGTGSAGIEAPAPERGACPECGS-ILEHEEGCVVCHSCGYSKC 751 (752)
T ss_pred CHHHHHHHHHHHHHHhccccccccccccccccccccCCCCCCCCCCc-ccEECCCCCcCCCCCCCCC
Confidence 356677777776554332221111011111 1112246999987 4322234567788887554
No 250
>PLN00188 enhanced disease resistance protein (EDR2); Provisional
Probab=22.41 E-value=1e+02 Score=30.79 Aligned_cols=30 Identities=17% Similarity=0.254 Sum_probs=26.7
Q ss_pred cCCeEEEEEeCChHHHHHHHHHHHHHHHHH
Q psy8222 11 TSSKSFAVHAATSTEKQEWMAHINKCIEDL 40 (198)
Q Consensus 11 t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~l 40 (198)
.+.+-..+-|.+.||=..||++|+.++++.
T Consensus 83 ~~~~~~~~~a~~~eea~~W~~a~~~a~~q~ 112 (719)
T PLN00188 83 EKYHRITMAAFNIQEALIWKEKIESVIDQH 112 (719)
T ss_pred CccccEEEecCCHHHHHHHHHHHHHHHhhh
Confidence 566778899999999999999999999963
No 251
>KOG2593|consensus
Probab=22.36 E-value=39 Score=31.69 Aligned_cols=34 Identities=26% Similarity=0.722 Sum_probs=27.5
Q ss_pred CCccccCCccCCCcc---------ccccccccCCceEeCCCCCC
Q psy8222 62 AAVCMHCKRTQFTVL---------SRRHHCRKCGSVVCAPCSNK 96 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~---------~RrhhCr~CG~vvC~~Cs~~ 96 (198)
.=.|+.|++ +|+.| .-..||-.||--+=..|+..
T Consensus 128 ~Y~Cp~C~k-kyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~~ 170 (436)
T KOG2593|consen 128 GYVCPNCQK-KYTSLEALQLLDNETGEFHCENCGGELVEDENKL 170 (436)
T ss_pred cccCCcccc-chhhhHHHHhhcccCceEEEecCCCchhcccccC
Confidence 346999999 98754 24799999999998888764
No 252
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=22.07 E-value=70 Score=22.53 Aligned_cols=13 Identities=31% Similarity=0.953 Sum_probs=8.2
Q ss_pred ccccccc--cCCceE
Q psy8222 77 SRRHHCR--KCGSVV 89 (198)
Q Consensus 77 ~RrhhCr--~CG~vv 89 (198)
+|.+.|. .||..|
T Consensus 25 ~~Y~qC~N~eCg~tF 39 (72)
T PRK09678 25 ERYHQCQNVNCSATF 39 (72)
T ss_pred eeeeecCCCCCCCEE
Confidence 4556776 677665
No 253
>KOG1311|consensus
Probab=22.06 E-value=53 Score=28.53 Aligned_cols=26 Identities=27% Similarity=0.546 Sum_probs=21.0
Q ss_pred CCCCccccCCccCCCccccccccccCCce
Q psy8222 60 NEAAVCMHCKRTQFTVLSRRHHCRKCGSV 88 (198)
Q Consensus 60 ~~~~~C~~C~~~~Fs~~~RrhhCr~CG~v 88 (198)
..+.+|..|++ -+.++-|||+-=|..
T Consensus 125 pRs~HCsvC~~---CV~rfDHHC~WvnnC 150 (299)
T KOG1311|consen 125 PRSSHCSVCNN---CVLRFDHHCPWLNNC 150 (299)
T ss_pred CCcccchhhcc---cccccCCCCCCccce
Confidence 46889999987 888899999876653
No 254
>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=21.92 E-value=39 Score=21.55 Aligned_cols=9 Identities=33% Similarity=1.198 Sum_probs=5.5
Q ss_pred eeeccchHH
Q psy8222 108 LRVCLTCYD 116 (198)
Q Consensus 108 ~RVC~~C~~ 116 (198)
.-+|..||.
T Consensus 23 ~dLC~~CF~ 31 (45)
T cd02336 23 YDLCPSCYQ 31 (45)
T ss_pred cccChHHHh
Confidence 456666665
No 255
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=21.74 E-value=33 Score=23.43 Aligned_cols=21 Identities=38% Similarity=1.124 Sum_probs=7.8
Q ss_pred ccccCCcc---CCCccccccccccCC
Q psy8222 64 VCMHCKRT---QFTVLSRRHHCRKCG 86 (198)
Q Consensus 64 ~C~~C~~~---~Fs~~~RrhhCr~CG 86 (198)
.|--|+++ +|.++. |.|..||
T Consensus 32 lCNDC~~~s~v~fH~lg--~KC~~C~ 55 (61)
T PF14599_consen 32 LCNDCNAKSEVPFHFLG--HKCSHCG 55 (61)
T ss_dssp EESSS--EEEEE--TT------TTTS
T ss_pred ECCCCCCccceeeeHhh--hcCCCCC
Confidence 47777762 455553 5566665
No 256
>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=21.65 E-value=46 Score=25.80 Aligned_cols=25 Identities=28% Similarity=0.713 Sum_probs=18.1
Q ss_pred CccccCCccCCCccccc-----cccccCCce
Q psy8222 63 AVCMHCKRTQFTVLSRR-----HHCRKCGSV 88 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~~Rr-----hhCr~CG~v 88 (198)
-.|..|+. +-+.+.+. .+|..||..
T Consensus 94 VlC~~C~s-pdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 94 VLCPECGS-PDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp SSCTSTSS-SSEEEEEETTCCEEEETTTSCE
T ss_pred EEcCCCCC-CccEEEEcCCEEEEEecccCCc
Confidence 46999999 77777543 677777763
No 257
>KOG1813|consensus
Probab=21.36 E-value=69 Score=28.72 Aligned_cols=29 Identities=34% Similarity=0.834 Sum_probs=20.7
Q ss_pred ccccCCccCCCccccccccccCCceEeCCCCCCe
Q psy8222 64 VCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKR 97 (198)
Q Consensus 64 ~C~~C~~~~Fs~~~RrhhCr~CG~vvC~~Cs~~~ 97 (198)
.|.+|++ .|- +--=-.||+.||..|+...
T Consensus 243 ~c~icr~-~f~----~pVvt~c~h~fc~~ca~~~ 271 (313)
T KOG1813|consen 243 KCFICRK-YFY----RPVVTKCGHYFCEVCALKP 271 (313)
T ss_pred ccccccc-ccc----cchhhcCCceeehhhhccc
Confidence 4999998 552 2223479999999997653
No 258
>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=21.18 E-value=53 Score=19.17 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=7.9
Q ss_pred cccccCCceE
Q psy8222 80 HHCRKCGSVV 89 (198)
Q Consensus 80 hhCr~CG~vv 89 (198)
+.|..||.++
T Consensus 2 ~~C~~CGy~y 11 (33)
T cd00350 2 YVCPVCGYIY 11 (33)
T ss_pred EECCCCCCEE
Confidence 5688899884
No 259
>KOG3362|consensus
Probab=21.04 E-value=92 Score=25.07 Aligned_cols=25 Identities=24% Similarity=0.653 Sum_probs=19.3
Q ss_pred CCCccccCCccCCCccccccccccCCceEeC
Q psy8222 61 EAAVCMHCKRTQFTVLSRRHHCRKCGSVVCA 91 (198)
Q Consensus 61 ~~~~C~~C~~~~Fs~~~RrhhCr~CG~vvC~ 91 (198)
..+.|.+|+- | -++-|-+||.-+|.
T Consensus 117 ~r~fCaVCG~--~----S~ysC~~CG~kyCs 141 (156)
T KOG3362|consen 117 LRKFCAVCGY--D----SKYSCVNCGTKYCS 141 (156)
T ss_pred cchhhhhcCC--C----chhHHHhcCCceee
Confidence 5678999983 3 35789999998885
No 260
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=20.94 E-value=36 Score=25.83 Aligned_cols=10 Identities=50% Similarity=1.431 Sum_probs=9.2
Q ss_pred cccccCCceE
Q psy8222 80 HHCRKCGSVV 89 (198)
Q Consensus 80 hhCr~CG~vv 89 (198)
|.|-+||.+|
T Consensus 3 H~CtrCG~vf 12 (112)
T COG3364 3 HQCTRCGEVF 12 (112)
T ss_pred ceeccccccc
Confidence 8899999997
No 261
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=20.84 E-value=2.4e+02 Score=24.86 Aligned_cols=25 Identities=12% Similarity=0.247 Sum_probs=16.8
Q ss_pred ChHHHHHHHHHHHHHHHHHHHhcCC
Q psy8222 22 TSTEKQEWMAHINKCIEDLLRKSGK 46 (198)
Q Consensus 22 s~~Ek~~Wi~~i~~~i~~ll~~~g~ 46 (198)
+.++-..|.+.|..++.......|.
T Consensus 195 ~~~~~~~l~~~i~~vl~~ai~~gGt 219 (273)
T COG0266 195 SLAQLALLHEAIKDVLADAIERGGT 219 (273)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 3445567788888777777666653
No 262
>PRK10445 endonuclease VIII; Provisional
Probab=20.73 E-value=2.8e+02 Score=23.83 Aligned_cols=25 Identities=4% Similarity=-0.036 Sum_probs=15.4
Q ss_pred ChHHHHHHHHHHHHHHHHHHHhcCC
Q psy8222 22 TSTEKQEWMAHINKCIEDLLRKSGK 46 (198)
Q Consensus 22 s~~Ek~~Wi~~i~~~i~~ll~~~g~ 46 (198)
|.++-....++|.+.+.......|.
T Consensus 191 s~~~~~~L~~~i~~vl~~ai~~gg~ 215 (263)
T PRK10445 191 NEAQLDALAHALLDIPRLSYATRGQ 215 (263)
T ss_pred CHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 4556666667777766666555443
No 263
>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=20.63 E-value=45 Score=17.14 Aligned_cols=9 Identities=33% Similarity=0.977 Sum_probs=4.7
Q ss_pred ccccCCceE
Q psy8222 81 HCRKCGSVV 89 (198)
Q Consensus 81 hCr~CG~vv 89 (198)
.|..||+.|
T Consensus 2 ~C~~C~~~f 10 (23)
T PF00096_consen 2 KCPICGKSF 10 (23)
T ss_dssp EETTTTEEE
T ss_pred CCCCCCCcc
Confidence 355555554
No 264
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=20.59 E-value=81 Score=21.59 Aligned_cols=31 Identities=29% Similarity=0.719 Sum_probs=21.6
Q ss_pred CCccccCCccCCCcccc--ccccccCCceEeCCC
Q psy8222 62 AAVCMHCKRTQFTVLSR--RHHCRKCGSVVCAPC 93 (198)
Q Consensus 62 ~~~C~~C~~~~Fs~~~R--rhhCr~CG~vvC~~C 93 (198)
...|..|+. ......+ ++-|.+||.+.=..|
T Consensus 9 ~~~CtSCg~-~i~p~e~~v~F~CPnCGe~~I~Rc 41 (61)
T COG2888 9 PPVCTSCGR-EIAPGETAVKFPCPNCGEVEIYRC 41 (61)
T ss_pred CceeccCCC-EeccCCceeEeeCCCCCceeeehh
Confidence 567999998 6544433 688999997654444
No 265
>CHL00112 rpl28 ribosomal protein L28; Provisional
Probab=20.32 E-value=1.1e+02 Score=20.84 Aligned_cols=15 Identities=13% Similarity=0.301 Sum_probs=11.7
Q ss_pred CCeeeccchHHhhcc
Q psy8222 106 KPLRVCLTCYDVLSR 120 (198)
Q Consensus 106 ~~~RVC~~C~~~l~~ 120 (198)
..++||..|...+..
T Consensus 47 ~kl~Vstr~Lrt~~k 61 (63)
T CHL00112 47 VKLKISTKAIKTLKK 61 (63)
T ss_pred EEEEEEHHHhhhccc
Confidence 567999999887653
No 266
>KOG3521|consensus
Probab=20.11 E-value=1.5e+02 Score=29.72 Aligned_cols=38 Identities=16% Similarity=0.466 Sum_probs=31.8
Q ss_pred cceEEEe------cCCeEEEEEeCChHHHHHHHHHHHHHHHHHH
Q psy8222 4 RNGWLIQ------TSSKSFAVHAATSTEKQEWMAHINKCIEDLL 41 (198)
Q Consensus 4 ~n~f~i~------t~~KSf~v~A~s~~Ek~~Wi~~i~~~i~~ll 41 (198)
+|+|++. +.+--|.+.+..+++...|.+.|..|...+.
T Consensus 487 pnsf~lVhLtEFh~a~~ayt~hcs~p~d~~~W~D~l~~Aq~~~Q 530 (846)
T KOG3521|consen 487 PNSFLLVHLTEFHTAQAAYTMHCSGPEDTLRWTDMLKMAQDELQ 530 (846)
T ss_pred CCceEEEeechhhhhhhhheeecCChhhHHHHHHHHHHHHHHHH
Confidence 5777765 6667788999999999999999999887654
No 267
>KOG4323|consensus
Probab=20.07 E-value=50 Score=31.28 Aligned_cols=27 Identities=22% Similarity=0.321 Sum_probs=21.5
Q ss_pred CccccCCccCCCccccccccccCCceE
Q psy8222 63 AVCMHCKRTQFTVLSRRHHCRKCGSVV 89 (198)
Q Consensus 63 ~~C~~C~~~~Fs~~~RrhhCr~CG~vv 89 (198)
..|..|..-.+..++|-..|+.|+..|
T Consensus 169 ~qc~vC~~g~~~~~NrmlqC~~C~~~f 195 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGNRMLQCDKCRQWY 195 (464)
T ss_pred ceeeeeecCCcCccceeeeecccccHH
Confidence 458888743788889999999999875
No 268
>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=20.03 E-value=38 Score=20.13 Aligned_cols=8 Identities=63% Similarity=1.605 Sum_probs=2.5
Q ss_pred ccccCCce
Q psy8222 81 HCRKCGSV 88 (198)
Q Consensus 81 hCr~CG~v 88 (198)
+|..||.+
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
Done!