Query psy16463
Match_columns 317
No_of_seqs 233 out of 1283
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 22:00:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16463.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16463hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5034 TNG2 Chromatin remodel 100.0 1.8E-37 4E-42 281.2 18.5 249 24-286 1-270 (271)
2 KOG1973|consensus 100.0 1.2E-34 2.6E-39 272.2 14.0 248 24-290 4-272 (274)
3 PF12998 ING: Inhibitor of gro 99.9 1.3E-24 2.7E-29 175.5 13.0 100 28-127 1-105 (105)
4 PF00628 PHD: PHD-finger; Int 98.8 8E-10 1.7E-14 77.9 1.2 44 239-285 1-50 (51)
5 smart00249 PHD PHD zinc finger 98.7 1.2E-08 2.7E-13 69.2 3.2 42 239-283 1-47 (47)
6 KOG1512|consensus 97.7 1.6E-05 3.5E-10 74.5 1.8 49 239-290 316-367 (381)
7 KOG4299|consensus 97.6 2E-05 4.3E-10 80.6 1.9 46 238-286 254-305 (613)
8 KOG0825|consensus 97.6 3.5E-05 7.5E-10 80.5 2.4 50 235-286 213-266 (1134)
9 KOG4323|consensus 97.5 3E-05 6.4E-10 77.6 1.5 50 237-289 171-227 (464)
10 KOG0954|consensus 97.5 5.3E-05 1.2E-09 78.7 2.0 54 230-286 264-321 (893)
11 KOG0956|consensus 97.2 0.00018 3.9E-09 74.4 2.2 48 238-286 7-57 (900)
12 PF13831 PHD_2: PHD-finger; PD 97.1 9.1E-05 2E-09 48.9 -0.5 34 248-284 2-36 (36)
13 KOG0383|consensus 96.9 0.00038 8.3E-09 73.1 1.7 42 238-284 48-92 (696)
14 KOG1244|consensus 96.7 0.00083 1.8E-08 62.9 1.8 47 237-286 281-331 (336)
15 cd04718 BAH_plant_2 BAH, or Br 96.6 0.001 2.2E-08 57.3 2.1 25 263-287 2-28 (148)
16 KOG1245|consensus 96.5 0.00049 1.1E-08 77.5 -0.9 50 236-288 1107-1160(1404)
17 KOG0955|consensus 96.5 0.0019 4E-08 70.7 3.3 49 237-288 220-271 (1051)
18 KOG1632|consensus 96.0 0.0027 5.8E-08 62.1 1.0 48 238-288 61-115 (345)
19 COG5141 PHD zinc finger-contai 95.0 0.0092 2E-07 60.1 1.0 43 239-284 195-241 (669)
20 KOG1844|consensus 94.9 0.014 3.1E-07 59.3 2.1 52 235-289 84-138 (508)
21 KOG1632|consensus 93.9 0.0081 1.7E-07 58.8 -2.1 50 233-285 235-294 (345)
22 KOG0957|consensus 92.7 0.11 2.5E-06 52.6 3.8 46 238-286 121-179 (707)
23 KOG0957|consensus 92.7 1.5 3.3E-05 44.8 11.6 44 239-285 546-597 (707)
24 PF13771 zf-HC5HC2H: PHD-like 88.4 0.25 5.4E-06 38.3 1.5 30 238-269 37-67 (90)
25 KOG2752|consensus 88.2 0.27 5.8E-06 47.3 1.7 31 236-269 127-165 (345)
26 PF07227 DUF1423: Protein of u 87.8 0.4 8.6E-06 48.2 2.8 45 241-288 133-194 (446)
27 PF13832 zf-HC5HC2H_2: PHD-zin 86.9 0.3 6.5E-06 39.4 1.1 30 238-269 56-86 (110)
28 KOG1473|consensus 82.8 0.74 1.6E-05 50.9 2.1 41 239-284 346-389 (1414)
29 KOG4443|consensus 75.7 1.6 3.5E-05 45.8 1.9 47 238-287 69-119 (694)
30 KOG3970|consensus 74.2 4.2 9.1E-05 37.7 3.9 57 240-300 53-117 (299)
31 PF10158 LOH1CR12: Tumour supp 72.4 59 0.0013 27.5 10.5 79 29-110 36-114 (131)
32 PF10497 zf-4CXXC_R1: Zinc-fin 69.8 3.2 6.9E-05 33.8 2.0 65 233-298 3-89 (105)
33 KOG3053|consensus 67.9 2.7 5.8E-05 39.6 1.2 70 237-307 20-101 (293)
34 TIGR00634 recN DNA repair prot 65.2 62 0.0013 33.7 10.8 105 24-128 283-399 (563)
35 PF08432 Vfa1: AAA-ATPase Vps4 65.1 6.9 0.00015 34.8 3.3 67 239-314 15-84 (182)
36 KOG0994|consensus 64.8 24 0.00051 40.0 7.7 40 90-129 1566-1605(1758)
37 PRK10869 recombination and rep 64.7 89 0.0019 32.6 11.9 39 91-129 357-395 (553)
38 KOG4216|consensus 64.5 3.9 8.6E-05 40.7 1.8 26 236-264 45-74 (479)
39 COG5415 Predicted integral mem 62.4 4.9 0.00011 36.8 1.8 33 40-72 13-45 (251)
40 KOG4443|consensus 61.8 2.3 5E-05 44.7 -0.4 45 238-285 19-70 (694)
41 PF07649 C1_3: C1-like domain; 60.5 2.2 4.8E-05 26.5 -0.5 27 239-268 2-30 (30)
42 PF03194 LUC7: LUC7 N_terminus 59.8 72 0.0016 30.0 9.2 72 48-119 89-164 (254)
43 COG3404 Methenyl tetrahydrofol 58.0 1.5E+02 0.0033 27.1 11.7 81 37-117 52-137 (208)
44 PF11690 DUF3287: Protein of u 56.5 63 0.0014 26.6 7.2 46 82-127 38-84 (109)
45 KOG1512|consensus 54.8 3.5 7.5E-05 39.4 -0.4 33 249-284 278-315 (381)
46 KOG2932|consensus 53.3 5.8 0.00012 38.4 0.8 38 238-285 91-131 (389)
47 PF13639 zf-RING_2: Ring finge 52.9 2.3 5.1E-05 28.4 -1.4 39 240-284 3-44 (44)
48 PHA02862 5L protein; Provision 52.4 5.5 0.00012 34.4 0.4 29 260-288 25-53 (156)
49 KOG1493|consensus 52.1 4.6 9.9E-05 31.2 -0.1 48 239-286 22-79 (84)
50 PF10367 Vps39_2: Vacuolar sor 50.8 13 0.00028 29.1 2.3 27 239-268 80-107 (109)
51 PF13341 RAG2_PHD: RAG2 PHD do 50.0 8.2 0.00018 29.3 1.0 33 249-283 29-68 (78)
52 PF10146 zf-C4H2: Zinc finger- 49.9 1.4E+02 0.0031 27.7 9.3 26 249-287 193-218 (230)
53 PF11781 RRN7: RNA polymerase 49.8 11 0.00023 24.8 1.4 25 251-285 9-33 (36)
54 KOG4460|consensus 49.6 1.7E+02 0.0037 30.8 10.5 34 28-61 570-604 (741)
55 KOG3579|consensus 49.0 18 0.00038 34.7 3.2 60 229-290 260-327 (352)
56 PRK15365 type III secretion sy 48.5 1.5E+02 0.0032 24.1 9.0 77 47-128 7-93 (107)
57 PF05384 DegS: Sensor protein 48.1 1.9E+02 0.0041 25.3 9.6 98 31-128 16-125 (159)
58 PF10796 Anti-adapt_IraP: Sigm 47.2 1.3E+02 0.0028 23.8 7.4 74 44-120 5-81 (87)
59 KOG4299|consensus 47.1 11 0.00023 39.6 1.6 44 237-285 47-94 (613)
60 COG5175 MOT2 Transcriptional r 45.6 6.9 0.00015 38.3 0.0 47 235-288 12-64 (480)
61 PF05130 FlgN: FlgN protein; 45.1 1.6E+02 0.0035 23.6 9.8 22 107-128 105-126 (143)
62 PF07496 zf-CW: CW-type Zinc F 45.0 13 0.00029 26.0 1.4 31 249-283 2-35 (50)
63 KOG2846|consensus 43.8 14 0.00031 35.9 1.8 39 250-293 220-258 (328)
64 PF08702 Fib_alpha: Fibrinogen 43.7 2.1E+02 0.0046 24.5 11.6 30 99-128 102-131 (146)
65 cd07625 BAR_Vps17p The Bin/Amp 43.6 2.7E+02 0.0059 25.8 13.8 115 12-127 89-205 (230)
66 KOG4628|consensus 43.2 22 0.00048 35.0 3.0 47 238-288 231-278 (348)
67 KOG2626|consensus 43.0 16 0.00035 37.7 2.2 53 237-292 20-82 (544)
68 PF04668 Tsg: Twisted gastrula 42.9 8.9 0.00019 32.6 0.3 12 260-271 102-116 (132)
69 KOG4552|consensus 42.2 2.5E+02 0.0055 25.9 9.4 20 109-128 75-94 (272)
70 COG5194 APC11 Component of SCF 41.8 5.8 0.00012 31.0 -0.9 43 240-286 23-79 (88)
71 PF04961 FTCD_C: Formiminotran 41.6 2.4E+02 0.0051 25.1 9.2 73 40-115 50-127 (184)
72 PHA02825 LAP/PHD finger-like p 40.8 10 0.00022 33.3 0.3 48 238-287 9-58 (162)
73 PF10046 BLOC1_2: Biogenesis o 40.4 86 0.0019 24.9 5.6 44 25-68 42-85 (99)
74 PF04111 APG6: Autophagy prote 39.2 3.6E+02 0.0079 26.0 12.2 37 33-69 48-84 (314)
75 PF13901 DUF4206: Domain of un 38.9 24 0.00051 31.9 2.4 39 239-287 154-199 (202)
76 PF12678 zf-rbx1: RING-H2 zinc 37.9 8.1 0.00017 29.1 -0.7 22 258-284 50-73 (73)
77 KOG1507|consensus 37.5 93 0.002 30.7 6.3 47 15-64 49-95 (358)
78 PF00130 C1_1: Phorbol esters/ 37.1 30 0.00065 23.7 2.2 33 236-271 10-46 (53)
79 PF01396 zf-C4_Topoisom: Topoi 36.9 28 0.0006 23.1 1.9 25 239-263 3-36 (39)
80 PRK10807 paraquat-inducible pr 36.6 5.2E+02 0.011 27.0 13.1 102 25-128 417-524 (547)
81 PRK14127 cell division protein 36.6 1.3E+02 0.0029 24.7 6.2 40 29-71 27-66 (109)
82 PF12095 DUF3571: Protein of u 36.5 54 0.0012 25.7 3.7 44 10-62 18-61 (83)
83 PF06160 EzrA: Septation ring 36.4 4.5E+02 0.0097 27.5 11.6 47 82-128 167-214 (560)
84 COG0497 RecN ATPase involved i 36.0 4.2E+02 0.0092 27.9 11.2 110 21-130 276-397 (557)
85 PF08746 zf-RING-like: RING-li 34.8 10 0.00022 25.8 -0.6 32 251-283 12-43 (43)
86 TIGR02338 gimC_beta prefoldin, 34.0 2.5E+02 0.0054 22.6 10.6 40 28-67 3-42 (110)
87 smart00744 RINGv The RING-vari 33.9 7.4 0.00016 27.1 -1.3 25 260-284 25-49 (49)
88 TIGR01562 FdhE formate dehydro 33.8 29 0.00063 33.6 2.2 11 250-262 210-220 (305)
89 KOG4515|consensus 33.1 3.8E+02 0.0081 24.4 9.7 44 29-72 100-143 (217)
90 PRK10244 anti-RssB factor; Pro 32.9 2.5E+02 0.0053 22.3 6.8 74 44-120 5-81 (88)
91 KOG1829|consensus 32.7 13 0.00028 39.0 -0.4 30 250-287 531-560 (580)
92 PRK14154 heat shock protein Gr 32.1 3.7E+02 0.0079 24.7 8.9 42 87-128 110-151 (208)
93 cd04476 RPA1_DBD_C RPA1_DBD_C: 32.1 27 0.00059 30.0 1.6 27 261-287 31-61 (166)
94 KOG1029|consensus 31.8 2E+02 0.0044 31.6 8.0 44 15-62 421-464 (1118)
95 PF05781 MRVI1: MRVI1 protein; 31.5 3E+02 0.0066 28.8 9.1 85 45-131 213-315 (538)
96 PF00641 zf-RanBP: Zn-finger i 31.4 24 0.00052 21.7 0.8 15 275-289 2-16 (30)
97 PF05008 V-SNARE: Vesicle tran 30.3 2.3E+02 0.0049 21.0 6.6 10 81-90 23-32 (79)
98 PF15446 zf-PHD-like: PHD/FYVE 30.2 31 0.00067 30.6 1.6 24 247-273 14-37 (175)
99 cd07627 BAR_Vps5p The Bin/Amph 29.9 4.1E+02 0.009 23.9 11.6 101 18-128 81-181 (216)
100 KOG1941|consensus 29.8 5.7 0.00012 39.6 -3.3 50 235-288 363-416 (518)
101 PHA02562 46 endonuclease subun 29.4 6.2E+02 0.013 25.7 11.4 23 106-128 260-282 (562)
102 KOG0996|consensus 29.3 6.1E+02 0.013 29.3 11.4 33 96-128 895-927 (1293)
103 KOG1244|consensus 28.6 15 0.00032 35.1 -0.7 44 238-284 225-282 (336)
104 cd07664 BAR_SNX2 The Bin/Amphi 28.6 4.8E+02 0.01 24.2 11.7 100 17-128 98-197 (234)
105 PRK03564 formate dehydrogenase 28.6 39 0.00084 32.8 2.1 9 278-286 253-261 (309)
106 COG1773 Rubredoxin [Energy pro 28.5 52 0.0011 23.8 2.2 10 276-285 35-44 (55)
107 PF07011 DUF1313: Protein of u 28.4 1.2E+02 0.0025 24.0 4.3 33 40-72 40-72 (87)
108 PF11221 Med21: Subunit 21 of 27.9 3.7E+02 0.0081 22.7 10.4 63 58-120 78-141 (144)
109 KOG1671|consensus 27.8 30 0.00064 31.5 1.1 21 264-284 155-177 (210)
110 cd07665 BAR_SNX1 The Bin/Amphi 27.4 5E+02 0.011 24.1 11.6 101 16-128 97-197 (234)
111 PF03107 C1_2: C1 domain; Int 27.1 62 0.0013 20.0 2.2 26 240-268 3-30 (30)
112 PLN03208 E3 ubiquitin-protein 26.9 30 0.00065 31.3 1.0 51 232-287 13-78 (193)
113 PF01627 Hpt: Hpt domain; Int 26.6 2.5E+02 0.0055 20.3 8.2 18 104-121 71-88 (90)
114 KOG0994|consensus 26.6 1.1E+03 0.024 27.6 12.9 19 18-36 1468-1486(1758)
115 PF09986 DUF2225: Uncharacteri 26.6 55 0.0012 29.8 2.7 44 237-286 5-57 (214)
116 PF13949 ALIX_LYPXL_bnd: ALIX 26.5 5.2E+02 0.011 23.9 10.9 45 28-72 22-66 (296)
117 KOG1246|consensus 26.3 51 0.0011 36.4 2.8 51 235-288 153-206 (904)
118 TIGR00153 conserved hypothetic 26.2 4.7E+02 0.01 23.3 10.4 61 10-70 10-71 (216)
119 PF10146 zf-C4H2: Zinc finger- 26.1 5.3E+02 0.011 23.9 10.8 10 239-248 196-206 (230)
120 KOG4215|consensus 26.1 32 0.00069 34.2 1.0 25 236-263 18-46 (432)
121 PF07888 CALCOCO1: Calcium bin 25.8 8E+02 0.017 25.9 11.9 31 97-128 428-458 (546)
122 KOG0995|consensus 25.8 6E+02 0.013 26.9 10.1 82 46-127 422-504 (581)
123 PF11793 FANCL_C: FANCL C-term 25.8 32 0.0007 25.7 0.8 47 239-286 4-64 (70)
124 PF02318 FYVE_2: FYVE-type zin 25.5 23 0.00049 29.1 -0.1 44 239-287 56-104 (118)
125 KOG2041|consensus 25.5 58 0.0013 35.3 2.9 53 231-288 1110-1167(1189)
126 cd00162 RING RING-finger (Real 25.4 15 0.00033 23.3 -0.9 26 258-285 18-43 (45)
127 PRK11637 AmiB activator; Provi 25.4 6.8E+02 0.015 24.9 10.5 26 39-64 44-69 (428)
128 PF15450 DUF4631: Domain of un 25.0 8.1E+02 0.018 25.6 11.2 14 24-37 311-324 (531)
129 PF08646 Rep_fac-A_C: Replicat 24.9 31 0.00068 29.0 0.7 27 261-287 15-47 (146)
130 COG0551 TopA Zn-finger domain 24.7 83 0.0018 26.3 3.3 43 238-285 18-68 (140)
131 smart00547 ZnF_RBZ Zinc finger 24.5 33 0.00071 20.2 0.5 13 276-288 1-13 (26)
132 PF01858 RB_A: Retinoblastoma- 24.1 79 0.0017 28.4 3.2 43 11-53 134-176 (194)
133 PF04216 FdhE: Protein involve 24.1 34 0.00074 32.4 0.8 26 237-264 172-209 (290)
134 PF10737 GerPC: Spore germinat 24.0 5.2E+02 0.011 23.1 8.6 43 30-74 88-136 (176)
135 PF13922 PHD_3: PHD domain of 24.0 12 0.00025 28.1 -1.8 28 238-271 34-61 (69)
136 PRK04778 septation ring format 23.9 8.4E+02 0.018 25.4 11.6 98 30-127 110-217 (569)
137 KOG1973|consensus 23.7 99 0.0022 29.3 3.9 100 28-128 26-126 (274)
138 cd07599 BAR_Rvs167p The Bin/Am 23.5 5.3E+02 0.012 23.0 11.5 21 99-119 154-174 (216)
139 KOG0704|consensus 23.5 52 0.0011 32.5 2.0 31 238-269 20-60 (386)
140 PF11855 DUF3375: Protein of u 22.6 8.4E+02 0.018 24.9 10.8 35 28-62 178-212 (478)
141 KOG3277|consensus 22.5 55 0.0012 28.7 1.7 19 239-259 81-111 (165)
142 KOG1952|consensus 22.4 37 0.00079 37.2 0.7 50 236-288 190-247 (950)
143 PF00645 zf-PARP: Poly(ADP-rib 22.2 20 0.00043 27.2 -1.0 10 261-270 39-48 (82)
144 PF11932 DUF3450: Protein of u 21.8 6.1E+02 0.013 23.3 8.7 38 83-120 131-168 (251)
145 COG4867 Uncharacterized protei 21.8 1.9E+02 0.004 29.7 5.4 32 37-68 121-152 (652)
146 COG1382 GimC Prefoldin, chaper 21.7 4.8E+02 0.01 21.8 11.2 89 38-128 2-104 (119)
147 PRK08032 fliD flagellar cappin 21.7 6.4E+02 0.014 25.6 9.5 45 28-72 392-436 (462)
148 PF10650 zf-C3H1: Putative zin 21.6 48 0.001 19.7 0.8 13 252-266 11-23 (23)
149 PF00412 LIM: LIM domain; Int 21.4 55 0.0012 22.5 1.3 40 241-285 3-55 (58)
150 PF15619 Lebercilin: Ciliary p 21.3 6E+02 0.013 22.8 12.8 38 29-66 48-85 (194)
151 PF08317 Spc7: Spc7 kinetochor 20.9 7.5E+02 0.016 23.8 12.6 29 100-128 141-169 (325)
152 PF00038 Filament: Intermediat 20.5 6.9E+02 0.015 23.4 9.0 10 119-128 294-303 (312)
153 KOG0971|consensus 20.5 1.1E+03 0.024 26.8 11.1 34 96-129 320-353 (1243)
154 TIGR00570 cdk7 CDK-activating 20.2 3.2E+02 0.0069 26.6 6.5 33 29-73 94-126 (309)
No 1
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=100.00 E-value=1.8e-37 Score=281.22 Aligned_cols=249 Identities=23% Similarity=0.426 Sum_probs=150.4
Q ss_pred hhhhHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHhCcCC----hHHHHHHHHHHHHHHHHHHH
Q psy16463 24 MYSVPYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIAS--QNGNKID----QFSRKRNLLRVQVALIAAQE 97 (317)
Q Consensus 24 ~~~a~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~--~~~k~~~----~~~~~~~~~~I~~~l~~a~e 97 (317)
+++++.|+||+|.|+|+|.|+.++|++|.++|.++.++++.|.+.+. +|....+ .+....+...|++.|-.++.
T Consensus 1 ~d~~~~Lnd~~d~l~n~P~et~~~~t~l~~iD~k~~d~~k~l~q~~si~k~~~~~~~~t~~e~ed~l~k~i~Ell~~a~~ 80 (271)
T COG5034 1 ADLFPGLNDITDHLANVPSETDIRFTELSEIDAKVCDIIKNLRQMISILKKIIDLDSQTYEEVEDGLLKEIRELLLKAIY 80 (271)
T ss_pred CchhHHHHHHHHHHHhCChhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhhcccCccccchhHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999999999999999999887765 3322222 23345688889999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHhccCcCcccchhhh---hhhccccccccc---ccc-------cccCCCCCCCcc
Q psy16463 98 IGDEKLSIMQQVQDVIEGKTRQIDGIFYNLPSVTSRREQE---AVETSVKHDEAV---STE-------KTQQSETPVAPK 164 (317)
Q Consensus 98 l~dEKv~LA~q~~dlVdkhirrLD~dl~~le~d~~~~e~~---~~~~~~~~~~~s---~~~-------~~~~~~~~~~~k 164 (317)
++.+|+.||+.+..+++||+++||..+.+...++.....+ .........+.+ +++ .+.++.-+...+
T Consensus 81 ~~~~~~~l~d~~~~l~~Rh~~~~d~~~a~~~h~~~~~~ie~~~~~~s~~~~~~~ss~a~~ss~~~~saassqgs~~t~~~ 160 (271)
T COG5034 81 IQKEKSDLADRAEKLLRRHRKLLDDRIAKRPHEKVAARIENCHDAVSRLERNSYSSAARRSSGEHRSAASSQGSRHTKLK 160 (271)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhHHHhhhhhhhhhhhhhhhhhhhhhhccccchhhhccccccccccccccccCchhH
Confidence 9999999999999999999999999998887543221111 000000000001 000 000000000000
Q ss_pred ccccccCcccccchhccCCCCCCCCCccccccCCCCCCCCCcccccccchhhcccccC-CCC-CCCCCCCCCCCCceeee
Q psy16463 165 KRQRKKNTEVDSEMIECSSTPLPRSSATIAVVKKPSTQSGGKKKKRKTKQQRECEKEA-TPP-PDEDLAIDPNEPTYCLC 242 (317)
Q Consensus 165 r~rr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~k~~~~~~~~~~~~~-~~~-~~~~~~~d~~e~~~C~C 242 (317)
.|....+... .++...+....+....+.+ ..+...+.. ....+. .+. .-...+..+++.+||+|
T Consensus 161 -~R~n~~~~k~-------~~p~~~S~r~~~~t~~sp~--v~~t~t~v~----e~~~~~s~~~~~vss~d~se~e~lYCfC 226 (271)
T COG5034 161 -KRKNIHNLKR-------RSPELSSKREVSFTLESPS--VPDTATRVK----EGNNGGSTKSRGVSSEDNSEGEELYCFC 226 (271)
T ss_pred -HHHhhccccc-------CCcchhhhccCCccCCCCC--cccchhhhh----cccCCCCccccCcCccccccCceeEEEe
Confidence 0000000000 0000000000000000000 000000000 000000 000 00111344678899999
Q ss_pred CCCCCCCeeeeCCCCCCCcceecccCCccCCCCCceeCcccccc
Q psy16463 243 NQVSFGQMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKA 286 (317)
Q Consensus 243 ~~~~~g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~ 286 (317)
++|+||+||+|||++|.++|||+.||||..+|+|+||||+|...
T Consensus 227 qqvSyGqMVaCDn~nCkrEWFH~~CVGLk~pPKG~WYC~eCk~~ 270 (271)
T COG5034 227 QQVSYGQMVACDNANCKREWFHLECVGLKEPPKGKWYCPECKKA 270 (271)
T ss_pred cccccccceecCCCCCchhheeccccccCCCCCCcEeCHHhHhc
Confidence 99999999999999999999999999999999999999999753
No 2
>KOG1973|consensus
Probab=100.00 E-value=1.2e-34 Score=272.25 Aligned_cols=248 Identities=28% Similarity=0.549 Sum_probs=155.4
Q ss_pred hhhhHHHHHHHHH----hhcChHHHHHHHHHHHHHHH--HHHHHHHHHH-HHHHHHhCcCC----hHHHHHHHHHHHHHH
Q psy16463 24 MYSVPYVETYLDI----VENLPDEIQRYLTKIRELDV--LYQSYMKEIE-HIASQNGNKID----QFSRKRNLLRVQVAL 92 (317)
Q Consensus 24 ~~~a~yLedyld~----ienLP~Elqr~l~lIRElD~--k~~~~~~~ie-~~~~~~~k~~~----~~~~~~~~~~I~~~l 92 (317)
++.+.+++++++. +.+||..++++|.+|.++|. +......+++ .....|.+... ..........|++.+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~l~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (274)
T KOG1973|consen 4 LDQAILIEEVDDDIDMAVQNLPRNLQHNFDVIEDIDIFGRSENQKKELDLKVAVEYMSKGRSQLSKPQKDPLLEAIRSAL 83 (274)
T ss_pred cchhhhhhhcccccccccccCCccchhHHHHHhhhhccchhHHHHhhhhhhhhhccccccccccCccccchhHHHHHHHH
Confidence 3456667777777 99999999999999999999 5577777776 66677765443 455677889999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccCcCcccchhhhhhhccccccccccccc-ccCCCCCC-Ccccccccc
Q psy16463 93 IAAQEIGDEKLSIMQQVQDVIEGKTRQIDGIFYNLPSVTSRREQEAVETSVKHDEAVSTEK-TQQSETPV-APKKRQRKK 170 (317)
Q Consensus 93 ~~a~el~dEKv~LA~q~~dlVdkhirrLD~dl~~le~d~~~~e~~~~~~~~~~~~~s~~~~-~~~~~~~~-~~kr~rr~~ 170 (317)
..+.+++|||+++|.+++++|.+|++++|..+..|+.++... .....+ ..++ ........ ...+.+...
T Consensus 84 ~~~~~~~~ek~~~~~~~~e~~~~~~~~~~~~~~~~e~~~~~~--~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~s 154 (274)
T KOG1973|consen 84 RKCKELSDEKVQIAMQTVELIPKHIGRLETALKSFEVELELA--KAESSS-------KRSSSLKSAKKKEREVFKEKKES 154 (274)
T ss_pred hhhhhhhhHHHHHHHHHHHhhHhhhcchhHHHHhcccchhhh--hhhccc-------ccccchhccCccccccccchhhc
Confidence 999999999999999999999999999999999888433111 000000 0000 00000000 000000000
Q ss_pred CcccccchhccCCCCCCCCCccccccCCCCCCCCCcccccc--------cchhhcccccCCCCCCCCCCCCCCCCceeee
Q psy16463 171 NTEVDSEMIECSSTPLPRSSATIAVVKKPSTQSGGKKKKRK--------TKQQRECEKEATPPPDEDLAIDPNEPTYCLC 242 (317)
Q Consensus 171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~k~~--------~~~~~~~~~~~~~~~~~~~~~d~~e~~~C~C 242 (317)
... +....+.......+........ ..+++++. +.... .....+..+.+...|+++++||+|
T Consensus 155 ~~~-----~~~~~s~~~~~~~~~~~~~~~~---~~rekk~~v~~~~~~~t~~~~--~s~~~~~~~~~~~~d~~e~~yC~C 224 (274)
T KOG1973|consen 155 KQG-----SSEKPSSVDKAKKGSKVNRRPC---GAREKKRKVVEAKKEKTPKNK--SSRPAESMESEEAVDPDEPTYCIC 224 (274)
T ss_pred CCC-----CCCCcccccccccccccccccc---hhhhhhhhhccccccccccCC--CCCcccccccccccCCCCCEEEEe
Confidence 000 0000000000000000000000 01111111 00000 000011223345789999999999
Q ss_pred CCCCCCCeeeeCCCCCCCcceecccCCccCCCCCceeCccccccccCC
Q psy16463 243 NQVSFGQMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKARSNA 290 (317)
Q Consensus 243 ~~~~~g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~~~~~ 290 (317)
++++||+||+|||++|+|+||||.||||+..|+|+||||.|+......
T Consensus 225 nqvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~PkgkWyC~~C~~~~~~~ 272 (274)
T KOG1973|consen 225 NQVSYGKMIGCDNPGCPIEWFHFTCVGLKTKPKGKWYCPRCKAENKKK 272 (274)
T ss_pred cccccccccccCCCCCCcceEEEeccccccCCCCcccchhhhhhhhcc
Confidence 999999999999999999999999999999999999999999876543
No 3
>PF12998 ING: Inhibitor of growth proteins N-terminal histone-binding; InterPro: IPR024610 Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. This entry represents the N-terminal histone binding domain found in inhibitor proteins.; PDB: 4AFL_A.
Probab=99.92 E-value=1.3e-24 Score=175.48 Aligned_cols=100 Identities=33% Similarity=0.478 Sum_probs=91.3
Q ss_pred HHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcC-----ChHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 28 PYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGNKI-----DQFSRKRNLLRVQVALIAAQEIGDEK 102 (317)
Q Consensus 28 ~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~k~~-----~~~~~~~~~~~I~~~l~~a~el~dEK 102 (317)
+|||+|+|+|++||.||+|+|++||+||.++++...+++..+.+|.+.. .++.+..++.+|+..|.+++.+++||
T Consensus 1 ~~le~f~d~~~~LP~el~r~l~~irelD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~l~deK 80 (105)
T PF12998_consen 1 TYLEDFLDSLENLPAELQRNLTLIRELDAKSQDLLEELDQQIQKFIKNHGSPSLSPEKRRELLKEIQEEYERALELSDEK 80 (105)
T ss_dssp HHHHHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTS--S-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHChHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5999999999999999999999999999999999999999999997633 34567889999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhccC
Q psy16463 103 LSIMQQVQDVIEGKTRQIDGIFYNL 127 (317)
Q Consensus 103 v~LA~q~~dlVdkhirrLD~dl~~l 127 (317)
|+||+++|++|++|++|||.++++|
T Consensus 81 v~lA~~~~d~v~~hi~rLD~dl~~f 105 (105)
T PF12998_consen 81 VALAQQAYDLVDRHIRRLDQDLKKF 105 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCT---
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 9999999999999999999999987
No 4
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=98.85 E-value=8e-10 Score=77.92 Aligned_cols=44 Identities=50% Similarity=1.412 Sum_probs=36.7
Q ss_pred ee-eeCCCC-CCCeeeeCCCCCCCcceecccCCccCC----CCCceeCccccc
Q psy16463 239 YC-LCNQVS-FGQMVMCDNDLCPHQWFHFSCVAVTNT----PKGKWYCPNCRK 285 (317)
Q Consensus 239 ~C-~C~~~~-~g~mi~Cd~~~C~~~wfH~~Cvgl~~~----p~~~w~C~~C~~ 285 (317)
|| +|++.. .++||.||. |. .|||..|++++.. +.+.|+|+.|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~--C~-~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDS--CN-RWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBST--TS-CEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCC--CC-hhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 68 899853 468999998 98 9999999998755 245899999975
No 5
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG1512|consensus
Probab=97.69 E-value=1.6e-05 Score=74.51 Aligned_cols=49 Identities=33% Similarity=0.864 Sum_probs=41.3
Q ss_pred ee-eeCCCCC-CCeeeeCCCCCCCcceecccCCccCCCCCceeCc-cccccccCC
Q psy16463 239 YC-LCNQVSF-GQMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCP-NCRKARSNA 290 (317)
Q Consensus 239 ~C-~C~~~~~-g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~-~C~~~~~~~ 290 (317)
.| +|++|.. .+|+.||. |. .-||.-||||...|.|.|.|. .|.....+.
T Consensus 316 lC~IC~~P~~E~E~~FCD~--CD-RG~HT~CVGL~~lP~G~WICD~~C~~~~~~t 367 (381)
T KOG1512|consen 316 LCRICLGPVIESEHLFCDV--CD-RGPHTLCVGLQDLPRGEWICDMRCREATLNT 367 (381)
T ss_pred hhhccCCcccchheecccc--cc-CCCCccccccccccCccchhhhHHHHhcCCC
Confidence 46 7998854 68999999 99 889999999999999999998 677665443
No 7
>KOG4299|consensus
Probab=97.64 E-value=2e-05 Score=80.63 Aligned_cols=46 Identities=39% Similarity=1.211 Sum_probs=36.6
Q ss_pred cee-eeCCCC-CCCeeeeCCCCCCCcceecccCCcc----CCCCCceeCcccccc
Q psy16463 238 TYC-LCNQVS-FGQMVMCDNDLCPHQWFHFSCVAVT----NTPKGKWYCPNCRKA 286 (317)
Q Consensus 238 ~~C-~C~~~~-~g~mi~Cd~~~C~~~wfH~~Cvgl~----~~p~~~w~C~~C~~~ 286 (317)
.|| .|++.. +-..||||. |+ .-||+.|+-.+ ..|.|.|||+.|.-+
T Consensus 254 ~fCsaCn~~~~F~~~i~CD~--Cp-~sFH~~CLePPl~~eniP~g~W~C~ec~~k 305 (613)
T KOG4299|consen 254 DFCSACNGSGLFNDIICCDG--CP-RSFHQTCLEPPLEPENIPPGSWFCPECKIK 305 (613)
T ss_pred HHHHHhCCccccccceeecC--Cc-hHHHHhhcCCCCCcccCCCCccccCCCeee
Confidence 399 899851 234599999 99 88999999855 346799999999855
No 8
>KOG0825|consensus
Probab=97.57 E-value=3.5e-05 Score=80.46 Aligned_cols=50 Identities=28% Similarity=0.902 Sum_probs=40.4
Q ss_pred CCCcee-eeCCCCC-CCeeeeCCCCCCCcceecccCCc--cCCCCCceeCcccccc
Q psy16463 235 NEPTYC-LCNQVSF-GQMVMCDNDLCPHQWFHFSCVAV--TNTPKGKWYCPNCRKA 286 (317)
Q Consensus 235 ~e~~~C-~C~~~~~-g~mi~Cd~~~C~~~wfH~~Cvgl--~~~p~~~w~C~~C~~~ 286 (317)
.+.+-| +|...+. ..||.||. |....||..|+.+ .+.|.+.|||+.|.-.
T Consensus 213 ~E~~~C~IC~~~DpEdVLLLCDs--CN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 213 QEEVKCDICTVHDPEDVLLLCDS--CNKVYYHVYCLDPDLSESPVNEWYCTNCSLL 266 (1134)
T ss_pred cccccceeeccCChHHhheeecc--cccceeeccccCcccccccccceecCcchhh
Confidence 455679 8997654 46999999 9966699999985 4579999999999844
No 9
>KOG4323|consensus
Probab=97.54 E-value=3e-05 Score=77.59 Aligned_cols=50 Identities=28% Similarity=0.814 Sum_probs=37.4
Q ss_pred CceeeeCCCC-CCCeeeeCCCCCCCcceecccCCccCC------CCCceeCccccccccC
Q psy16463 237 PTYCLCNQVS-FGQMVMCDNDLCPHQWFHFSCVAVTNT------PKGKWYCPNCRKARSN 289 (317)
Q Consensus 237 ~~~C~C~~~~-~g~mi~Cd~~~C~~~wfH~~Cvgl~~~------p~~~w~C~~C~~~~~~ 289 (317)
-.||.|+++. +..||+|+. |. .|||-.|.-.... +...|||..|......
T Consensus 171 c~vC~~g~~~~~NrmlqC~~--C~-~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~ 227 (464)
T KOG4323|consen 171 CSVCYCGGPGAGNRMLQCDK--CR-QWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKK 227 (464)
T ss_pred eeeeecCCcCccceeeeecc--cc-cHHHHHhccCCCCHhhccCccceEeehhhccchhh
Confidence 4566777663 347999999 98 9999999874333 3469999999976543
No 10
>KOG0954|consensus
Probab=97.46 E-value=5.3e-05 Score=78.69 Aligned_cols=54 Identities=31% Similarity=0.848 Sum_probs=45.4
Q ss_pred CCCCCCCCcee-eeCCCCC---CCeeeeCCCCCCCcceecccCCccCCCCCceeCcccccc
Q psy16463 230 LAIDPNEPTYC-LCNQVSF---GQMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKA 286 (317)
Q Consensus 230 ~~~d~~e~~~C-~C~~~~~---g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~ 286 (317)
..+.-++++.| ||..++. .+||.||. |. --.|..|.||...|.|.|+|..|.-.
T Consensus 264 lgie~dedviCDvCrspD~e~~neMVfCd~--Cn-~cVHqaCyGIle~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 264 LGIEYDEDVICDVCRSPDSEEANEMVFCDK--CN-ICVHQACYGILEVPEGPWLCRTCALG 321 (893)
T ss_pred ceeeccccceeceecCCCccccceeEEecc--ch-hHHHHhhhceeecCCCCeeehhcccc
Confidence 34555688999 9998743 47999999 98 67999999999999999999998743
No 11
>KOG0956|consensus
Probab=97.19 E-value=0.00018 Score=74.39 Aligned_cols=48 Identities=27% Similarity=0.895 Sum_probs=41.4
Q ss_pred ceeeeCCCC-C--CCeeeeCCCCCCCcceecccCCccCCCCCceeCcccccc
Q psy16463 238 TYCLCNQVS-F--GQMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKA 286 (317)
Q Consensus 238 ~~C~C~~~~-~--g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~ 286 (317)
-+|+|-+.- | ..+|-||+..|. ..+|-.|.||..+|.|.|||..|...
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCs-VAVHQaCYGIvqVPtGpWfCrKCesq 57 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCS-VAVHQACYGIVQVPTGPWFCRKCESQ 57 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCce-eeeehhcceeEecCCCchhhhhhhhh
Confidence 378997652 2 359999999998 89999999999999999999999855
No 12
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=97.11 E-value=9.1e-05 Score=48.93 Aligned_cols=34 Identities=38% Similarity=1.045 Sum_probs=20.4
Q ss_pred CCeeeeCCCCCCCcceecccCCccCCCCC-ceeCcccc
Q psy16463 248 GQMVMCDNDLCPHQWFHFSCVAVTNTPKG-KWYCPNCR 284 (317)
Q Consensus 248 g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~-~w~C~~C~ 284 (317)
..||.|++ |. -++|.+|.|+...+.+ .|+|..|.
T Consensus 2 n~ll~C~~--C~-v~VH~~CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDN--CN-VAVHQSCYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SS--S---EEEHHHHT-SS--SS-----HHH-
T ss_pred CceEEeCC--CC-CcCChhhCCcccCCCCCcEECCcCC
Confidence 46999999 98 7899999999988876 89999884
No 13
>KOG0383|consensus
Probab=96.90 E-value=0.00038 Score=73.15 Aligned_cols=42 Identities=38% Similarity=1.062 Sum_probs=35.5
Q ss_pred cee-eeCCCCCCCeeeeCCCCCCCcceecccCCcc--CCCCCceeCcccc
Q psy16463 238 TYC-LCNQVSFGQMVMCDNDLCPHQWFHFSCVAVT--NTPKGKWYCPNCR 284 (317)
Q Consensus 238 ~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cvgl~--~~p~~~w~C~~C~ 284 (317)
-+| +|.. +|+.|+||. |+ .|||..|.+.+ ..|.+.|.|+.|.
T Consensus 48 e~c~ic~~--~g~~l~c~t--C~-~s~h~~cl~~pl~~~p~~~~~c~Rc~ 92 (696)
T KOG0383|consen 48 EACRICAD--GGELLWCDT--CP-ASFHASCLGPPLTPQPNGEFICPRCF 92 (696)
T ss_pred hhhhhhcC--CCcEEEecc--cc-HHHHHHccCCCCCcCCccceeeeeec
Confidence 455 9998 799999999 99 99999999854 4456779999995
No 14
>KOG1244|consensus
Probab=96.67 E-value=0.00083 Score=62.89 Aligned_cols=47 Identities=30% Similarity=0.966 Sum_probs=37.7
Q ss_pred Ccee-eeCCCCC-CCeeeeCCCCCCCcceecccCC--ccCCCCCceeCcccccc
Q psy16463 237 PTYC-LCNQVSF-GQMVMCDNDLCPHQWFHFSCVA--VTNTPKGKWYCPNCRKA 286 (317)
Q Consensus 237 ~~~C-~C~~~~~-g~mi~Cd~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~ 286 (317)
-.|| +|+-... .+++.||. |. .-||+.|+. +.++|.|.|-|-.|...
T Consensus 281 ck~csicgtsenddqllfcdd--cd-rgyhmyclsppm~eppegswsc~KOG~~ 331 (336)
T KOG1244|consen 281 CKYCSICGTSENDDQLLFCDD--CD-RGYHMYCLSPPMVEPPEGSWSCHLCLEE 331 (336)
T ss_pred cceeccccCcCCCceeEeecc--cC-CceeeEecCCCcCCCCCCchhHHHHHHH
Confidence 3567 7876543 57999998 99 889999998 45678899999999754
No 15
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=96.64 E-value=0.001 Score=57.32 Aligned_cols=25 Identities=36% Similarity=1.184 Sum_probs=21.9
Q ss_pred eecccCC--ccCCCCCceeCccccccc
Q psy16463 263 FHFSCVA--VTNTPKGKWYCPNCRKAR 287 (317)
Q Consensus 263 fH~~Cvg--l~~~p~~~w~C~~C~~~~ 287 (317)
||+.|+. |+..|.|+|+||.|..+.
T Consensus 2 ~H~~CL~Ppl~~~P~g~W~Cp~C~~~~ 28 (148)
T cd04718 2 FHLCCLRPPLKEVPEGDWICPFCEVEK 28 (148)
T ss_pred cccccCCCCCCCCCCCCcCCCCCcCCC
Confidence 8999998 677899999999999654
No 16
>KOG1245|consensus
Probab=96.51 E-value=0.00049 Score=77.55 Aligned_cols=50 Identities=34% Similarity=0.994 Sum_probs=40.7
Q ss_pred CCcee-eeCCCCC-CCeeeeCCCCCCCcceecccCC--ccCCCCCceeCcccccccc
Q psy16463 236 EPTYC-LCNQVSF-GQMVMCDNDLCPHQWFHFSCVA--VTNTPKGKWYCPNCRKARS 288 (317)
Q Consensus 236 e~~~C-~C~~~~~-g~mi~Cd~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~~~ 288 (317)
....| +|..... -.|+-||. |. .|||+.|+. +...|.+.|+||.|+....
T Consensus 1107 ~~~~c~~cr~k~~~~~m~lc~~--c~-~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1107 VNALCKVCRRKKQDEKMLLCDE--CL-SGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred chhhhhhhhhcccchhhhhhHh--hh-hhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence 34578 8976533 37999999 97 999999987 5677899999999998754
No 17
>KOG0955|consensus
Probab=96.49 E-value=0.0019 Score=70.75 Aligned_cols=49 Identities=27% Similarity=0.784 Sum_probs=40.1
Q ss_pred CceeeeCCCCC---CCeeeeCCCCCCCcceecccCCccCCCCCceeCcccccccc
Q psy16463 237 PTYCLCNQVSF---GQMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKARS 288 (317)
Q Consensus 237 ~~~C~C~~~~~---g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~~~ 288 (317)
..+|||..... ...|.||+ |. -.+|..|+|++..|.|.|+|-.|.....
T Consensus 220 ~~C~iC~~~~~~n~n~ivfCD~--Cn-l~VHq~Cygi~~ipeg~WlCr~Cl~s~~ 271 (1051)
T KOG0955|consen 220 AVCCICLDGECQNSNVIVFCDG--CN-LAVHQECYGIPFIPEGQWLCRRCLQSPQ 271 (1051)
T ss_pred ccceeecccccCCCceEEEcCC--Cc-chhhhhccCCCCCCCCcEeehhhccCcC
Confidence 34559987532 46999999 99 6799999999999999999999986543
No 18
>KOG1632|consensus
Probab=95.95 E-value=0.0027 Score=62.09 Aligned_cols=48 Identities=29% Similarity=0.764 Sum_probs=38.9
Q ss_pred ceeeeCCCCCC--CeeeeCCCCCCCcceeccc--CCccCC---CCCceeCcccccccc
Q psy16463 238 TYCLCNQVSFG--QMVMCDNDLCPHQWFHFSC--VAVTNT---PKGKWYCPNCRKARS 288 (317)
Q Consensus 238 ~~C~C~~~~~g--~mi~Cd~~~C~~~wfH~~C--vgl~~~---p~~~w~C~~C~~~~~ 288 (317)
.||.|..+... +|+.||. |. .|||..| ||++.. +...|||..|.....
T Consensus 61 ~~~~~~~~~~p~~~~~~cd~--C~-~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~~ 115 (345)
T KOG1632|consen 61 RYCKCYKPCDPDDLMEQCDL--CE-DWYHGECWEVGTAEKEAPKEDPKVCDECKEAQD 115 (345)
T ss_pred chhhcccccCchhhhhcccc--cc-ccccccccccCchhhcCCccccccccccchhhh
Confidence 38888877544 8999998 98 9999999 997643 458999999986553
No 19
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=95.00 E-value=0.0092 Score=60.08 Aligned_cols=43 Identities=33% Similarity=0.868 Sum_probs=36.7
Q ss_pred ee-eeCCCCC---CCeeeeCCCCCCCcceecccCCccCCCCCceeCcccc
Q psy16463 239 YC-LCNQVSF---GQMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCR 284 (317)
Q Consensus 239 ~C-~C~~~~~---g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~ 284 (317)
.| +|..... .-+|.||+ |. -..|-+|.||.-.|.|.|+|-.|.
T Consensus 195 ~C~~c~~t~~eN~naiVfCdg--C~-i~VHq~CYGI~f~peG~WlCrkCi 241 (669)
T COG5141 195 ICTKCTSTHNENSNAIVFCDG--CE-ICVHQSCYGIQFLPEGFWLCRKCI 241 (669)
T ss_pred hhHhccccccCCcceEEEecC--cc-hhhhhhcccceecCcchhhhhhhc
Confidence 47 7876543 45999999 99 568999999999999999999996
No 20
>KOG1844|consensus
Probab=94.87 E-value=0.014 Score=59.31 Aligned_cols=52 Identities=27% Similarity=0.628 Sum_probs=41.9
Q ss_pred CCCceeeeCCC-C-CCCeeeeCCCCCCCcceecccCCccCCC-CCceeCccccccccC
Q psy16463 235 NEPTYCLCNQV-S-FGQMVMCDNDLCPHQWFHFSCVAVTNTP-KGKWYCPNCRKARSN 289 (317)
Q Consensus 235 ~e~~~C~C~~~-~-~g~mi~Cd~~~C~~~wfH~~Cvgl~~~p-~~~w~C~~C~~~~~~ 289 (317)
...+.|.|+.. + .|.||+|+. |. .|-|.-|+|....- .+.|.|..|......
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~~--c~-~Wqh~~C~g~~~~~~p~~y~c~~c~~~~~~ 138 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCDW--CG-RWQHKICCGSFKSTKPDKYVCEICTPRNKE 138 (508)
T ss_pred CcccccccccccCCCceeeCCcc--cC-cccCceeeeecCCCCchhceeeeecccccc
Confidence 35567999866 3 589999999 99 99999999975544 489999999976543
No 21
>KOG1632|consensus
Probab=93.88 E-value=0.0081 Score=58.79 Aligned_cols=50 Identities=28% Similarity=0.689 Sum_probs=38.2
Q ss_pred CCCCCcee-eeCCCCC--CCeeeeCCCCCCCcceecccCCccCCCC---Cc----eeCccccc
Q psy16463 233 DPNEPTYC-LCNQVSF--GQMVMCDNDLCPHQWFHFSCVAVTNTPK---GK----WYCPNCRK 285 (317)
Q Consensus 233 d~~e~~~C-~C~~~~~--g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~---~~----w~C~~C~~ 285 (317)
++.+.++| .|+.... -+||+|+- |. .|||..||.+...++ .. |+|++|..
T Consensus 235 ~~~~~~~~~~cg~~~~~~~~~~~~~~--~e-~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 235 PDYSKLICDPCGLSDANKKFEICCDL--CE-SWFHGDCVQIFEARKRLNEIRNEVYKCPHCTV 294 (345)
T ss_pred cccccccccccCcchHHHHHHHHHHH--HH-HHhcccccccccchhhhhhhhccceecCceee
Confidence 33445677 6776432 36999998 98 999999999987764 34 99999986
No 22
>KOG0957|consensus
Probab=92.70 E-value=0.11 Score=52.58 Aligned_cols=46 Identities=30% Similarity=0.855 Sum_probs=33.6
Q ss_pred ceeee-CCC--CCCCeeeeCCCCCCCcceecccCCccCC---C-------CCceeCcccccc
Q psy16463 238 TYCLC-NQV--SFGQMVMCDNDLCPHQWFHFSCVAVTNT---P-------KGKWYCPNCRKA 286 (317)
Q Consensus 238 ~~C~C-~~~--~~g~mi~Cd~~~C~~~wfH~~Cvgl~~~---p-------~~~w~C~~C~~~ 286 (317)
++|+| ++- +-|++|+||+ |.+ -.|-.|.|+... | ..-|||..|+-.
T Consensus 121 iCcVClg~rs~da~ei~qCd~--CGi-~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~G 179 (707)
T KOG0957|consen 121 ICCVCLGQRSVDAGEILQCDK--CGI-NVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYG 179 (707)
T ss_pred EEEEeecCccccccceeeccc--cCc-eecccccccccccccCCCCccCCCCchhhhhHhcC
Confidence 56699 333 4589999999 995 489999996521 2 147999999743
No 23
>KOG0957|consensus
Probab=92.67 E-value=1.5 Score=44.76 Aligned_cols=44 Identities=32% Similarity=0.962 Sum_probs=33.5
Q ss_pred ee-eeCCCC-CCCeeeeCCCCCCCcceecccCC--ccCCCCC----ceeCccccc
Q psy16463 239 YC-LCNQVS-FGQMVMCDNDLCPHQWFHFSCVA--VTNTPKG----KWYCPNCRK 285 (317)
Q Consensus 239 ~C-~C~~~~-~g~mi~Cd~~~C~~~wfH~~Cvg--l~~~p~~----~w~C~~C~~ 285 (317)
-| ||.... .-.++.||. |. --||+.|+. |+..|+. -|.|..|-.
T Consensus 546 sCgiCkks~dQHll~~CDt--C~-lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk 597 (707)
T KOG0957|consen 546 SCGICKKSTDQHLLTQCDT--CH-LHYHLGCLSPPLTRLPKKNKNFGWQCSECDK 597 (707)
T ss_pred eeeeeccchhhHHHhhcch--hh-ceeeccccCCccccCcccccCcceeeccccc
Confidence 48 898742 235889999 98 679999998 5566653 699999943
No 24
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=88.40 E-value=0.25 Score=38.27 Aligned_cols=30 Identities=27% Similarity=0.729 Sum_probs=25.8
Q ss_pred cee-eeCCCCCCCeeeeCCCCCCCcceecccCC
Q psy16463 238 TYC-LCNQVSFGQMVMCDNDLCPHQWFHFSCVA 269 (317)
Q Consensus 238 ~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cvg 269 (317)
..| +|+.. +|-.|.|..+.|. .+||+.|.-
T Consensus 37 ~~C~~C~~~-~Ga~i~C~~~~C~-~~fH~~CA~ 67 (90)
T PF13771_consen 37 LKCSICKKK-GGACIGCSHPGCS-RSFHVPCAR 67 (90)
T ss_pred CCCcCCCCC-CCeEEEEeCCCCC-cEEChHHHc
Confidence 357 89985 6899999999998 999999964
No 25
>KOG2752|consensus
Probab=88.21 E-value=0.27 Score=47.29 Aligned_cols=31 Identities=32% Similarity=0.937 Sum_probs=24.7
Q ss_pred CCceeeeCCCCC-------CCeeeeCCCCCCCccee-cccCC
Q psy16463 236 EPTYCLCNQVSF-------GQMVMCDNDLCPHQWFH-FSCVA 269 (317)
Q Consensus 236 e~~~C~C~~~~~-------g~mi~Cd~~~C~~~wfH-~~Cvg 269 (317)
.-.||.|..+.. |+|++|-- |+ .||| -.|+.
T Consensus 127 qG~~C~Cd~~Ypdp~~~~e~~m~QC~i--CE-DWFHce~c~~ 165 (345)
T KOG2752|consen 127 QGLFCKCDTPYPDPVRTEEGEMLQCVI--CE-DWFHCEGCMQ 165 (345)
T ss_pred cceeEEecCCCCCccccccceeeeEEe--cc-chhcccccCc
Confidence 457999987732 57999988 99 9999 77765
No 26
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=87.84 E-value=0.4 Score=48.22 Aligned_cols=45 Identities=22% Similarity=0.676 Sum_probs=31.4
Q ss_pred eeCCCCC----CCeeeeCCCCCCCcceecccC--------CccCC-C----CCceeCcccccccc
Q psy16463 241 LCNQVSF----GQMVMCDNDLCPHQWFHFSCV--------AVTNT-P----KGKWYCPNCRKARS 288 (317)
Q Consensus 241 ~C~~~~~----g~mi~Cd~~~C~~~wfH~~Cv--------gl~~~-p----~~~w~C~~C~~~~~ 288 (317)
+|++.++ .-||.||. |. .|-|..|. |.+.. + .+.|||..|-....
T Consensus 133 iC~kfD~~~n~~~Wi~Cd~--Cg-H~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~se 194 (446)
T PF07227_consen 133 ICSKFDDNKNTCSWIGCDV--CG-HWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSE 194 (446)
T ss_pred ccCCcccCCCCeeEEeccC--CC-ceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhh
Confidence 7877533 25999998 98 99999993 21111 1 24899999986644
No 27
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=86.89 E-value=0.3 Score=39.42 Aligned_cols=30 Identities=27% Similarity=0.704 Sum_probs=25.6
Q ss_pred cee-eeCCCCCCCeeeeCCCCCCCcceecccCC
Q psy16463 238 TYC-LCNQVSFGQMVMCDNDLCPHQWFHFSCVA 269 (317)
Q Consensus 238 ~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cvg 269 (317)
..| +|+.. .|-.|.|..+.|. .+||..|.-
T Consensus 56 ~~C~iC~~~-~G~~i~C~~~~C~-~~fH~~CA~ 86 (110)
T PF13832_consen 56 LKCSICGKS-GGACIKCSHPGCS-TAFHPTCAR 86 (110)
T ss_pred CcCcCCCCC-CceeEEcCCCCCC-cCCCHHHHH
Confidence 346 99986 7889999999998 999999953
No 28
>KOG1473|consensus
Probab=82.85 E-value=0.74 Score=50.93 Aligned_cols=41 Identities=32% Similarity=1.027 Sum_probs=35.5
Q ss_pred ee-eeCCCCCCCeeeeCCCCCCCcceecccCCcc--CCCCCceeCcccc
Q psy16463 239 YC-LCNQVSFGQMVMCDNDLCPHQWFHFSCVAVT--NTPKGKWYCPNCR 284 (317)
Q Consensus 239 ~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cvgl~--~~p~~~w~C~~C~ 284 (317)
.| ||++ .|..+||++ |+ .-+|..||..+ ..|...|-|.-|.
T Consensus 346 hcrf~~d--~~~~lc~Et--~p-rvvhlEcv~hP~~~~~s~~~e~evc~ 389 (1414)
T KOG1473|consen 346 HCRFCHD--LGDLLCCET--CP-RVVHLECVFHPRFAVPSAFWECEVCN 389 (1414)
T ss_pred cccccCc--ccceeeccc--CC-ceEEeeecCCccccCCCccchhhhhh
Confidence 58 9998 699999999 99 88999999855 4577899999997
No 29
>KOG4443|consensus
Probab=75.71 E-value=1.6 Score=45.84 Aligned_cols=47 Identities=26% Similarity=0.839 Sum_probs=32.8
Q ss_pred cee-eeCCC-CCCCeeeeCCCCCCCcceecccCCc--cCCCCCceeCccccccc
Q psy16463 238 TYC-LCNQV-SFGQMVMCDNDLCPHQWFHFSCVAV--TNTPKGKWYCPNCRKAR 287 (317)
Q Consensus 238 ~~C-~C~~~-~~g~mi~Cd~~~C~~~wfH~~Cvgl--~~~p~~~w~C~~C~~~~ 287 (317)
+.| .|+.. +..-+..|+. |. .-||..|... +..+.|.|+|+.|..-+
T Consensus 69 rvCe~c~~~gD~~kf~~Ck~--cD-vsyh~yc~~P~~~~v~sg~~~ckk~~~c~ 119 (694)
T KOG4443|consen 69 RVCEACGTTGDPKKFLLCKR--CD-VSYHCYCQKPPNDKVPSGPWLCKKCTRCR 119 (694)
T ss_pred eeeeeccccCCccccccccc--cc-ccccccccCCccccccCcccccHHHHhhh
Confidence 345 46532 1234667888 97 7899999874 45678999999887543
No 30
>KOG3970|consensus
Probab=74.24 E-value=4.2 Score=37.67 Aligned_cols=57 Identities=23% Similarity=0.588 Sum_probs=36.0
Q ss_pred e-eeCCC-CCCCeeeeCCCCCCCcceecccCCc-----cCCC-CCceeCccccccccCCCcchhHHHHH
Q psy16463 240 C-LCNQV-SFGQMVMCDNDLCPHQWFHFSCVAV-----TNTP-KGKWYCPNCRKARSNAVRPKKQLVER 300 (317)
Q Consensus 240 C-~C~~~-~~g~mi~Cd~~~C~~~wfH~~Cvgl-----~~~p-~~~w~C~~C~~~~~~~~~~~~~~~~~ 300 (317)
| +|+-+ ..|+-+.- .| |..||+.|+.- +... .--|.||-|...-.+...-..+....
T Consensus 53 C~LC~t~La~gdt~RL---vC-yhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~a 117 (299)
T KOG3970|consen 53 CRLCNTPLASGDTTRL---VC-YHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEA 117 (299)
T ss_pred CceeCCccccCcceee---hh-hhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHH
Confidence 8 89876 23554443 26 58899999872 2211 23589999998876665544443333
No 31
>PF10158 LOH1CR12: Tumour suppressor protein; InterPro: IPR018780 This entry represents a region of 130 amino acids that is the most conserved part of some hypothetical proteins involved in loss of heterozygosity, and thus, tumour suppression []. The exact function of these proteins is not known.
Probab=72.37 E-value=59 Score=27.53 Aligned_cols=79 Identities=11% Similarity=0.189 Sum_probs=48.8
Q ss_pred HHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 29 YVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGNKIDQFSRKRNLLRVQVALIAAQEIGDEKLSIMQQ 108 (317)
Q Consensus 29 yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~k~~~~~~~~~~~~~I~~~l~~a~el~dEKv~LA~q 108 (317)
|-+.|-.+.+.+=.|=...-..|+++|..+..+...+.+..+.|.+-.... ..+..|...+.+++.+=++=+.+..+
T Consensus 36 ~Q~HL~~cA~~Va~~Q~~L~~riKevd~~~~~l~~~~~erqk~~~k~ae~L---~kv~els~~L~~~~~lL~~~v~~ie~ 112 (131)
T PF10158_consen 36 YQEHLNQCAEAVAFDQNALAKRIKEVDQEIAKLLQQMVERQKRFAKFAEQL---EKVNELSQQLSRCQSLLNQTVPSIET 112 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555566666677777888899999999999988887777664322222 12445555566555543444444443
Q ss_pred HH
Q psy16463 109 VQ 110 (317)
Q Consensus 109 ~~ 110 (317)
+.
T Consensus 113 LN 114 (131)
T PF10158_consen 113 LN 114 (131)
T ss_pred HH
Confidence 33
No 32
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=69.79 E-value=3.2 Score=33.81 Aligned_cols=65 Identities=26% Similarity=0.559 Sum_probs=39.3
Q ss_pred CCCCCcee-eeCCCCCCCeeee----CCCCC---CCcceecccCCcc-------CCCCCceeCccccc-------cccCC
Q psy16463 233 DPNEPTYC-LCNQVSFGQMVMC----DNDLC---PHQWFHFSCVAVT-------NTPKGKWYCPNCRK-------ARSNA 290 (317)
Q Consensus 233 d~~e~~~C-~C~~~~~g~mi~C----d~~~C---~~~wfH~~Cvgl~-------~~p~~~w~C~~C~~-------~~~~~ 290 (317)
|+..-..| .|.+...+..+.| .+..| . .-|=..|+-.. ......|.||.|+. .+.+.
T Consensus 3 d~~~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~-~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiCnCs~Crrk~g 81 (105)
T PF10497_consen 3 DSVNGKTCHQCRQKTLDFKTICTGHWKNSSCRGCR-GKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGICNCSFCRRKRG 81 (105)
T ss_pred cCCCCCCchhhcCCCCCCceEcCCCCCCCCCccCc-ceehHhHHHHHHhhhHHHHhcCCceECCCCCCeeCCHhhhccCC
Confidence 34445678 8988766766677 33447 6 44667785421 11347899999985 23344
Q ss_pred CcchhHHH
Q psy16463 291 VRPKKQLV 298 (317)
Q Consensus 291 ~~~~~~~~ 298 (317)
+.|-+.+.
T Consensus 82 ~~PTg~l~ 89 (105)
T PF10497_consen 82 WAPTGILY 89 (105)
T ss_pred CCCcHHHH
Confidence 55554444
No 33
>KOG3053|consensus
Probab=67.86 E-value=2.7 Score=39.60 Aligned_cols=70 Identities=20% Similarity=0.430 Sum_probs=46.5
Q ss_pred Ccee-eeCCCCCC----Ceee-eCCCCCCCcceecccCC--ccCC----CCCceeCccccccccCCCcchhHHHHHHHHh
Q psy16463 237 PTYC-LCNQVSFG----QMVM-CDNDLCPHQWFHFSCVA--VTNT----PKGKWYCPNCRKARSNAVRPKKQLVERLEKY 304 (317)
Q Consensus 237 ~~~C-~C~~~~~g----~mi~-Cd~~~C~~~wfH~~Cvg--l~~~----p~~~w~C~~C~~~~~~~~~~~~~~~~~~~~~ 304 (317)
..+| +|-..+-+ .||. |-...- ..|.|-+|+- +.+. +...-.||+|..+.-.++-....+...|++.
T Consensus 20 eR~CWiCF~TdeDn~~a~WV~PCrCRGt-~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~~~~~~Le~~ 98 (293)
T KOG3053|consen 20 ERCCWICFATDEDNRLAAWVHPCRCRGT-TKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLGPFDRVLERL 98 (293)
T ss_pred ceeEEEEeccCcccchhhhcccccccCc-cHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccChHHHHHHHh
Confidence 4688 79654322 3443 321224 4999999987 3333 2357899999999887777777777777776
Q ss_pred hhh
Q psy16463 305 NKE 307 (317)
Q Consensus 305 ~k~ 307 (317)
.+-
T Consensus 99 d~~ 101 (293)
T KOG3053|consen 99 DIL 101 (293)
T ss_pred hhH
Confidence 543
No 34
>TIGR00634 recN DNA repair protein RecN. All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.
Probab=65.16 E-value=62 Score=33.68 Aligned_cols=105 Identities=16% Similarity=0.136 Sum_probs=57.3
Q ss_pred hhhhHHHHHHHHHhhcCh---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-----cCChHHHHHHHH---HHHHH-
Q psy16463 24 MYSVPYVETYLDIVENLP---DEIQRYLTKIRELDVLYQSYMKEIEHIASQNGN-----KIDQFSRKRNLL---RVQVA- 91 (317)
Q Consensus 24 ~~~a~yLedyld~ienLP---~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~k-----~~~~~~~~~~~~---~I~~~- 91 (317)
-+++.-|.+|++.++.=| .+|+..+..++.+-.++.....++-...+++.+ .......+.+.. .+++.
T Consensus 283 ~d~~~~l~~~~~~l~~dp~~L~ele~RL~~l~~LkrKyg~s~e~l~~~~~~l~~eL~~l~~~~~~le~L~~el~~l~~~l 362 (563)
T TIGR00634 283 EEATRELQNYLDELEFDPERLNEIEERLAQIKRLKRKYGASVEEVLEYAEKIKEELDQLDDSDESLEALEEEVDKLEEEL 362 (563)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 344556677777776667 445555555555555554333232222222211 111111222222 33333
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccCc
Q psy16463 92 LIAAQEIGDEKLSIMQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 92 l~~a~el~dEKv~LA~q~~dlVdkhirrLD~dl~~le 128 (317)
...+.+|...-...|..+-..|..+++.|...-..|.
T Consensus 363 ~~~a~~Ls~~R~~~a~~l~~~v~~~l~~L~m~~~~f~ 399 (563)
T TIGR00634 363 DKAAVALSLIRRKAAERLAKRVEQELKALAMEKAEFT 399 (563)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcEEE
Confidence 3445667777777888888899999998877666665
No 35
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=65.15 E-value=6.9 Score=34.82 Aligned_cols=67 Identities=27% Similarity=0.431 Sum_probs=41.4
Q ss_pred ee-eeCCCCCCCeeeeCCCCCCCcceecccCC-ccCCCCCceeCcccccccc-CCCcchhHHHHHHHHhhhhhhhhhcc
Q psy16463 239 YC-LCNQVSFGQMVMCDNDLCPHQWFHFSCVA-VTNTPKGKWYCPNCRKARS-NAVRPKKQLVERLEKYNKEKQEKIGN 314 (317)
Q Consensus 239 ~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cvg-l~~~p~~~w~C~~C~~~~~-~~~~~~~~~~~~~~~~~k~~~~~~~~ 314 (317)
-| ||..|+..-||.=++ -.||| .|-. |. +.-||.-=..... ...+....+..++++++++-+++.+.
T Consensus 15 ~C~IC~KpsttVL~t~~~----~DfFY-~C~~HL~----D~~F~~p~~~~~~~~~~~k~~el~~eiekvkke~Eekq~~ 84 (182)
T PF08432_consen 15 ACFICYKPSTTVLITPDN----KDFFY-VCPSHLK----DRQFATPIYDEEYVEAKKKKKELEEEIEKVKKEYEEKQKW 84 (182)
T ss_pred ceeEecCCCceEEecCCC----CCeEE-eCccccc----CcccCCCCCCHHHHHHHhhHHHHHHHHHHHHHHHHHHhHH
Confidence 49 899998877876555 38997 7865 33 3366653222211 12234455778888888877766553
No 36
>KOG0994|consensus
Probab=64.82 E-value=24 Score=39.97 Aligned_cols=40 Identities=13% Similarity=0.088 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccCcC
Q psy16463 90 VALIAAQEIGDEKLSIMQQVQDVIEGKTRQIDGIFYNLPS 129 (317)
Q Consensus 90 ~~l~~a~el~dEKv~LA~q~~dlVdkhirrLD~dl~~le~ 129 (317)
+....+++.+|+-...|+.+..-++..|+.....|.+.++
T Consensus 1566 e~V~eaL~~Ad~Aq~~a~~ai~~a~~~~~~a~~~l~kv~~ 1605 (1758)
T KOG0994|consen 1566 EDVVEALEEADVAQGEAQDAIQGADRDIRLAQQLLAKVQE 1605 (1758)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 3444455555566666666666666666655555555553
No 37
>PRK10869 recombination and repair protein; Provisional
Probab=64.73 E-value=89 Score=32.60 Aligned_cols=39 Identities=13% Similarity=0.166 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccCcC
Q psy16463 91 ALIAAQEIGDEKLSIMQQVQDVIEGKTRQIDGIFYNLPS 129 (317)
Q Consensus 91 ~l~~a~el~dEKv~LA~q~~dlVdkhirrLD~dl~~le~ 129 (317)
.+..+.+|+..-...|..+-..|..+++.|...=..|..
T Consensus 357 l~~~A~~LS~~R~~aA~~l~~~v~~~L~~L~m~~a~f~v 395 (553)
T PRK10869 357 ALETAQKLHQSRQRYAKELAQLITESMHELSMPHGKFTI 395 (553)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCcEEEE
Confidence 344566777778888999999999999998877776663
No 38
>KOG4216|consensus
Probab=64.50 E-value=3.9 Score=40.65 Aligned_cols=26 Identities=31% Similarity=0.865 Sum_probs=20.1
Q ss_pred CCcee-eeCCCCCC---CeeeeCCCCCCCccee
Q psy16463 236 EPTYC-LCNQVSFG---QMVMCDNDLCPHQWFH 264 (317)
Q Consensus 236 e~~~C-~C~~~~~g---~mi~Cd~~~C~~~wfH 264 (317)
|.+-| +|++.+.| -.|-|++ |. .+|-
T Consensus 45 EvIPCKiCGDKSSGiHYGVITCEG--CK-GFFR 74 (479)
T KOG4216|consen 45 EIIPCKICGDKSSGIHYGVITCEG--CK-GFFR 74 (479)
T ss_pred EEEeeeeccCCCCcceeeeEeecc--ch-Hhhh
Confidence 34569 99998776 4889999 98 7764
No 39
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=62.45 E-value=4.9 Score=36.83 Aligned_cols=33 Identities=18% Similarity=0.270 Sum_probs=25.9
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 40 LPDEIQRYLTKIRELDVLYQSYMKEIEHIASQN 72 (317)
Q Consensus 40 LP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~ 72 (317)
+-.+|.|.=..|.++|..+-.++..+.+..-.|
T Consensus 13 ~~~~L~rle~qi~q~~~~~~~~qs~l~~~~~r~ 45 (251)
T COG5415 13 YTADLSRLESQIHQLDVALKKSQSILSQWQSRL 45 (251)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446788888999999999888877777765554
No 40
>KOG4443|consensus
Probab=61.81 E-value=2.3 Score=44.72 Aligned_cols=45 Identities=36% Similarity=0.924 Sum_probs=31.7
Q ss_pred cee-eeCCCC---CCCeeeeCCCCCCCcceecccCCccCC---CCCceeCccccc
Q psy16463 238 TYC-LCNQVS---FGQMVMCDNDLCPHQWFHFSCVAVTNT---PKGKWYCPNCRK 285 (317)
Q Consensus 238 ~~C-~C~~~~---~g~mi~Cd~~~C~~~wfH~~Cvgl~~~---p~~~w~C~~C~~ 285 (317)
..| +|+... -|-|+.|.+ |. .-||..||.+-.. -.+-|-||.|+.
T Consensus 19 ~mc~l~~s~G~~~ag~m~ac~~--c~-~~yH~~cvt~~~~~~~l~~gWrC~~crv 70 (694)
T KOG4443|consen 19 LMCPLCGSSGKGRAGRLLACSD--CG-QKYHPYCVTSWAQHAVLSGGWRCPSCRV 70 (694)
T ss_pred hhhhhhccccccccCcchhhhh--hc-ccCCcchhhHHHhHHHhcCCcccCCcee
Confidence 346 676432 267999998 98 8899999984322 134599999984
No 41
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=60.48 E-value=2.2 Score=26.49 Aligned_cols=27 Identities=26% Similarity=0.597 Sum_probs=11.2
Q ss_pred ee-eeCCCCCC-CeeeeCCCCCCCcceecccC
Q psy16463 239 YC-LCNQVSFG-QMVMCDNDLCPHQWFHFSCV 268 (317)
Q Consensus 239 ~C-~C~~~~~g-~mi~Cd~~~C~~~wfH~~Cv 268 (317)
.| +|+.+.++ .+-.|.. |. -++|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~--Cd-f~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSE--CD-FDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TT--T------HHHH
T ss_pred cCCcCCCcCCCCceEECcc--CC-CccChhcC
Confidence 36 78888666 7888988 99 67898874
No 42
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=59.75 E-value=72 Score=29.95 Aligned_cols=72 Identities=17% Similarity=0.204 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCcCC---hHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q psy16463 48 LTKIRELDVLYQSYMKEIEHIASQNGNKID---QFSRKRNLLRVQVALIAAQEIGDE-KLSIMQQVQDVIEGKTRQ 119 (317)
Q Consensus 48 l~lIRElD~k~~~~~~~ie~~~~~~~k~~~---~~~~~~~~~~I~~~l~~a~el~dE-Kv~LA~q~~dlVdkhirr 119 (317)
-.+|+++|.++......|+.....-..... ......+-.+|...+..+-+|+.+ +|.-|..+...|+.--..
T Consensus 89 ~~~i~d~drrI~~~k~RL~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~e 164 (254)
T PF03194_consen 89 QRLIRDCDRRIERAKERLEQTQEEQAKEADEEKAEKIDELDEKIGELLKEAEELGEEGDVDEAQKLMEEVEKLKEE 164 (254)
T ss_pred HHHHHHHHHHHHHHHHHHHhCccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356777777777766666554332211111 222345667899999999999987 899999888877754433
No 43
>COG3404 Methenyl tetrahydrofolate cyclohydrolase [Amino acid transport and metabolism]
Probab=58.02 E-value=1.5e+02 Score=27.06 Aligned_cols=81 Identities=15% Similarity=0.167 Sum_probs=52.3
Q ss_pred hhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-----cCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 37 VENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGN-----KIDQFSRKRNLLRVQVALIAAQEIGDEKLSIMQQVQD 111 (317)
Q Consensus 37 ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~k-----~~~~~~~~~~~~~I~~~l~~a~el~dEKv~LA~q~~d 111 (317)
-++.-.|...+|..+.++-..+..+..+-.+-+..+.. ....+++......||..+..+.+.--+=+.++-++++
T Consensus 52 Y~~~d~e~k~i~~~~~~ik~~l~~lidkD~eAf~~im~AyKlPK~teEEK~~R~~~lQ~Alk~Aa~vP~~ia~~~~~~l~ 131 (208)
T COG3404 52 YEDYDDEMKEILEELQKIKAELLALIDKDEEAFNLIMAAYKLPKSTEEEKAARRKALQNALKEAAKVPLDIATLMVDLLE 131 (208)
T ss_pred hhhhhhhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHH
Confidence 45566778888888888888888877765555555432 2233345556778999998888755555555555555
Q ss_pred HHHHHH
Q psy16463 112 VIEGKT 117 (317)
Q Consensus 112 lVdkhi 117 (317)
++..-+
T Consensus 132 l~e~l~ 137 (208)
T COG3404 132 LLEKLV 137 (208)
T ss_pred HHHHHH
Confidence 554443
No 44
>PF11690 DUF3287: Protein of unknown function (DUF3287); InterPro: IPR021704 This eukaryotic family of proteins has no known function.
Probab=56.45 E-value=63 Score=26.64 Aligned_cols=46 Identities=20% Similarity=0.295 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhHhccC
Q psy16463 82 KRNLLRVQVALIAAQEIGDEKLSIMQQVQDV-IEGKTRQIDGIFYNL 127 (317)
Q Consensus 82 ~~~~~~I~~~l~~a~el~dEKv~LA~q~~dl-VdkhirrLD~dl~~l 127 (317)
++...-|+.--..-+++.+|+-.|..++.+| |++-++.|+++-..-
T Consensus 38 ~ea~~F~~kV~~qH~~~~~e~r~L~kKi~~l~veRkmr~Les~p~~W 84 (109)
T PF11690_consen 38 KEAYDFIDKVVDQHQRYCDERRKLRKKIQDLRVERKMRALESHPFDW 84 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCChHHH
Confidence 3333334444444457888999999999997 999999999875443
No 45
>KOG1512|consensus
Probab=54.82 E-value=3.5 Score=39.45 Aligned_cols=33 Identities=27% Similarity=0.670 Sum_probs=25.6
Q ss_pred CeeeeCCCCCCCcceecccCCccCCC-----CCceeCcccc
Q psy16463 249 QMVMCDNDLCPHQWFHFSCVAVTNTP-----KGKWYCPNCR 284 (317)
Q Consensus 249 ~mi~Cd~~~C~~~wfH~~Cvgl~~~p-----~~~w~C~~C~ 284 (317)
-||+|.. |. -.+|..||.++..- .=.|.|..|+
T Consensus 278 S~I~C~~--C~-~~~HP~Ci~M~~elv~~~KTY~W~C~~C~ 315 (381)
T KOG1512|consen 278 SWIVCKP--CA-TRPHPYCVAMIPELVGQYKTYFWKCSSCE 315 (381)
T ss_pred cceeecc--cc-cCCCCcchhcCHHHHhHHhhcchhhcccH
Confidence 5999988 98 67999999876442 2368888776
No 46
>KOG2932|consensus
Probab=53.32 E-value=5.8 Score=38.41 Aligned_cols=38 Identities=26% Similarity=0.818 Sum_probs=27.1
Q ss_pred cee-eeCCC--CCCCeeeeCCCCCCCcceecccCCccCCCCCceeCccccc
Q psy16463 238 TYC-LCNQV--SFGQMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRK 285 (317)
Q Consensus 238 ~~C-~C~~~--~~g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~ 285 (317)
-+| -|..+ -||.||-|+. .|-+.|..... .-.||.|..
T Consensus 91 HfCd~Cd~PI~IYGRmIPCkH------vFCl~CAr~~~----dK~Cp~C~d 131 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIPCKH------VFCLECARSDS----DKICPLCDD 131 (389)
T ss_pred EeecccCCcceeeecccccch------hhhhhhhhcCc----cccCcCccc
Confidence 467 69887 4899999985 36778876653 346777763
No 47
>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=52.95 E-value=2.3 Score=28.43 Aligned_cols=39 Identities=33% Similarity=0.670 Sum_probs=22.1
Q ss_pred e-eeCCCC-CC-CeeeeCCCCCCCcceecccCCccCCCCCceeCcccc
Q psy16463 240 C-LCNQVS-FG-QMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCR 284 (317)
Q Consensus 240 C-~C~~~~-~g-~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~ 284 (317)
| ||...- .+ .++.. . |. ..||..|+.--.. ....||.|+
T Consensus 3 C~IC~~~~~~~~~~~~l-~--C~-H~fh~~Ci~~~~~--~~~~CP~CR 44 (44)
T PF13639_consen 3 CPICLEEFEDGEKVVKL-P--CG-HVFHRSCIKEWLK--RNNSCPVCR 44 (44)
T ss_dssp ETTTTCBHHTTSCEEEE-T--TS-EEEEHHHHHHHHH--HSSB-TTTH
T ss_pred CcCCChhhcCCCeEEEc-c--CC-CeeCHHHHHHHHH--hCCcCCccC
Confidence 5 776552 23 34433 3 87 8999999862111 124898885
No 48
>PHA02862 5L protein; Provisional
Probab=52.37 E-value=5.5 Score=34.43 Aligned_cols=29 Identities=17% Similarity=0.304 Sum_probs=21.9
Q ss_pred CcceecccCCccCCCCCceeCcccccccc
Q psy16463 260 HQWFHFSCVAVTNTPKGKWYCPNCRKARS 288 (317)
Q Consensus 260 ~~wfH~~Cvgl~~~p~~~w~C~~C~~~~~ 288 (317)
+.|.|-+|+..=-.+.++-+|+.|..+..
T Consensus 25 ~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 25 YKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred chhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 49999999873224456789999997763
No 49
>KOG1493|consensus
Probab=52.08 E-value=4.6 Score=31.23 Aligned_cols=48 Identities=38% Similarity=0.840 Sum_probs=31.4
Q ss_pred ee-eeCCCCCCCeeeeC--CCCCCCcc------eecccCC-ccCCCCCceeCcccccc
Q psy16463 239 YC-LCNQVSFGQMVMCD--NDLCPHQW------FHFSCVA-VTNTPKGKWYCPNCRKA 286 (317)
Q Consensus 239 ~C-~C~~~~~g~mi~Cd--~~~C~~~w------fH~~Cvg-l~~~p~~~w~C~~C~~~ 286 (317)
.| +|+.+..|---.|- +++||+-| ||..|+- --..|..+-.||-|+..
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~ 79 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQT 79 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhe
Confidence 58 99987666333333 24588666 8999974 22345556889999864
No 50
>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=50.83 E-value=13 Score=29.14 Aligned_cols=27 Identities=22% Similarity=0.624 Sum_probs=16.5
Q ss_pred ee-eeCCCCCCCeeeeCCCCCCCcceecccC
Q psy16463 239 YC-LCNQVSFGQMVMCDNDLCPHQWFHFSCV 268 (317)
Q Consensus 239 ~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cv 268 (317)
.| +|+++-+...+.--. |. .-||+.|.
T Consensus 80 ~C~vC~k~l~~~~f~~~p--~~-~v~H~~C~ 107 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFP--CG-HVVHYSCI 107 (109)
T ss_pred CccCcCCcCCCceEEEeC--CC-eEEecccc
Confidence 48 999984432222222 43 66999997
No 51
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=50.01 E-value=8.2 Score=29.28 Aligned_cols=33 Identities=24% Similarity=0.787 Sum_probs=19.0
Q ss_pred CeeeeCCCCCCCcceecccCCccCCC-------CCceeCccc
Q psy16463 249 QMVMCDNDLCPHQWFHFSCVAVTNTP-------KGKWYCPNC 283 (317)
Q Consensus 249 ~mi~Cd~~~C~~~wfH~~Cvgl~~~p-------~~~w~C~~C 283 (317)
-||.|.+. = -.|.|..|+.|.+.- ..+|||.+=
T Consensus 29 AMI~cs~~-~-GHWvhaqCm~LsE~~L~~LSq~n~KYfC~dH 68 (78)
T PF13341_consen 29 AMIFCSRG-G-GHWVHAQCMDLSETMLIQLSQENTKYFCNDH 68 (78)
T ss_dssp -EEEE-ST-T--EEEETGGGT--HHHHHHHHHSSS-B--TTT
T ss_pred eEEEEeCC-C-ceEeEeecccchHHHHHHHccCCceEEEhhh
Confidence 49999974 3 389999999986542 368999753
No 52
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=49.89 E-value=1.4e+02 Score=27.67 Aligned_cols=26 Identities=35% Similarity=0.858 Sum_probs=18.4
Q ss_pred CeeeeCCCCCCCcceecccCCccCCCCCceeCccccccc
Q psy16463 249 QMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKAR 287 (317)
Q Consensus 249 ~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~~ 287 (317)
-|-.|.+ |. .-.|-. .| .||-|..+-
T Consensus 193 PMK~C~s--C~-qqIHRN------AP----iCPlCK~Ks 218 (230)
T PF10146_consen 193 PMKTCQS--CH-QQIHRN------AP----ICPLCKAKS 218 (230)
T ss_pred CcchhHh--HH-HHHhcC------CC----CCccccccc
Confidence 4888988 96 767732 33 599998763
No 53
>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=49.82 E-value=11 Score=24.79 Aligned_cols=25 Identities=32% Similarity=0.975 Sum_probs=17.3
Q ss_pred eeeCCCCCCCcceecccCCccCCCCCceeCccccc
Q psy16463 251 VMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRK 285 (317)
Q Consensus 251 i~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~ 285 (317)
+.|.. |.-.||. ...|.|||..|-.
T Consensus 9 ~~C~~--C~~~~~~--------~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPV--CGSRWFY--------SDDGFYYCDRCGH 33 (36)
T ss_pred CcCCC--CCCeEeE--------ccCCEEEhhhCce
Confidence 45766 7755664 4568999998854
No 54
>KOG4460|consensus
Probab=49.62 E-value=1.7e+02 Score=30.79 Aligned_cols=34 Identities=21% Similarity=0.258 Sum_probs=26.1
Q ss_pred HHHHHHHHHhhcChHHHHHHHHHHHHH-HHHHHHH
Q psy16463 28 PYVETYLDIVENLPDEIQRYLTKIREL-DVLYQSY 61 (317)
Q Consensus 28 ~yLedyld~ienLP~Elqr~l~lIREl-D~k~~~~ 61 (317)
.+-|+||..-.-.-.||||+..+|... |.+.|++
T Consensus 570 vfrEqYi~~~dlV~~e~qrH~~~l~~~k~~QlQ~l 604 (741)
T KOG4460|consen 570 VFREQYILKQDLVKEEIQRHVKLLCDQKKKQLQDL 604 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 577999999998999999999888654 4444443
No 55
>KOG3579|consensus
Probab=48.96 E-value=18 Score=34.75 Aligned_cols=60 Identities=32% Similarity=0.748 Sum_probs=40.2
Q ss_pred CCCCCCCCCcee-eeCCC-CCCCeeeeCCCCCCCcceecccCC--ccCC-CCCceeCc---cccccccCC
Q psy16463 229 DLAIDPNEPTYC-LCNQV-SFGQMVMCDNDLCPHQWFHFSCVA--VTNT-PKGKWYCP---NCRKARSNA 290 (317)
Q Consensus 229 ~~~~d~~e~~~C-~C~~~-~~g~mi~Cd~~~C~~~wfH~~Cvg--l~~~-p~~~w~C~---~C~~~~~~~ 290 (317)
+...-+..+++| +|+.- ..--+|+|-. -++.-|-|.|-. |... ..+..||| .|---+...
T Consensus 260 ~s~~A~~apLcCTLC~ERLEDTHFVQCPS--Vp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPLvgS~v 327 (352)
T KOG3579|consen 260 DSGAAPSAPLCCTLCHERLEDTHFVQCPS--VPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPLVGSNV 327 (352)
T ss_pred ccccCCCCceeehhhhhhhccCceeecCC--CcccceecccCHHHHHhhcCCCceeCCCCCcCcccCCcc
Confidence 345677888999 89864 2345899976 665668888876 3322 35899998 465444444
No 56
>PRK15365 type III secretion system chaperone SseA; Provisional
Probab=48.53 E-value=1.5e+02 Score=24.11 Aligned_cols=77 Identities=13% Similarity=0.109 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHH------HHHHHhC---cCChHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Q psy16463 47 YLTKIRELDVLYQSYMKEIEH------IASQNGN---KIDQFSRKRNLLRVQVALIAAQ-EIGDEKLSIMQQVQDVIEGK 116 (317)
Q Consensus 47 ~l~lIRElD~k~~~~~~~ie~------~~~~~~k---~~~~~~~~~~~~~I~~~l~~a~-el~dEKv~LA~q~~dlVdkh 116 (317)
.|+++++|..+|..+...+.+ .+..++. ..++.. ++.+..+...|=... .+..||.++... |...
T Consensus 7 ~~~~l~DL~~rYs~L~s~lkKfkq~q~~I~q~L~eRA~~d~ka-RE~l~rLd~aFP~G~~~~~qE~~k~m~~----i~~~ 81 (107)
T PRK15365 7 AFSEYRDLEQSYMQLNHCLKKFHQIRAKVSQQLAERAESPKKS-RETESILHNLFPQGVAGVNQEAEKDLKK----IVSL 81 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHH-HHHHHHHHHHCcchhhHHhHHHHHHHHH----HHHH
Confidence 477888888888765444322 2222222 233333 334445555554433 446677665554 4488
Q ss_pred HHHHHhHhccCc
Q psy16463 117 TRQIDGIFYNLP 128 (317)
Q Consensus 117 irrLD~dl~~le 128 (317)
.++|+..|+.+-
T Consensus 82 FKQLEt~LKnln 93 (107)
T PRK15365 82 FKQLEVRLKQLN 93 (107)
T ss_pred HHHHHHHHHhcC
Confidence 899999998887
No 57
>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction
Probab=48.08 E-value=1.9e+02 Score=25.31 Aligned_cols=98 Identities=13% Similarity=0.197 Sum_probs=57.0
Q ss_pred HHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcC------ChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 31 ETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGNKI------DQFSRKRNLLRVQVALIAAQEIGDEKLS 104 (317)
Q Consensus 31 edyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~k~~------~~~~~~~~~~~I~~~l~~a~el~dEKv~ 104 (317)
++..+-.++-=.|+.+.-.+|.++-..+.....++|.+-..+...- +..-..-.-..|+..|..|.+++-+..-
T Consensus 16 ~qIf~I~E~~R~E~~~l~~EL~evk~~v~~~I~evD~Le~~er~aR~rL~eVS~~f~~ysE~dik~AYe~A~~lQ~~L~~ 95 (159)
T PF05384_consen 16 EQIFEIAEQARQEYERLRKELEEVKEEVSEVIEEVDKLEKRERQARQRLAEVSRNFDRYSEEDIKEAYEEAHELQVRLAM 95 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHHHHHHHHH
Confidence 4444445555567777777777777777777777777655542210 0000000123578888888777755444
Q ss_pred HHHH------HHHHHHHHHHHHHhHhccCc
Q psy16463 105 IMQQ------VQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 105 LA~q------~~dlVdkhirrLD~dl~~le 128 (317)
+-.+ --|-+++.+++|..-+++.+
T Consensus 96 ~re~E~qLr~rRD~LErrl~~l~~tierAE 125 (159)
T PF05384_consen 96 LREREKQLRERRDELERRLRNLEETIERAE 125 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4433 34556677777776666555
No 58
>PF10796 Anti-adapt_IraP: Sigma-S stabilisation anti-adaptor protein ; InterPro: IPR019732 This entry is conserved in Enterobacteriaceae. It is one of a series of proteins, expressed by these bacteria in response to stress, that help to regulate Sigma-S, the stationary phase sigma factor of Escherichia coli and Salmonella. IraP is essential for Sigma-S stabilisation in some but not all starvation conditions []. ; GO: 0005737 cytoplasm
Probab=47.19 E-value=1.3e+02 Score=23.80 Aligned_cols=74 Identities=16% Similarity=0.208 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH---HHHHhCcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 44 IQRYLTKIRELDVLYQSYMKEIEHI---ASQNGNKIDQFSRKRNLLRVQVALIAAQEIGDEKLSIMQQVQDVIEGKTRQI 120 (317)
Q Consensus 44 lqr~l~lIRElD~k~~~~~~~ie~~---~~~~~k~~~~~~~~~~~~~I~~~l~~a~el~dEKv~LA~q~~dlVdkhirrL 120 (317)
|...|-.|-++|....++..+++.+ +.-.+...+...+.+++..|...+..+..-+++=.. .-.+|+.+++++|
T Consensus 5 i~~lL~KlA~~e~esKeL~AqVEAleivitALL~~l~~~~~~~~i~~I~~Ai~~a~~~~~~~~~---sd~eLL~~~~~~L 81 (87)
T PF10796_consen 5 IAELLAKLAEKEAESKELTAQVEALEIVITALLRTLDQGGRQEMIESIEKAIEDASPSSDVPLK---SDAELLLQYVKKL 81 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHhcccCCccch---HHHHHHHHHHHHH
Confidence 5567788889999999888887664 444444556677888999999988877753333221 2345666666665
No 59
>KOG4299|consensus
Probab=47.13 E-value=11 Score=39.64 Aligned_cols=44 Identities=34% Similarity=0.902 Sum_probs=34.7
Q ss_pred Ccee-eeCCCCCCCeeeeCCCCCCCcceecccCCccCCCC---CceeCccccc
Q psy16463 237 PTYC-LCNQVSFGQMVMCDNDLCPHQWFHFSCVAVTNTPK---GKWYCPNCRK 285 (317)
Q Consensus 237 ~~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~---~~w~C~~C~~ 285 (317)
.+.| +|.+ +|...||+. |+ .-||..|.+....|. ..|.|..|..
T Consensus 47 ~ts~~~~~~--~gn~~~~~~--~~-~s~h~~~~~~~~sp~~~~~~~~~~~~~~ 94 (613)
T KOG4299|consen 47 ATSCGICKS--GGNLLCCDH--CP-ASFHLECDKPPLSPDLKGSEINCSRCPK 94 (613)
T ss_pred hhhcchhhh--cCCcccccc--Cc-cccchhccCcccCcccccccccccCCCc
Confidence 3457 8887 788899999 99 899999999766664 5677777765
No 60
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=45.57 E-value=6.9 Score=38.33 Aligned_cols=47 Identities=23% Similarity=0.609 Sum_probs=24.8
Q ss_pred CCCcee-eeCCCC---CCCeee--eCCCCCCCcceecccCCccCCCCCceeCcccccccc
Q psy16463 235 NEPTYC-LCNQVS---FGQMVM--CDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKARS 288 (317)
Q Consensus 235 ~e~~~C-~C~~~~---~g~mi~--Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~~~ 288 (317)
||..|| +|=.+- ...+.- |.-..|.+-|-| |... -.--||.|+++..
T Consensus 12 deed~cplcie~mditdknf~pc~cgy~ic~fc~~~-----irq~--lngrcpacrr~y~ 64 (480)
T COG5175 12 DEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNN-----IRQN--LNGRCPACRRKYD 64 (480)
T ss_pred cccccCcccccccccccCCcccCCcccHHHHHHHHH-----HHhh--ccCCChHhhhhcc
Confidence 344579 897652 222333 444456544544 2111 1346999998764
No 61
>PF05130 FlgN: FlgN protein; InterPro: IPR007809 Flagella synthesis protein FlgN is an export chaperone involved in flagellar synthesis []. This entry represents a FlgN-like domain, consisting of a 4 long helices bundle, where the last helix is shorter than the three others.; GO: 0009296 flagellum assembly, 0019861 flagellum; PDB: 2FUP_A 3OPC_A.
Probab=45.05 E-value=1.6e+02 Score=23.58 Aligned_cols=22 Identities=14% Similarity=0.231 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHHHhHhccCc
Q psy16463 107 QQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 107 ~q~~dlVdkhirrLD~dl~~le 128 (317)
..-..+|..++..++.-+..+.
T Consensus 105 ~~N~~ll~~~~~~~~~~l~~l~ 126 (143)
T PF05130_consen 105 ERNQQLLEQALEFVQQLLNLLQ 126 (143)
T ss_dssp HHHHHHHHHCCHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 3334455555555555555555
No 62
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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 CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=45.03 E-value=13 Score=25.95 Aligned_cols=31 Identities=29% Similarity=0.737 Sum_probs=15.7
Q ss_pred CeeeeCCCCCCCcceecccCCccC---CCCCceeCccc
Q psy16463 249 QMVMCDNDLCPHQWFHFSCVAVTN---TPKGKWYCPNC 283 (317)
Q Consensus 249 ~mi~Cd~~~C~~~wfH~~Cvgl~~---~p~~~w~C~~C 283 (317)
.+|+||. |. .|=.+. .++.. .-.+.|||..-
T Consensus 2 ~WVQCd~--C~-KWR~lp-~~~~~~~~~~~d~W~C~~n 35 (50)
T PF07496_consen 2 YWVQCDS--CL-KWRRLP-EEVDPIREELPDPWYCSMN 35 (50)
T ss_dssp EEEE-TT--T---EEEE--CCHHCTSCCSSTT--GGGS
T ss_pred eEEECCC--CC-ceeeCC-hhhCcccccCCCeEEcCCC
Confidence 4799998 97 997776 44332 11249999873
No 63
>KOG2846|consensus
Probab=43.82 E-value=14 Score=35.92 Aligned_cols=39 Identities=18% Similarity=0.480 Sum_probs=28.8
Q ss_pred eeeeCCCCCCCcceecccCCccCCCCCceeCccccccccCCCcc
Q psy16463 250 MVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKARSNAVRP 293 (317)
Q Consensus 250 mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~~~~~~~~ 293 (317)
-+-|.+ |. .|..|+....-+--.|||+.|...++.+..+
T Consensus 220 ALIC~~--C~---~HNGla~~ee~~yi~F~C~~Cn~LN~~~k~~ 258 (328)
T KOG2846|consen 220 ALICSQ--CH---HHNGLARKEEYEYITFRCPHCNALNPAKKSP 258 (328)
T ss_pred hhcchh--hc---cccCcCChhhcCceEEECccccccCCCcCCc
Confidence 344655 95 4999998765566689999999888766553
No 64
>PF08702 Fib_alpha: Fibrinogen alpha/beta chain family; InterPro: IPR012290 Fibrinogen plays key roles in both blood clotting and platelet aggregation. During blood clot formation, the conversion of soluble fibrinogen to insoluble fibrin is triggered by thrombin, resulting in the polymerisation of fibrin, which forms a soft clot; this is then converted to a hard clot by factor XIIIA, which cross-links fibrin molecules. Platelet aggregation involves the binding of the platelet protein receptor integrin alpha(IIb)-beta(3) to the C-terminal D domain of fibrinogen []. In addition to platelet aggregation, platelet-fibrinogen interaction mediates both adhesion and fibrin clot retraction. Fibrinogen occurs as a dimer, where each monomer is composed of three non-identical chains, alpha, beta and gamma, linked together by several disulphide bonds []. The N-terminals of all six chains come together to form the centre of the molecule (E domain), from which the monomers extend in opposite directions as coiled coils, followed by C-terminal globular domains (D domains). Therefore, the domain composition is: D-coil-E-coil-D. At each end, the C-terminal of the alpha chain extends beyond the D domain as a protuberance that is important for cross-linking the molecule. During clot formation, the N-terminal fragments of the alpha and beta chains (within the E domain) in fibrinogen are cleaved by thrombin, releasing fibrinopeptides A and B, respectively, and producing fibrin. This cleavage results in the exposure of four binding sites on the E domain, each of which can bind to a D domain from different fibrin molecules. The binding of fibrin molecules produces a polymer consisting of a lattice network of fibrins that form a long, branching, flexible fibre [, ]. Fibrin fibres interact with platelets to increase the size of the clot, as well as with several different proteins and cells, thereby promoting the inflammatory response and concentrating the cells required for wound repair at the site of damage. This entry represents the coiled-coil domain and part of the N-terminal E domain found in all three fibrinogen polypeptides, namely the alpha, beta and gamma chains. More information about these proteins can be found at Protein of the Month: Fibrinogen [].; GO: 0005102 receptor binding, 0030674 protein binding, bridging, 0007165 signal transduction, 0030168 platelet activation, 0051258 protein polymerization, 0005577 fibrinogen complex; PDB: 1LWU_D 1N73_D 1M1J_B 1JY2_R 1JY3_R 1RF0_A 2H43_D 1RE4_D 2XNY_D 2HPC_D ....
Probab=43.69 E-value=2.1e+02 Score=24.55 Aligned_cols=30 Identities=7% Similarity=0.126 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHhccCc
Q psy16463 99 GDEKLSIMQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 99 ~dEKv~LA~q~~dlVdkhirrLD~dl~~le 128 (317)
...-+.+-+.+++-....|.+|+.++..++
T Consensus 102 ~~~~I~~Lq~~~~~~~~ki~~Le~~i~~~~ 131 (146)
T PF08702_consen 102 QPSNIRVLQNILRSNRQKIQRLEQDIDQQE 131 (146)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346778888888888899999999987766
No 65
>cd07625 BAR_Vps17p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps17p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Vsp17p forms a dimer with Vps5p, the yeast counterpart of human SNX1, and is part of the retromer complex that mediates the transport of the carboxypeptidase Y receptor Vps10p from endosomes to Golgi. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=43.59 E-value=2.7e+02 Score=25.80 Aligned_cols=115 Identities=10% Similarity=-0.053 Sum_probs=69.5
Q ss_pred cccccchhhhhhhhhhHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC--cCChHHHHHHHHHHH
Q psy16463 12 SPNMLNQAVLEAMYSVPYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGN--KIDQFSRKRNLLRVQ 89 (317)
Q Consensus 12 ~~~m~~~a~~e~~~~a~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~k--~~~~~~~~~~~~~I~ 89 (317)
|++...+|..+....+..|.+|+..+..+-.-|....-.||++-.-.+.+...- ....++.. ...+..-.+.+..|+
T Consensus 89 ~dl~~~QA~~d~~tl~d~L~~~~~~~~~vKealtnR~~~~re~~qAq~~~~~K~-~~~~rlk~s~~i~~~KvdeA~~~l~ 167 (230)
T cd07625 89 GDIDSIQATVDMATLYDGLEWISRDAYVVKEALTNRHLLMRELIQAQQNTKSKQ-EAARRLKAKRDINPLKVDEAIRQLE 167 (230)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhcCCCCChHhHHHHHHHHH
Confidence 577788888888888888999999888888888888888888866655555433 33334422 222433344444444
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccC
Q psy16463 90 VALIAAQEIGDEKLSIMQQVQDVIEGKTRQIDGIFYNL 127 (317)
Q Consensus 90 ~~l~~a~el~dEKv~LA~q~~dlVdkhirrLD~dl~~l 127 (317)
+.-....++...=-.|...|..-+.++......++...
T Consensus 168 eA~~~e~~l~~k~~rIs~nm~~E~~rf~~~~~~dl~~~ 205 (230)
T cd07625 168 EATKHEHDLSLKLKRITGNMLIERKEWTDWTEEDLQSA 205 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44333444444333455555555555555555555443
No 66
>KOG4628|consensus
Probab=43.24 E-value=22 Score=35.04 Aligned_cols=47 Identities=23% Similarity=0.546 Sum_probs=28.2
Q ss_pred ceeeeCCC-CCCCeeeeCCCCCCCcceecccCCccCCCCCceeCcccccccc
Q psy16463 238 TYCLCNQV-SFGQMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKARS 288 (317)
Q Consensus 238 ~~C~C~~~-~~g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~~~ 288 (317)
++|||-.- -.|+-+.==. |. .-||..||..=-... .-+||-|+..-.
T Consensus 231 ~CaIClEdY~~GdklRiLP--C~-H~FH~~CIDpWL~~~-r~~CPvCK~di~ 278 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRILP--CS-HKFHVNCIDPWLTQT-RTFCPVCKRDIR 278 (348)
T ss_pred eEEEeecccccCCeeeEec--CC-CchhhccchhhHhhc-CccCCCCCCcCC
Confidence 45599754 1266555444 65 559999996211111 347999997643
No 67
>KOG2626|consensus
Probab=43.02 E-value=16 Score=37.67 Aligned_cols=53 Identities=21% Similarity=0.595 Sum_probs=35.2
Q ss_pred CceeeeCCCCC--CCeeeeCCCCCCCcceecccCCccC-----CC---CCceeCccccccccCCCc
Q psy16463 237 PTYCLCNQVSF--GQMVMCDNDLCPHQWFHFSCVAVTN-----TP---KGKWYCPNCRKARSNAVR 292 (317)
Q Consensus 237 ~~~C~C~~~~~--g~mi~Cd~~~C~~~wfH~~Cvgl~~-----~p---~~~w~C~~C~~~~~~~~~ 292 (317)
.++|+|+.-.. -.-++|.. |- .|||..|+-... .| .-.+.|-.|...+...+.
T Consensus 20 ~~~~y~e~~r~l~~~elqcs~--cl-k~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~~~e~f~ 82 (544)
T KOG2626|consen 20 ATVCYCEGERNLGIVELQCST--CL-KWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPSGREHFE 82 (544)
T ss_pred ccccccccccccCceeeEeee--cc-cccccccccccccccccCCcccceeEEeccccCcchhhhh
Confidence 46899986533 35788988 95 999986654221 12 247899999977544333
No 68
>PF04668 Tsg: Twisted gastrulation (Tsg) protein conserved region; InterPro: IPR006761 Tsg was identified in Drosophila melanogaster as being required to specify the dorsal-most structures in the embryo, for example the amnioserosa. Biochemical experiments have revealed three key properties of Tsg: it can synergistically inhibit Dpp/BMP action in both D. melanogaster and vertebrates by forming a tripartite complete between itself, SOG/chordin and a BMP ligand; Tsg seems to enhance the Tld/BMP-1-mediated cleavage rate of SOG/chordin and may change the preference of site utilisation; Tsg can promote the dissociation of chordin cysteine-rich-containing fragments from the ligand to inhibit BMP signalling [, ].
Probab=42.91 E-value=8.9 Score=32.61 Aligned_cols=12 Identities=50% Similarity=1.068 Sum_probs=9.2
Q ss_pred Ccceeccc---CCcc
Q psy16463 260 HQWFHFSC---VAVT 271 (317)
Q Consensus 260 ~~wfH~~C---vgl~ 271 (317)
|+|||..| ||.+
T Consensus 102 YRWFHdgCCECVG~~ 116 (132)
T PF04668_consen 102 YRWFHDGCCECVGPT 116 (132)
T ss_pred ceeeccchhhccCch
Confidence 89999965 6643
No 69
>KOG4552|consensus
Probab=42.23 E-value=2.5e+02 Score=25.92 Aligned_cols=20 Identities=15% Similarity=0.306 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHHhHhccCc
Q psy16463 109 VQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 109 ~~dlVdkhirrLD~dl~~le 128 (317)
+.+.++.|+.+=|.++.+|+
T Consensus 75 ~m~~Lea~VEkrD~~IQqLq 94 (272)
T KOG4552|consen 75 LMRTLEAHVEKRDEVIQQLQ 94 (272)
T ss_pred HHHHHHHHHHHhHHHHHHHH
Confidence 33344444444444444444
No 70
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=41.81 E-value=5.8 Score=30.95 Aligned_cols=43 Identities=33% Similarity=0.702 Sum_probs=25.1
Q ss_pred e-eeCCCCCCCeeeeCC-----CCCCCc------ceecccCC--ccCCCCCceeCcccccc
Q psy16463 240 C-LCNQVSFGQMVMCDN-----DLCPHQ------WFHFSCVA--VTNTPKGKWYCPNCRKA 286 (317)
Q Consensus 240 C-~C~~~~~g~mi~Cd~-----~~C~~~------wfH~~Cvg--l~~~p~~~w~C~~C~~~ 286 (317)
| +|+-...|.-+.|-. ..|++. .||+.|+. |.. +-.||.|+..
T Consensus 23 CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T----k~~CPld~q~ 79 (88)
T COG5194 23 CAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT----KGVCPLDRQT 79 (88)
T ss_pred hhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh----CCCCCCCCce
Confidence 6 776544444444433 335544 49999986 332 4578887743
No 71
>PF04961 FTCD_C: Formiminotransferase-cyclodeaminase; InterPro: IPR007044 Enzymes containing the cyclodeaminase domain function in channeling one-carbon units to the folate pool. In most cases, this domain catalyses the cyclisation of formimidoyltetrahydrofolate to methenyltetrahydrofolate as shown in reaction (1). In the methylotrophic bacterium Methylobacterium extorquens, however, it catalyses the interconversion of formyltetrahydrofolate and methylenetetrahydrofolate [],as shown in reaction (2) (1) 5-formimidoyltetrahydrofolate = 5,10-methenyltetrahydrofolate + NH(3) (2) 10- formyltetrahydrofolate = 5,10-methenyltetrahydrofolate + H(2)O In prokaryotes, this domain mostly occurs on its own, while in eukaryotes it is fused to a glutamate formiminotransferase domain (which catalyses the previous step in the pathway) to form the bifunctional enzyme formiminotransferase-cyclodeaminase []. The eukaryotic enzyme is a circular tetramer of homodimers [], while the prokaryotic enzyme is a dimer [, ]. The crystal structure of the cyclodeaminase enzyme (Q9X1P6 from SWISSPROT) from Thermaotogoa maritima has been studied []. It is a homodimer, where each monomer is composed of six alpha helices arranged in an up and down helical bundle, forming a novel fold. The location of the active site is not known, but sequence alignments revealed two clusters of conserved residues located in a deep pocket within the dimmer interface. This pocket was large enough to accommodate the reaction product and it was postulated that this is the active site.; GO: 0003824 catalytic activity, 0044237 cellular metabolic process; PDB: 2PFD_C 1O5H_B.
Probab=41.65 E-value=2.4e+02 Score=25.06 Aligned_cols=73 Identities=18% Similarity=0.149 Sum_probs=42.1
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc-----CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 40 LPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGNK-----IDQFSRKRNLLRVQVALIAAQEIGDEKLSIMQQVQDVIE 114 (317)
Q Consensus 40 LP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~k~-----~~~~~~~~~~~~I~~~l~~a~el~dEKv~LA~q~~dlVd 114 (317)
+-.+++..+..+.++=.++..+.++=.+-+..|++. ...+++......|++.+..+.+.- ++++...+++++
T Consensus 50 ~~~~~~~~~~~~~~~~~~ll~l~d~D~~af~~~~~a~klPk~T~eek~~R~~~i~~al~~A~~vP---l~~a~~~~~~l~ 126 (184)
T PF04961_consen 50 VEEELKEIIEKLEELREELLDLADEDAEAFNAVMAAYKLPKETDEEKAARSEAIQEALKEAAEVP---LEIARLCLELLE 126 (184)
T ss_dssp GHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCTS---SGGGTTTHHHHHHHHHHHHHHHH---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHhhHHHHHHHHHHHHHHHH---HHHHHHHHHHHH
Confidence 334666666666666666655555555555555442 123334445667888888877643 455555555555
Q ss_pred H
Q psy16463 115 G 115 (317)
Q Consensus 115 k 115 (317)
-
T Consensus 127 ~ 127 (184)
T PF04961_consen 127 L 127 (184)
T ss_dssp H
T ss_pred H
Confidence 4
No 72
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=40.85 E-value=10 Score=33.27 Aligned_cols=48 Identities=15% Similarity=0.310 Sum_probs=29.4
Q ss_pred cee-eeCCCCCCCeee-eCCCCCCCcceecccCCccCCCCCceeCccccccc
Q psy16463 238 TYC-LCNQVSFGQMVM-CDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKAR 287 (317)
Q Consensus 238 ~~C-~C~~~~~g~mi~-Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~~ 287 (317)
..| +|.+... .++. |...+- +.|.|-+|+..=-...+...|+.|....
T Consensus 9 ~~CRIC~~~~~-~~~~PC~CkGs-~k~VH~sCL~rWi~~s~~~~CeiC~~~Y 58 (162)
T PHA02825 9 KCCWICKDEYD-VVTNYCNCKNE-NKIVHKECLEEWINTSKNKSCKICNGPY 58 (162)
T ss_pred CeeEecCCCCC-CccCCcccCCC-chHHHHHHHHHHHhcCCCCcccccCCeE
Confidence 468 8977532 2222 321112 4799999997332345678999998654
No 73
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=40.38 E-value=86 Score=24.95 Aligned_cols=44 Identities=16% Similarity=0.234 Sum_probs=0.0
Q ss_pred hhhHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 25 YSVPYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHI 68 (317)
Q Consensus 25 ~~a~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~ 68 (317)
+.+.-|..+++.+..+=.+|+.++..|-++|.++..+..-+..+
T Consensus 42 ~~~~~l~~~~~~l~~k~~~l~~~l~~Id~Ie~~V~~LE~~v~~L 85 (99)
T PF10046_consen 42 DIAAGLEKNLEDLNQKYEELQPYLQQIDQIEEQVTELEQTVYEL 85 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 74
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=39.21 E-value=3.6e+02 Score=26.00 Aligned_cols=37 Identities=22% Similarity=0.333 Sum_probs=19.0
Q ss_pred HHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 33 YLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIA 69 (317)
Q Consensus 33 yld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~ 69 (317)
+.+.+..|-.|-.+.+.++.+|+....++.+++..+.
T Consensus 48 ~~~el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~le 84 (314)
T PF04111_consen 48 LEEELEKLEQEEEELLQELEELEKEREELDQELEELE 84 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444445555555555555555555555544433
No 75
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=38.92 E-value=24 Score=31.92 Aligned_cols=39 Identities=36% Similarity=0.899 Sum_probs=27.7
Q ss_pred ee-eeCCCC--C----CCeeeeCCCCCCCcceecccCCccCCCCCceeCccccccc
Q psy16463 239 YC-LCNQVS--F----GQMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKAR 287 (317)
Q Consensus 239 ~C-~C~~~~--~----g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~~ 287 (317)
.| +|+... | ...+.|.. |. .-||-.|..- -.||.|.+-+
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~--C~-~v~H~~C~~~-------~~CpkC~R~~ 199 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPK--CK-SVFHKSCFRK-------KSCPKCARRQ 199 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCc--Cc-cccchhhcCC-------CCCCCcHhHh
Confidence 47 787541 2 24678988 98 8899999962 2399998653
No 76
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=37.95 E-value=8.1 Score=29.12 Aligned_cols=22 Identities=41% Similarity=1.130 Sum_probs=15.1
Q ss_pred CCCcceecccCC--ccCCCCCceeCcccc
Q psy16463 258 CPHQWFHFSCVA--VTNTPKGKWYCPNCR 284 (317)
Q Consensus 258 C~~~wfH~~Cvg--l~~~p~~~w~C~~C~ 284 (317)
|. ..||+.|+. +... ..||-|+
T Consensus 50 C~-H~FH~~Ci~~Wl~~~----~~CP~CR 73 (73)
T PF12678_consen 50 CG-HIFHFHCISQWLKQN----NTCPLCR 73 (73)
T ss_dssp TS-EEEEHHHHHHHHTTS----SB-TTSS
T ss_pred cC-CCEEHHHHHHHHhcC----CcCCCCC
Confidence 77 779999986 3322 3899886
No 77
>KOG1507|consensus
Probab=37.47 E-value=93 Score=30.72 Aligned_cols=47 Identities=17% Similarity=0.234 Sum_probs=32.5
Q ss_pred ccchhhhhhhhhhHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 15 MLNQAVLEAMYSVPYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKE 64 (317)
Q Consensus 15 m~~~a~~e~~~~a~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ 64 (317)
++++.....-..+.+. .+.|++||.-+++.+.-||.|-.++.++..+
T Consensus 49 ~~~~~~~r~~~l~~~~---s~~v~~Lp~~Vk~Rv~aLk~lQ~~~~~ie~~ 95 (358)
T KOG1507|consen 49 LLSALDGRLASLAGLL---SDMVENLPPAVKNRVLALKNLQLECDEIEAK 95 (358)
T ss_pred hhcccchhhhcccCCC---chhhhhcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444333334444 4557889999999999999999998876544
No 78
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=37.14 E-value=30 Score=23.75 Aligned_cols=33 Identities=30% Similarity=0.637 Sum_probs=24.0
Q ss_pred CCcee-eeCCCC---CCCeeeeCCCCCCCcceecccCCcc
Q psy16463 236 EPTYC-LCNQVS---FGQMVMCDNDLCPHQWFHFSCVAVT 271 (317)
Q Consensus 236 e~~~C-~C~~~~---~g~mi~Cd~~~C~~~wfH~~Cvgl~ 271 (317)
.+.+| +|+..- ...-+.|.. |. -.+|-.|+...
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~--C~-~~~H~~C~~~~ 46 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSW--CG-LVCHKKCLSKV 46 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETT--TT--EEETTGGCTS
T ss_pred CCCCCcccCcccCCCCCCeEEECC--CC-ChHhhhhhhhc
Confidence 46789 899875 346788988 98 67999998743
No 79
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=36.86 E-value=28 Score=23.07 Aligned_cols=25 Identities=24% Similarity=0.546 Sum_probs=16.4
Q ss_pred ee-eeCCC------CCCCeeeeCC-CCCCC-cce
Q psy16463 239 YC-LCNQV------SFGQMVMCDN-DLCPH-QWF 263 (317)
Q Consensus 239 ~C-~C~~~------~~g~mi~Cd~-~~C~~-~wf 263 (317)
.| .|+.. .+|.+++|.+ |.|.+ .|+
T Consensus 3 ~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~~~~ 36 (39)
T PF01396_consen 3 KCPKCGGPLVLRRGKKGKFLGCSNYPECKYTEPL 36 (39)
T ss_pred CCCCCCceeEEEECCCCCEEECCCCCCcCCeEeC
Confidence 36 67643 3478899998 78874 443
No 80
>PRK10807 paraquat-inducible protein B; Provisional
Probab=36.64 E-value=5.2e+02 Score=27.04 Aligned_cols=102 Identities=14% Similarity=0.093 Sum_probs=47.1
Q ss_pred hhhHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHHHHHHHHHHHH---
Q psy16463 25 YSVPYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGNKIDQFSRKRNLLRVQVALIAAQEIGDE--- 101 (317)
Q Consensus 25 ~~a~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~k~~~~~~~~~~~~~I~~~l~~a~el~dE--- 101 (317)
.+..-+.++++.|+.|| |..+++.+...=.....++++++.....+.+-..+.....+..++++.+..+...-.+
T Consensus 417 ~l~~~~~~il~kin~lp--le~i~~~l~~tL~~~~~tl~~l~~~l~~l~~ll~~~~~~~Lp~~L~~TL~~l~~~l~~~~~ 494 (547)
T PRK10807 417 QIQQKLMEALDKINNLP--LNPMIEQATSTLSESQRTMRELQTTLDSLNKITSSQSMQQLPADMQKTLRELNRSMQGFQP 494 (547)
T ss_pred HHHHHHHHHHHHHhcCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 34567889999999999 5555554322222223333444444433322222333333444555444433321111
Q ss_pred ---HHHHHHHHHHHHHHHHHHHHhHhccCc
Q psy16463 102 ---KLSIMQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 102 ---Kv~LA~q~~dlVdkhirrLD~dl~~le 128 (317)
-.+-.++++.-|++-+|.|..-+..|+
T Consensus 495 ~s~~~~~l~~tl~~l~~~~r~lr~l~~~L~ 524 (547)
T PRK10807 495 GSPAYNKMVADMQRLDQVLRELQPVLKTLN 524 (547)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 111222344445555555555444444
No 81
>PRK14127 cell division protein GpsB; Provisional
Probab=36.62 E-value=1.3e+02 Score=24.70 Aligned_cols=40 Identities=20% Similarity=0.349 Sum_probs=24.5
Q ss_pred HHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 29 YVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQ 71 (317)
Q Consensus 29 yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~ 71 (317)
=+++|||.|. .++.....++.+|-.+...+..+|++.-..
T Consensus 27 EVD~FLd~V~---~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~ 66 (109)
T PRK14127 27 EVDKFLDDVI---KDYEAFQKEIEELQQENARLKAQVDELTKQ 66 (109)
T ss_pred HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3566666665 466666666666666666666665554443
No 82
>PF12095 DUF3571: Protein of unknown function (DUF3571); InterPro: IPR021954 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 85 to 97 amino acids in length. ; PDB: 2KRX_A.
Probab=36.48 E-value=54 Score=25.74 Aligned_cols=44 Identities=16% Similarity=0.363 Sum_probs=26.5
Q ss_pred CCcccccchhhhhhhhhhHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHH
Q psy16463 10 QQSPNMLNQAVLEAMYSVPYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYM 62 (317)
Q Consensus 10 ~~~~~m~~~a~~e~~~~a~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~ 62 (317)
++.--|++++.. ...|..++...++||.+|++.-+ +|..++.++
T Consensus 18 ~~~Eqflt~~El-----l~~Lk~~L~~~~~LP~dL~~~~s----~~~qa~~Ll 61 (83)
T PF12095_consen 18 GQPEQFLTPEEL-----LEKLKEWLQNQDDLPPDLAKFSS----VEEQAQYLL 61 (83)
T ss_dssp SS-SEEE-HHHH-----HHHHHHHHHHTTTS-HHHHH-------HHHHHHHHH
T ss_pred CCCcccCCHHHH-----HHHHHHHHHcCCCCCHHHHhCCC----HHHHHHHHH
Confidence 344445555444 78999999999999999987544 445544443
No 83
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=36.43 E-value=4.5e+02 Score=27.47 Aligned_cols=47 Identities=11% Similarity=0.333 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHhHhccCc
Q psy16463 82 KRNLLRVQVALIAAQEIGDE-KLSIMQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 82 ~~~~~~I~~~l~~a~el~dE-Kv~LA~q~~dlVdkhirrLD~dl~~le 128 (317)
+..+..|...|....++-.. =..=|..++.-+..++..|+..+..+-
T Consensus 167 e~~L~~ie~~F~~f~~lt~~GD~~~A~eil~~l~~~~~~l~~~~e~IP 214 (560)
T PF06160_consen 167 EKQLENIEEEFSEFEELTENGDYLEAREILEKLKEETDELEEIMEDIP 214 (560)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 44555555555555554433 334455566666666666665555443
No 84
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=36.05 E-value=4.2e+02 Score=27.93 Aligned_cols=110 Identities=12% Similarity=0.138 Sum_probs=60.0
Q ss_pred hhhhhhhHHHHHHHHHhhcChHHHHHHHHHHHHHHH---HHHHHHHH----HHHHHHHHhC-cCChHHHHHHH---HHHH
Q psy16463 21 LEAMYSVPYVETYLDIVENLPDEIQRYLTKIRELDV---LYQSYMKE----IEHIASQNGN-KIDQFSRKRNL---LRVQ 89 (317)
Q Consensus 21 ~e~~~~a~yLedyld~ienLP~Elqr~l~lIRElD~---k~~~~~~~----ie~~~~~~~k-~~~~~~~~~~~---~~I~ 89 (317)
.+.-+++.-|.+|++.++-=|.+|......|..|-. ||.-...+ .++....+.. .........+- ..++
T Consensus 276 ~~l~ea~~el~~~~~~le~Dp~~L~~ve~Rl~~L~~l~RKY~~~~~~l~~~~~~~~~el~~L~~~~~~~~~Le~~~~~l~ 355 (557)
T COG0497 276 YELEEASEELRAYLDELEFDPNRLEEVEERLFALKSLARKYGVTIEDLLEYLDKIKEELAQLDNSEESLEALEKEVKKLK 355 (557)
T ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH
Confidence 333444556677777777777776665555444433 33221111 1111111111 01111112222 2333
Q ss_pred -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccCcCc
Q psy16463 90 -VALIAAQEIGDEKLSIMQQVQDVIEGKTRQIDGIFYNLPSV 130 (317)
Q Consensus 90 -~~l~~a~el~dEKv~LA~q~~dlVdkhirrLD~dl~~le~d 130 (317)
+.+..|..|+..-...|..+-..|...++.|-..-..|..+
T Consensus 356 ~~~~~~A~~Ls~~R~~~A~~L~~~v~~eL~~L~Me~a~F~ve 397 (557)
T COG0497 356 AELLEAAEALSAIRKKAAKELEKEVTAELKALAMEKARFTVE 397 (557)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceEEEE
Confidence 33455778888888899999999999999988777777743
No 85
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=34.79 E-value=10 Score=25.82 Aligned_cols=32 Identities=28% Similarity=0.592 Sum_probs=14.8
Q ss_pred eeeCCCCCCCcceecccCCccCCCCCceeCccc
Q psy16463 251 VMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNC 283 (317)
Q Consensus 251 i~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C 283 (317)
+.|.+++|... +|..|+.-.-.....--||.|
T Consensus 12 ~~C~~~~C~~r-~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 12 QRCSNRDCNVR-LHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp EE-SS--S--E-E-HHHHHHHTTT-SS-B-TTT
T ss_pred ccCCCCccCch-HHHHHHHHHHhcCCCCCCcCC
Confidence 56888889855 699998733222222278877
No 86
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=33.96 E-value=2.5e+02 Score=22.55 Aligned_cols=40 Identities=20% Similarity=0.338 Sum_probs=25.8
Q ss_pred HHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 28 PYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEH 67 (317)
Q Consensus 28 ~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~ 67 (317)
+.+++.+..+..|-.+++...+.+..|+....+...-+++
T Consensus 3 ~~~q~~~~~~q~~q~~~~~l~~q~~~le~~~~E~~~v~~e 42 (110)
T TIGR02338 3 PQVQNQLAQLQQLQQQLQAVATQKQQVEAQLKEAEKALEE 42 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666666666677777777777777777665544433
No 87
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=33.95 E-value=7.4 Score=27.14 Aligned_cols=25 Identities=20% Similarity=0.493 Sum_probs=15.6
Q ss_pred CcceecccCCccCCCCCceeCcccc
Q psy16463 260 HQWFHFSCVAVTNTPKGKWYCPNCR 284 (317)
Q Consensus 260 ~~wfH~~Cvgl~~~p~~~w~C~~C~ 284 (317)
+.|||.+|+.-=....+...||.|.
T Consensus 25 ~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 25 LKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred hhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3799999986211122345788873
No 88
>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=33.80 E-value=29 Score=33.57 Aligned_cols=11 Identities=27% Similarity=1.108 Sum_probs=7.8
Q ss_pred eeeeCCCCCCCcc
Q psy16463 250 MVMCDNDLCPHQW 262 (317)
Q Consensus 250 mi~Cd~~~C~~~w 262 (317)
++.|.- |..+|
T Consensus 210 yL~Csl--C~teW 220 (305)
T TIGR01562 210 YLSCSL--CATEW 220 (305)
T ss_pred EEEcCC--CCCcc
Confidence 666766 77777
No 89
>KOG4515|consensus
Probab=33.10 E-value=3.8e+02 Score=24.36 Aligned_cols=44 Identities=7% Similarity=0.129 Sum_probs=31.0
Q ss_pred HHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 29 YVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQN 72 (317)
Q Consensus 29 yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~ 72 (317)
|-++|--+.+.+-.|=.+....++++|..+..+........+.|
T Consensus 100 ~Q~Hl~~cA~aVA~dQn~lv~r~K~v~~s~~tLf~~~~~~qk~y 143 (217)
T KOG4515|consen 100 LQEHLAVCAKAVAADQNKLVARCKSVEASMITLFEETRAHQKQY 143 (217)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666677777777778888888888888777766655554444
No 90
>PRK10244 anti-RssB factor; Provisional
Probab=32.86 E-value=2.5e+02 Score=22.32 Aligned_cols=74 Identities=11% Similarity=0.129 Sum_probs=48.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH---HHHHhCcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 44 IQRYLTKIRELDVLYQSYMKEIEHI---ASQNGNKIDQFSRKRNLLRVQVALIAAQEIGDEKLSIMQQVQDVIEGKTRQI 120 (317)
Q Consensus 44 lqr~l~lIRElD~k~~~~~~~ie~~---~~~~~k~~~~~~~~~~~~~I~~~l~~a~el~dEKv~LA~q~~dlVdkhirrL 120 (317)
|-..|-.|-++|....++..+++.+ +.-.+..++.+...++...|+..+..+.+-+ -.+-..-.+|+-.|++||
T Consensus 5 I~elL~KlA~ke~esKeL~AQVEAlellitAlL~~~~~~~~~~li~~Ie~Ai~~a~~~~---~~~~~~D~eLL~~~v~~L 81 (88)
T PRK10244 5 IAELLAKLAQKEEESKELTAQVEALELLVTAMLRTMGKNGQQELIEQVEGAINAVSKPD---DSVPDSDTELLLTYVNKL 81 (88)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHHhcccc---ccccchHHHHHHHHHHHH
Confidence 4456777888899888888887664 4444445555556778888888887664422 233344456677777765
No 91
>KOG1829|consensus
Probab=32.69 E-value=13 Score=39.02 Aligned_cols=30 Identities=27% Similarity=0.755 Sum_probs=22.5
Q ss_pred eeeeCCCCCCCcceecccCCccCCCCCceeCccccccc
Q psy16463 250 MVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKAR 287 (317)
Q Consensus 250 mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~~ 287 (317)
-.-|+. |. .|||-.|....... ||.|.+-+
T Consensus 531 ~~rC~~--C~-avfH~~C~~r~s~~-----CPrC~R~q 560 (580)
T KOG1829|consen 531 TRRCST--CL-AVFHKKCLRRKSPC-----CPRCERRQ 560 (580)
T ss_pred ceeHHH--HH-HHHHHHHHhccCCC-----CCchHHHH
Confidence 467888 97 99999998654222 99998553
No 92
>PRK14154 heat shock protein GrpE; Provisional
Probab=32.09 E-value=3.7e+02 Score=24.65 Aligned_cols=42 Identities=12% Similarity=0.046 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccCc
Q psy16463 87 RVQVALIAAQEIGDEKLSIMQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 87 ~I~~~l~~a~el~dEKv~LA~q~~dlVdkhirrLD~dl~~le 128 (317)
-|-+.|.+|+......-.....+++=|+--.++|..-|+++-
T Consensus 110 pVlDnLeRAL~~~~~~~~~~~~l~eGvemi~k~l~~vL~k~G 151 (208)
T PRK14154 110 PVADSLIHGLESPASEDPQVKSMRDGMSLTLDLLHNTLAKHG 151 (208)
T ss_pred hHHhHHHHHHhcccccchhHHHHHHHHHHHHHHHHHHHHHCC
Confidence 345666666653222222234556666666666777766665
No 93
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=32.05 E-value=27 Score=30.02 Aligned_cols=27 Identities=26% Similarity=0.767 Sum_probs=17.4
Q ss_pred cceecccCC----ccCCCCCceeCccccccc
Q psy16463 261 QWFHFSCVA----VTNTPKGKWYCPNCRKAR 287 (317)
Q Consensus 261 ~wfH~~Cvg----l~~~p~~~w~C~~C~~~~ 287 (317)
.||...|-. +...+.+.|+|+.|....
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCcC
Confidence 466666653 333333789999998653
No 94
>KOG1029|consensus
Probab=31.83 E-value=2e+02 Score=31.62 Aligned_cols=44 Identities=25% Similarity=0.234 Sum_probs=29.5
Q ss_pred ccchhhhhhhhhhHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHH
Q psy16463 15 MLNQAVLEAMYSVPYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYM 62 (317)
Q Consensus 15 m~~~a~~e~~~~a~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~ 62 (317)
|+|+-+.|.-.+.. |. ....+|-.||.-.-..+++|+.+++++.
T Consensus 421 m~~Qk~reqe~iv~-~n---ak~~ql~~eletLn~k~qqls~kl~Dvr 464 (1118)
T KOG1029|consen 421 MLNQKNREQEWIVY-LN---AKKKQLQQELETLNFKLQQLSGKLQDVR 464 (1118)
T ss_pred HHhhhhHHHHHHHH-HH---HHHHHHHHHHHHHHHHHHHHhhhhhhhe
Confidence 77777777655542 22 2345566777777788888888888754
No 95
>PF05781 MRVI1: MRVI1 protein; InterPro: IPR008677 This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene []. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP []. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins [].
Probab=31.48 E-value=3e+02 Score=28.78 Aligned_cols=85 Identities=13% Similarity=0.151 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc----CChHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHH
Q psy16463 45 QRYLTKIRELDVLYQSYMKEIEHIASQNGNK----IDQFSRKRNLLRVQVALIAAQE--------------IGDEKLSIM 106 (317)
Q Consensus 45 qr~l~lIRElD~k~~~~~~~ie~~~~~~~k~----~~~~~~~~~~~~I~~~l~~a~e--------------l~dEKv~LA 106 (317)
+|.-...|+-|..=.++.++|+.....+..- .+..+..+++.+++..+.-+.. +..|+- .
T Consensus 213 ~R~~~~eR~RdlaEeNl~kEi~~~~~~l~~l~~lc~~d~e~~e~~~kl~~~l~~l~~~~~rvss~AE~lGAv~QE~R--~ 290 (538)
T PF05781_consen 213 KRLKLEERSRDLAEENLKKEIENCLKLLESLAPLCWEDNESREIIQKLQKSLDVLHQCATRVSSRAEMLGAVHQESR--V 290 (538)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHH--H
Confidence 4555566666766667777766655444221 1112223333333333322111 123443 4
Q ss_pred HHHHHHHHHHHHHHHhHhccCcCcc
Q psy16463 107 QQVQDVIEGKTRQIDGIFYNLPSVT 131 (317)
Q Consensus 107 ~q~~dlVdkhirrLD~dl~~le~d~ 131 (317)
..+.+++..|+..|..-+++..+++
T Consensus 291 SkAvevM~qhvenLkr~~~kehaeL 315 (538)
T PF05781_consen 291 SKAVEVMIQHVENLKRMYEKEHAEL 315 (538)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5788999999999999888888544
No 96
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=31.44 E-value=24 Score=21.70 Aligned_cols=15 Identities=33% Similarity=1.068 Sum_probs=10.2
Q ss_pred CCceeCccccccccC
Q psy16463 275 KGKWYCPNCRKARSN 289 (317)
Q Consensus 275 ~~~w~C~~C~~~~~~ 289 (317)
.|.|.|+.|...+..
T Consensus 2 ~g~W~C~~C~~~N~~ 16 (30)
T PF00641_consen 2 EGDWKCPSCTFMNPA 16 (30)
T ss_dssp SSSEEETTTTEEEES
T ss_pred CcCccCCCCcCCchH
Confidence 367888888765543
No 97
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=30.28 E-value=2.3e+02 Score=20.99 Aligned_cols=10 Identities=20% Similarity=0.285 Sum_probs=3.7
Q ss_pred HHHHHHHHHH
Q psy16463 81 RKRNLLRVQV 90 (317)
Q Consensus 81 ~~~~~~~I~~ 90 (317)
+...+..|+.
T Consensus 23 r~~~i~~~e~ 32 (79)
T PF05008_consen 23 RKSLIREIER 32 (79)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 3333333333
No 98
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=30.23 E-value=31 Score=30.62 Aligned_cols=24 Identities=25% Similarity=0.726 Sum_probs=20.2
Q ss_pred CCCeeeeCCCCCCCcceecccCCccCC
Q psy16463 247 FGQMVMCDNDLCPHQWFHFSCVAVTNT 273 (317)
Q Consensus 247 ~g~mi~Cd~~~C~~~wfH~~Cvgl~~~ 273 (317)
-|.||.|-+ |. .-||-.|+|....
T Consensus 14 kG~Lv~CQG--Cs-~sYHk~CLG~Rs~ 37 (175)
T PF15446_consen 14 KGPLVYCQG--CS-SSYHKACLGPRSQ 37 (175)
T ss_pred CCCeEEcCc--cC-hHHHhhhcCCccc
Confidence 389999988 98 7899999996544
No 99
>cd07627 BAR_Vps5p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps5p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Vsp5p is the yeast counterpart of human SNX1 and is part of the retromer complex, which functions in the endosome-to-Golgi retrieval of vacuolar protein sorting receptor Vps10p, the Golgi-resident membrane protein A-ALP, and endopeptidase Kex2. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in
Probab=29.85 E-value=4.1e+02 Score=23.85 Aligned_cols=101 Identities=7% Similarity=0.054 Sum_probs=48.4
Q ss_pred hhhhhhhhhhHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHHHHHHHH
Q psy16463 18 QAVLEAMYSVPYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGNKIDQFSRKRNLLRVQVALIAAQE 97 (317)
Q Consensus 18 ~a~~e~~~~a~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~k~~~~~~~~~~~~~I~~~l~~a~e 97 (317)
.+..+.......|.+|+-.+..+=.=|.+..........-..++.+ +.....++.. .+. .+...+..+..++..
T Consensus 81 ~a~~e~~~l~~~L~ey~r~~~Svk~~~~~R~~~~~~~~~~~~~L~k-~~~~~~Kl~~-~~~-s~~~K~~~~~~ei~~--- 154 (216)
T cd07627 81 QALQDVLTLGVTLDEYIRSIGSVRAAFAQRQKLWQYWQSAESELSK-KKAQLEKLKR-QGK-TQQEKLNSLLSELEE--- 154 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhc-cCC-ChHHHHHHHHHHHHH---
Confidence 3444444555566666666665555555554444433322222221 1111222211 110 112223333333333
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHhccCc
Q psy16463 98 IGDEKLSIMQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 98 l~dEKv~LA~q~~dlVdkhirrLD~dl~~le 128 (317)
...++..|.+-|+.|...+++ ++..|+
T Consensus 155 -~e~~~~~a~~~~e~is~~~k~---El~rF~ 181 (216)
T cd07627 155 -AERRASELKKEFEEVSELIKS---ELERFE 181 (216)
T ss_pred -HHHHHHHHHHHHHHHHHHHHH---HHHHHH
Confidence 346788888888888877765 555565
No 100
>KOG1941|consensus
Probab=29.83 E-value=5.7 Score=39.62 Aligned_cols=50 Identities=36% Similarity=0.824 Sum_probs=31.3
Q ss_pred CCCcee-eeCCCCCC---CeeeeCCCCCCCcceecccCCccCCCCCceeCcccccccc
Q psy16463 235 NEPTYC-LCNQVSFG---QMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKARS 288 (317)
Q Consensus 235 ~e~~~C-~C~~~~~g---~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~~~ 288 (317)
.-..|| +|++- +| +-++--- |. ..||..|+--.-...+.--||.|++-+.
T Consensus 363 e~~L~Cg~CGe~-~Glk~e~LqALp--Cs-HIfH~rCl~e~L~~n~~rsCP~CrklrS 416 (518)
T KOG1941|consen 363 ETELYCGLCGES-IGLKNERLQALP--CS-HIFHLRCLQEILENNGTRSCPNCRKLRS 416 (518)
T ss_pred HHhhhhhhhhhh-hcCCcccccccc--hh-HHHHHHHHHHHHHhCCCCCCccHHHHHh
Confidence 345799 99975 44 2222222 54 5699999862223456788999994443
No 101
>PHA02562 46 endonuclease subunit; Provisional
Probab=29.39 E-value=6.2e+02 Score=25.74 Aligned_cols=23 Identities=13% Similarity=0.187 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHhHhccCc
Q psy16463 106 MQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 106 A~q~~dlVdkhirrLD~dl~~le 128 (317)
+...+..++.-+..++..+..+.
T Consensus 260 l~~~~~~~~~~l~~~~~~~~~~~ 282 (562)
T PHA02562 260 LNTAAAKIKSKIEQFQKVIKMYE 282 (562)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 44444445555555555555553
No 102
>KOG0996|consensus
Probab=29.29 E-value=6.1e+02 Score=29.32 Aligned_cols=33 Identities=21% Similarity=0.343 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHhccCc
Q psy16463 96 QEIGDEKLSIMQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 96 ~el~dEKv~LA~q~~dlVdkhirrLD~dl~~le 128 (317)
.++.++|++.-..=.+-|-..|..|.+++.++.
T Consensus 895 ~~i~~e~~q~qk~kv~~~~~~~~~l~~~i~k~~ 927 (1293)
T KOG0996|consen 895 DEIGGEKVQAQKDKVEKINEQLDKLEADIAKLT 927 (1293)
T ss_pred HHhhchhhHHhHHHHHHHHHHHHHHHHHHHHhH
Confidence 345555555544444444444555544444444
No 103
>KOG1244|consensus
Probab=28.64 E-value=15 Score=35.09 Aligned_cols=44 Identities=32% Similarity=0.786 Sum_probs=29.5
Q ss_pred cee-eeCCCC-----C---CCeeeeCCCCCCCcceecccCCccCC-----CCCceeCcccc
Q psy16463 238 TYC-LCNQVS-----F---GQMVMCDNDLCPHQWFHFSCVAVTNT-----PKGKWYCPNCR 284 (317)
Q Consensus 238 ~~C-~C~~~~-----~---g~mi~Cd~~~C~~~wfH~~Cvgl~~~-----p~~~w~C~~C~ 284 (317)
-|| ||=..+ . .++|.|.. |. .-=|.+|+..+.. ..-.|.|-+|.
T Consensus 225 ~YCDFclgdsr~nkkt~~peelvscsd--cg-rsghpsclqft~nm~~avk~yrwqcieck 282 (336)
T KOG1244|consen 225 PYCDFCLGDSRENKKTGMPEELVSCSD--CG-RSGHPSCLQFTANMIAAVKTYRWQCIECK 282 (336)
T ss_pred cccceeccccccccccCCchhhcchhh--cC-CCCCcchhhhhHHHHHHHHhheeeeeecc
Confidence 389 884332 1 36999987 98 7779999886543 22467666664
No 104
>cd07664 BAR_SNX2 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX2 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures effcient cargo sorting by facilitating proper membrane localization
Probab=28.63 E-value=4.8e+02 Score=24.15 Aligned_cols=100 Identities=9% Similarity=0.065 Sum_probs=59.0
Q ss_pred chhhhhhhhhhHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHHHHHHH
Q psy16463 17 NQAVLEAMYSVPYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGNKIDQFSRKRNLLRVQVALIAAQ 96 (317)
Q Consensus 17 ~~a~~e~~~~a~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~k~~~~~~~~~~~~~I~~~l~~a~ 96 (317)
.+|..+.+.....|++|+-.|..+-.=|.+.....+.......++.+.-. ...++..... ...+..+..++..+
T Consensus 98 ~qa~~d~~~l~e~L~eYiR~i~svK~~f~~R~k~~~~~~~a~~~L~kkr~-~~~Kl~~~~k----~dK~~~~~~ev~~~- 171 (234)
T cd07664 98 DQAFADFYLFSELLGDYIRLIAAVKGVFDQRMKCWQKWQDAQVTLQKKRE-AEAKLQYANK----PDKLQQAKDEIKEW- 171 (234)
T ss_pred HHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhhcCc----hhHHHHHHHHHHHH-
Confidence 45555556666788888888888877777777777766655554443322 2233321111 12233444444433
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHhccCc
Q psy16463 97 EIGDEKLSIMQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 97 el~dEKv~LA~q~~dlVdkhirrLD~dl~~le 128 (317)
..++..|..-|+.|...+++ ++..|+
T Consensus 172 ---e~~~~~a~~~fe~Is~~~k~---El~rFe 197 (234)
T cd07664 172 ---EAKVQQGERDFEQISKTIRK---EVGRFE 197 (234)
T ss_pred ---HHHHHHHHHHHHHHHHHHHH---HHHHHH
Confidence 36778888888887776664 555565
No 105
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=28.63 E-value=39 Score=32.80 Aligned_cols=9 Identities=22% Similarity=0.531 Sum_probs=6.8
Q ss_pred eeCcccccc
Q psy16463 278 WYCPNCRKA 286 (317)
Q Consensus 278 w~C~~C~~~ 286 (317)
..|..|..-
T Consensus 253 e~C~~C~~Y 261 (309)
T PRK03564 253 ESCGDCGTY 261 (309)
T ss_pred eeccccccc
Confidence 579999754
No 106
>COG1773 Rubredoxin [Energy production and conversion]
Probab=28.48 E-value=52 Score=23.81 Aligned_cols=10 Identities=40% Similarity=1.414 Sum_probs=9.0
Q ss_pred CceeCccccc
Q psy16463 276 GKWYCPNCRK 285 (317)
Q Consensus 276 ~~w~C~~C~~ 285 (317)
..|+||.|-.
T Consensus 35 d~w~CP~Cg~ 44 (55)
T COG1773 35 DDWVCPECGV 44 (55)
T ss_pred CccCCCCCCC
Confidence 6899999986
No 107
>PF07011 DUF1313: Protein of unknown function (DUF1313); InterPro: IPR009741 This family consists of several hypothetical plant proteins of around 100 residues in length. The function of this family is unknown.
Probab=28.43 E-value=1.2e+02 Score=24.03 Aligned_cols=33 Identities=24% Similarity=0.342 Sum_probs=24.7
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 40 LPDEIQRYLTKIRELDVLYQSYMKEIEHIASQN 72 (317)
Q Consensus 40 LP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~ 72 (317)
.|.-|.|++.|||||-.-+...+.--..+-..|
T Consensus 40 ~PdnL~RNV~LIrELN~NI~rVv~lY~dLs~sF 72 (87)
T PF07011_consen 40 IPDNLSRNVGLIRELNGNISRVVDLYSDLSSSF 72 (87)
T ss_pred CCchhhHhHHHHHHHHhhHHHHHHHHHHHhHHH
Confidence 899999999999999877766665555554444
No 108
>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.
Probab=27.86 E-value=3.7e+02 Score=22.71 Aligned_cols=63 Identities=13% Similarity=0.123 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 58 YQSYMKEIEHIASQNGN-KIDQFSRKRNLLRVQVALIAAQEIGDEKLSIMQQVQDVIEGKTRQI 120 (317)
Q Consensus 58 ~~~~~~~ie~~~~~~~k-~~~~~~~~~~~~~I~~~l~~a~el~dEKv~LA~q~~dlVdkhirrL 120 (317)
+....+.|+.++..+-. +.+.....+.+..+..++..+-+--.++|.-+..++..|+.-|+.+
T Consensus 78 Ii~kakqIe~LIdsLPg~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~i~~i 141 (144)
T PF11221_consen 78 IIRKAKQIEYLIDSLPGIEVSEEEQLKRIKELEEENEEAEEELQEAVKEAEELLKQVQELIREI 141 (144)
T ss_dssp HHHHHHHHHHHHHHSTTSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445667777777633 3344444556666777776666656677777777777777666543
No 109
>KOG1671|consensus
Probab=27.83 E-value=30 Score=31.54 Aligned_cols=21 Identities=38% Similarity=1.007 Sum_probs=15.1
Q ss_pred ecccCCccCCC-CCceeCc-ccc
Q psy16463 264 HFSCVAVTNTP-KGKWYCP-NCR 284 (317)
Q Consensus 264 H~~Cvgl~~~p-~~~w~C~-~C~ 284 (317)
|+.||-+...- .|.|||| +|.
T Consensus 155 hLGCVp~~~AGd~gg~~CPCHGS 177 (210)
T KOG1671|consen 155 HLGCVPIANAGDYGGYYCPCHGS 177 (210)
T ss_pred cccccccccccccCceecccccc
Confidence 99999775443 4789999 443
No 110
>cd07665 BAR_SNX1 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX1 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures effcient cargo sorting by facilitating proper membrane localization
Probab=27.44 E-value=5e+02 Score=24.07 Aligned_cols=101 Identities=7% Similarity=0.060 Sum_probs=53.9
Q ss_pred cchhhhhhhhhhHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHHHHHH
Q psy16463 16 LNQAVLEAMYSVPYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGNKIDQFSRKRNLLRVQVALIAA 95 (317)
Q Consensus 16 ~~~a~~e~~~~a~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~k~~~~~~~~~~~~~I~~~l~~a 95 (317)
-.+|..+.+.....|+||+-.|..+-.-|.......+..-.-.+++.+ ......++..... ...+..+..++..+
T Consensus 97 ~~qa~qd~~~f~e~l~eYiRli~SVK~~f~~R~k~~~~~~~~~~~l~k-Kr~~~~Kl~~~~~----~dK~~~a~~Ev~e~ 171 (234)
T cd07665 97 QEQANNDFFLLAELLADYIRLLSAVRGAFDQRMKTWQRWQDAQAMLQK-KREAEARLLWANK----PDKLQQAKDEIAEW 171 (234)
T ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhcCC----chHHHHHHHHHHHH
Confidence 344555556666778888877776665555544444333222222222 1222223321111 12333445555544
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHhccCc
Q psy16463 96 QEIGDEKLSIMQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 96 ~el~dEKv~LA~q~~dlVdkhirrLD~dl~~le 128 (317)
. .|+.-|..-|+-|.+.|++ ++..|+
T Consensus 172 e----~k~~~a~~~fe~is~~ik~---El~rFe 197 (234)
T cd07665 172 E----SRVTQYERDFERISATVRK---EVIRFE 197 (234)
T ss_pred H----HHHHHHHHHHHHHHHHHHH---HHHHHH
Confidence 4 6888888888888777765 666676
No 111
>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=27.13 E-value=62 Score=19.99 Aligned_cols=26 Identities=27% Similarity=0.724 Sum_probs=19.9
Q ss_pred e-eeCCCCCCC-eeeeCCCCCCCcceecccC
Q psy16463 240 C-LCNQVSFGQ-MVMCDNDLCPHQWFHFSCV 268 (317)
Q Consensus 240 C-~C~~~~~g~-mi~Cd~~~C~~~wfH~~Cv 268 (317)
| +|++...|. +-.|+. |. --+|..|+
T Consensus 3 C~~C~~~~~~~~~Y~C~~--c~-f~lh~~Ca 30 (30)
T PF03107_consen 3 CDVCRRKIDGFYFYHCSE--CC-FTLHVRCA 30 (30)
T ss_pred CCCCCCCcCCCEeEEeCC--CC-CeEcCccC
Confidence 7 788877787 888966 87 45788874
No 112
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=26.90 E-value=30 Score=31.34 Aligned_cols=51 Identities=20% Similarity=0.497 Sum_probs=30.0
Q ss_pred CCCCCCcee-eeCCCCCCCeeeeCCCCCCCcceecccCC--ccC------------CCCCceeCccccccc
Q psy16463 232 IDPNEPTYC-LCNQVSFGQMVMCDNDLCPHQWFHFSCVA--VTN------------TPKGKWYCPNCRKAR 287 (317)
Q Consensus 232 ~d~~e~~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cvg--l~~------------~p~~~w~C~~C~~~~ 287 (317)
.+..+...| ||.+......+ -. |. .+|++.|+- +.. ......-||.|+..-
T Consensus 13 ~~~~~~~~CpICld~~~dPVv--T~--CG-H~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~I 78 (193)
T PLN03208 13 VDSGGDFDCNICLDQVRDPVV--TL--CG-HLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDV 78 (193)
T ss_pred ccCCCccCCccCCCcCCCcEE--cC--CC-chhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcC
Confidence 444555678 99886433333 12 66 677888874 110 123467899999653
No 113
>PF01627 Hpt: Hpt domain; InterPro: IPR008207 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents a domain present at the N terminus in proteins which undergo autophosphorylation. The group includes, the gliding motility regulatory protein from Myxococcus xanthus and a number of bacterial chemotaxis proteins.; GO: 0004871 signal transducer activity, 0000160 two-component signal transduction system (phosphorelay); PDB: 3KYJ_A 3KYI_A 3IQT_A 1Y6D_A 2LD6_A 1TQG_A 2R25_A 1OXB_A 1QSP_B 1C03_B ....
Probab=26.64 E-value=2.5e+02 Score=20.31 Aligned_cols=18 Identities=22% Similarity=0.326 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy16463 104 SIMQQVQDVIEGKTRQID 121 (317)
Q Consensus 104 ~LA~q~~dlVdkhirrLD 121 (317)
.+..++++.|...+.+|.
T Consensus 71 ~~~~~~~~~l~~~l~~l~ 88 (90)
T PF01627_consen 71 EELEQLLDELEAMLEQLR 88 (90)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHh
Confidence 566677777777776664
No 114
>KOG0994|consensus
Probab=26.57 E-value=1.1e+03 Score=27.65 Aligned_cols=19 Identities=16% Similarity=0.139 Sum_probs=8.1
Q ss_pred hhhhhhhhhhHHHHHHHHH
Q psy16463 18 QAVLEAMYSVPYVETYLDI 36 (317)
Q Consensus 18 ~a~~e~~~~a~yLedyld~ 36 (317)
.++.|.-.++.-|-+|+..
T Consensus 1468 ~s~~el~~Li~~v~~Flt~ 1486 (1758)
T KOG0994|consen 1468 ESNRELRNLIQQVRDFLTQ 1486 (1758)
T ss_pred HHHHHHHHHHHHHHHHhcC
Confidence 3333333444444555443
No 115
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=26.55 E-value=55 Score=29.79 Aligned_cols=44 Identities=27% Similarity=0.653 Sum_probs=26.7
Q ss_pred Ccee-eeCCCCC--------CCeeeeCCCCCCCcceecccCCccCCCCCceeCcccccc
Q psy16463 237 PTYC-LCNQVSF--------GQMVMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKA 286 (317)
Q Consensus 237 ~~~C-~C~~~~~--------g~mi~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~ 286 (317)
.+.| +|++... +-++.=|.+.|+ |+.=| .+-.-.-|.||+|--.
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~----~Y~~v--nP~~Y~V~vCP~CgyA 57 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCP----RYKGV--NPLFYEVWVCPHCGYA 57 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCcc----ccCCC--CCeeeeEEECCCCCCc
Confidence 4569 8987622 346677777786 22212 2222367999999743
No 116
>PF13949 ALIX_LYPXL_bnd: ALIX V-shaped domain binding to HIV ; PDB: 2XS1_A 2XS8_A 2R03_A 2R02_A 2OEX_B 2OEV_A 2OJQ_A 2R05_A.
Probab=26.49 E-value=5.2e+02 Score=23.91 Aligned_cols=45 Identities=16% Similarity=0.240 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 28 PYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQN 72 (317)
Q Consensus 28 ~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~ 72 (317)
..++.+.+.+..|+.-.++.-+.|.++.....+-..+-+....+|
T Consensus 22 ~g~~~l~~~l~~l~~~~~~~~~~L~e~~~~L~~E~~ed~~~r~~~ 66 (296)
T PF13949_consen 22 GGIEKLEESLQELPELSQEVRSILDEIEEMLDEEEREDEQLRAKY 66 (296)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred CChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345555555555555555555555555555555444445555555
No 117
>KOG1246|consensus
Probab=26.30 E-value=51 Score=36.44 Aligned_cols=51 Identities=27% Similarity=0.800 Sum_probs=35.9
Q ss_pred CCCcee-eeCCCCCCCeeeeCCCCCCCcceecccCCc--cCCCCCceeCcccccccc
Q psy16463 235 NEPTYC-LCNQVSFGQMVMCDNDLCPHQWFHFSCVAV--TNTPKGKWYCPNCRKARS 288 (317)
Q Consensus 235 ~e~~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cvgl--~~~p~~~w~C~~C~~~~~ 288 (317)
.....| .|.....-.++.|+. |. .=+|..|..+ +..+.+.|.|+.|.....
T Consensus 153 ~~~~~~~~~~k~~~~~~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 206 (904)
T KOG1246|consen 153 IDYPQCNTCSKGKEEKLLLCDS--CD-DSYHTYCLRPPLTRVPDGDWRCPKCIPTPE 206 (904)
T ss_pred ccchhhhccccCCCccceeccc--cc-CcccccccCCCCCcCCcCcccCCccccccc
Confidence 333446 676643223448888 97 8899999874 555689999999997743
No 118
>TIGR00153 conserved hypothetical protein TIGR00153. An apparent homolog with a suggested function is Pit accessory protein from Sinorhizobium meliloti, which may be involved in phosphate (Pi) transport.
Probab=26.16 E-value=4.7e+02 Score=23.32 Aligned_cols=61 Identities=10% Similarity=0.062 Sum_probs=40.8
Q ss_pred CCcccccchhhhhhhhhhHHHHHHHHHhh-cChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 10 QQSPNMLNQAVLEAMYSVPYVETYLDIVE-NLPDEIQRYLTKIRELDVLYQSYMKEIEHIAS 70 (317)
Q Consensus 10 ~~~~~m~~~a~~e~~~~a~yLedyld~ie-nLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~ 70 (317)
|+||..+.....-....+..|.+.++... +--.++...+..|+++..+.-.+..+|...+.
T Consensus 10 ~~s~~~l~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~~~I~~lE~eaD~i~~~i~~~L~ 71 (216)
T TIGR00153 10 GHERDNERQHIEKVGECVQLLIKSFELLKSGNNEKDEELRKEIIEIEHEADEIKREIRLNLE 71 (216)
T ss_pred hCCCccHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence 56777666655544555666666665553 22235778899999999999888888766553
No 119
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=26.13 E-value=5.3e+02 Score=23.88 Aligned_cols=10 Identities=30% Similarity=0.617 Sum_probs=6.1
Q ss_pred ee-eeCCCCCC
Q psy16463 239 YC-LCNQVSFG 248 (317)
Q Consensus 239 ~C-~C~~~~~g 248 (317)
.| -|++.-..
T Consensus 196 ~C~sC~qqIHR 206 (230)
T PF10146_consen 196 TCQSCHQQIHR 206 (230)
T ss_pred hhHhHHHHHhc
Confidence 46 78876444
No 120
>KOG4215|consensus
Probab=26.10 E-value=32 Score=34.22 Aligned_cols=25 Identities=28% Similarity=0.951 Sum_probs=18.8
Q ss_pred CCcee-eeCCCCCC---CeeeeCCCCCCCcce
Q psy16463 236 EPTYC-LCNQVSFG---QMVMCDNDLCPHQWF 263 (317)
Q Consensus 236 e~~~C-~C~~~~~g---~mi~Cd~~~C~~~wf 263 (317)
...+| +|++-+.| -.|.||+ |. .+|
T Consensus 18 ~~~~CaICGDkaTGKHYGA~SCdG--CK-GFF 46 (432)
T KOG4215|consen 18 VAEFCAICGDKATGKHYGAISCDG--CK-GFF 46 (432)
T ss_pred ccchhheeCCcccccccceeecCc--ch-HHH
Confidence 34579 99988766 3779999 98 665
No 121
>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Q61026 from SWISSPROT), and thus enhances transcriptional activation by a number of nuclear receptors. CoCoA has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region [].
Probab=25.83 E-value=8e+02 Score=25.85 Aligned_cols=31 Identities=10% Similarity=0.186 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHhccCc
Q psy16463 97 EIGDEKLSIMQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 97 el~dEKv~LA~q~~dlVdkhirrLD~dl~~le 128 (317)
-++.||=+|..--.+|. .+|++|+..|.++-
T Consensus 428 v~qkEKEql~~EkQeL~-~yi~~Le~r~~~~~ 458 (546)
T PF07888_consen 428 VAQKEKEQLQEEKQELL-EYIERLEQRLDKVA 458 (546)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHHHHHHhh
Confidence 34568888888777776 48999998887775
No 122
>KOG0995|consensus
Probab=25.79 E-value=6e+02 Score=26.86 Aligned_cols=82 Identities=11% Similarity=0.058 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-hCcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHh
Q psy16463 46 RYLTKIRELDVLYQSYMKEIEHIASQN-GNKIDQFSRKRNLLRVQVALIAAQEIGDEKLSIMQQVQDVIEGKTRQIDGIF 124 (317)
Q Consensus 46 r~l~lIRElD~k~~~~~~~ie~~~~~~-~k~~~~~~~~~~~~~I~~~l~~a~el~dEKv~LA~q~~dlVdkhirrLD~dl 124 (317)
.+..+..++-..+++...++..+.+.+ ........+.+.+..|...+..+..+-..|...|.....--+.|+..|+..+
T Consensus 422 ~l~el~~ei~~~~~~~~~~~~tLq~~~~~~~~~i~E~~~~l~~~~~el~~~~~~~~~~k~e~eee~~k~~~E~e~le~~l 501 (581)
T KOG0995|consen 422 LLKELLDEISEELHEAENELETLQEHFSNKASTIEEKIQILGEIELELKKAESKYELKKEEAEEEWKKCRKEIEKLEEEL 501 (581)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_pred ccC
Q psy16463 125 YNL 127 (317)
Q Consensus 125 ~~l 127 (317)
..+
T Consensus 502 ~~l 504 (581)
T KOG0995|consen 502 LNL 504 (581)
T ss_pred HHH
No 123
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=25.79 E-value=32 Score=25.67 Aligned_cols=47 Identities=28% Similarity=0.631 Sum_probs=18.9
Q ss_pred ee-eeCCCC--CC--CeeeeCCCCCCCcceecccCC-----ccCCC----CCceeCcccccc
Q psy16463 239 YC-LCNQVS--FG--QMVMCDNDLCPHQWFHFSCVA-----VTNTP----KGKWYCPNCRKA 286 (317)
Q Consensus 239 ~C-~C~~~~--~g--~mi~Cd~~~C~~~wfH~~Cvg-----l~~~p----~~~w~C~~C~~~ 286 (317)
.| ||...- .+ .-+.|+++.|. .-||..|+- +.... .-.+-||.|...
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~n~~C~-~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~ 64 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCPNPSCG-KKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSP 64 (70)
T ss_dssp S-SSS--SS-TT-----B--S-TT-----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SE
T ss_pred CCCcCCcEecCCCCcCceEcCCcccC-CHHHHHHHHHHHHHcccCCeeecccccCCcCCCCe
Confidence 46 787642 23 35889988898 789999986 11111 124679999865
No 124
>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=25.51 E-value=23 Score=29.12 Aligned_cols=44 Identities=27% Similarity=0.740 Sum_probs=26.2
Q ss_pred ee-eeCCCCCCCe----eeeCCCCCCCcceecccCCccCCCCCceeCccccccc
Q psy16463 239 YC-LCNQVSFGQM----VMCDNDLCPHQWFHFSCVAVTNTPKGKWYCPNCRKAR 287 (317)
Q Consensus 239 ~C-~C~~~~~g~m----i~Cd~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~~ 287 (317)
.| .|+.+ +|++ .-|.. |. ..+=-.|-.. ......|+|.-|...+
T Consensus 56 ~C~~C~~~-fg~l~~~~~~C~~--C~-~~VC~~C~~~-~~~~~~WlC~vC~k~r 104 (118)
T PF02318_consen 56 HCARCGKP-FGFLFNRGRVCVD--CK-HRVCKKCGVY-SKKEPIWLCKVCQKQR 104 (118)
T ss_dssp B-TTTS-B-CSCTSTTCEEETT--TT-EEEETTSEEE-TSSSCCEEEHHHHHHH
T ss_pred chhhhCCc-ccccCCCCCcCCc--CC-ccccCccCCc-CCCCCCEEChhhHHHH
Confidence 68 78876 4433 44655 87 4444455443 3445789999998653
No 125
>KOG2041|consensus
Probab=25.46 E-value=58 Score=35.31 Aligned_cols=53 Identities=28% Similarity=0.716 Sum_probs=33.3
Q ss_pred CCCCCCC-cee-eeCCCCCCCeeeeCCCCCCCcceecccCCccCCC---CCceeCcccccccc
Q psy16463 231 AIDPNEP-TYC-LCNQVSFGQMVMCDNDLCPHQWFHFSCVAVTNTP---KGKWYCPNCRKARS 288 (317)
Q Consensus 231 ~~d~~e~-~~C-~C~~~~~g~mi~Cd~~~C~~~wfH~~Cvgl~~~p---~~~w~C~~C~~~~~ 288 (317)
++||+.+ +-| +|+-+-..--++|.- |. .-| ..|+.-. .| .--|.||.|.....
T Consensus 1110 p~d~~~~~vdc~~cg~~i~~~~~~c~e--c~-~kf-P~CiasG-~pIt~~~fWlC~~CkH~a~ 1167 (1189)
T KOG2041|consen 1110 PVDPNSAKVDCSVCGAKIDPYDLQCSE--CQ-TKF-PVCIASG-RPITDNIFWLCPRCKHRAH 1167 (1189)
T ss_pred CCCCCccceeeeecCCcCCccCCCChh--hc-CcC-ceeeccC-CccccceEEEccccccccc
Confidence 4566654 468 798764444568866 87 434 6787522 12 23799999986543
No 126
>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=25.38 E-value=15 Score=23.27 Aligned_cols=26 Identities=38% Similarity=0.721 Sum_probs=16.5
Q ss_pred CCCcceecccCCccCCCCCceeCccccc
Q psy16463 258 CPHQWFHFSCVAVTNTPKGKWYCPNCRK 285 (317)
Q Consensus 258 C~~~wfH~~Cvgl~~~p~~~w~C~~C~~ 285 (317)
|. ..||..|+..... .+...||.|+.
T Consensus 18 C~-H~~c~~C~~~~~~-~~~~~Cp~C~~ 43 (45)
T cd00162 18 CG-HVFCRSCIDKWLK-SGKNTCPLCRT 43 (45)
T ss_pred CC-ChhcHHHHHHHHH-hCcCCCCCCCC
Confidence 65 5589999852111 14567999975
No 127
>PRK11637 AmiB activator; Provisional
Probab=25.36 E-value=6.8e+02 Score=24.89 Aligned_cols=26 Identities=8% Similarity=0.109 Sum_probs=12.3
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 39 NLPDEIQRYLTKIRELDVLYQSYMKE 64 (317)
Q Consensus 39 nLP~Elqr~l~lIRElD~k~~~~~~~ 64 (317)
.+-.+|...-..|.++...+.++..+
T Consensus 44 ~~~~~l~~l~~qi~~~~~~i~~~~~~ 69 (428)
T PRK11637 44 DNRDQLKSIQQDIAAKEKSVRQQQQQ 69 (428)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444555555555555554444333
No 128
>PF15450 DUF4631: Domain of unknown function (DUF4631)
Probab=24.99 E-value=8.1e+02 Score=25.64 Aligned_cols=14 Identities=7% Similarity=0.022 Sum_probs=10.2
Q ss_pred hhhhHHHHHHHHHh
Q psy16463 24 MYSVPYVETYLDIV 37 (317)
Q Consensus 24 ~~~a~yLedyld~i 37 (317)
-+++.||..||..+
T Consensus 311 eeL~~~L~~~lea~ 324 (531)
T PF15450_consen 311 EELATKLQENLEAM 324 (531)
T ss_pred HHHHHHHHHHHHHH
Confidence 45677888888775
No 129
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=24.91 E-value=31 Score=29.00 Aligned_cols=27 Identities=30% Similarity=0.802 Sum_probs=16.2
Q ss_pred cceecccC--C----ccCCCCCceeCccccccc
Q psy16463 261 QWFHFSCV--A----VTNTPKGKWYCPNCRKAR 287 (317)
Q Consensus 261 ~wfH~~Cv--g----l~~~p~~~w~C~~C~~~~ 287 (317)
.||...|. . +.....|.|+|+.|....
T Consensus 15 ~~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 15 NWYYPACPNEKCNKKVTENGDGSYRCEKCNKTV 47 (146)
T ss_dssp TTEEEE-TSTTTS-B-EEETTTEEEETTTTEEE
T ss_pred CcEECCCCCccCCCEeecCCCcEEECCCCCCcC
Confidence 45666666 2 333334789999998663
No 130
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=24.72 E-value=83 Score=26.34 Aligned_cols=43 Identities=26% Similarity=0.603 Sum_probs=25.9
Q ss_pred cee-eeCCC------CCCCeeeeCC-CCCCCcceecccCCccCCCCCceeCccccc
Q psy16463 238 TYC-LCNQV------SFGQMVMCDN-DLCPHQWFHFSCVAVTNTPKGKWYCPNCRK 285 (317)
Q Consensus 238 ~~C-~C~~~------~~g~mi~Cd~-~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~ 285 (317)
.-| .|+.. .+|.|++|++ +.|.+ ...- ........|-||.|..
T Consensus 18 ~~Cp~Cg~~m~~~~~~~g~f~gCs~yP~C~~----~~~~-~~~~~~~~~~Cp~C~~ 68 (140)
T COG0551 18 QICPKCGKNMVKKFGKYGIFLGCSNYPKCDY----YEPE-KAIAEKTGVKCPKCGK 68 (140)
T ss_pred ccCCcCCCeeEEEEccCCeEEEeCCCCCCCC----Cccc-ccccccCceeCCCCCC
Confidence 458 78865 4578999998 78872 1100 1111234688888874
No 131
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=24.49 E-value=33 Score=20.15 Aligned_cols=13 Identities=38% Similarity=1.068 Sum_probs=9.9
Q ss_pred CceeCcccccccc
Q psy16463 276 GKWYCPNCRKARS 288 (317)
Q Consensus 276 ~~w~C~~C~~~~~ 288 (317)
+.|.|+.|...+.
T Consensus 1 g~W~C~~C~~~N~ 13 (26)
T smart00547 1 GDWECPACTFLNF 13 (26)
T ss_pred CcccCCCCCCcCh
Confidence 5799999975543
No 132
>PF01858 RB_A: Retinoblastoma-associated protein A domain; InterPro: IPR002720 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and Simian virus 40 (SV40) large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion appears to be required for the stable folding of the B box (see IPR002719 from INTERPRO). Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the A-box is on N-terminal side of the B-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1O9K_A 3POM_A 1GH6_B 1N4M_A 4ELL_B 1AD6_A 1GUX_A 2R7G_C 4ELJ_A.
Probab=24.12 E-value=79 Score=28.39 Aligned_cols=43 Identities=21% Similarity=0.326 Sum_probs=30.1
Q ss_pred CcccccchhhhhhhhhhHHHHHHHHHhhcChHHHHHHHHHHHH
Q psy16463 11 QSPNMLNQAVLEAMYSVPYVETYLDIVENLPDEIQRYLTKIRE 53 (317)
Q Consensus 11 ~~~~m~~~a~~e~~~~a~yLedyld~ienLP~Elqr~l~lIRE 53 (317)
.-|..+.-.++.|.|-.-++|-|+-....||.+|.++|..|-|
T Consensus 134 ~FPwiL~~~~i~~f~f~KvIE~~Vr~~~~Lpr~lvkHL~~IEE 176 (194)
T PF01858_consen 134 SFPWILEVFDIHPFDFYKVIESFVRHEDGLPRELVKHLNSIEE 176 (194)
T ss_dssp STTHHHHHTT--HHHHHTTHHHHHHH-TT--HHHHHHHHHHHH
T ss_pred cchHHHHhcCCChhhHhhHHHHHHHccccCCHHHHHHHHHHHH
Confidence 3455566666667777788999999999999999999988765
No 133
>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=24.09 E-value=34 Score=32.41 Aligned_cols=26 Identities=27% Similarity=0.890 Sum_probs=12.5
Q ss_pred Ccee-eeCCCCC----------C-CeeeeCCCCCCCccee
Q psy16463 237 PTYC-LCNQVSF----------G-QMVMCDNDLCPHQWFH 264 (317)
Q Consensus 237 ~~~C-~C~~~~~----------g-~mi~Cd~~~C~~~wfH 264 (317)
.-|| +||..+. | -++.|.- |..+|-+
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~--C~t~W~~ 209 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSL--CGTEWRF 209 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETT--T--EEE-
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCC--CCCeeee
Confidence 3589 9997621 3 4888987 9989943
No 134
>PF10737 GerPC: Spore germination protein GerPC; InterPro: IPR019673 GerPC is required for the formation of functionally normal spores. The gerP locus encodes a number of proteins which are thought to be involved in the establishment of normal spore coat structure and/or permeability, which allows the access of germinants to their receptor [].
Probab=24.01 E-value=5.2e+02 Score=23.05 Aligned_cols=43 Identities=21% Similarity=0.318 Sum_probs=29.4
Q ss_pred HHHHHHHhhcChHHHHHHHHHH-HHHHHHHH-----HHHHHHHHHHHHHhC
Q psy16463 30 VETYLDIVENLPDEIQRYLTKI-RELDVLYQ-----SYMKEIEHIASQNGN 74 (317)
Q Consensus 30 Ledyld~ienLP~Elqr~l~lI-RElD~k~~-----~~~~~ie~~~~~~~k 74 (317)
+..||+ ..+|..|.+.-... +.||..+. ++.++|+++++-|++
T Consensus 88 v~~yL~--~e~p~~l~~~e~~~~~~ld~~y~~~IieDIrKQl~~RI~~Ylq 136 (176)
T PF10737_consen 88 VHQYLE--EEAPQRLEQLEQQYNVPLDDSYRSFIIEDIRKQLPQRIQFYLQ 136 (176)
T ss_pred HHHHHH--HHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHhHHHHHHHHh
Confidence 445555 35677777766655 35677665 567789999999976
No 135
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=24.00 E-value=12 Score=28.13 Aligned_cols=28 Identities=29% Similarity=0.857 Sum_probs=23.7
Q ss_pred ceeeeCCCCCCCeeeeCCCCCCCcceecccCCcc
Q psy16463 238 TYCLCNQVSFGQMVMCDNDLCPHQWFHFSCVAVT 271 (317)
Q Consensus 238 ~~C~C~~~~~g~mi~Cd~~~C~~~wfH~~Cvgl~ 271 (317)
.-|.|.- .-||-|-. |. .+-|-.|+|..
T Consensus 34 ~~C~C~L---kAMi~Cq~--CG-AFCHDDCIgps 61 (69)
T PF13922_consen 34 NKCACSL---KAMIMCQG--CG-AFCHDDCIGPS 61 (69)
T ss_pred cccccch---HHHHHHhh--cc-chhccccccHH
Confidence 4588986 68999988 98 88999999865
No 136
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=23.87 E-value=8.4e+02 Score=25.42 Aligned_cols=98 Identities=12% Similarity=0.194 Sum_probs=41.6
Q ss_pred HHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC---------cCChHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 30 VETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNGN---------KIDQFSRKRNLLRVQVALIAAQEIGD 100 (317)
Q Consensus 30 Ledyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~k---------~~~~~~~~~~~~~I~~~l~~a~el~d 100 (317)
+++.|+.++.-=.+|..-|+.|.+.+.+-.....++...++.+.+ +.....-+..+..|...|....+|-.
T Consensus 110 ~~~~l~~~e~~~~~i~~~l~~l~~~e~~nr~~v~~l~~~y~~~rk~ll~~~~~~G~a~~~le~~l~~~e~~f~~f~~l~~ 189 (569)
T PRK04778 110 IESLLDLIEEDIEQILEELQELLESEEKNREEVEQLKDLYRELRKSLLANRFSFGPALDELEKQLENLEEEFSQFVELTE 189 (569)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 444455554333444445555555555544444444444444322 11112233344445444443333221
Q ss_pred H-HHHHHHHHHHHHHHHHHHHHhHhccC
Q psy16463 101 E-KLSIMQQVQDVIEGKTRQIDGIFYNL 127 (317)
Q Consensus 101 E-Kv~LA~q~~dlVdkhirrLD~dl~~l 127 (317)
. -..=|..+++-+..|+..|+..+..+
T Consensus 190 ~Gd~~~A~e~l~~l~~~~~~l~~~~~~i 217 (569)
T PRK04778 190 SGDYVEAREILDQLEEELAALEQIMEEI 217 (569)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 12224444455555555555544443
No 137
>KOG1973|consensus
Probab=23.66 E-value=99 Score=29.26 Aligned_cols=100 Identities=12% Similarity=0.066 Sum_probs=63.6
Q ss_pred HHHHHHHHHhhcChHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 28 PYVETYLDIVENLPDEIQRYLTKIRELD-VLYQSYMKEIEHIASQNGNKIDQFSRKRNLLRVQVALIAAQEIGDEKLSIM 106 (317)
Q Consensus 28 ~yLedyld~ienLP~Elqr~l~lIRElD-~k~~~~~~~ie~~~~~~~k~~~~~~~~~~~~~I~~~l~~a~el~dEKv~LA 106 (317)
.++...++.|..+.... +......++| ..+....+....+...+..........+.+..+.+....-.+++...+.+.
T Consensus 26 ~~~~~~f~~l~~~~~~~-~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ek~~~~~~~~e~~ 104 (274)
T KOG1973|consen 26 RNLQHNFDVIEDIDIFG-RSENQKKELDLKVAVEYMSKGRSQLSKPQKDPLLEAIRSALRKCKELSDEKVQIAMQTVELI 104 (274)
T ss_pred ccchhHHHHHhhhhccc-hhHHHHhhhhhhhhhccccccccccCccccchhHHHHHHHHhhhhhhhhHHHHHHHHHHHhh
Confidence 45555555565555444 7778888888 444444444443222222222222334445555666666778888999999
Q ss_pred HHHHHHHHHHHHHHHhHhccCc
Q psy16463 107 QQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 107 ~q~~dlVdkhirrLD~dl~~le 128 (317)
...+.-.+.|+.+++.++....
T Consensus 105 ~~~~~~~~~~~~~~e~~~~~~~ 126 (274)
T KOG1973|consen 105 PKHIGRLETALKSFEVELELAK 126 (274)
T ss_pred HhhhcchhHHHHhcccchhhhh
Confidence 9999999999998888888773
No 138
>cd07599 BAR_Rvs167p The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Reduced viability upon starvation protein 167 and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of fungal proteins with similarity to Saccharomyces cerevisiae Reduced viability upon starvation protein 167 (Rvs167p) and Schizosaccharomyces pombe Hob1 (homolog of Bin1). S. cerevisiae Rvs167p plays a role in regulation of the actin cytoskeleton, endocytosis, and sporulation. It forms a heterodimer with another BAR domain protein Rvs161p. Rvs161p and Rvs167p share common functions but are not interchangeable. Their BAR domains cannot be replaced with each other and the overexpression of one cannot suppress the mutant phenotypes of the other. Rvs167p also interacts with the GTPase activating protein (GAP) Gyp5p, which is involved in ER to Golgi vesicle trafficking. BAR domains fo
Probab=23.54 E-value=5.3e+02 Score=22.99 Aligned_cols=21 Identities=10% Similarity=0.121 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy16463 99 GDEKLSIMQQVQDVIEGKTRQ 119 (317)
Q Consensus 99 ~dEKv~LA~q~~dlVdkhirr 119 (317)
+++++..|...|+.++.+++.
T Consensus 154 ae~~l~~a~~~y~~lN~~Lk~ 174 (216)
T cd07599 154 LERKLEEAKEEYEALNELLKS 174 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 468899999999999988764
No 139
>KOG0704|consensus
Probab=23.48 E-value=52 Score=32.48 Aligned_cols=31 Identities=26% Similarity=0.539 Sum_probs=17.9
Q ss_pred ceee-eCCC-------CCCCeee--eCCCCCCCcceecccCC
Q psy16463 238 TYCL-CNQV-------SFGQMVM--CDNDLCPHQWFHFSCVA 269 (317)
Q Consensus 238 ~~C~-C~~~-------~~g~mi~--Cd~~~C~~~wfH~~Cvg 269 (317)
..|+ |+.+ +||-+|| |.+..=. --.|.+||.
T Consensus 20 k~CfeC~a~NPQWvSvsyGIfICLECSG~HRg-LGVhiSFVR 60 (386)
T KOG0704|consen 20 KKCFECGAPNPQWVSVSYGIFICLECSGKHRG-LGVHISFVR 60 (386)
T ss_pred CceeecCCCCCCeEeecccEEEEEecCCcccc-cceeeEEEE
Confidence 4685 9865 5677777 3331111 236777775
No 140
>PF11855 DUF3375: Protein of unknown function (DUF3375); InterPro: IPR021804 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length.
Probab=22.61 E-value=8.4e+02 Score=24.94 Aligned_cols=35 Identities=23% Similarity=0.400 Sum_probs=29.6
Q ss_pred HHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHH
Q psy16463 28 PYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYM 62 (317)
Q Consensus 28 ~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~ 62 (317)
.-+.+++.-...||.+|.+.=..+|+||..+.+-+
T Consensus 178 er~~~i~~la~~L~~DFr~V~~~~r~l~r~lr~~i 212 (478)
T PF11855_consen 178 ERARQILQLARELPADFRRVEDNFRELDRALRERI 212 (478)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44567888889999999999999999999996543
No 141
>KOG3277|consensus
Probab=22.48 E-value=55 Score=28.67 Aligned_cols=19 Identities=42% Similarity=0.996 Sum_probs=13.2
Q ss_pred ee-eeCCCCC----------C-CeeeeCCCCCC
Q psy16463 239 YC-LCNQVSF----------G-QMVMCDNDLCP 259 (317)
Q Consensus 239 ~C-~C~~~~~----------g-~mi~Cd~~~C~ 259 (317)
.| +|+.-+. | -+|.|++ |.
T Consensus 81 TCkvCntRs~ktisk~AY~~GvVivqC~g--C~ 111 (165)
T KOG3277|consen 81 TCKVCNTRSTKTISKQAYEKGVVIVQCPG--CK 111 (165)
T ss_pred EeeccCCccccccChhhhhCceEEEECCC--Cc
Confidence 38 8986532 3 3889988 86
No 142
>KOG1952|consensus
Probab=22.37 E-value=37 Score=37.19 Aligned_cols=50 Identities=24% Similarity=0.755 Sum_probs=33.2
Q ss_pred CCcee-eeCCC-CC-CCeeeeCCCCCCCcceecccCCc---c--CCCCCceeCcccccccc
Q psy16463 236 EPTYC-LCNQV-SF-GQMVMCDNDLCPHQWFHFSCVAV---T--NTPKGKWYCPNCRKARS 288 (317)
Q Consensus 236 e~~~C-~C~~~-~~-g~mi~Cd~~~C~~~wfH~~Cvgl---~--~~p~~~w~C~~C~~~~~ 288 (317)
..+-| ||-.- .+ -.|-.|.. | |.-||+.|+.- . ......|-||.|.....
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~s--C-YhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKS--C-YHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred CceEEEEeeeeccccCCceecch--h-hhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 34458 88543 22 35778988 9 69999999862 1 11236899999985443
No 143
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=22.20 E-value=20 Score=27.20 Aligned_cols=10 Identities=30% Similarity=1.281 Sum_probs=8.7
Q ss_pred cceecccCCc
Q psy16463 261 QWFHFSCVAV 270 (317)
Q Consensus 261 ~wfH~~Cvgl 270 (317)
.|||+.|+..
T Consensus 39 ~W~H~~C~~~ 48 (82)
T PF00645_consen 39 KWYHWDCFFK 48 (82)
T ss_dssp EEEEHHHHHH
T ss_pred ceECcccccc
Confidence 8999999864
No 144
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=21.80 E-value=6.1e+02 Score=23.28 Aligned_cols=38 Identities=21% Similarity=0.142 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 83 RNLLRVQVALIAAQEIGDEKLSIMQQVQDVIEGKTRQI 120 (317)
Q Consensus 83 ~~~~~I~~~l~~a~el~dEKv~LA~q~~dlVdkhirrL 120 (317)
..+..++..+..+.--.-||+...-.+|..-...-+.+
T Consensus 131 ~Rl~~L~~~l~~~dv~~~ek~r~vlea~~~E~~yg~~i 168 (251)
T PF11932_consen 131 ERLARLRAMLDDADVSLAEKFRRVLEAYQIEMEYGRTI 168 (251)
T ss_pred HHHHHHHHhhhccCCCHHHHHHHHHHHHHHHHHhCCce
Confidence 33444444444333223344444444444433333333
No 145
>COG4867 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=21.77 E-value=1.9e+02 Score=29.75 Aligned_cols=32 Identities=16% Similarity=0.252 Sum_probs=23.9
Q ss_pred hhcChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 37 VENLPDEIQRYLTKIRELDVLYQSYMKEIEHI 68 (317)
Q Consensus 37 ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~ 68 (317)
|++||.--..-++++-+.|.+.++.....++.
T Consensus 121 ~~~lpes~a~av~el~~y~w~s~~ar~k~eqi 152 (652)
T COG4867 121 LDALPESPAKAVQELAEYRWRSGQAREKYEQI 152 (652)
T ss_pred hccCCcchHHHHHHHHHhcchhhHHHHHHHHH
Confidence 67788878888888888888888776655443
No 146
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=21.69 E-value=4.8e+02 Score=21.81 Aligned_cols=89 Identities=19% Similarity=0.252 Sum_probs=44.3
Q ss_pred hcChHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHh---C---cCChHHHHHHHHH-----HHHHHHHHHHHHHHHH
Q psy16463 38 ENLPDEIQRYLTKIRELDVLYQSYMKE---IEHIASQNG---N---KIDQFSRKRNLLR-----VQVALIAAQEIGDEKL 103 (317)
Q Consensus 38 enLP~Elqr~l~lIRElD~k~~~~~~~---ie~~~~~~~---k---~~~~~~~~~~~~~-----I~~~l~~a~el~dEKv 103 (317)
.+||.+++..+.....|-...+.+.-+ ++..++... . ..+.. ...+.. |......+..=-+++.
T Consensus 2 ~~lpp~~q~~l~q~QqLq~ql~~~~~qk~~le~qL~E~~~al~Ele~l~eD--~~vYk~VG~llvk~~k~~~~~eL~er~ 79 (119)
T COG1382 2 EQLPPEVQAQLAQLQQLQQQLQKVILQKQQLEAQLKEIEKALEELEKLDED--APVYKKVGNLLVKVSKEEAVDELEERK 79 (119)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcc--cHHHHHhhhHHhhhhHHHHHHHHHHHH
Confidence 567777777777777777766665433 222222211 0 00000 011222 2223333333334565
Q ss_pred HHHHHHHHHHHHHHHHHHhHhccCc
Q psy16463 104 SIMQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 104 ~LA~q~~dlVdkhirrLD~dl~~le 128 (317)
.....=...+++..++|+..++.+.
T Consensus 80 E~Le~ri~tLekQe~~l~e~l~eLq 104 (119)
T COG1382 80 ETLELRIKTLEKQEEKLQERLEELQ 104 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555555666666666666666666
No 147
>PRK08032 fliD flagellar capping protein; Reviewed
Probab=21.67 E-value=6.4e+02 Score=25.62 Aligned_cols=45 Identities=9% Similarity=0.195 Sum_probs=21.8
Q ss_pred HHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 28 PYVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQN 72 (317)
Q Consensus 28 ~yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~ 72 (317)
.||+.|+..-.-|......+-..|+.||.++..+...++.+.+.|
T Consensus 392 ~~l~~~~~~~G~l~~~~~~l~~~i~~l~~~i~~~~~rl~~~e~rl 436 (462)
T PRK08032 392 TNLKSWLSTTGIIKTATDGVNKTLKKLTKQYNAVSDSIDATIARY 436 (462)
T ss_pred HHHHHHHcCCccchhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555544444444444445555555555555555544444433
No 148
>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.
Probab=21.63 E-value=48 Score=19.75 Aligned_cols=13 Identities=31% Similarity=1.020 Sum_probs=9.2
Q ss_pred eeCCCCCCCcceecc
Q psy16463 252 MCDNDLCPHQWFHFS 266 (317)
Q Consensus 252 ~Cd~~~C~~~wfH~~ 266 (317)
-|..++| .|.||.
T Consensus 11 ~Cnd~~C--~~QHfr 23 (23)
T PF10650_consen 11 VCNDPDC--EFQHFR 23 (23)
T ss_pred eeCCCCC--CccccC
Confidence 4766789 488973
No 149
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=21.39 E-value=55 Score=22.52 Aligned_cols=40 Identities=23% Similarity=0.651 Sum_probs=21.7
Q ss_pred eeCCCCC-CCee-eeCCCCCCCcceecccCC-------ccCCC----CCceeCccccc
Q psy16463 241 LCNQVSF-GQMV-MCDNDLCPHQWFHFSCVA-------VTNTP----KGKWYCPNCRK 285 (317)
Q Consensus 241 ~C~~~~~-g~mi-~Cd~~~C~~~wfH~~Cvg-------l~~~p----~~~w~C~~C~~ 285 (317)
.|+++-. ++++ .-.+ ..||..|+. |.... .++.||..|-.
T Consensus 3 ~C~~~I~~~~~~~~~~~-----~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~ 55 (58)
T PF00412_consen 3 RCGKPIYGTEIVIKAMG-----KFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQ 55 (58)
T ss_dssp TTSSBESSSSEEEEETT-----EEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHH
T ss_pred CCCCCccCcEEEEEeCC-----cEEEccccccCCCCCccCCCeeEeECCEEECHHHHh
Confidence 4666644 3333 3444 446888764 22221 36788887754
No 150
>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease
Probab=21.29 E-value=6e+02 Score=22.80 Aligned_cols=38 Identities=21% Similarity=0.266 Sum_probs=29.8
Q ss_pred HHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16463 29 YVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIE 66 (317)
Q Consensus 29 yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie 66 (317)
-|..|-+.=..||.-|+++-.+||.|=.++........
T Consensus 48 AL~k~e~~e~~Lpqll~~h~eEvr~Lr~~LR~~q~~~r 85 (194)
T PF15619_consen 48 ALQKYEDTEAELPQLLQRHNEEVRVLRERLRKSQEQER 85 (194)
T ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46778888888999999999999988888776555433
No 151
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=20.95 E-value=7.5e+02 Score=23.76 Aligned_cols=29 Identities=7% Similarity=0.267 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhccCc
Q psy16463 100 DEKLSIMQQVQDVIEGKTRQIDGIFYNLP 128 (317)
Q Consensus 100 dEKv~LA~q~~dlVdkhirrLD~dl~~le 128 (317)
++..++-..+.+.++.|+..|+.|.+.|.
T Consensus 141 eWR~~ll~gl~~~L~~~~~~L~~D~~~L~ 169 (325)
T PF08317_consen 141 EWRMQLLEGLKEGLEENLELLQEDYAKLD 169 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666666666666666666665555
No 152
>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....
Probab=20.53 E-value=6.9e+02 Score=23.37 Aligned_cols=10 Identities=10% Similarity=0.119 Sum_probs=4.8
Q ss_pred HHHhHhccCc
Q psy16463 119 QIDGIFYNLP 128 (317)
Q Consensus 119 rLD~dl~~le 128 (317)
.||..|..+.
T Consensus 294 ~Ld~EIatYR 303 (312)
T PF00038_consen 294 ALDAEIATYR 303 (312)
T ss_dssp HHHHHHHHHH
T ss_pred hHHHHHHHHH
Confidence 4555554443
No 153
>KOG0971|consensus
Probab=20.46 E-value=1.1e+03 Score=26.77 Aligned_cols=34 Identities=15% Similarity=0.304 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHhccCcC
Q psy16463 96 QEIGDEKLSIMQQVQDVIEGKTRQIDGIFYNLPS 129 (317)
Q Consensus 96 ~el~dEKv~LA~q~~dlVdkhirrLD~dl~~le~ 129 (317)
.++++|+..--++=+++....+..|+.||+.|.+
T Consensus 320 KEmAEERaesLQ~eve~lkEr~deletdlEILKa 353 (1243)
T KOG0971|consen 320 KEMAEERAESLQQEVEALKERVDELETDLEILKA 353 (1243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788899988888899999999999999998874
No 154
>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=20.25 E-value=3.2e+02 Score=26.63 Aligned_cols=33 Identities=15% Similarity=0.204 Sum_probs=17.1
Q ss_pred HHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy16463 29 YVETYLDIVENLPDEIQRYLTKIRELDVLYQSYMKEIEHIASQNG 73 (317)
Q Consensus 29 yLedyld~ienLP~Elqr~l~lIRElD~k~~~~~~~ie~~~~~~~ 73 (317)
-.+|||+.|+.| .|.|+-.+|... ++..+.+|.
T Consensus 94 ~yNdYLE~vEdi------i~nL~~~~d~~~------te~~l~~y~ 126 (309)
T TIGR00570 94 EYNDYLEEVEDI------VYNLTNNIDLEN------TKKKIETYQ 126 (309)
T ss_pred HHHHHHHHHHHH------HHHhhcCCcHHH------HHHHHHHHH
Confidence 346677766544 244455566522 444455553
Done!