Query 028291
Match_columns 211
No_of_seqs 112 out of 688
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 09:14:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028291.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028291hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1984 Vesicle coat complex C 100.0 9.2E-55 2E-59 412.4 17.0 189 18-206 268-474 (1007)
2 KOG1985 Vesicle coat complex C 100.0 1.6E-47 3.5E-52 362.1 13.9 172 31-205 164-349 (887)
3 COG5028 Vesicle coat complex C 100.0 8.8E-47 1.9E-51 355.0 13.7 186 18-206 132-333 (861)
4 PLN00162 transport protein sec 100.0 4.9E-41 1.1E-45 326.5 17.8 161 35-207 7-176 (761)
5 PTZ00395 Sec24-related protein 100.0 6.7E-38 1.5E-42 308.4 15.5 198 4-206 622-1007(1560)
6 KOG1986 Vesicle coat complex C 100.0 1.4E-31 2.9E-36 250.8 11.8 162 33-209 5-175 (745)
7 COG5047 SEC23 Vesicle coat com 100.0 2.2E-28 4.8E-33 225.4 12.0 160 34-208 6-175 (755)
8 PF04810 zf-Sec23_Sec24: Sec23 99.5 3.6E-15 7.9E-20 93.8 1.8 34 87-120 1-34 (40)
9 PF04811 Sec23_trunk: Sec23/Se 99.4 3.1E-13 6.7E-18 115.4 8.4 59 149-208 1-61 (243)
10 cd01479 Sec24-like Sec24-like: 99.4 3.9E-13 8.5E-18 115.4 8.6 59 149-207 1-61 (244)
11 cd01468 trunk_domain trunk dom 99.4 6.4E-13 1.4E-17 113.4 8.3 59 149-208 1-61 (239)
12 cd01478 Sec23-like Sec23-like: 97.8 3.9E-05 8.4E-10 67.0 6.0 36 149-187 1-36 (267)
13 cd01463 vWA_VGCC_like VWA Volt 96.7 0.0056 1.2E-07 50.0 7.0 53 149-203 11-63 (190)
14 PF13768 VWA_3: von Willebrand 96.4 0.0086 1.9E-07 46.9 5.7 45 154-201 3-47 (155)
15 cd01456 vWA_ywmD_type VWA ywmD 96.0 0.019 4.1E-07 47.5 6.0 53 147-200 16-73 (206)
16 cd01472 vWA_collagen von Wille 96.0 0.024 5.2E-07 44.9 6.4 47 154-202 3-52 (164)
17 cd01471 vWA_micronemal_protein 95.9 0.021 4.5E-07 46.2 5.9 47 154-201 3-52 (186)
18 cd01477 vWA_F09G8-8_type VWA F 95.9 0.022 4.7E-07 47.3 6.1 49 151-201 19-76 (193)
19 cd01475 vWA_Matrilin VWA_Matri 95.9 0.026 5.7E-07 47.4 6.7 51 151-202 2-54 (224)
20 cd01464 vWA_subfamily VWA subf 95.8 0.019 4.1E-07 46.2 5.2 48 154-202 6-58 (176)
21 cd01461 vWA_interalpha_trypsin 95.8 0.029 6.2E-07 44.1 6.1 50 151-202 2-51 (171)
22 cd01466 vWA_C3HC4_type VWA C3H 95.8 0.022 4.7E-07 45.0 5.4 46 154-201 3-48 (155)
23 cd01469 vWA_integrins_alpha_su 95.7 0.033 7.1E-07 45.1 6.4 47 154-201 3-51 (177)
24 TIGR03788 marine_srt_targ mari 95.7 0.029 6.4E-07 54.0 6.9 53 148-202 268-320 (596)
25 cd01481 vWA_collagen_alpha3-VI 95.5 0.05 1.1E-06 43.7 6.8 47 154-201 3-51 (165)
26 cd01482 vWA_collagen_alphaI-XI 95.5 0.041 8.9E-07 43.7 6.0 46 154-201 3-51 (164)
27 cd01480 vWA_collagen_alpha_1-V 95.4 0.041 8.9E-07 44.8 5.8 47 153-201 4-59 (186)
28 cd01465 vWA_subgroup VWA subgr 95.2 0.052 1.1E-06 42.7 5.7 47 153-201 2-48 (170)
29 COG4245 TerY Uncharacterized p 95.1 0.042 9.1E-07 45.8 4.9 48 154-202 6-58 (207)
30 PF13519 VWA_2: von Willebrand 94.6 0.11 2.5E-06 40.1 6.2 46 154-201 2-51 (172)
31 cd01474 vWA_ATR ATR (Anthrax T 94.5 0.12 2.5E-06 41.9 6.3 49 151-201 4-52 (185)
32 cd00198 vWFA Von Willebrand fa 94.5 0.11 2.4E-06 39.1 5.8 47 153-201 2-51 (161)
33 smart00327 VWA von Willebrand 94.5 0.13 2.9E-06 40.0 6.3 49 152-201 2-52 (177)
34 PRK13685 hypothetical protein; 94.1 0.17 3.7E-06 45.1 6.9 51 151-202 88-142 (326)
35 cd01476 VWA_integrin_invertebr 94.1 0.23 5E-06 38.9 6.9 42 154-198 3-47 (163)
36 TIGR03436 acidobact_VWFA VWFA- 93.9 0.21 4.6E-06 43.5 7.1 50 150-202 52-102 (296)
37 cd01450 vWFA_subfamily_ECM Von 93.7 0.17 3.7E-06 38.8 5.5 47 154-201 3-51 (161)
38 cd01473 vWA_CTRP CTRP for CS 93.7 0.19 4.2E-06 41.4 6.0 48 154-201 3-52 (192)
39 cd01467 vWA_BatA_type VWA BatA 92.9 0.3 6.5E-06 38.9 5.9 46 153-201 4-55 (180)
40 cd01451 vWA_Magnesium_chelatas 91.6 0.42 9.2E-06 38.4 5.3 46 153-199 2-48 (178)
41 cd01454 vWA_norD_type norD typ 91.3 0.29 6.3E-06 39.1 4.1 46 153-199 2-48 (174)
42 cd01470 vWA_complement_factors 90.4 0.96 2.1E-05 36.9 6.4 14 189-202 39-52 (198)
43 cd01458 vWA_ku Ku70/Ku80 N-ter 90.3 0.83 1.8E-05 38.1 6.1 45 153-199 3-57 (218)
44 PTZ00441 sporozoite surface pr 89.3 0.84 1.8E-05 44.0 5.9 51 151-201 42-94 (576)
45 TIGR00868 hCaCC calcium-activa 88.9 1.2 2.7E-05 45.0 6.9 49 152-201 305-354 (863)
46 PF09967 DUF2201: VWA-like dom 88.5 1.1 2.4E-05 34.5 5.2 43 155-201 2-44 (126)
47 cd01462 VWA_YIEM_type VWA YIEM 88.1 0.68 1.5E-05 35.9 3.8 47 154-202 3-50 (152)
48 PRK13406 bchD magnesium chelat 87.9 1.2 2.5E-05 43.3 5.9 48 150-199 400-448 (584)
49 PRK00398 rpoP DNA-directed RNA 87.6 0.46 9.9E-06 30.2 2.1 28 88-119 3-30 (46)
50 cd01453 vWA_transcription_fact 86.3 2.1 4.7E-05 34.8 5.9 47 153-200 5-59 (183)
51 TIGR02031 BchD-ChlD magnesium 86.2 1.5 3.3E-05 42.5 5.7 48 150-199 406-454 (589)
52 PF13719 zinc_ribbon_5: zinc-r 84.7 0.59 1.3E-05 28.5 1.4 31 88-118 2-33 (37)
53 cd01452 VWA_26S_proteasome_sub 84.5 4 8.7E-05 33.8 6.7 47 153-201 5-60 (187)
54 PF02905 EBV-NA1: Epstein Barr 82.5 2.9 6.2E-05 32.7 4.7 33 170-202 112-146 (146)
55 PF09082 DUF1922: Domain of un 81.4 1 2.2E-05 31.4 1.7 25 88-118 3-27 (68)
56 TIGR02442 Cob-chelat-sub cobal 81.1 2.9 6.3E-05 40.8 5.4 48 150-198 464-512 (633)
57 COG1240 ChlD Mg-chelatase subu 80.9 2.5 5.5E-05 36.9 4.3 48 150-197 77-124 (261)
58 COG2888 Predicted Zn-ribbon RN 80.8 0.6 1.3E-05 31.7 0.4 27 82-118 32-58 (61)
59 cd01460 vWA_midasin VWA_Midasi 79.2 4 8.7E-05 35.7 5.1 55 150-207 59-118 (266)
60 cd00350 rubredoxin_like Rubred 78.1 1.4 3.1E-05 26.0 1.4 24 90-119 3-26 (33)
61 smart00661 RPOL9 RNA polymeras 77.9 1.2 2.7E-05 28.5 1.2 27 90-118 2-28 (52)
62 PF09723 Zn-ribbon_8: Zinc rib 77.8 1.1 2.5E-05 27.9 0.9 29 89-118 6-34 (42)
63 PF08271 TF_Zn_Ribbon: TFIIB z 75.9 2.6 5.6E-05 26.3 2.2 26 90-118 2-27 (43)
64 PRK14890 putative Zn-ribbon RN 75.8 1.2 2.5E-05 30.2 0.6 26 84-119 32-57 (59)
65 PF02318 FYVE_2: FYVE-type zin 75.3 2.1 4.5E-05 32.7 2.0 31 88-118 71-102 (118)
66 cd01457 vWA_ORF176_type VWA OR 72.9 7.1 0.00015 31.8 4.8 46 153-200 4-58 (199)
67 cd00730 rubredoxin Rubredoxin; 71.7 1.6 3.5E-05 28.5 0.5 30 90-119 3-43 (50)
68 TIGR00578 ku70 ATP-dependent D 70.8 11 0.00023 36.6 6.1 47 153-199 12-67 (584)
69 smart00834 CxxC_CXXC_SSSS Puta 70.0 2.3 5E-05 25.7 0.9 29 89-118 6-34 (41)
70 PRK12380 hydrogenase nickel in 69.4 2.9 6.3E-05 31.8 1.5 28 87-120 69-96 (113)
71 PF13717 zinc_ribbon_4: zinc-r 69.1 2.8 6.1E-05 25.3 1.2 31 88-118 2-33 (36)
72 TIGR01053 LSD1 zinc finger dom 68.4 4.2 9.1E-05 23.9 1.7 26 89-118 2-27 (31)
73 PRK12860 transcriptional activ 67.8 2.6 5.6E-05 35.2 1.0 31 85-118 131-162 (189)
74 PF08792 A2L_zn_ribbon: A2L zi 67.7 7.9 0.00017 23.0 2.9 28 87-118 2-29 (33)
75 COG1996 RPC10 DNA-directed RNA 67.3 3 6.6E-05 27.2 1.1 27 88-118 6-32 (49)
76 TIGR02605 CxxC_CxxC_SSSS putat 67.2 2.7 5.8E-05 27.0 0.8 30 89-119 6-35 (52)
77 PF10058 DUF2296: Predicted in 67.2 4.5 9.7E-05 26.8 1.9 33 86-118 20-52 (54)
78 TIGR00100 hypA hydrogenase nic 66.5 3.7 8E-05 31.3 1.6 29 87-121 69-97 (115)
79 PRK03681 hypA hydrogenase nick 66.2 3.7 8E-05 31.2 1.6 28 87-120 69-97 (114)
80 PF11781 RRN7: RNA polymerase 65.8 5.7 0.00012 24.1 2.0 26 88-118 8-33 (36)
81 PF14803 Nudix_N_2: Nudix N-te 64.6 2 4.4E-05 25.8 -0.1 28 91-118 3-30 (34)
82 PRK12722 transcriptional activ 64.0 3 6.5E-05 34.7 0.7 30 86-118 132-162 (187)
83 PRK03954 ribonuclease P protei 64.0 5.6 0.00012 30.8 2.2 31 89-119 65-102 (121)
84 KOG2353 L-type voltage-depende 63.9 14 0.0003 38.6 5.6 73 127-201 198-273 (1104)
85 PF13240 zinc_ribbon_2: zinc-r 63.3 2.7 5.9E-05 22.9 0.2 21 90-118 1-21 (23)
86 PF07282 OrfB_Zn_ribbon: Putat 62.9 4.9 0.00011 27.2 1.6 27 88-118 28-54 (69)
87 smart00401 ZnF_GATA zinc finge 62.9 4 8.7E-05 26.7 1.0 31 88-118 3-33 (52)
88 PF07754 DUF1610: Domain of un 62.2 5.9 0.00013 22.0 1.4 24 91-118 1-24 (24)
89 KOG3799 Rab3 effector RIM1 and 60.5 4.9 0.00011 31.9 1.3 28 87-118 88-115 (169)
90 COG1096 Predicted RNA-binding 60.1 6.9 0.00015 32.6 2.2 27 88-120 149-175 (188)
91 TIGR02098 MJ0042_CXXC MJ0042 f 59.3 5.7 0.00012 23.8 1.2 30 89-118 3-33 (38)
92 PF12760 Zn_Tnp_IS1595: Transp 59.2 10 0.00022 23.9 2.4 27 89-118 19-45 (46)
93 PF00301 Rubredoxin: Rubredoxi 58.8 2.3 5E-05 27.4 -0.7 10 109-118 33-42 (47)
94 PF03604 DNA_RNApol_7kD: DNA d 58.2 6.9 0.00015 23.2 1.4 13 85-97 14-26 (32)
95 smart00659 RPOLCX RNA polymera 57.2 8.9 0.00019 24.3 1.9 25 89-118 3-27 (44)
96 COG2051 RPS27A Ribosomal prote 56.6 13 0.00028 25.8 2.7 28 88-118 19-46 (67)
97 PRK00432 30S ribosomal protein 56.2 6.1 0.00013 25.7 1.0 24 89-118 21-45 (50)
98 PF13408 Zn_ribbon_recom: Reco 54.2 8.1 0.00018 24.8 1.4 32 86-118 3-34 (58)
99 smart00132 LIM Zinc-binding do 53.4 11 0.00024 21.7 1.8 29 90-118 1-35 (39)
100 PF05762 VWA_CoxE: VWA domain 52.9 18 0.00039 30.4 3.6 47 149-201 54-101 (222)
101 PRK00564 hypA hydrogenase nick 52.2 5.8 0.00012 30.3 0.5 29 86-120 69-98 (117)
102 TIGR01384 TFS_arch transcripti 52.1 8.9 0.00019 28.2 1.5 24 90-119 2-25 (104)
103 PF06943 zf-LSD1: LSD1 zinc fi 51.2 12 0.00026 20.9 1.6 11 107-117 13-23 (25)
104 PF08274 PhnA_Zn_Ribbon: PhnA 50.0 9 0.00019 22.4 1.0 26 88-118 2-27 (30)
105 PF01927 Mut7-C: Mut7-C RNAse 49.5 10 0.00022 29.9 1.6 31 88-118 91-132 (147)
106 PF00320 GATA: GATA zinc finge 48.8 5.2 0.00011 24.1 -0.2 28 91-118 1-28 (36)
107 PF00092 VWA: von Willebrand f 48.7 36 0.00077 26.2 4.6 23 183-206 33-56 (178)
108 cd02342 ZZ_UBA_plant Zinc fing 48.7 11 0.00024 23.9 1.3 23 89-118 1-23 (43)
109 TIGR00311 aIF-2beta translatio 47.4 20 0.00044 28.1 2.9 29 88-119 97-127 (133)
110 PF06827 zf-FPG_IleRS: Zinc fi 47.0 11 0.00024 21.4 1.0 26 90-117 3-28 (30)
111 PRK03824 hypA hydrogenase nick 46.5 12 0.00026 29.3 1.5 34 87-120 69-117 (135)
112 PF13894 zf-C2H2_4: C2H2-type 46.2 9.7 0.00021 19.4 0.7 8 111-118 1-8 (24)
113 PF01155 HypA: Hydrogenase exp 44.6 6 0.00013 29.9 -0.5 28 87-120 69-96 (113)
114 PF10571 UPF0547: Uncharacteri 44.5 8.8 0.00019 21.6 0.3 21 90-118 2-22 (26)
115 COG0675 Transposase and inacti 44.1 12 0.00027 32.1 1.4 23 87-118 308-330 (364)
116 COG1592 Rubrerythrin [Energy p 43.8 12 0.00025 30.6 1.1 13 107-119 131-143 (166)
117 PHA00626 hypothetical protein 43.8 22 0.00048 23.9 2.2 11 108-118 21-31 (59)
118 PF09297 zf-NADH-PPase: NADH p 42.9 25 0.00054 20.3 2.1 25 90-118 5-29 (32)
119 PF02891 zf-MIZ: MIZ/SP-RING z 42.8 7.5 0.00016 25.1 -0.2 31 88-118 15-49 (50)
120 PF13831 PHD_2: PHD-finger; PD 42.5 3.7 8E-05 24.8 -1.5 32 86-117 2-36 (36)
121 smart00778 Prim_Zn_Ribbon Zinc 42.5 21 0.00044 21.8 1.8 27 90-118 5-33 (37)
122 PRK00762 hypA hydrogenase nick 41.9 12 0.00025 28.9 0.8 33 87-120 69-102 (124)
123 PF05280 FlhC: Flagellar trans 41.5 8.8 0.00019 31.5 0.0 31 85-118 131-162 (175)
124 PF15288 zf-CCHC_6: Zinc knuck 41.3 9.9 0.00021 23.7 0.2 9 89-97 2-10 (40)
125 cd00729 rubredoxin_SM Rubredox 41.3 14 0.0003 21.9 0.9 9 110-118 2-10 (34)
126 COG1545 Predicted nucleic-acid 41.0 45 0.00098 26.2 4.0 64 87-161 28-93 (140)
127 PRK00420 hypothetical protein; 40.9 19 0.00042 27.5 1.8 25 89-118 24-48 (112)
128 PRK10997 yieM hypothetical pro 40.3 45 0.00098 31.8 4.5 49 152-203 324-374 (487)
129 PRK14810 formamidopyrimidine-D 40.3 24 0.00052 30.8 2.6 28 89-118 245-272 (272)
130 COG1645 Uncharacterized Zn-fin 40.1 20 0.00043 28.2 1.8 24 89-118 29-52 (131)
131 COG3357 Predicted transcriptio 39.9 10 0.00022 28.0 0.1 28 87-118 57-84 (97)
132 COG1198 PriA Primosomal protei 38.3 1.3E+02 0.0028 30.3 7.5 105 87-201 443-566 (730)
133 PF14581 SseB_C: SseB protein 37.9 1.2E+02 0.0026 22.2 5.7 44 149-198 46-90 (108)
134 PF08879 WRC: WRC; InterPro: 37.5 15 0.00032 23.6 0.6 10 106-115 10-19 (46)
135 PF05117 DUF695: Family of unk 37.4 1.1E+02 0.0024 23.3 5.7 41 166-207 57-97 (136)
136 PRK00415 rps27e 30S ribosomal 36.7 44 0.00095 22.6 2.8 28 88-118 11-38 (59)
137 PF04032 Rpr2: RNAse P Rpr2/Rp 36.2 16 0.00034 25.6 0.6 31 88-118 46-85 (85)
138 TIGR00686 phnA alkylphosphonat 35.2 31 0.00068 26.2 2.1 27 88-119 2-28 (109)
139 COG1571 Predicted DNA-binding 35.2 20 0.00044 33.5 1.3 74 57-135 314-393 (421)
140 PRK12286 rpmF 50S ribosomal pr 34.8 28 0.00062 23.2 1.7 25 86-119 25-49 (57)
141 PRK12496 hypothetical protein; 34.6 17 0.00037 29.4 0.7 25 89-119 128-152 (164)
142 cd02344 ZZ_HERC2 Zinc finger, 33.9 26 0.00057 22.3 1.3 23 89-118 1-23 (45)
143 PRK08270 anaerobic ribonucleos 33.2 20 0.00044 35.4 1.0 25 86-119 624-648 (656)
144 PF12874 zf-met: Zinc-finger o 32.7 22 0.00048 18.7 0.8 8 111-118 1-8 (25)
145 PF06007 PhnJ: Phosphonate met 32.7 24 0.00052 30.7 1.3 26 89-114 236-264 (277)
146 PF10263 SprT-like: SprT-like 32.0 26 0.00056 27.3 1.3 31 86-118 121-151 (157)
147 PF06677 Auto_anti-p27: Sjogre 31.8 41 0.00089 21.0 1.9 24 89-117 18-41 (41)
148 PF00130 C1_1: Phorbol esters/ 31.5 33 0.00071 21.7 1.5 28 86-118 9-36 (53)
149 cd00202 ZnF_GATA Zinc finger D 31.4 8.7 0.00019 25.3 -1.3 29 90-118 1-29 (54)
150 PF02150 RNA_POL_M_15KD: RNA p 31.4 56 0.0012 19.4 2.4 26 90-118 3-28 (35)
151 PF09943 DUF2175: Uncharacteri 31.2 27 0.00058 26.2 1.2 10 109-118 1-10 (101)
152 PRK13130 H/ACA RNA-protein com 31.2 29 0.00062 23.2 1.2 23 86-118 3-25 (56)
153 PF12773 DZR: Double zinc ribb 30.5 17 0.00038 22.8 0.1 29 86-119 10-38 (50)
154 COG1998 RPS31 Ribosomal protei 30.5 28 0.00061 22.8 1.1 26 89-118 20-45 (51)
155 PRK01103 formamidopyrimidine/5 30.2 45 0.00098 29.0 2.6 26 91-118 248-273 (274)
156 COG0266 Nei Formamidopyrimidin 30.2 34 0.00074 30.1 1.9 28 89-118 246-273 (273)
157 cd02338 ZZ_PCMF_like Zinc fing 29.7 35 0.00075 21.9 1.4 23 89-118 1-23 (49)
158 KOG3886 GTP-binding protein [S 29.6 1.4E+02 0.003 26.3 5.4 42 152-195 83-124 (295)
159 COG2023 RPR2 RNase P subunit R 28.7 42 0.00091 25.4 1.9 30 89-118 57-90 (105)
160 TIGR01031 rpmF_bact ribosomal 28.6 40 0.00086 22.3 1.6 24 86-118 24-47 (55)
161 COG0275 Predicted S-adenosylme 28.5 89 0.0019 28.1 4.2 29 169-198 219-247 (314)
162 PF06061 Baculo_ME53: Baculovi 28.4 20 0.00044 32.4 0.2 87 109-203 91-189 (327)
163 PF13453 zf-TFIIB: Transcripti 28.0 41 0.00089 20.5 1.5 10 88-97 19-28 (41)
164 COG1773 Rubredoxin [Energy pro 27.8 34 0.00074 22.8 1.1 11 108-118 34-44 (55)
165 TIGR00006 S-adenosyl-methyltra 27.5 86 0.0019 28.0 4.0 31 167-198 213-243 (305)
166 PRK07218 replication factor A; 27.5 30 0.00065 32.4 1.1 23 86-118 295-317 (423)
167 PRK06393 rpoE DNA-directed RNA 27.5 23 0.00051 24.4 0.3 21 89-119 6-26 (64)
168 PF04216 FdhE: Protein involve 26.8 45 0.00098 29.2 2.1 30 87-118 171-205 (290)
169 PRK14892 putative transcriptio 26.8 48 0.001 24.7 1.9 33 86-119 19-51 (99)
170 smart00400 ZnF_CHCC zinc finge 26.6 88 0.0019 20.1 3.0 22 100-121 13-34 (55)
171 PRK12336 translation initiatio 26.5 68 0.0015 26.8 3.0 29 88-119 98-128 (201)
172 cd02340 ZZ_NBR1_like Zinc fing 26.4 43 0.00093 20.9 1.3 22 89-118 1-22 (43)
173 COG2956 Predicted N-acetylgluc 26.3 30 0.00064 31.6 0.8 25 86-118 352-376 (389)
174 PF14353 CpXC: CpXC protein 25.8 62 0.0013 24.5 2.5 11 109-119 37-47 (128)
175 PRK13945 formamidopyrimidine-D 25.8 55 0.0012 28.7 2.4 27 90-118 256-282 (282)
176 PRK00050 16S rRNA m(4)C1402 me 25.4 99 0.0021 27.5 4.0 31 167-198 209-239 (296)
177 PF05191 ADK_lid: Adenylate ki 25.4 24 0.00052 21.3 0.1 26 91-118 4-29 (36)
178 PF13465 zf-H2C2_2: Zinc-finge 25.0 46 0.00099 18.2 1.2 12 107-118 11-22 (26)
179 PF08273 Prim_Zn_Ribbon: Zinc- 24.9 35 0.00075 21.2 0.7 26 91-117 6-33 (40)
180 PRK10445 endonuclease VIII; Pr 24.6 64 0.0014 28.0 2.6 26 90-117 237-262 (263)
181 PRK08351 DNA-directed RNA poly 24.2 32 0.00069 23.4 0.5 21 90-120 5-25 (61)
182 PRK07562 ribonucleotide-diphos 24.1 59 0.0013 34.5 2.5 26 88-118 1190-1215(1220)
183 PRK00423 tfb transcription ini 23.7 75 0.0016 28.2 2.9 30 86-118 9-38 (310)
184 COG2093 DNA-directed RNA polym 23.6 29 0.00062 23.8 0.2 23 90-120 6-28 (64)
185 TIGR00595 priA primosomal prot 23.4 33 0.00072 32.6 0.6 11 88-98 222-232 (505)
186 PF09779 Ima1_N: Ima1 N-termin 23.4 39 0.00084 26.3 0.9 29 89-119 1-29 (131)
187 PRK04351 hypothetical protein; 23.3 59 0.0013 25.9 1.9 31 86-118 110-140 (149)
188 PHA02942 putative transposase; 23.2 46 0.001 30.5 1.5 27 87-118 324-350 (383)
189 COG1644 RPB10 DNA-directed RNA 23.1 28 0.00061 23.8 0.1 13 87-99 3-15 (63)
190 PF01873 eIF-5_eIF-2B: Domain 23.0 68 0.0015 24.8 2.2 28 88-118 93-122 (125)
191 PRK14811 formamidopyrimidine-D 22.7 69 0.0015 27.9 2.4 27 90-118 237-263 (269)
192 PRK04016 DNA-directed RNA poly 22.6 34 0.00074 23.4 0.4 13 87-99 3-15 (62)
193 PRK10220 hypothetical protein; 22.6 69 0.0015 24.4 2.1 27 88-119 3-29 (111)
194 cd04931 ACT_PAH ACT domain of 22.5 1.3E+02 0.0028 21.8 3.4 32 150-183 53-84 (90)
195 PF00362 Integrin_beta: Integr 22.0 1.4E+02 0.0031 27.9 4.5 48 150-199 101-150 (426)
196 PRK11827 hypothetical protein; 22.0 69 0.0015 21.7 1.8 28 87-118 7-34 (60)
197 PF11130 TraC_F_IV: F pilus as 21.9 1.6E+02 0.0035 24.4 4.5 41 155-199 29-70 (235)
198 PF11524 SeleniumBinding: Sele 21.7 43 0.00093 23.9 0.7 37 170-207 33-69 (81)
199 smart00290 ZnF_UBP Ubiquitin C 21.7 62 0.0013 20.1 1.5 20 90-119 1-20 (50)
200 TIGR00354 polC DNA polymerase, 21.6 42 0.0009 34.7 0.9 23 86-118 623-645 (1095)
201 PF02591 DUF164: Putative zinc 21.5 45 0.00097 21.7 0.8 13 86-98 44-56 (56)
202 PF05741 zf-nanos: Nanos RNA b 21.5 30 0.00064 23.1 -0.1 14 109-122 32-45 (55)
203 PF04502 DUF572: Family of unk 21.4 97 0.0021 27.7 3.2 41 78-118 30-85 (324)
204 PRK05452 anaerobic nitric oxid 21.4 43 0.00093 31.6 0.9 34 86-119 423-467 (479)
205 KOG1074 Transcriptional repres 21.4 34 0.00074 34.7 0.2 34 85-118 350-389 (958)
206 PF00096 zf-C2H2: Zinc finger, 21.2 40 0.00086 17.3 0.4 8 111-118 1-8 (23)
207 KOG3768 DEAD box RNA helicase 21.2 1.9E+02 0.004 28.8 5.0 47 152-198 2-57 (888)
208 PRK12366 replication factor A; 21.1 64 0.0014 31.7 2.1 27 87-119 531-557 (637)
209 COG2260 Predicted Zn-ribbon RN 21.1 46 0.001 22.5 0.8 22 87-118 4-25 (59)
210 PF06524 NOA36: NOA36 protein; 21.0 56 0.0012 28.8 1.4 15 104-118 136-150 (314)
211 PF14599 zinc_ribbon_6: Zinc-r 21.0 41 0.00089 22.8 0.5 10 88-97 48-57 (61)
212 PLN00032 DNA-directed RNA poly 21.0 41 0.00088 23.6 0.5 13 87-99 3-15 (71)
213 smart00653 eIF2B_5 domain pres 21.0 1.1E+02 0.0023 23.2 2.8 28 88-118 80-109 (110)
214 PF14952 zf-tcix: Putative tre 20.9 42 0.00091 21.4 0.5 12 86-97 9-20 (44)
215 PRK07111 anaerobic ribonucleos 20.9 44 0.00096 33.5 0.9 24 86-118 678-701 (735)
216 COG0846 SIR2 NAD-dependent pro 20.8 54 0.0012 28.4 1.4 18 87-104 145-163 (250)
217 PRK03988 translation initiatio 20.6 1.1E+02 0.0024 24.1 3.0 29 88-119 102-132 (138)
218 smart00187 INB Integrin beta s 20.5 3.5E+02 0.0077 25.4 6.7 48 150-198 98-146 (423)
219 PF01283 Ribosomal_S26e: Ribos 20.5 57 0.0012 25.0 1.3 16 83-98 15-30 (113)
220 PF00025 Arf: ADP-ribosylation 20.3 1.9E+02 0.0042 22.7 4.4 30 150-183 81-110 (175)
221 PF05907 DUF866: Eukaryotic pr 20.2 1E+02 0.0022 24.9 2.7 32 88-119 30-73 (161)
No 1
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=9.2e-55 Score=412.41 Aligned_cols=189 Identities=48% Similarity=0.972 Sum_probs=181.5
Q ss_pred CCCCCCcceeEecCCCCCCCCeeEeeccccCCCHHhhhhcCCceEEEEecCCCCCCCCCCCceeccCCCCceecCCCCeE
Q 028291 18 KPPPPVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGY 97 (211)
Q Consensus 18 ~~pp~~~~~~~~~d~gn~~p~~iR~T~~~~P~t~~~~~~~~iPlg~vv~Pf~~~~~~e~~vP~v~~~~~~p~RC~~C~aY 97 (211)
.+||++||+|++.|||||+|+|||+|+|+||.|.++++.++||||++|+||+.+...|+++|+||+++.+|+||+||+||
T Consensus 268 ~~PPl~TTd~~~~DqGN~sPr~mr~T~Y~iP~T~Dl~~as~iPLalvIqPfa~l~p~E~~~~vVd~g~sgPvRC~RCkaY 347 (1007)
T KOG1984|consen 268 QPPPLVTTDFFIQDQGNCSPRFMRCTMYTIPCTNDLLKASQIPLALVIQPFATLTPNEAPVPVVDLGESGPVRCNRCKAY 347 (1007)
T ss_pred CCCCCcccceEEeccCCCCcchheeecccCCccHhHHHhcCCcceeEecccccCCcccCCCceecCCCCCCcchhhhhhh
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EccceEEEeCCceEEEecCCC--------------CCcccCCCCCCCCCCcceEEEechhhhcc--CCCCcEEEEEEEcc
Q 028291 98 RNPFMEFVDNGKSFVCNFCGL--------------DGRCLDADERPELCRGTVEFAASREFMMR--NVMPPVYFFLIDVS 161 (211)
Q Consensus 98 iNp~~~~~~~g~~w~C~~C~~--------------~~~~~d~~~rpEL~~~tvE~~~p~~y~~r--~~~pp~yvFvIDvS 161 (211)
||||++|+.+|++|+||||+. +|+|.|.+.||||..|+|||+++++|+++ ++.||+|||+||||
T Consensus 348 inPFmqF~~~gr~f~Cn~C~~~n~vp~~yf~~L~~~grr~D~~erpEL~~Gt~dfvatk~Y~~~~k~p~ppafvFmIDVS 427 (1007)
T KOG1984|consen 348 INPFMQFIDGGRKFICNFCGSKNQVPDDYFNHLGPTGRRVDVEERPELCLGTVDFVATKDYCRKTKPPKPPAFVFMIDVS 427 (1007)
T ss_pred cCcceEEecCCceEEecCCCccccCChhhcccCCCcccccccccCchhcccccceeeehhhhhcCCCCCCceEEEEEEee
Confidence 999999999999999999998 36789999999999999999999999987 89999999999999
Q ss_pred hhhHhhcHHHHHHHHHHHHHhcCCCCC--cEEEEEEeCCeEEEeecC
Q 028291 162 TDAVQTGATAAACSAIMQVISDLPINI--FVVGLLKLKIWWMCILYG 206 (211)
Q Consensus 162 ~~a~~~g~l~~v~~sL~~~l~~lp~~~--~~Vg~Itfd~~i~~~~~~ 206 (211)
++|+++|++.+++++|++.|+.++.+. ++|||||||++|+.|.+-
T Consensus 428 y~Ai~~G~~~a~ce~ik~~l~~lp~~~p~~~Vgivtfd~tvhFfnl~ 474 (1007)
T KOG1984|consen 428 YNAISNGAVKAACEAIKSVLEDLPREEPNIRVGIVTFDKTVHFFNLS 474 (1007)
T ss_pred hhhhhcchHHHHHHHHHHHHhhcCccCCceEEEEEEecceeEeeccC
Confidence 999999999999999999999999643 899999999999988764
No 2
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.6e-47 Score=362.13 Aligned_cols=172 Identities=39% Similarity=0.724 Sum_probs=160.7
Q ss_pred CCCCCCCCeeEeeccccCCCHHhhhhcCCceEEEEecCCCCCCCCCCCceeccCCCCceecCCCCeEEccceEEEeCCce
Q 028291 31 DTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKS 110 (211)
Q Consensus 31 d~gn~~p~~iR~T~~~~P~t~~~~~~~~iPlg~vv~Pf~~~~~~e~~vP~v~~~~~~p~RC~~C~aYiNp~~~~~~~g~~ 110 (211)
+..||+|+|+|+|+++||.+.++++|++||||++|+||++.. +..++|++. ...|+||++||+|||||+.|++.|++
T Consensus 164 ~~~nc~p~y~RsTl~~iP~t~sLl~kskLPlglvv~Pf~~~~-d~~~~p~~~--~~~IvRCr~CRtYiNPFV~fid~gr~ 240 (887)
T KOG1985|consen 164 ESSNCSPSYVRSTLSAIPQTQSLLKKSKLPLGLVVHPFAHLD-DIDPLPVIT--STLIVRCRRCRTYINPFVEFIDQGRR 240 (887)
T ss_pred cccCCCHHHHHHHHHhCCccHHHHHhcCCCceEEEeeccccc-ccCCCCccc--CCceeeehhhhhhcCCeEEecCCCce
Confidence 568999999999999999999999999999999999999887 445577665 67899999999999999999999999
Q ss_pred EEEecCCC-------------CCcccCCCCCCCCCCcceEEEechhhhccCCCCcEEEEEEEcchhhHhhcHHHHHHHHH
Q 028291 111 FVCNFCGL-------------DGRCLDADERPELCRGTVEFAASREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAI 177 (211)
Q Consensus 111 w~C~~C~~-------------~~~~~d~~~rpEL~~~tvE~~~p~~y~~r~~~pp~yvFvIDvS~~a~~~g~l~~v~~sL 177 (211)
|+||+|+. ++.+.|..+||||++++|||++|.||+.|+|+|++||||||||..|+|+|++++++++|
T Consensus 241 WrCNlC~~~NdvP~~f~~~~~t~~~~~~~~RpEl~~s~vE~iAP~eYmlR~P~Pavy~FliDVS~~a~ksG~L~~~~~sl 320 (887)
T KOG1985|consen 241 WRCNLCGRVNDVPDDFDWDPLTGAYGDPYSRPELTSSVVEFIAPSEYMLRPPQPAVYVFLIDVSISAIKSGYLETVARSL 320 (887)
T ss_pred eeechhhhhcCCcHHhhcCccccccCCcccCccccceeEEEecCcccccCCCCCceEEEEEEeehHhhhhhHHHHHHHHH
Confidence 99999999 24578899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCC-cEEEEEEeCCeEEEeec
Q 028291 178 MQVISDLPINI-FVVGLLKLKIWWMCILY 205 (211)
Q Consensus 178 ~~~l~~lp~~~-~~Vg~Itfd~~i~~~~~ 205 (211)
++.|+.||.+. ++|||||||++|+.|..
T Consensus 321 L~~LD~lpgd~Rt~igfi~fDs~ihfy~~ 349 (887)
T KOG1985|consen 321 LENLDALPGDPRTRIGFITFDSTIHFYSV 349 (887)
T ss_pred HHhhhcCCCCCcceEEEEEeeceeeEEec
Confidence 99999999666 99999999999998764
No 3
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=100.00 E-value=8.8e-47 Score=355.02 Aligned_cols=186 Identities=35% Similarity=0.693 Sum_probs=172.7
Q ss_pred CCCCCCcceeEecCCCCCCCCeeEeeccccCCCHHhhhhcCCceEEEEecCCCCCCCCCCCceeccCCCCceecCCCCeE
Q 028291 18 KPPPPVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGY 97 (211)
Q Consensus 18 ~~pp~~~~~~~~~d~gn~~p~~iR~T~~~~P~t~~~~~~~~iPlg~vv~Pf~~~~~~e~~vP~v~~~~~~p~RC~~C~aY 97 (211)
..||+ ++.++..|++|++|+|+|+|+|++|.+.+++++++||||+||+||.++.+.+.++|+++ +..|+||++||+|
T Consensus 132 ~~ppl-tt~~~~~e~~n~~p~yvrsT~yaiP~t~dl~~~skiPfgLVI~Pf~~l~~e~~~vpl~~--d~~ivRCrrCrsY 208 (861)
T COG5028 132 IVPPL-TTNFVGSEQSNCSPKYVRSTMYAIPETNDLLKKSKIPFGLVIRPFLELYPEEDPVPLVE--DGSIVRCRRCRSY 208 (861)
T ss_pred CCCCc-ccceeeeccCCCCHHHHHHHHhhCCCchhHHHhcCCCceEEeehhhhcCccCCCCccCC--CCcchhhhhhHhh
Confidence 45677 99999999999999999999999999999999999999999999999988788889877 3458999999999
Q ss_pred EccceEEEeCCceEEEecCCCC--------------CcccCCCCCCCCCCcceEEEechhhhccCCCCcEEEEEEEcchh
Q 028291 98 RNPFMEFVDNGKSFVCNFCGLD--------------GRCLDADERPELCRGTVEFAASREFMMRNVMPPVYFFLIDVSTD 163 (211)
Q Consensus 98 iNp~~~~~~~g~~w~C~~C~~~--------------~~~~d~~~rpEL~~~tvE~~~p~~y~~r~~~pp~yvFvIDvS~~ 163 (211)
||||++|+.+|++|+||+|+.. ..|.|.+.|+||.+++|||++|++|+.|.+.||+|||+||||..
T Consensus 209 iNPfv~fi~~g~kw~CNiC~~kN~vp~~~~~~~~~~~~r~d~~~r~El~~~vvdf~ap~~Y~~~~p~P~~yvFlIDVS~~ 288 (861)
T COG5028 209 INPFVQFIEQGRKWRCNICRSKNDVPEGFDNPSGPNDPRSDRYSRPELKSGVVDFLAPKEYSLRQPPPPVYVFLIDVSFE 288 (861)
T ss_pred cCceEEEecCCcEEEEeeccccccCcccccCcCCCCCccccccccchhhceeeEEecccceeeccCCCCEEEEEEEeehH
Confidence 9999999999999999999982 23566889999999999999999999999999999999999999
Q ss_pred hHhhcHHHHHHHHHHHHHhcCCCCC--cEEEEEEeCCeEEEeecC
Q 028291 164 AVQTGATAAACSAIMQVISDLPINI--FVVGLLKLKIWWMCILYG 206 (211)
Q Consensus 164 a~~~g~l~~v~~sL~~~l~~lp~~~--~~Vg~Itfd~~i~~~~~~ 206 (211)
++++|++.++.++|++.|+.+|+-+ ++|+||.||+.|+.++..
T Consensus 289 a~~~g~~~a~~r~Il~~l~~~~~~dpr~kIaii~fD~sl~ffk~s 333 (861)
T COG5028 289 AIKNGLVKAAIRAILENLDQIPNFDPRTKIAIICFDSSLHFFKLS 333 (861)
T ss_pred hhhcchHHHHHHHHHhhccCCCCCCCcceEEEEEEcceeeEEecC
Confidence 9999999999999999999998865 999999999999988753
No 4
>PLN00162 transport protein sec23; Provisional
Probab=100.00 E-value=4.9e-41 Score=326.48 Aligned_cols=161 Identities=25% Similarity=0.332 Sum_probs=144.9
Q ss_pred CCCCeeEeeccccCCCHHhhhhcCCceEEEEecCCCCCCCCCCCceeccCCCCceecCCCCeEEccceEEEeCCceEEEe
Q 028291 35 CSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKSFVCN 114 (211)
Q Consensus 35 ~~p~~iR~T~~~~P~t~~~~~~~~iPlg~vv~Pf~~~~~~e~~vP~v~~~~~~p~RC~~C~aYiNp~~~~~~~g~~w~C~ 114 (211)
.+-++||+|||+||.++.++++++|||||+|+||++.. ++|+++ ++|+||++|+|||||||+|+.+|++|+||
T Consensus 7 e~~~gvR~s~n~~P~t~~~~~~~~iPlg~v~tPl~~~~----~vp~v~---~~pvRC~~CraylNPf~~~d~~~~~W~C~ 79 (761)
T PLN00162 7 EAIDGVRMSWNVWPSSKIEASKCVIPLAALYTPLKPLP----ELPVLP---YDPLRCRTCRAVLNPYCRVDFQAKIWICP 79 (761)
T ss_pred cccCceEeeeecCCCCHHHHhcCCCCeEEEEecCCcCC----CCCcCC---CCCCccCCCcCEECCceEEecCCCEEEcc
Confidence 35689999999999999999999999999999999864 288887 67999999999999999999999999999
Q ss_pred cCCCCCc----c---cCCCCCCCC--CCcceEEEechhhhccCCCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCC
Q 028291 115 FCGLDGR----C---LDADERPEL--CRGTVEFAASREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLP 185 (211)
Q Consensus 115 ~C~~~~~----~---~d~~~rpEL--~~~tvE~~~p~~y~~r~~~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp 185 (211)
||+..|. + .+.+.+||| +++||||++|+ |..+++.||+|+||||+|..+++ ++.++++|+++|+.||
T Consensus 80 ~C~~~N~~P~~Y~~~~~~~~p~EL~p~~~TvEY~~p~-~~~~~~~pp~fvFvID~s~~~~~---l~~lk~sl~~~L~~LP 155 (761)
T PLN00162 80 FCFQRNHFPPHYSSISETNLPAELFPQYTTVEYTLPP-GSGGAPSPPVFVFVVDTCMIEEE---LGALKSALLQAIALLP 155 (761)
T ss_pred CCCCCCCCchHhcccCccCCChhhcCCceeEEEECCC-CCCCCCCCcEEEEEEecchhHHH---HHHHHHHHHHHHHhCC
Confidence 9999542 2 235678899 89999999998 88899999999999999998876 5668899999999999
Q ss_pred CCCcEEEEEEeCCeEEEeecCC
Q 028291 186 INIFVVGLLKLKIWWMCILYGN 207 (211)
Q Consensus 186 ~~~~~Vg~Itfd~~i~~~~~~~ 207 (211)
++ ++|||||||++|+.+.++.
T Consensus 156 ~~-a~VGlITF~s~V~~~~L~~ 176 (761)
T PLN00162 156 EN-ALVGLITFGTHVHVHELGF 176 (761)
T ss_pred CC-CEEEEEEECCEEEEEEcCC
Confidence 99 7999999999999999874
No 5
>PTZ00395 Sec24-related protein; Provisional
Probab=100.00 E-value=6.7e-38 Score=308.39 Aligned_cols=198 Identities=24% Similarity=0.409 Sum_probs=168.8
Q ss_pred CCceEEeccCCCCcCCCCCCcceeEecCCCCCCCCeeEeeccccCCCHHhhhhcCCceEEEEecCCCCCCCCCCCceecc
Q 028291 4 SSVILYETRQGKSVKPPPPVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDF 83 (211)
Q Consensus 4 ~~~~~~~t~~~~~~~~pp~~~~~~~~~d~gn~~p~~iR~T~~~~P~t~~~~~~~~iPlg~vv~Pf~~~~~~e~~vP~v~~ 83 (211)
....+|+|+++ ..||+.+++|+++|+|||+|+|||+|||.||.+.++++.++||||++|+||+.+.++| +||.++.
T Consensus 622 ~~~~~~~t~k~---~~pp~~~~~~~~~dtgn~dP~~~r~tmY~iP~~~~~~~~~~iP~gi~v~Pfa~~~~~e-~~~~~~~ 697 (1560)
T PTZ00395 622 KNLKVFETCKY---ISPPSYYQPYISIDTGKADPRFLKSTLYQIPLFSETLKLSQIPFGIIVNPFACLNEGE-GIDKIDM 697 (1560)
T ss_pred ccchhhhhccC---CCCCCCCCceEEeecCCCChhhhhhhhhcCcchHHHHHhcCCCceeecchhhhcCCCC-CCcccch
Confidence 44578999965 4589999999999999999999999999999999999999999999999999988765 4898886
Q ss_pred C--------CCCceecCCCCeEEccceEEEeCCceEEEecCCCCCc------------------c-cCCC----CCCCCC
Q 028291 84 G--------ESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGR------------------C-LDAD----ERPELC 132 (211)
Q Consensus 84 ~--------~~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~~~------------------~-~d~~----~rpEL~ 132 (211)
. +.+|+||.+|+||+|+++.|+.. ++++|+||++... + .|.. ..--|.
T Consensus 698 ~~~~~d~~~~~~~~rc~~c~~y~~~~~~~~~~-~~~~c~~c~~~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 776 (1560)
T PTZ00395 698 KDIINDKEENIEILRCPKCLGYLHATILEDIS-SSVQCVFCDTDFLINENVLFDIFQYNEKIGHKESDHNEHGNSLSPLL 776 (1560)
T ss_pred hhcccchhhccceeecchhHhhhcchheeccc-ceEEEEecCCcchhhHHHHHHHHHHhhhhccccccccccccccchhh
Confidence 4 24799999999999999999866 7899999999311 1 1111 112367
Q ss_pred CcceEEEechhhhc------------------------------------------------------------------
Q 028291 133 RGTVEFAASREFMM------------------------------------------------------------------ 146 (211)
Q Consensus 133 ~~tvE~~~p~~y~~------------------------------------------------------------------ 146 (211)
.|+||+++|+-|+.
T Consensus 777 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 856 (1560)
T PTZ00395 777 KGSVDIIIPPIYYHNVNKFKLTYTYLNKNINQTAFMITNKIMSFTKHISNSLVANDSKGGNKATSASAFGDSGDANFLAG 856 (1560)
T ss_pred cCceeEEccchhhccCCccceeeehhhcchhhhhhhhhhhhhhhhhhhcchheecccccccccchhhhcccccccccccc
Confidence 89999999887641
Q ss_pred --------------------------------------------------------------------------------
Q 028291 147 -------------------------------------------------------------------------------- 146 (211)
Q Consensus 147 -------------------------------------------------------------------------------- 146 (211)
T Consensus 857 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 936 (1560)
T PTZ00395 857 GGYTNYGGAGGYNTYDNQSGYNNHDVVNNRGGSGAGNHLYGKDHDVQNFDNVMDNANFTIHDMKNLICEKNGEPDSAKIR 936 (1560)
T ss_pred cccccccccccccccccccccccccccccccccCcCcccccCcccccchhhhccCCceeeecchhhhhcccCCchhhhhh
Confidence
Q ss_pred -----------cCCCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEEEeecC
Q 028291 147 -----------RNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWMCILYG 206 (211)
Q Consensus 147 -----------r~~~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~~~~~~ 206 (211)
+.++||+|+||||||+.||++|++.+++++|+++|+.|+++.++|||||||+.|+.|-+.
T Consensus 937 ~~~~~~~~~~~~~p~PP~YvFLIDVS~~AVkSGLl~tacesIK~sLDsL~dpRTRVGIITFDSsLHFYNLk 1007 (1560)
T PTZ00395 937 RNSFLAKYPQVKNMLPPYFVFVVECSYNAIYNNITYTILEGIRYAVQNVKCPQTKIAIITFNSSIYFYHCK 1007 (1560)
T ss_pred ccchhhccccccCCCCCEEEEEEECCHHHHhhChHHHHHHHHHHHHhcCCCCCcEEEEEEecCcEEEEecC
Confidence 136789999999999999999999999999999999998655999999999999988774
No 6
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.97 E-value=1.4e-31 Score=250.85 Aligned_cols=162 Identities=27% Similarity=0.402 Sum_probs=140.2
Q ss_pred CCCCCCeeEeeccccCCCHHhhhhcCCceEEEEecCCCCCCCCCCCceeccCCCCceecCCCCeEEccceEEEeCCceEE
Q 028291 33 GNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKSFV 112 (211)
Q Consensus 33 gn~~p~~iR~T~~~~P~t~~~~~~~~iPlg~vv~Pf~~~~~~e~~vP~v~~~~~~p~RC~~C~aYiNp~~~~~~~g~~w~ 112 (211)
.+..-++||+|||.||+++....++.+|++++++||.+..+ +|.+. ++|+||++|+||+||||.++.+.+.|.
T Consensus 5 ~~e~~dGvR~twnvwPs~~~~~~~~vvPla~lytPl~e~~~----~~~~~---y~P~~C~~C~AvlNPyc~vd~~a~~W~ 77 (745)
T KOG1986|consen 5 DIEEIDGVRFTWNVWPSTRAEASRTVVPLACLYTPLKERPD----LPPIQ---YDPLRCSKCGAVLNPYCSVDFRAKSWI 77 (745)
T ss_pred ccccCCCcccccccCCCcccccccccccHHHhccccccCCC----CCccC---CCCchhccchhhcCcceeecccCceEe
Confidence 35667899999999999999999999999999999997653 56565 899999999999999999999999999
Q ss_pred EecCCCCC----cc--cCCCCCC-CC--CCcceEEEechhhhccCCCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhc
Q 028291 113 CNFCGLDG----RC--LDADERP-EL--CRGTVEFAASREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISD 183 (211)
Q Consensus 113 C~~C~~~~----~~--~d~~~rp-EL--~~~tvE~~~p~~y~~r~~~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~ 183 (211)
|+||...| .+ +...+.| || ++.+|||.+++. +..||+|+||||++.... .++.++++|+.+|+.
T Consensus 78 CpfC~qrN~~p~~Y~~is~~n~P~el~Pq~stvEy~l~~~----~~~ppvf~fVvDtc~~ee---eL~~LkssL~~~l~l 150 (745)
T KOG1986|consen 78 CPFCNQRNPFPPHYSGISENNLPPELLPQYSTVEYTLSPG----RVSPPVFVFVVDTCMDEE---ELQALKSSLKQSLSL 150 (745)
T ss_pred ccccccCCCCChhhcccCccCCChhhcCCcceeEEecCCC----CCCCceEEEEEeeccChH---HHHHHHHHHHHHHhh
Confidence 99999954 23 2233444 88 789999999854 345999999999998764 378999999999999
Q ss_pred CCCCCcEEEEEEeCCeEEEeecCCcc
Q 028291 184 LPINIFVVGLLKLKIWWMCILYGNEH 209 (211)
Q Consensus 184 lp~~~~~Vg~Itfd~~i~~~~~~~~~ 209 (211)
||++ ++|||||||+.|.++++|-++
T Consensus 151 LP~~-alvGlItfg~~v~v~el~~~~ 175 (745)
T KOG1986|consen 151 LPEN-ALVGLITFGTMVQVHELGFEE 175 (745)
T ss_pred CCCc-ceEEEEEecceEEEEEcCCCc
Confidence 9999 799999999999999998764
No 7
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=99.95 E-value=2.2e-28 Score=225.40 Aligned_cols=160 Identities=25% Similarity=0.414 Sum_probs=137.9
Q ss_pred CCCCCeeEeeccccCCCHHhhhhcCCceEEEEecCCCCCCCCCCCceeccCCCCceecCC-CCeEEccceEEEeCCceEE
Q 028291 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCC-CRGYRNPFMEFVDNGKSFV 112 (211)
Q Consensus 34 n~~p~~iR~T~~~~P~t~~~~~~~~iPlg~vv~Pf~~~~~~e~~vP~v~~~~~~p~RC~~-C~aYiNp~~~~~~~g~~w~ 112 (211)
+.+-++||+|||+||.|+..+.++.+|++++|+||++.+. +++.. ++|+.|.. |+||+||||.++.+++.|+
T Consensus 6 iee~dgir~twnvfpat~~da~~~~iPia~lY~Pl~e~~~----~~v~~---yepv~C~~pC~avlnpyC~id~r~~~W~ 78 (755)
T COG5047 6 IEENDGIRLTWNVFPATRGDATRTVIPIACLYTPLHEDDA----LTVNY---YEPVKCTAPCKAVLNPYCHIDERNQSWI 78 (755)
T ss_pred hccccceEEEEecccCCccccccccccHHHhccccccccc----cCccc---CCCceecccchhhcCcceeeccCCceEe
Confidence 4567899999999999999999999999999999998643 44443 88999999 9999999999999999999
Q ss_pred EecCCCCC----cccC--CCC-CCCC--CCcceEEEechhhhccCCCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhc
Q 028291 113 CNFCGLDG----RCLD--ADE-RPEL--CRGTVEFAASREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISD 183 (211)
Q Consensus 113 C~~C~~~~----~~~d--~~~-rpEL--~~~tvE~~~p~~y~~r~~~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~ 183 (211)
|+||...+ .+.| ..+ -+|| ++.||||++++. ...||+|+||||++.... -+.+++++|+..|..
T Consensus 79 CpfCnqrn~lp~qy~~iS~~~LplellpqssTiey~lskp----~~~ppvf~fvvD~~~D~e---~l~~Lkdslivslsl 151 (755)
T COG5047 79 CPFCNQRNTLPPQYRDISNANLPLELLPQSSTIEYTLSKP----VILPPVFFFVVDACCDEE---ELTALKDSLIVSLSL 151 (755)
T ss_pred cceecCCCCCChhhcCCCcccCCccccCCCceEEEEccCC----ccCCceEEEEEEeecCHH---HHHHHHHHHHHHHhc
Confidence 99999954 3333 233 3488 799999999863 457999999999998554 379999999999999
Q ss_pred CCCCCcEEEEEEeCCeEEEeecCCc
Q 028291 184 LPINIFVVGLLKLKIWWMCILYGNE 208 (211)
Q Consensus 184 lp~~~~~Vg~Itfd~~i~~~~~~~~ 208 (211)
+|++ ++||||||+..|.++++|-+
T Consensus 152 lppe-aLvglItygt~i~v~el~ae 175 (755)
T COG5047 152 LPPE-ALVGLITYGTSIQVHELNAE 175 (755)
T ss_pred CCcc-ceeeEEEecceeEEEecccc
Confidence 9999 79999999999999988754
No 8
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=99.52 E-value=3.6e-15 Score=93.83 Aligned_cols=34 Identities=56% Similarity=1.255 Sum_probs=24.5
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDG 120 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~~ 120 (211)
+|+||++|+||||||++|+.+|++|+|+||++.+
T Consensus 1 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 1 GPVRCRRCRAYLNPFCQFDDGGKTWICNFCGTKN 34 (40)
T ss_dssp -S-B-TTT--BS-TTSEEETTTTEEEETTT--EE
T ss_pred CccccCCCCCEECCcceEcCCCCEEECcCCCCcC
Confidence 4899999999999999999999999999999843
No 9
>PF04811 Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: IPR006896 COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger (IPR006895 from INTERPRO), an alpha/beta trunk domain, an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes the Sec23/24 alpha/beta trunk domain, which is formed from a single, approximately 250-residue segment plugged into the beta-barrel between strands beta-1 and beta-19. The trunk has an alpha/beta fold with a vWA topology, and it forms the dimer interface, primarily involving strand beta-14 on Sec23 and Sec24; in addition, the trunk domain of Sec23 contacts Sar1.; GO: 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EGD_A 2NUP_A 3EG9_A 3EFO_A 3EGX_A 2NUT_A 1PD0_A 1PD1_A 1M2V_B 1PCX_A ....
Probab=99.44 E-value=3.1e-13 Score=115.41 Aligned_cols=59 Identities=29% Similarity=0.443 Sum_probs=51.1
Q ss_pred CCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCC--CCCcEEEEEEeCCeEEEeecCCc
Q 028291 149 VMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLP--INIFVVGLLKLKIWWMCILYGNE 208 (211)
Q Consensus 149 ~~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp--~~~~~Vg~Itfd~~i~~~~~~~~ 208 (211)
|+||+|+||||+|.+|+++|++++++++|+++|+.|| ++ ++|||||||+.|+++.++.+
T Consensus 1 P~pp~y~FvID~s~~av~~g~~~~~~~sl~~~l~~l~~~~~-~~vgiitfd~~V~~y~l~~~ 61 (243)
T PF04811_consen 1 PQPPVYVFVIDVSYEAVQSGLLQSLIESLKSALDSLPGDER-TRVGIITFDSSVHFYNLSSS 61 (243)
T ss_dssp -S--EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTSSTSTT--EEEEEEESSSEEEEETTTT
T ss_pred CCCCEEEEEEECchhhhhccHHHHHHHHHHHHHHhccCCCC-cEEEEEEeCCEEEEEECCCC
Confidence 6899999999999999999999999999999999999 55 89999999999999988763
No 10
>cd01479 Sec24-like Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24
Probab=99.43 E-value=3.9e-13 Score=115.41 Aligned_cols=59 Identities=32% Similarity=0.525 Sum_probs=55.3
Q ss_pred CCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCC-C-cEEEEEEeCCeEEEeecCC
Q 028291 149 VMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPIN-I-FVVGLLKLKIWWMCILYGN 207 (211)
Q Consensus 149 ~~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~-~-~~Vg~Itfd~~i~~~~~~~ 207 (211)
|+||+|+||||+|..++++|++++++++|+++|+.+|++ . ++|||||||+.|+.+.++.
T Consensus 1 p~pp~~~FvIDvs~~a~~~g~~~~~~~si~~~L~~lp~~~~~~~VgiITfd~~v~~y~l~~ 61 (244)
T cd01479 1 PQPAVYVFLIDVSYNAIKSGLLATACEALLSNLDNLPGDDPRTRVGFITFDSTLHFFNLKS 61 (244)
T ss_pred CCCCEEEEEEEccHHHHhhChHHHHHHHHHHHHHhcCCCCCCeEEEEEEECCeEEEEECCC
Confidence 579999999999999999999999999999999999987 3 8999999999999998864
No 11
>cd01468 trunk_domain trunk domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface. Some members of this family possess a partial MIDAS motif that is a characteristic feature of most vWA domain proteins.
Probab=99.41 E-value=6.4e-13 Score=113.45 Aligned_cols=59 Identities=27% Similarity=0.407 Sum_probs=55.3
Q ss_pred CCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCC--CCCcEEEEEEeCCeEEEeecCCc
Q 028291 149 VMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLP--INIFVVGLLKLKIWWMCILYGNE 208 (211)
Q Consensus 149 ~~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp--~~~~~Vg~Itfd~~i~~~~~~~~ 208 (211)
|+||+|+||||+|.+|+++|++++++++|+++|+.|| ++ ++|||||||++|+.+.++..
T Consensus 1 p~pp~~vFvID~s~~ai~~~~l~~~~~sl~~~l~~lp~~~~-~~igiITf~~~V~~~~~~~~ 61 (239)
T cd01468 1 PQPPVFVFVIDVSYEAIKEGLLQALKESLLASLDLLPGDPR-ARVGLITYDSTVHFYNLSSD 61 (239)
T ss_pred CCCCEEEEEEEcchHhccccHHHHHHHHHHHHHHhCCCCCC-cEEEEEEeCCeEEEEECCCC
Confidence 5899999999999999999999999999999999999 66 89999999999999988743
No 12
>cd01478 Sec23-like Sec23-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 23 is very similar to Sec24. The Sec23 and Sec24
Probab=97.81 E-value=3.9e-05 Score=66.97 Aligned_cols=36 Identities=31% Similarity=0.557 Sum_probs=33.6
Q ss_pred CCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCC
Q 028291 149 VMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPIN 187 (211)
Q Consensus 149 ~~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~ 187 (211)
|.||+|+||||+|..+++ +++++++|+++|+.||++
T Consensus 1 p~pp~~vFviDvs~~~~e---l~~l~~sl~~~L~~lP~~ 36 (267)
T cd01478 1 TSPPVFLFVVDTCMDEEE---LDALKESLIMSLSLLPPN 36 (267)
T ss_pred CCCCEEEEEEECccCHHH---HHHHHHHHHHHHHhCCCC
Confidence 578999999999999887 678999999999999999
No 13
>cd01463 vWA_VGCC_like VWA Voltage gated Calcium channel like: Voltage-gated calcium channels are a complex of five proteins: alpha 1, beta 1, gamma, alpha 2 and delta. The alpha 2 and delta subunits result from proteolytic processing of a single gene product and carries at its N-terminus the VWA and cache domains, The alpha 2 delta gene family has orthologues in D. melanogaster and C. elegans but none have been detected in aither A. thaliana or yeast. The exact biochemical function of the VWA domain is not known but the alpha 2 delta complex has been shown to regulate various functional properties of the channel complex.
Probab=96.73 E-value=0.0056 Score=49.98 Aligned_cols=53 Identities=15% Similarity=0.134 Sum_probs=43.3
Q ss_pred CCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEEEe
Q 028291 149 VMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWMCI 203 (211)
Q Consensus 149 ~~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~~~ 203 (211)
..|-..+||||+|.. +...-++.++++++.+++.+++++ +||+|+|+..+...
T Consensus 11 ~~p~~vv~llD~SgS-M~~~~l~~ak~~~~~ll~~l~~~d-~v~lv~F~~~~~~~ 63 (190)
T cd01463 11 TSPKDIVILLDVSGS-MTGQRLHLAKQTVSSILDTLSDND-FFNIITFSNEVNPV 63 (190)
T ss_pred cCCceEEEEEECCCC-CCcHHHHHHHHHHHHHHHhCCCCC-EEEEEEeCCCeeEE
Confidence 456789999999864 333357889999999999999884 99999999998743
No 14
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=96.38 E-value=0.0086 Score=46.92 Aligned_cols=45 Identities=16% Similarity=0.198 Sum_probs=38.3
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEE
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWM 201 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~ 201 (211)
.+||||+|... + |..+.++++|+.+|+.|++++ ++.||.||....
T Consensus 3 vvilvD~S~Sm-~-g~~~~~k~al~~~l~~L~~~d-~fnii~f~~~~~ 47 (155)
T PF13768_consen 3 VVILVDTSGSM-S-GEKELVKDALRAILRSLPPGD-RFNIIAFGSSVR 47 (155)
T ss_pred EEEEEeCCCCC-C-CcHHHHHHHHHHHHHhCCCCC-EEEEEEeCCEee
Confidence 68999998744 3 333899999999999999995 999999999876
No 15
>cd01456 vWA_ywmD_type VWA ywmD type:Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=95.96 E-value=0.019 Score=47.46 Aligned_cols=53 Identities=19% Similarity=0.153 Sum_probs=42.3
Q ss_pred cCCCCcEEEEEEEcchhhHh-----hcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeE
Q 028291 147 RNVMPPVYFFLIDVSTDAVQ-----TGATAAACSAIMQVISDLPINIFVVGLLKLKIWW 200 (211)
Q Consensus 147 r~~~pp~yvFvIDvS~~a~~-----~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i 200 (211)
....+..++||||+|..-.. ..-++.+++++...++.++++ .+||+++|++.+
T Consensus 16 ~~~~~~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~l~~~-~~v~lv~F~~~~ 73 (206)
T cd01456 16 EPQLPPNVAIVLDNSGSMREVDGGGETRLDNAKAALDETANALPDG-TRLGLWTFSGDG 73 (206)
T ss_pred ccCCCCcEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHhCCCC-ceEEEEEecCCC
Confidence 45577889999999864320 235789999999999999888 499999999853
No 16
>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.
Probab=95.95 E-value=0.024 Score=44.85 Aligned_cols=47 Identities=17% Similarity=0.126 Sum_probs=37.3
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCC---CCCcEEEEEEeCCeEEE
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLP---INIFVVGLLKLKIWWMC 202 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp---~~~~~Vg~Itfd~~i~~ 202 (211)
.+||||+|. ++...-++.++++++.++..+. +. .+||+|+|+.....
T Consensus 3 vv~vlD~Sg-Sm~~~~~~~~k~~~~~~~~~l~~~~~~-~~~giv~Fs~~~~~ 52 (164)
T cd01472 3 IVFLVDGSE-SIGLSNFNLVKDFVKRVVERLDIGPDG-VRVGVVQYSDDPRT 52 (164)
T ss_pred EEEEEeCCC-CCCHHHHHHHHHHHHHHHhhcccCCCC-eEEEEEEEcCceeE
Confidence 589999986 4444467889999999988875 33 69999999988773
No 17
>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell. In association with invasion, T. gondii sequentially discharges three sets of secretory organelles beginning with the micronemes, which contain adhesive proteins involved in parasite attachment to a host cell. Deployed as protein complexes, several micronemal proteins possess vertebrate-derived adhesive sequences that function in binding receptors. The VWA domain likely mediates the protein-protein interactions of these with their interacting partners.
Probab=95.91 E-value=0.021 Score=46.17 Aligned_cols=47 Identities=11% Similarity=0.076 Sum_probs=37.3
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCC---CCCcEEEEEEeCCeEE
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLP---INIFVVGLLKLKIWWM 201 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp---~~~~~Vg~Itfd~~i~ 201 (211)
++||||.|..--....++.+++.+...++.+. ++ ++||+|+|+....
T Consensus 3 v~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~-~~vglv~Fs~~~~ 52 (186)
T cd01471 3 LYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDE-INLYLVTFSTNAK 52 (186)
T ss_pred EEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCc-eEEEEEEecCCce
Confidence 68999998754333337889999999998775 34 7999999999877
No 18
>cd01477 vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of mo
Probab=95.90 E-value=0.022 Score=47.28 Aligned_cols=49 Identities=16% Similarity=0.110 Sum_probs=37.7
Q ss_pred CcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCC---------CCcEEEEEEeCCeEE
Q 028291 151 PPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPI---------NIFVVGLLKLKIWWM 201 (211)
Q Consensus 151 pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~---------~~~~Vg~Itfd~~i~ 201 (211)
..-.+||||.|.. +..+-|+.+++.++..+..+.. . ++||+|+|++..+
T Consensus 19 ~~DivfvlD~S~S-m~~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~-~rVGlV~fs~~a~ 76 (193)
T cd01477 19 WLDIVFVVDNSKG-MTQGGLWQVRATISSLFGSSSQIGTDYDDPRS-TRVGLVTYNSNAT 76 (193)
T ss_pred eeeEEEEEeCCCC-cchhhHHHHHHHHHHHHhhccccccccCCCCC-cEEEEEEccCceE
Confidence 4568999999864 3333478899999888776543 3 7999999999876
No 19
>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
Probab=95.88 E-value=0.026 Score=47.36 Aligned_cols=51 Identities=25% Similarity=0.256 Sum_probs=39.0
Q ss_pred CcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCC--cEEEEEEeCCeEEE
Q 028291 151 PPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINI--FVVGLLKLKIWWMC 202 (211)
Q Consensus 151 pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~--~~Vg~Itfd~~i~~ 202 (211)
|.-.+||||.|.. +...-++.+++.++.+++.+.-.. ++||+|+|+.....
T Consensus 2 ~~DlvfllD~S~S-m~~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~~~ 54 (224)
T cd01475 2 PTDLVFLIDSSRS-VRPENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTVKQ 54 (224)
T ss_pred CccEEEEEeCCCC-CCHHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCceeE
Confidence 3458999999864 333347889999999998874321 79999999998873
No 20
>cd01464 vWA_subfamily VWA subfamily: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=95.78 E-value=0.019 Score=46.16 Aligned_cols=48 Identities=13% Similarity=0.169 Sum_probs=36.8
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCC-----cEEEEEEeCCeEEE
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLPINI-----FVVGLLKLKIWWMC 202 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~-----~~Vg~Itfd~~i~~ 202 (211)
.+||||+|. ++...-++.++++++..++.+.++. .+||+|+|++..+.
T Consensus 6 v~~llD~Sg-SM~~~~~~~~k~a~~~~~~~l~~~~~~~~~~~v~ii~F~~~a~~ 58 (176)
T cd01464 6 IYLLLDTSG-SMAGEPIEALNQGLQMLQSELRQDPYALESVEISVITFDSAARV 58 (176)
T ss_pred EEEEEECCC-CCCChHHHHHHHHHHHHHHHHhcChhhccccEEEEEEecCCceE
Confidence 689999986 4444457888898888888875431 58999999998764
No 21
>cd01461 vWA_interalpha_trypsin_inhibitor vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to the extracellular matrix by binding to hyaluronic acid. The heavy chains carry the VWA domain with a conserved MIDAS motif. Although the exact role of the VWA domains remains unknown, it has been speculated to be involved in mediating protein-protein interactions with the components of the extracellular matrix.
Probab=95.78 E-value=0.029 Score=44.12 Aligned_cols=50 Identities=18% Similarity=0.211 Sum_probs=40.3
Q ss_pred CcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEEE
Q 028291 151 PPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWMC 202 (211)
Q Consensus 151 pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~~ 202 (211)
|.-++||+|+|.. +...-++.++++|...+..++.+ .+|++++|++....
T Consensus 2 ~~~v~~vlD~S~S-M~~~~~~~~~~al~~~l~~l~~~-~~~~l~~Fs~~~~~ 51 (171)
T cd01461 2 PKEVVFVIDTSGS-MSGTKIEQTKEALLTALKDLPPG-DYFNIIGFSDTVEE 51 (171)
T ss_pred CceEEEEEECCCC-CCChhHHHHHHHHHHHHHhCCCC-CEEEEEEeCCCcee
Confidence 4568999999864 33334788999999999999888 49999999988663
No 22
>cd01466 vWA_C3HC4_type VWA C3HC4-type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most,
Probab=95.77 E-value=0.022 Score=45.04 Aligned_cols=46 Identities=17% Similarity=0.075 Sum_probs=37.4
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEE
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWM 201 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~ 201 (211)
.+||||.|. ++...-++.+++++..+++.|++. .+||+|+|+...+
T Consensus 3 v~~vlD~S~-SM~~~rl~~ak~a~~~l~~~l~~~-~~~~li~F~~~~~ 48 (155)
T cd01466 3 LVAVLDVSG-SMAGDKLQLVKHALRFVISSLGDA-DRLSIVTFSTSAK 48 (155)
T ss_pred EEEEEECCC-CCCcHHHHHHHHHHHHHHHhCCCc-ceEEEEEecCCcc
Confidence 579999986 444334788999999999999988 4999999998655
No 23
>cd01469 vWA_integrins_alpha_subunit Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration. Integrins consist of an alpha and a beta sub-unit. Each sub-unit has a large extracellular portion, a single transmembrane segment and a short cytoplasmic domain. The N-terminal domains of the alpha and beta subunits associate to form the integrin headpiece, which contains the ligand binding site, whereas the C-terminal segments traverse the plasma membrane and mediate interaction with the cytoskeleton and with signalling proteins.The VWA domains present in the alpha subunits of integrins seem to be a chordate specific radiation of the gene family being found only in vertebrates. They mediate protein-protein interactions.
Probab=95.73 E-value=0.033 Score=45.08 Aligned_cols=47 Identities=17% Similarity=0.171 Sum_probs=37.5
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCC--cEEEEEEeCCeEE
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLPINI--FVVGLLKLKIWWM 201 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~--~~Vg~Itfd~~i~ 201 (211)
.+||||.|..- ...-++.+++.++..++.+.... ++||+|+|+...+
T Consensus 3 i~fvlD~S~S~-~~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~~ 51 (177)
T cd01469 3 IVFVLDGSGSI-YPDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESFR 51 (177)
T ss_pred EEEEEeCCCCC-CHHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCcee
Confidence 68999998653 22347889999999999876532 8999999999876
No 24
>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein. Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092).
Probab=95.68 E-value=0.029 Score=54.02 Aligned_cols=53 Identities=19% Similarity=0.236 Sum_probs=43.6
Q ss_pred CCCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEEE
Q 028291 148 NVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWMC 202 (211)
Q Consensus 148 ~~~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~~ 202 (211)
.+.|..++||||+|. ++..+-++.+++++..+|..|++++ +|+||.|++.+..
T Consensus 268 ~~~p~~vvfvlD~Sg-SM~g~~i~~ak~al~~~l~~L~~~d-~~~ii~F~~~~~~ 320 (596)
T TIGR03788 268 QVLPRELVFVIDTSG-SMAGESIEQAKSALLLALDQLRPGD-RFNIIQFDSDVTL 320 (596)
T ss_pred cCCCceEEEEEECCC-CCCCccHHHHHHHHHHHHHhCCCCC-EEEEEEECCcceE
Confidence 345667999999986 4443457889999999999999985 9999999998874
No 25
>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=95.53 E-value=0.05 Score=43.75 Aligned_cols=47 Identities=23% Similarity=0.245 Sum_probs=38.0
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCC--cEEEEEEeCCeEE
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLPINI--FVVGLLKLKIWWM 201 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~--~~Vg~Itfd~~i~ 201 (211)
.+|+||.|. ++...-++.+++.++.+++.+.-.. ++||+|+|+....
T Consensus 3 ivfllD~S~-Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~ 51 (165)
T cd01481 3 IVFLIDGSD-NVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPR 51 (165)
T ss_pred EEEEEeCCC-CcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCee
Confidence 589999976 4444568999999999999876432 8999999998876
No 26
>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=95.47 E-value=0.041 Score=43.68 Aligned_cols=46 Identities=20% Similarity=0.098 Sum_probs=36.2
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCC---CCCcEEEEEEeCCeEE
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLP---INIFVVGLLKLKIWWM 201 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp---~~~~~Vg~Itfd~~i~ 201 (211)
.+||+|.|..--+. -++.+++.++.+++.+. +. .+||+|+|++...
T Consensus 3 v~~vlD~S~Sm~~~-~~~~~k~~~~~l~~~~~~~~~~-~rvgli~fs~~~~ 51 (164)
T cd01482 3 IVFLVDGSWSIGRS-NFNLVRSFLSSVVEAFEIGPDG-VQVGLVQYSDDPR 51 (164)
T ss_pred EEEEEeCCCCcChh-hHHHHHHHHHHHHhheeeCCCc-eEEEEEEECCCee
Confidence 68999998644333 46889999998888763 34 7999999999876
No 27
>cd01480 vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=95.35 E-value=0.041 Score=44.80 Aligned_cols=47 Identities=15% Similarity=0.113 Sum_probs=35.5
Q ss_pred EEEEEEEcchhhHhhcHHHHHHHHHHHHHhcC---------CCCCcEEEEEEeCCeEE
Q 028291 153 VYFFLIDVSTDAVQTGATAAACSAIMQVISDL---------PINIFVVGLLKLKIWWM 201 (211)
Q Consensus 153 ~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~l---------p~~~~~Vg~Itfd~~i~ 201 (211)
-.+||||.|. ++...-++.+++.++.+++.+ +++ .+||+|+|+....
T Consensus 4 dvv~vlD~S~-Sm~~~~~~~~k~~~~~~~~~l~~~~~~~i~~~~-~rvglv~fs~~~~ 59 (186)
T cd01480 4 DITFVLDSSE-SVGLQNFDITKNFVKRVAERFLKDYYRKDPAGS-WRVGVVQYSDQQE 59 (186)
T ss_pred eEEEEEeCCC-ccchhhHHHHHHHHHHHHHHHhhhhccCCCCCc-eEEEEEEecCCce
Confidence 4789999986 444334677888888888877 334 6999999998866
No 28
>cd01465 vWA_subgroup VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if n
Probab=95.18 E-value=0.052 Score=42.68 Aligned_cols=47 Identities=15% Similarity=0.058 Sum_probs=38.1
Q ss_pred EEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEE
Q 028291 153 VYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWM 201 (211)
Q Consensus 153 ~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~ 201 (211)
.++||+|+|..- ..+-++.+++++..++..++.+ .+||+++|+....
T Consensus 2 ~~~~vlD~S~SM-~~~~~~~~k~a~~~~~~~l~~~-~~v~li~f~~~~~ 48 (170)
T cd01465 2 NLVFVIDRSGSM-DGPKLPLVKSALKLLVDQLRPD-DRLAIVTYDGAAE 48 (170)
T ss_pred cEEEEEECCCCC-CChhHHHHHHHHHHHHHhCCCC-CEEEEEEecCCcc
Confidence 378999998643 3233788999999999999888 4999999998765
No 29
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=95.07 E-value=0.042 Score=45.75 Aligned_cols=48 Identities=13% Similarity=0.123 Sum_probs=38.0
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCC-----cEEEEEEeCCeEEE
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLPINI-----FVVGLLKLKIWWMC 202 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~-----~~Vg~Itfd~~i~~ 202 (211)
.+|++|+|.. +.-.-++++..+|+.+++.|..+. +.++|||||..+..
T Consensus 6 ~~lllDtSgS-M~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~~a~~ 58 (207)
T COG4245 6 CYLLLDTSGS-MIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGPARV 58 (207)
T ss_pred EEEEEecCcc-cccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecCcceE
Confidence 4578999864 444457889999999999887774 78999999987663
No 30
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=94.60 E-value=0.11 Score=40.13 Aligned_cols=46 Identities=22% Similarity=0.234 Sum_probs=35.1
Q ss_pred EEEEEEcchhhHhh----cHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEE
Q 028291 154 YFFLIDVSTDAVQT----GATAAACSAIMQVISDLPINIFVVGLLKLKIWWM 201 (211)
Q Consensus 154 yvFvIDvS~~a~~~----g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~ 201 (211)
.+||||.|..--.. ..++.+++++..+++.+|++ +||+++|+....
T Consensus 2 vv~v~D~SgSM~~~~~~~~~~~~~~~~~~~~~~~~~~~--~v~l~~f~~~~~ 51 (172)
T PF13519_consen 2 VVFVLDNSGSMNGYDGNRTRIDQAKDALNELLANLPGD--RVGLVSFSDSSR 51 (172)
T ss_dssp EEEEEE-SGGGGTTTSSS-HHHHHHHHHHHHHHHHTTS--EEEEEEESTSCE
T ss_pred EEEEEECCcccCCCCCCCcHHHHHHHHHHHHHHHCCCC--EEEEEEeccccc
Confidence 68999999743322 25889999999999998844 999999997644
No 31
>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax. ATR is the cellular receptor for the anthrax protective antigen and facilitates entry of the toxin into cells. The VWA domain in ATR contains the toxin binding site and mediates interaction with protective antigen. The binding is mediated by divalent cations that binds to the MIDAS motif. These proteins are a family of vertebrate ECM receptors expressed by endothelial cells.
Probab=94.53 E-value=0.12 Score=41.95 Aligned_cols=49 Identities=10% Similarity=0.099 Sum_probs=32.4
Q ss_pred CcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEE
Q 028291 151 PPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWM 201 (211)
Q Consensus 151 pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~ 201 (211)
+.-.+|+||.|.. +... ....++.++.+++.+.....+||+|+|++...
T Consensus 4 ~~Dvv~llD~SgS-m~~~-~~~~~~~~~~l~~~~~~~~~rvglv~Fs~~~~ 52 (185)
T cd01474 4 HFDLYFVLDKSGS-VAAN-WIEIYDFVEQLVDRFNSPGLRFSFITFSTRAT 52 (185)
T ss_pred ceeEEEEEeCcCc-hhhh-HHHHHHHHHHHHHHcCCCCcEEEEEEecCCce
Confidence 3458999999864 3332 33445666766665432226999999998766
No 32
>cd00198 vWFA Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.
Probab=94.48 E-value=0.11 Score=39.10 Aligned_cols=47 Identities=26% Similarity=0.205 Sum_probs=38.5
Q ss_pred EEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCC---CCcEEEEEEeCCeEE
Q 028291 153 VYFFLIDVSTDAVQTGATAAACSAIMQVISDLPI---NIFVVGLLKLKIWWM 201 (211)
Q Consensus 153 ~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~---~~~~Vg~Itfd~~i~ 201 (211)
.++|+||.|... ....++.+++.+..++..+.. . .+||++.|+....
T Consensus 2 ~v~~viD~S~Sm-~~~~~~~~~~~~~~~~~~~~~~~~~-~~i~v~~f~~~~~ 51 (161)
T cd00198 2 DIVFLLDVSGSM-GGEKLDKAKEALKALVSSLSASPPG-DRVGLVTFGSNAR 51 (161)
T ss_pred cEEEEEeCCCCc-CcchHHHHHHHHHHHHHhcccCCCC-cEEEEEEecCccc
Confidence 378999998754 446788999999999999887 4 6999999997544
No 33
>smart00327 VWA von Willebrand factor (vWF) type A domain. VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.
Probab=94.48 E-value=0.13 Score=39.96 Aligned_cols=49 Identities=20% Similarity=0.129 Sum_probs=38.5
Q ss_pred cEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCC--CcEEEEEEeCCeEE
Q 028291 152 PVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPIN--IFVVGLLKLKIWWM 201 (211)
Q Consensus 152 p~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~--~~~Vg~Itfd~~i~ 201 (211)
-.++|+||+|..- ....++.+++.+...+..+... ..+||+++|+....
T Consensus 2 ~~v~l~vD~S~SM-~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ii~f~~~~~ 52 (177)
T smart00327 2 LDVVFLLDGSGSM-GPNRFEKAKEFVLKLVEQLDIGPDGDRVGLVTFSDDAT 52 (177)
T ss_pred ccEEEEEeCCCcc-chHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeCCCce
Confidence 3578999998644 3456788999999999988773 27999999998655
No 34
>PRK13685 hypothetical protein; Provisional
Probab=94.07 E-value=0.17 Score=45.13 Aligned_cols=51 Identities=27% Similarity=0.236 Sum_probs=40.2
Q ss_pred CcEEEEEEEcchhhHh----hcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEEE
Q 028291 151 PPVYFFLIDVSTDAVQ----TGATAAACSAIMQVISDLPINIFVVGLLKLKIWWMC 202 (211)
Q Consensus 151 pp~yvFvIDvS~~a~~----~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~~ 202 (211)
+-..+||||+|..-.. ..-++.++++++..++.+++++ +||+|+|+...+.
T Consensus 88 ~~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l~~~d-~vglv~Fa~~a~~ 142 (326)
T PRK13685 88 RAVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELTPGI-NLGLIAFAGTATV 142 (326)
T ss_pred CceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhCCCCC-eEEEEEEcCceee
Confidence 3468999999864221 1357889999999999997774 9999999998763
No 35
>cd01476 VWA_integrin_invertebrates VWA_integrin (invertebrates): Integrins are a family of cell surface receptors that have diverse functions in cell-cell and cell-extracellular matrix interactions. Because of their involvement in many biologically important adhesion processes, integrins are conserved across a wide range of multicellular animals. Integrins from invertebrates have been identified from six phyla. There are no data to date to suggest any immunological functions for the invertebrate integrins. The members of this sub-group have the conserved MIDAS motif that is charateristic of this domain suggesting the involvement of the integrins in the recognition and binding of multi-ligands.
Probab=94.07 E-value=0.23 Score=38.94 Aligned_cols=42 Identities=21% Similarity=0.260 Sum_probs=33.6
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCC---CCcEEEEEEeCC
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLPI---NIFVVGLLKLKI 198 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~---~~~~Vg~Itfd~ 198 (211)
++|++|+|. ++.. -++..++.++.++..+.. . .+||+|+|+.
T Consensus 3 v~~llD~S~-Sm~~-~~~~~~~~~~~~~~~l~~~~~~-~~v~lv~f~~ 47 (163)
T cd01476 3 LLFVLDSSG-SVRG-KFEKYKKYIERIVEGLEIGPTA-TRVALITYSG 47 (163)
T ss_pred EEEEEeCCc-chhh-hHHHHHHHHHHHHHhcCCCCCC-cEEEEEEEcC
Confidence 689999986 4443 367788889999888754 4 6999999999
No 36
>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain. Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196.
Probab=93.92 E-value=0.21 Score=43.48 Aligned_cols=50 Identities=18% Similarity=0.141 Sum_probs=40.2
Q ss_pred CCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhc-CCCCCcEEEEEEeCCeEEE
Q 028291 150 MPPVYFFLIDVSTDAVQTGATAAACSAIMQVISD-LPINIFVVGLLKLKIWWMC 202 (211)
Q Consensus 150 ~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~-lp~~~~~Vg~Itfd~~i~~ 202 (211)
.|...+||||+|..- + +.+..+++++...++. +.++ .+||+|+|+..+..
T Consensus 52 ~p~~vvlvlD~SgSM-~-~~~~~a~~a~~~~l~~~l~~~-d~v~lv~f~~~~~~ 102 (296)
T TIGR03436 52 LPLTVGLVIDTSGSM-R-NDLDRARAAAIRFLKTVLRPN-DRVFVVTFNTRLRL 102 (296)
T ss_pred CCceEEEEEECCCCc-h-HHHHHHHHHHHHHHHhhCCCC-CEEEEEEeCCceeE
Confidence 578899999998633 3 3467888999999987 7667 49999999998874
No 37
>cd01450 vWFA_subfamily_ECM Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A
Probab=93.70 E-value=0.17 Score=38.84 Aligned_cols=47 Identities=23% Similarity=0.191 Sum_probs=36.0
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCC--CcEEEEEEeCCeEE
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLPIN--IFVVGLLKLKIWWM 201 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~--~~~Vg~Itfd~~i~ 201 (211)
.+|++|+|. ++....++.+++.+...+..+... ..+||+++|+....
T Consensus 3 i~~llD~S~-Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~ 51 (161)
T cd01450 3 IVFLLDGSE-SVGPENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVR 51 (161)
T ss_pred EEEEEeCCC-CcCHHHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCce
Confidence 579999986 444446788889999998887652 16999999997654
No 38
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=93.67 E-value=0.19 Score=41.39 Aligned_cols=48 Identities=17% Similarity=0.128 Sum_probs=35.3
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCC--cEEEEEEeCCeEE
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLPINI--FVVGLLKLKIWWM 201 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~--~~Vg~Itfd~~i~ 201 (211)
.+|+||.|..--+..+-..+++.++.+++.+.-.. ++||+|+|++..+
T Consensus 3 i~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~ 52 (192)
T cd01473 3 LTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNR 52 (192)
T ss_pred EEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCce
Confidence 58999998744333333357888888888765432 8999999999876
No 39
>cd01467 vWA_BatA_type VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=92.90 E-value=0.3 Score=38.85 Aligned_cols=46 Identities=17% Similarity=0.135 Sum_probs=33.3
Q ss_pred EEEEEEEcchhhHhh------cHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEE
Q 028291 153 VYFFLIDVSTDAVQT------GATAAACSAIMQVISDLPINIFVVGLLKLKIWWM 201 (211)
Q Consensus 153 ~yvFvIDvS~~a~~~------g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~ 201 (211)
-++|+||+|.. +.. .-++.++..+...+...+++ +||+|+|+....
T Consensus 4 ~vv~vlD~S~S-M~~~~~~~~~r~~~a~~~~~~~~~~~~~~--~v~lv~f~~~~~ 55 (180)
T cd01467 4 DIMIALDVSGS-MLAQDFVKPSRLEAAKEVLSDFIDRREND--RIGLVVFAGAAF 55 (180)
T ss_pred eEEEEEECCcc-cccccCCCCCHHHHHHHHHHHHHHhCCCC--eEEEEEEcCCee
Confidence 47999999863 321 13567777777777766543 999999998776
No 40
>cd01451 vWA_Magnesium_chelatase Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto). In chlorophyll biosynthesis, insertion of Mg2+ into protoporphyrin IX is catalysed by magnesium chelatase in an ATP-dependent reaction. Magnesium chelatase is a three sub-unit (BchI, BchD and BchH) enzyme with a novel arrangement of domains: the C-terminal helical domain is located behind the nucleotide binding site. The BchD domain contains a AAA domain at its N-terminus and a VWA domain at its C-terminus. The VWA domain has been speculated to be involved in mediating protein-protein interactions.
Probab=91.59 E-value=0.42 Score=38.43 Aligned_cols=46 Identities=22% Similarity=0.272 Sum_probs=32.8
Q ss_pred EEEEEEEcchhhHhhcHHHHHHHHHHHHHhc-CCCCCcEEEEEEeCCe
Q 028291 153 VYFFLIDVSTDAVQTGATAAACSAIMQVISD-LPINIFVVGLLKLKIW 199 (211)
Q Consensus 153 ~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~-lp~~~~~Vg~Itfd~~ 199 (211)
..+|+||+|..--...-++.+++++...+.. +..+ .+||+|+|+..
T Consensus 2 ~v~lvlD~SgSM~~~~rl~~ak~a~~~~~~~~~~~~-d~v~lv~F~~~ 48 (178)
T cd01451 2 LVIFVVDASGSMAARHRMAAAKGAVLSLLRDAYQRR-DKVALIAFRGT 48 (178)
T ss_pred eEEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCC-CEEEEEEECCC
Confidence 3689999986322121478888888888864 4556 49999999853
No 41
>cd01454 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial denitrification has been established as NO3- ------ NO2- ------ NO ------- N2O --------- N2. This reaction generally occurs under oxygen limiting conditions. Genetic and biochemical studies have shown that the first srep of the biochemical pathway is catalyzed by periplasmic nitrate reductases. This family is widely present in proteobacteria and firmicutes. This version of the domain is also present in some archaeal members. The function of the vWA domain in this sub-group is not known. Members of this subgroup have a conserved MIDAS motif.
Probab=91.34 E-value=0.29 Score=39.10 Aligned_cols=46 Identities=15% Similarity=0.096 Sum_probs=34.4
Q ss_pred EEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCC-CCcEEEEEEeCCe
Q 028291 153 VYFFLIDVSTDAVQTGATAAACSAIMQVISDLPI-NIFVVGLLKLKIW 199 (211)
Q Consensus 153 ~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~-~~~~Vg~Itfd~~ 199 (211)
+++|+||+|..-....-++.+++++..+++.+.. + -++|+++|+..
T Consensus 2 ~v~~llD~SgSM~~~~kl~~ak~a~~~l~~~l~~~~-d~~~l~~F~~~ 48 (174)
T cd01454 2 AVTLLLDLSGSMRSDRRIDVAKKAAVLLAEALEACG-VPHAILGFTTD 48 (174)
T ss_pred EEEEEEECCCCCCCCcHHHHHHHHHHHHHHHHHHcC-CcEEEEEecCC
Confidence 5789999987432213578888888887777765 5 49999999876
No 42
>cd01470 vWA_complement_factors Complement factors B and C2 are two critical proteases for complement activation. They both contain three CCP or Sushi domains, a trypsin-type serine protease domain and a single VWA domain with a conserved metal ion dependent adhesion site referred commonly as the MIDAS motif. Orthologues of these molecules are found from echinoderms to chordates. During complement activation, the CCP domains are cleaved off, resulting in the formation of an active protease that cleaves and activates complement C3. Complement C2 is in the classical pathway and complement B is in the alternative pathway. The interaction of C2 with C4 and of factor B with C3b are both dependent on Mg2+ binding sites within the VWA domains and the VWA domain of factor B has been shown to mediate the binding of C3. This is consistent with the common inferred function of VWA domains as magnesium-dependent protein interaction domains.
Probab=90.38 E-value=0.96 Score=36.89 Aligned_cols=14 Identities=0% Similarity=-0.444 Sum_probs=11.8
Q ss_pred cEEEEEEeCCeEEE
Q 028291 189 FVVGLLKLKIWWMC 202 (211)
Q Consensus 189 ~~Vg~Itfd~~i~~ 202 (211)
.+||+|+|++....
T Consensus 39 ~~v~li~Fs~~~~~ 52 (198)
T cd01470 39 PRYEIISYASDPKE 52 (198)
T ss_pred ceEEEEEecCCceE
Confidence 59999999987763
No 43
>cd01458 vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.
Probab=90.33 E-value=0.83 Score=38.05 Aligned_cols=45 Identities=24% Similarity=0.339 Sum_probs=34.4
Q ss_pred EEEEEEEcchhhHh------hcHHHHHHHHHHHHHhc----CCCCCcEEEEEEeCCe
Q 028291 153 VYFFLIDVSTDAVQ------TGATAAACSAIMQVISD----LPINIFVVGLLKLKIW 199 (211)
Q Consensus 153 ~yvFvIDvS~~a~~------~g~l~~v~~sL~~~l~~----lp~~~~~Vg~Itfd~~ 199 (211)
..+|+||+|..-.+ ..-|+.+++.+...++. .+.+ +||+|.|++.
T Consensus 3 ~ivf~iDvS~SM~~~~~~~~~s~l~~a~~~i~~~~~~ki~~~~~D--~vGlilf~t~ 57 (218)
T cd01458 3 SVVFLVDVSPSMFESKDGEYESPFEEALKCIRQLMKSKIISSPKD--LVGVVFYGTE 57 (218)
T ss_pred EEEEEEeCCHHHcCCCCCCCCChHHHHHHHHHHHHHhceeCCCCC--eEEEEEEccc
Confidence 47999999963321 24588899999999986 4444 9999999986
No 44
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=89.30 E-value=0.84 Score=44.05 Aligned_cols=51 Identities=12% Similarity=0.044 Sum_probs=38.3
Q ss_pred CcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCC--CcEEEEEEeCCeEE
Q 028291 151 PPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPIN--IFVVGLLKLKIWWM 201 (211)
Q Consensus 151 pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~--~~~Vg~Itfd~~i~ 201 (211)
..-.+||||+|..--...+++.++..++.+++.+... .+.||+++|++...
T Consensus 42 ~lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~r 94 (576)
T PTZ00441 42 EVDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNTT 94 (576)
T ss_pred CceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCce
Confidence 4569999999864433455577888888888877432 27899999999876
No 45
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=88.85 E-value=1.2 Score=44.99 Aligned_cols=49 Identities=10% Similarity=0.057 Sum_probs=35.6
Q ss_pred cEEEEEEEcchhhHhhcHHHHHHHHHHHHH-hcCCCCCcEEEEEEeCCeEE
Q 028291 152 PVYFFLIDVSTDAVQTGATAAACSAIMQVI-SDLPINIFVVGLLKLKIWWM 201 (211)
Q Consensus 152 p~yvFvIDvS~~a~~~g~l~~v~~sL~~~l-~~lp~~~~~Vg~Itfd~~i~ 201 (211)
...+||||+|..-....-++.++++++..| +.++++ .+||+|+|++..+
T Consensus 305 r~VVLVLDvSGSM~g~dRL~~lkqAA~~fL~~~l~~~-DrVGLVtFsssA~ 354 (863)
T TIGR00868 305 RIVCLVLDKSGSMTVEDRLKRMNQAAKLFLLQTVEKG-SWVGMVTFDSAAY 354 (863)
T ss_pred ceEEEEEECCccccccCHHHHHHHHHHHHHHHhCCCC-CEEEEEEECCcee
Confidence 568999999974322224677777877765 456777 4999999999865
No 46
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=88.53 E-value=1.1 Score=34.54 Aligned_cols=43 Identities=12% Similarity=0.110 Sum_probs=35.2
Q ss_pred EEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEE
Q 028291 155 FFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWM 201 (211)
Q Consensus 155 vFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~ 201 (211)
+++||+|. ++....++.++..+..+++.. + ..|-+|.||..|+
T Consensus 2 ~vaiDtSG-Sis~~~l~~fl~ev~~i~~~~--~-~~v~vi~~D~~v~ 44 (126)
T PF09967_consen 2 VVAIDTSG-SISDEELRRFLSEVAGILRRF--P-AEVHVIQFDAEVQ 44 (126)
T ss_pred EEEEECCC-CCCHHHHHHHHHHHHHHHHhC--C-CCEEEEEECCEee
Confidence 68999986 555557888899999988888 3 3688999999998
No 47
>cd01462 VWA_YIEM_type VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=88.14 E-value=0.68 Score=35.87 Aligned_cols=47 Identities=13% Similarity=0.038 Sum_probs=31.5
Q ss_pred EEEEEEcchhhHhhcHHHHHHHHHHHHHhcCC-CCCcEEEEEEeCCeEEE
Q 028291 154 YFFLIDVSTDAVQTGATAAACSAIMQVISDLP-INIFVVGLLKLKIWWMC 202 (211)
Q Consensus 154 yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp-~~~~~Vg~Itfd~~i~~ 202 (211)
++|+||+|..- ...-++..+..+..++..+. .+ .+|++|+|+.....
T Consensus 3 v~illD~SgSM-~~~k~~~a~~~~~~l~~~~~~~~-~~v~li~F~~~~~~ 50 (152)
T cd01462 3 VILLVDQSGSM-YGAPEEVAKAVALALLRIALAEN-RDTYLILFDSEFQT 50 (152)
T ss_pred EEEEEECCCCC-CCCHHHHHHHHHHHHHHHHHHcC-CcEEEEEeCCCceE
Confidence 78999998643 32234556666666666554 35 48999999988443
No 48
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=87.86 E-value=1.2 Score=43.30 Aligned_cols=48 Identities=19% Similarity=0.173 Sum_probs=36.6
Q ss_pred CCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhc-CCCCCcEEEEEEeCCe
Q 028291 150 MPPVYFFLIDVSTDAVQTGATAAACSAIMQVISD-LPINIFVVGLLKLKIW 199 (211)
Q Consensus 150 ~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~-lp~~~~~Vg~Itfd~~ 199 (211)
.+-..+||||+|..- ...-+..++.++...|.. +...+ +||+|+|+..
T Consensus 400 ~~~~vvfvvD~SGSM-~~~rl~~aK~a~~~ll~~ay~~rD-~v~lI~F~g~ 448 (584)
T PRK13406 400 SETTTIFVVDASGSA-ALHRLAEAKGAVELLLAEAYVRRD-QVALVAFRGR 448 (584)
T ss_pred CCccEEEEEECCCCC-cHhHHHHHHHHHHHHHHhhcCCCC-EEEEEEECCC
Confidence 457899999999853 334578899999998865 44554 9999999654
No 49
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.63 E-value=0.46 Score=30.15 Aligned_cols=28 Identities=25% Similarity=0.668 Sum_probs=20.2
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
..+|.+|++-+ .++.....+.|+.||..
T Consensus 3 ~y~C~~CG~~~----~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREV----ELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEE----EECCCCCceECCCCCCe
Confidence 46899999963 23334447999999984
No 50
>cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.
Probab=86.32 E-value=2.1 Score=34.85 Aligned_cols=47 Identities=13% Similarity=0.118 Sum_probs=32.7
Q ss_pred EEEEEEEcchhhHh----hcHHHHHHHHHHHHHhcC---CCCCcEEEEEEe-CCeE
Q 028291 153 VYFFLIDVSTDAVQ----TGATAAACSAIMQVISDL---PINIFVVGLLKL-KIWW 200 (211)
Q Consensus 153 ~yvFvIDvS~~a~~----~g~l~~v~~sL~~~l~~l---p~~~~~Vg~Itf-d~~i 200 (211)
..+|+||+|..-.. -.-++.+++.+...++.+ ..+ .+||+|+| +..-
T Consensus 5 ~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~-~~vglv~f~~~~a 59 (183)
T cd01453 5 HLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPI-SQLGIISIKNGRA 59 (183)
T ss_pred EEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCcc-ccEEEEEEcCCcc
Confidence 47899999865221 124788899998888754 222 49999999 5533
No 51
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=86.19 E-value=1.5 Score=42.48 Aligned_cols=48 Identities=15% Similarity=0.180 Sum_probs=36.4
Q ss_pred CCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhc-CCCCCcEEEEEEeCCe
Q 028291 150 MPPVYFFLIDVSTDAVQTGATAAACSAIMQVISD-LPINIFVVGLLKLKIW 199 (211)
Q Consensus 150 ~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~-lp~~~~~Vg~Itfd~~ 199 (211)
..-.++||||.|. ++..+-++.++.++..++.. +...+ +||+|+|+..
T Consensus 406 ~~~~v~fvvD~SG-SM~~~rl~~aK~av~~Ll~~~~~~~D-~v~Li~F~~~ 454 (589)
T TIGR02031 406 SGRLLIFVVDASG-SAAVARMSEAKGAVELLLGEAYVHRD-QVSLIAFRGT 454 (589)
T ss_pred cCceEEEEEECCC-CCChHHHHHHHHHHHHHHHhhccCCC-EEEEEEECCC
Confidence 4456889999997 44444588899999998875 34454 8999999754
No 52
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=84.73 E-value=0.59 Score=28.45 Aligned_cols=31 Identities=23% Similarity=0.561 Sum_probs=20.8
Q ss_pred ceecCCCCeEEc-cceEEEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRN-PFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiN-p~~~~~~~g~~w~C~~C~~ 118 (211)
.++|.+|++-.+ +-.++...|++.+|+-|++
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCc
Confidence 467888887655 3334555677788888875
No 53
>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.
Probab=84.49 E-value=4 Score=33.82 Aligned_cols=47 Identities=21% Similarity=0.107 Sum_probs=33.5
Q ss_pred EEEEEEEcchhhHh----hcHHHHHHHHHHHH----HhcCCCCCcEEEEEEeCC-eEE
Q 028291 153 VYFFLIDVSTDAVQ----TGATAAACSAIMQV----ISDLPINIFVVGLLKLKI-WWM 201 (211)
Q Consensus 153 ~yvFvIDvS~~a~~----~g~l~~v~~sL~~~----l~~lp~~~~~Vg~Itfd~-~i~ 201 (211)
+-+++||+|....+ =.-+++.++.+... ++..|++ +||+|+|.. .-+
T Consensus 5 a~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np~~--~vGlv~fag~~a~ 60 (187)
T cd01452 5 ATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPEN--NVGLMTMAGNSPE 60 (187)
T ss_pred EEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCCCc--cEEEEEecCCceE
Confidence 57899999965332 12367777777766 4667766 899999998 443
No 54
>PF02905 EBV-NA1: Epstein Barr virus nuclear antigen-1, DNA-binding domain; InterPro: IPR004186 The Epstein-Barr virus (strain GD1) nuclear antigen 1 (EBNA1) binds to and activates DNA replication from the latent origin of replication. The crystal structure of the DNA-binding and dimerization domains were solved [], and it was found that EBNA1 appears to bind DNA via two independent regions, the core and the flanking DNA-binding domains. This DNA-binding domain has a ferredoxin-like fold.; GO: 0003677 DNA binding, 0003688 DNA replication origin binding, 0006260 DNA replication, 0006275 regulation of DNA replication, 0045893 positive regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1B3T_B 1VHI_B.
Probab=82.53 E-value=2.9 Score=32.70 Aligned_cols=33 Identities=18% Similarity=0.022 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHhcCCCCC--cEEEEEEeCCeEEE
Q 028291 170 TAAACSAIMQVISDLPINI--FVVGLLKLKIWWMC 202 (211)
Q Consensus 170 l~~v~~sL~~~l~~lp~~~--~~Vg~Itfd~~i~~ 202 (211)
.+.++++|+..+..-|... ++|-+++||..|++
T Consensus 112 Ae~vkDAi~Dyi~T~P~PT~~~~Vt~~~Fd~~V~L 146 (146)
T PF02905_consen 112 AECVKDAIRDYIMTRPQPTCNTQVTVCSFDDGVML 146 (146)
T ss_dssp HHHHHHHHHHHHCTS-TTGGGEEEEEEEEEEEE--
T ss_pred HHHHHHHHHHHhcCCCCCCcceEEEEEeCCCCCcC
Confidence 4679999999999887765 89999999998864
No 55
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=81.38 E-value=1 Score=31.39 Aligned_cols=25 Identities=32% Similarity=0.860 Sum_probs=17.6
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
+.|| +|+.| .|. +++.+.-+| .||.
T Consensus 3 ifrC-~Cgr~--lya--~e~~kTkkC-~CG~ 27 (68)
T PF09082_consen 3 IFRC-DCGRY--LYA--KEGAKTKKC-VCGK 27 (68)
T ss_dssp EEEE-TTS----EEE--ETT-SEEEE-TTTE
T ss_pred EEEe-cCCCE--EEe--cCCcceeEe-cCCC
Confidence 6899 79998 454 467788899 9998
No 56
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=81.07 E-value=2.9 Score=40.80 Aligned_cols=48 Identities=23% Similarity=0.324 Sum_probs=34.3
Q ss_pred CCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhc-CCCCCcEEEEEEeCC
Q 028291 150 MPPVYFFLIDVSTDAVQTGATAAACSAIMQVISD-LPINIFVVGLLKLKI 198 (211)
Q Consensus 150 ~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~-lp~~~~~Vg~Itfd~ 198 (211)
....++||||+|..-...+-+..++.++..++.. +... -+||+|+|+.
T Consensus 464 ~~~~vv~vvD~SgSM~~~~rl~~ak~a~~~ll~~a~~~~-D~v~lI~F~g 512 (633)
T TIGR02442 464 AGNLVIFVVDASGSMAARGRMAAAKGAVLSLLRDAYQKR-DKVALITFRG 512 (633)
T ss_pred CCceEEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCC-CEEEEEEECC
Confidence 3457889999997543333567788888877754 4445 4999999974
No 57
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=80.88 E-value=2.5 Score=36.86 Aligned_cols=48 Identities=19% Similarity=0.209 Sum_probs=33.7
Q ss_pred CCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeC
Q 028291 150 MPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLK 197 (211)
Q Consensus 150 ~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd 197 (211)
...-+|||||.|..-.-.+-.++++-++...|..--...-+|++|+|.
T Consensus 77 ~g~lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~dAYq~RdkvavI~F~ 124 (261)
T COG1240 77 AGNLIVFVVDASGSMAARRRMAAAKGAALSLLRDAYQRRDKVAVIAFR 124 (261)
T ss_pred cCCcEEEEEeCcccchhHHHHHHHHHHHHHHHHHHHHccceEEEEEec
Confidence 345699999999643323347888888888886532222499999997
No 58
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=80.80 E-value=0.6 Score=31.68 Aligned_cols=27 Identities=37% Similarity=0.972 Sum_probs=14.8
Q ss_pred ccCCCCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 82 DFGESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 82 ~~~~~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
+.|+..|.||.+||-. |..|+|+-||.
T Consensus 32 nCGe~~I~Rc~~CRk~----------g~~Y~Cp~CGF 58 (61)
T COG2888 32 NCGEVEIYRCAKCRKL----------GNPYRCPKCGF 58 (61)
T ss_pred CCCceeeehhhhHHHc----------CCceECCCcCc
Confidence 3445556666666533 44456666654
No 59
>cd01460 vWA_midasin VWA_Midasin: Midasin is a member of the AAA ATPase family. The proteins of this family are unified by their common archetectural organization that is based upon a conserved ATPase domain. The AAA domain of midasin contains six tandem AAA protomers. The AAA domains in midasin is followed by a D/E rich domain that is following by a VWA domain. The members of this subgroup have a conserved MIDAS motif. The function of this domain is not exactly known although it has been speculated to play a crucial role in midasin function.
Probab=79.22 E-value=4 Score=35.72 Aligned_cols=55 Identities=11% Similarity=0.067 Sum_probs=38.0
Q ss_pred CCcEEEEEEEcchhhHhhc----HHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEE-EeecCC
Q 028291 150 MPPVYFFLIDVSTDAVQTG----ATAAACSAIMQVISDLPINIFVVGLLKLKIWWM-CILYGN 207 (211)
Q Consensus 150 ~pp~yvFvIDvS~~a~~~g----~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~-~~~~~~ 207 (211)
.....+++||.|..-.++. -++ .+..|..+|..++.+ +||++.|+..++ +..+++
T Consensus 59 r~~qIvlaID~S~SM~~~~~~~~ale-ak~lIs~al~~Le~g--~vgVv~Fg~~~~~v~Plt~ 118 (266)
T cd01460 59 RDYQILIAIDDSKSMSENNSKKLALE-SLCLVSKALTLLEVG--QLGVCSFGEDVQILHPFDE 118 (266)
T ss_pred cCceEEEEEecchhcccccccccHHH-HHHHHHHHHHhCcCC--cEEEEEeCCCceEeCCCCC
Confidence 4678999999986422211 133 455777777888777 899999999977 333433
No 60
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=78.11 E-value=1.4 Score=25.99 Aligned_cols=24 Identities=25% Similarity=0.559 Sum_probs=16.1
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
+|..|+=...+- ...|.|++|+..
T Consensus 3 ~C~~CGy~y~~~------~~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGE------EAPWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCC------cCCCcCcCCCCc
Confidence 678887443332 246999999874
No 61
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=77.85 E-value=1.2 Score=28.45 Aligned_cols=27 Identities=30% Similarity=0.556 Sum_probs=18.4
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
-|..|+..|-+- -..++..|+|+-|+.
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCC
Confidence 488999976332 122234899999997
No 62
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=77.80 E-value=1.1 Score=27.90 Aligned_cols=29 Identities=21% Similarity=0.430 Sum_probs=24.1
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
-||..|+....-+..+.. .....|+-||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 689999988877777766 56799999998
No 63
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=75.89 E-value=2.6 Score=26.26 Aligned_cols=26 Identities=31% Similarity=0.724 Sum_probs=20.0
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
+|.+|++-- ..++.....++|.-||.
T Consensus 2 ~Cp~Cg~~~---~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKE---IVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSE---EEEETTTTEEEETTT-B
T ss_pred CCcCCcCCc---eEEcCCCCeEECCCCCC
Confidence 699999842 46677777899999998
No 64
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=75.82 E-value=1.2 Score=30.23 Aligned_cols=26 Identities=35% Similarity=0.859 Sum_probs=15.0
Q ss_pred CCCCceecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 84 GESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 84 ~~~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
|+..|.||.+||-. +..|+|+-||..
T Consensus 32 G~~~I~RC~~CRk~----------~~~Y~CP~CGF~ 57 (59)
T PRK14890 32 GEVIIYRCEKCRKQ----------SNPYTCPKCGFE 57 (59)
T ss_pred CCeeEeechhHHhc----------CCceECCCCCCc
Confidence 34446666666643 345667777653
No 65
>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=75.31 E-value=2.1 Score=32.69 Aligned_cols=31 Identities=13% Similarity=0.268 Sum_probs=26.1
Q ss_pred ceecCCCCeEEccceEEEe-CCceEEEecCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVD-NGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~-~g~~w~C~~C~~ 118 (211)
...|..|+-.+..-|.+.. ....|.|++|..
T Consensus 71 ~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 71 GRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQK 102 (118)
T ss_dssp CEEETTTTEEEETTSEEETSSSCCEEEHHHHH
T ss_pred CCcCCcCCccccCccCCcCCCCCCEEChhhHH
Confidence 4889999999998888874 567899999976
No 66
>cd01457 vWA_ORF176_type VWA ORF176 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most
Probab=72.90 E-value=7.1 Score=31.85 Aligned_cols=46 Identities=13% Similarity=0.071 Sum_probs=28.5
Q ss_pred EEEEEEEcchhhHhh------cHHHHHHHHHHHHHhc---CCCCCcEEEEEEeCCeE
Q 028291 153 VYFFLIDVSTDAVQT------GATAAACSAIMQVISD---LPINIFVVGLLKLKIWW 200 (211)
Q Consensus 153 ~yvFvIDvS~~a~~~------g~l~~v~~sL~~~l~~---lp~~~~~Vg~Itfd~~i 200 (211)
-++|+||.|..-... .-++.+++++..++.. +..+ .++++.|+...
T Consensus 4 dvv~~ID~SgSM~~~~~~~~~~k~~~ak~~~~~l~~~~~~~D~d--~i~l~~f~~~~ 58 (199)
T cd01457 4 DYTLLIDKSGSMAEADEAKERSRWEEAQESTRALARKCEEYDSD--GITVYLFSGDF 58 (199)
T ss_pred CEEEEEECCCcCCCCCCCCCchHHHHHHHHHHHHHHHHHhcCCC--CeEEEEecCCc
Confidence 489999998643211 0245556666555554 4333 68889988764
No 67
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=71.75 E-value=1.6 Score=28.53 Aligned_cols=30 Identities=30% Similarity=0.666 Sum_probs=19.0
Q ss_pred ecCCCCeEEccc-----------eEEEeCCceEEEecCCCC
Q 028291 90 RCCCCRGYRNPF-----------MEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 90 RC~~C~aYiNp~-----------~~~~~~g~~w~C~~C~~~ 119 (211)
+|..|+=..+|- +.|..--..|+|++|+..
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 677777665643 234334456999999863
No 68
>TIGR00578 ku70 ATP-dependent DNA helicase ii, 70 kDa subunit (ku70). Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast.
Probab=70.75 E-value=11 Score=36.62 Aligned_cols=47 Identities=13% Similarity=0.072 Sum_probs=32.2
Q ss_pred EEEEEEEcchhhHh-------hcHHHHHHHHHHHHHhcC-CCCC-cEEEEEEeCCe
Q 028291 153 VYFFLIDVSTDAVQ-------TGATAAACSAIMQVISDL-PINI-FVVGLLKLKIW 199 (211)
Q Consensus 153 ~yvFvIDvS~~a~~-------~g~l~~v~~sL~~~l~~l-p~~~-~~Vg~Itfd~~ 199 (211)
+.||+||+|..-.+ ..-|+.+++++..+++.. -.+. ..||++.|++.
T Consensus 12 ailflIDvs~sM~~~~~~~~~~s~~~~al~~i~~l~q~kIis~~~D~vGivlfgT~ 67 (584)
T TIGR00578 12 SLIFLVDASKAMFEESQGEDELTPFDMSIQCIQSVYTSKIISSDKDLLAVVFYGTE 67 (584)
T ss_pred EEEEEEECCHHHcCCCcCcCcCChHHHHHHHHHHHHHhcCCCCCCCeEEEEEEecc
Confidence 68999999975332 123567777777777752 2111 59999999974
No 69
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=69.98 E-value=2.3 Score=25.70 Aligned_cols=29 Identities=24% Similarity=0.396 Sum_probs=20.7
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
-||..|+........... +....|+-||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 589999987665554433 55688999987
No 70
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=69.36 E-value=2.9 Score=31.77 Aligned_cols=28 Identities=14% Similarity=0.284 Sum_probs=20.4
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDG 120 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~~ 120 (211)
.-.||..|+.. |......|.|+-||...
T Consensus 69 ~~~~C~~Cg~~------~~~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 69 AQAWCWDCSQV------VEIHQHDAQCPHCHGER 96 (113)
T ss_pred cEEEcccCCCE------EecCCcCccCcCCCCCC
Confidence 45899999954 33444568899999743
No 71
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=69.08 E-value=2.8 Score=25.31 Aligned_cols=31 Identities=19% Similarity=0.526 Sum_probs=18.4
Q ss_pred ceecCCCCeEEc-cceEEEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRN-PFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiN-p~~~~~~~g~~w~C~~C~~ 118 (211)
.++|.+|++-.+ +=-++-..|.+.+|.-|++
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence 367777777544 2222344567777777765
No 72
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=68.37 E-value=4.2 Score=23.91 Aligned_cols=26 Identities=27% Similarity=0.594 Sum_probs=17.8
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
++|..|+.-|- .-.+.++++|.+|.+
T Consensus 2 ~~C~~C~t~L~----yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 2 VVCGGCRTLLM----YPRGASSVRCALCQT 27 (31)
T ss_pred cCcCCCCcEee----cCCCCCeEECCCCCe
Confidence 46888887653 224677888888865
No 73
>PRK12860 transcriptional activator FlhC; Provisional
Probab=67.83 E-value=2.6 Score=35.16 Aligned_cols=31 Identities=35% Similarity=0.801 Sum_probs=22.2
Q ss_pred CCCceecCCCCe-EEccceEEEeCCceEEEecCCC
Q 028291 85 ESGLVRCCCCRG-YRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 85 ~~~p~RC~~C~a-YiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.-...+|.+|++ ||-. ..+....++|++|.-
T Consensus 131 ~L~l~~C~~Cgg~fv~~---~~e~~~~f~CplC~~ 162 (189)
T PRK12860 131 MLQLARCCRCGGKFVTH---AHDLRHNFVCGLCQP 162 (189)
T ss_pred CeeeccCCCCCCCeecc---ccccCCCCcCCCCCC
Confidence 345799999997 5422 224556799999996
No 74
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=67.69 E-value=7.9 Score=23.00 Aligned_cols=28 Identities=32% Similarity=0.660 Sum_probs=19.4
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.+.+|..|++-+ -+.......+|.+|+.
T Consensus 2 ~~~~C~~C~~~~----i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 2 NLKKCSKCGGNG----IVNKEDDYEVCIFCGS 29 (33)
T ss_pred CceEcCCCCCCe----EEEecCCeEEcccCCc
Confidence 357899998864 2223444689999986
No 75
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=67.28 E-value=3 Score=27.20 Aligned_cols=27 Identities=22% Similarity=0.625 Sum_probs=20.4
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.=+|.+|++-+ ..+.......|+-||+
T Consensus 6 ~Y~C~~Cg~~~----~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREV----ELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCee----ehhhccCceeCCCCCc
Confidence 45889999876 4455666788999988
No 76
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=67.24 E-value=2.7 Score=27.00 Aligned_cols=30 Identities=23% Similarity=0.490 Sum_probs=21.7
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
-||.+|+....-+..+.. .....|+.||..
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~ 35 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-DPLATCPECGGE 35 (52)
T ss_pred EEeCCCCCEeEEEEecCC-CCCCCCCCCCCC
Confidence 589999986665554443 446789999984
No 77
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=67.20 E-value=4.5 Score=26.81 Aligned_cols=33 Identities=15% Similarity=0.282 Sum_probs=23.1
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
..++-|++|++-=.-+-+-+...-+|+|..|+.
T Consensus 20 r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 20 RYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred ceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 457889999986433324444555899999986
No 78
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=66.55 E-value=3.7 Score=31.28 Aligned_cols=29 Identities=14% Similarity=0.085 Sum_probs=20.7
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCCCCc
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGR 121 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~~~ 121 (211)
.-.||.+|+.. |......|.|+-||....
T Consensus 69 ~~~~C~~Cg~~------~~~~~~~~~CP~Cgs~~~ 97 (115)
T TIGR00100 69 VECECEDCSEE------VSPEIDLYRCPKCHGIML 97 (115)
T ss_pred cEEEcccCCCE------EecCCcCccCcCCcCCCc
Confidence 45899999965 333334689999998543
No 79
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=66.18 E-value=3.7 Score=31.24 Aligned_cols=28 Identities=21% Similarity=0.312 Sum_probs=19.5
Q ss_pred CceecCCCCeEEccceEEEeCCc-eEEEecCCCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGK-SFVCNFCGLDG 120 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~-~w~C~~C~~~~ 120 (211)
.-.||.+|+.+ |..... .|.|+-||...
T Consensus 69 ~~~~C~~Cg~~------~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 69 AECWCETCQQY------VTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred cEEEcccCCCe------eecCCccCCcCcCcCCCC
Confidence 45899999964 333222 38899999754
No 80
>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=65.81 E-value=5.7 Score=24.08 Aligned_cols=26 Identities=19% Similarity=0.562 Sum_probs=18.9
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
..+|..|++. +.. .+...|.|.-||+
T Consensus 8 ~~~C~~C~~~---~~~--~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGSR---WFY--SDDGFYYCDRCGH 33 (36)
T ss_pred CCcCCCCCCe---EeE--ccCCEEEhhhCce
Confidence 3679999999 333 3333699999986
No 81
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=64.62 E-value=2 Score=25.78 Aligned_cols=28 Identities=29% Similarity=0.597 Sum_probs=12.4
Q ss_pred cCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 91 C~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
|..|++-+.--.--.++..+++|.-|+.
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred cccccChhhhhcCCCCCccceECCCCCC
Confidence 7777776533222224556788888874
No 82
>PRK12722 transcriptional activator FlhC; Provisional
Probab=64.01 E-value=3 Score=34.71 Aligned_cols=30 Identities=37% Similarity=0.781 Sum_probs=21.5
Q ss_pred CCceecCCCCe-EEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRG-YRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~a-YiNp~~~~~~~g~~w~C~~C~~ 118 (211)
-...+|.+|++ ||-. ..+....++|++|.-
T Consensus 132 L~l~~C~~Cgg~fv~~---~~e~~~~f~CplC~~ 162 (187)
T PRK12722 132 LQLSSCNCCGGHFVTH---AHDPVGSFVCGLCQP 162 (187)
T ss_pred EeeccCCCCCCCeecc---ccccCCCCcCCCCCC
Confidence 45789999997 5422 223456799999998
No 83
>PRK03954 ribonuclease P protein component 4; Validated
Probab=63.98 E-value=5.6 Score=30.81 Aligned_cols=31 Identities=19% Similarity=0.391 Sum_probs=20.9
Q ss_pred eecCCCCeEEccc----eEEEeCC---ceEEEecCCCC
Q 028291 89 VRCCCCRGYRNPF----MEFVDNG---KSFVCNFCGLD 119 (211)
Q Consensus 89 ~RC~~C~aYiNp~----~~~~~~g---~~w~C~~C~~~ 119 (211)
--|++|.++|=|- +.+..++ -.++|..||..
T Consensus 65 ~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~ 102 (121)
T PRK03954 65 RYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHI 102 (121)
T ss_pred HHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCE
Confidence 4599999998663 3343322 23489999983
No 84
>KOG2353 consensus L-type voltage-dependent Ca2+ channel, alpha2/delta subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=63.95 E-value=14 Score=38.62 Aligned_cols=73 Identities=15% Similarity=0.131 Sum_probs=55.4
Q ss_pred CCCCCCCcceEEEech---hhhccCCCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEE
Q 028291 127 ERPELCRGTVEFAASR---EFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWM 201 (211)
Q Consensus 127 ~rpEL~~~tvE~~~p~---~y~~r~~~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~ 201 (211)
.+++=+..++|+.... -|......|-..+|++|+|. ++..-.++.++..+.++|+.|-+++ .|-++||++.+.
T Consensus 198 W~~~~~~~~idl~D~R~r~Wyi~aAt~pKdiviLlD~Sg-Sm~g~~~~lak~tv~~iLdtLs~~D-fvni~tf~~~~~ 273 (1104)
T KOG2353|consen 198 WFDNNTDNSIDLYDCRNRSWYIQAATSPKDIVILLDVSG-SMSGLRLDLAKQTVNEILDTLSDND-FVNILTFNSEVN 273 (1104)
T ss_pred CccCCCCCcceeeecccccccccccCCccceEEEEeccc-cccchhhHHHHHHHHHHHHhcccCC-eEEEEeeccccC
Confidence 3344355666665543 34555677889999999986 5554557889999999999999996 999999998876
No 85
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=63.28 E-value=2.7 Score=22.90 Aligned_cols=21 Identities=29% Similarity=0.607 Sum_probs=11.8
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
+|.+|++-+..-.+| |+-||+
T Consensus 1 ~Cp~CG~~~~~~~~f--------C~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKF--------CPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcc--------hhhhCC
Confidence 477777765443332 666664
No 86
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=62.88 E-value=4.9 Score=27.24 Aligned_cols=27 Identities=26% Similarity=0.639 Sum_probs=21.7
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
--.|..|+...-- ...++.|.|.-||.
T Consensus 28 Sq~C~~CG~~~~~----~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 28 SQTCPRCGHRNKK----RRSGRVFTCPNCGF 54 (69)
T ss_pred ccCccCccccccc----ccccceEEcCCCCC
Confidence 4568999988655 45788999999998
No 87
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=62.85 E-value=4 Score=26.66 Aligned_cols=31 Identities=29% Similarity=0.608 Sum_probs=26.0
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
+.+|.+|++--.|..+-...|..-.||-|+.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl 33 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGL 33 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccH
Confidence 5789999988888777666777799999998
No 88
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=62.17 E-value=5.9 Score=22.00 Aligned_cols=24 Identities=29% Similarity=0.707 Sum_probs=15.8
Q ss_pred cCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 91 C~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
|.+|+.-|-|.-+ +..|.|+-||.
T Consensus 1 C~sC~~~i~~r~~----~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQ----AVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCccc----CceEeCCCCCC
Confidence 6667776665443 55688888873
No 89
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.45 E-value=4.9 Score=31.86 Aligned_cols=28 Identities=29% Similarity=0.522 Sum_probs=20.7
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.+--|.+|++-+..- .+.-+|+||+|..
T Consensus 88 q~r~CARCGGrv~lr----sNKv~wvcnlc~k 115 (169)
T KOG3799|consen 88 QTRFCARCGGRVSLR----SNKVMWVCNLCRK 115 (169)
T ss_pred hhhHHHhcCCeeeec----cCceEEeccCCcH
Confidence 355678899875443 3566899999998
No 90
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=60.13 E-value=6.9 Score=32.56 Aligned_cols=27 Identities=30% Similarity=0.652 Sum_probs=21.8
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDG 120 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~~ 120 (211)
-.||++|++-|= ..+.+.+|+-||..-
T Consensus 149 ~A~CsrC~~~L~------~~~~~l~Cp~Cg~tE 175 (188)
T COG1096 149 YARCSRCRAPLV------KKGNMLKCPNCGNTE 175 (188)
T ss_pred EEEccCCCcceE------EcCcEEECCCCCCEE
Confidence 479999999743 267899999999843
No 91
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=59.29 E-value=5.7 Score=23.77 Aligned_cols=30 Identities=23% Similarity=0.492 Sum_probs=13.8
Q ss_pred eecCCCCeEEc-cceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRN-PFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiN-p~~~~~~~g~~w~C~~C~~ 118 (211)
++|.+|++-.. +--.+...+....|+-|++
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~ 33 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGH 33 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCC
Confidence 45666666311 1111222344566666664
No 92
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=59.24 E-value=10 Score=23.88 Aligned_cols=27 Identities=15% Similarity=0.461 Sum_probs=19.0
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
+.|.+|++- . +..+ .+.+.|.|.-|++
T Consensus 19 ~~CP~Cg~~-~-~~~~-~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-K-HYRL-KTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-e-eEEe-CCCCeEECCCCCC
Confidence 669999987 2 2222 3356899999985
No 93
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=58.84 E-value=2.3 Score=27.45 Aligned_cols=10 Identities=40% Similarity=1.185 Sum_probs=5.4
Q ss_pred ceEEEecCCC
Q 028291 109 KSFVCNFCGL 118 (211)
Q Consensus 109 ~~w~C~~C~~ 118 (211)
..|+|+.|+.
T Consensus 33 ~~w~CP~C~a 42 (47)
T PF00301_consen 33 DDWVCPVCGA 42 (47)
T ss_dssp TT-B-TTTSS
T ss_pred CCCcCcCCCC
Confidence 3488888875
No 94
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=58.15 E-value=6.9 Score=23.16 Aligned_cols=13 Identities=23% Similarity=0.467 Sum_probs=9.5
Q ss_pred CCCceecCCCCeE
Q 028291 85 ESGLVRCCCCRGY 97 (211)
Q Consensus 85 ~~~p~RC~~C~aY 97 (211)
..+++||..|+.-
T Consensus 14 ~~~~irC~~CG~R 26 (32)
T PF03604_consen 14 PGDPIRCPECGHR 26 (32)
T ss_dssp TSSTSSBSSSS-S
T ss_pred CCCcEECCcCCCe
Confidence 4678899999864
No 95
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=57.22 E-value=8.9 Score=24.26 Aligned_cols=25 Identities=20% Similarity=0.381 Sum_probs=15.8
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
-+|.+|++-+..- .+..-+|+-||+
T Consensus 3 Y~C~~Cg~~~~~~-----~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIK-----SKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecC-----CCCceECCCCCc
Confidence 3677777754432 344577888877
No 96
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=56.57 E-value=13 Score=25.84 Aligned_cols=28 Identities=25% Similarity=0.553 Sum_probs=22.6
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
-++|..|+-- -+-|.......+|..||.
T Consensus 19 ~VkCpdC~N~---q~vFshast~V~C~~CG~ 46 (67)
T COG2051 19 RVKCPDCGNE---QVVFSHASTVVTCLICGT 46 (67)
T ss_pred EEECCCCCCE---EEEeccCceEEEeccccc
Confidence 4899999854 555666788899999998
No 97
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=56.20 E-value=6.1 Score=25.71 Aligned_cols=24 Identities=21% Similarity=0.541 Sum_probs=17.2
Q ss_pred eecCCCCe-EEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRG-YRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~a-YiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.-|.+|++ +|-+. ...|.|.-|+.
T Consensus 21 ~fCP~Cg~~~m~~~------~~r~~C~~Cgy 45 (50)
T PRK00432 21 KFCPRCGSGFMAEH------LDRWHCGKCGY 45 (50)
T ss_pred CcCcCCCcchhecc------CCcEECCCcCC
Confidence 47999998 44332 24799999986
No 98
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=54.18 E-value=8.1 Score=24.84 Aligned_cols=32 Identities=22% Similarity=0.345 Sum_probs=22.6
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.+.++|..|+..|..... ......|.|.-+..
T Consensus 3 ~g~l~C~~CG~~m~~~~~-~~~~~yy~C~~~~~ 34 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRKR-KGKYRYYRCSNRRR 34 (58)
T ss_pred CCcEEcccCCcEeEEEEC-CCCceEEEcCCCcC
Confidence 467999999998877543 23346788887554
No 99
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=53.40 E-value=11 Score=21.70 Aligned_cols=29 Identities=28% Similarity=0.540 Sum_probs=16.0
Q ss_pred ecCCCCeEEccc-eEEEeCCce-----EEEecCCC
Q 028291 90 RCCCCRGYRNPF-MEFVDNGKS-----FVCNFCGL 118 (211)
Q Consensus 90 RC~~C~aYiNp~-~~~~~~g~~-----w~C~~C~~ 118 (211)
||..|+-.|-+- ..+...++. |.|..|+.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~ 35 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGK 35 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCC
Confidence 577787777664 223333333 45666654
No 100
>PF05762 VWA_CoxE: VWA domain containing CoxE-like protein; InterPro: IPR008912 This group of proteins contains a VWA type domain and the function of this family is unknown. It is found as part of a CO oxidising (Cox) system operon in several bacteria [].
Probab=52.88 E-value=18 Score=30.35 Aligned_cols=47 Identities=15% Similarity=0.156 Sum_probs=28.5
Q ss_pred CCCc-EEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEE
Q 028291 149 VMPP-VYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWM 201 (211)
Q Consensus 149 ~~pp-~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~ 201 (211)
+..| .+|+++|+|. +++ ++...++..+.++....+ .+.++.|+..+.
T Consensus 54 ~~~~~~lvvl~DvSG-SM~-~~s~~~l~~~~~l~~~~~----~~~~f~F~~~l~ 101 (222)
T PF05762_consen 54 PRKPRRLVVLCDVSG-SMA-GYSEFMLAFLYALQRQFR----RVRVFVFSTRLT 101 (222)
T ss_pred cCCCccEEEEEeCCC-ChH-HHHHHHHHHHHHHHHhCC----CEEEEEEeeehh
Confidence 4445 8999999996 443 344444444444444443 566777877665
No 101
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=52.16 E-value=5.8 Score=30.32 Aligned_cols=29 Identities=24% Similarity=0.510 Sum_probs=18.9
Q ss_pred CCceecCCCCeEEccceEEEeCCceE-EEecCCCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSF-VCNFCGLDG 120 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w-~C~~C~~~~ 120 (211)
....||.+|+.+ |......+ .|+-||...
T Consensus 69 p~~~~C~~Cg~~------~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 69 KVELECKDCSHV------FKPNALDYGVCEKCHSKN 98 (117)
T ss_pred CCEEEhhhCCCc------cccCCccCCcCcCCCCCc
Confidence 346899999954 22222234 599999854
No 102
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=52.05 E-value=8.9 Score=28.19 Aligned_cols=24 Identities=29% Similarity=0.719 Sum_probs=19.1
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
.|.+|++.|.|- +..+.|..|+..
T Consensus 2 fC~~Cg~~l~~~------~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPK------NGVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccC------CCeEECcCCCCc
Confidence 599999999652 347999999984
No 103
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=51.19 E-value=12 Score=20.93 Aligned_cols=11 Identities=27% Similarity=0.640 Sum_probs=6.0
Q ss_pred CCceEEEecCC
Q 028291 107 NGKSFVCNFCG 117 (211)
Q Consensus 107 ~g~~w~C~~C~ 117 (211)
+...++|..|.
T Consensus 13 GA~sVrCa~C~ 23 (25)
T PF06943_consen 13 GAPSVRCACCH 23 (25)
T ss_pred CCCCeECCccC
Confidence 44556666654
No 104
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=50.05 E-value=9 Score=22.35 Aligned_cols=26 Identities=31% Similarity=0.699 Sum_probs=13.0
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.+.|..|++=-+= .+|..++|+-|++
T Consensus 2 ~p~Cp~C~se~~y-----~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 2 LPKCPLCGSEYTY-----EDGELLVCPECGH 27 (30)
T ss_dssp S---TTT-----E-----E-SSSEEETTTTE
T ss_pred CCCCCCCCCccee-----ccCCEEeCCcccc
Confidence 3578888874222 5677899999974
No 105
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=49.52 E-value=10 Score=29.87 Aligned_cols=31 Identities=26% Similarity=0.597 Sum_probs=21.7
Q ss_pred ceecCCCCeEEccceE-----------EEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRNPFME-----------FVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~-----------~~~~g~~w~C~~C~~ 118 (211)
.-||..|.+-+-+-.+ +.....-|+|+-||+
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~k 132 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGK 132 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCC
Confidence 5899999995543222 223356899999998
No 106
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=48.78 E-value=5.2 Score=24.06 Aligned_cols=28 Identities=36% Similarity=0.727 Sum_probs=18.4
Q ss_pred cCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 91 C~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
|.+|++==.|..+-...|....||-|+.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~ 28 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGL 28 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHH
Confidence 7788887778777777788779999874
No 107
>PF00092 VWA: von Willebrand factor type A domain; InterPro: IPR002035 The von Willebrand factor is a large multimeric glycoprotein found in blood plasma. Mutant forms are involved in the aetiology of bleeding disorders []. In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins [, , ]. Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands []. A number of human diseases arise from mutations in VWA domains. Secondary structure prediction from 75 aligned vWF sequences has revealed a largely alternating sequence of alpha-helices and beta-strands []. Fold recognition algorithms were used to score sequence compatibility with a library of known structures: the vWF domain fold was predicted to be a doubly-wound, open, twisted beta-sheet flanked by alpha-helices []. 3D structures have been determined for the I-domains of integrins CD11b (with bound magnesium) [] and CD11a (with bound manganese) []. The domain adopts a classic alpha/beta Rossmann fold and contains an unusual metal ion coordination site at its surface. It has been suggested that this site represents a general metal ion-dependent adhesion site (MIDAS) for binding protein ligands []. The residues constituting the MIDAS motif in the CD11b and CD11a I-domains are completely conserved, but the manner in which the metal ion is coordinated differs slightly [].; GO: 0005515 protein binding; PDB: 2XGG_B 3ZQK_B 3GXB_A 3PPV_A 3PPX_A 3PPW_A 3PPY_A 1CQP_B 3TCX_B 2ICA_A ....
Probab=48.71 E-value=36 Score=26.15 Aligned_cols=23 Identities=9% Similarity=-0.181 Sum_probs=16.4
Q ss_pred cCCCCCcEEEEEEeCCeEE-EeecC
Q 028291 183 DLPINIFVVGLLKLKIWWM-CILYG 206 (211)
Q Consensus 183 ~lp~~~~~Vg~Itfd~~i~-~~~~~ 206 (211)
..+.. ++||+|+|+.... .+.++
T Consensus 33 ~~~~~-~rv~iv~f~~~~~~~~~~~ 56 (178)
T PF00092_consen 33 ISNNG-TRVGIVTFSDSARVLFSLT 56 (178)
T ss_dssp BSTTS-EEEEEEEESSSEEEEEETT
T ss_pred ccccc-cccceeeeecccccccccc
Confidence 34444 8999999999887 44443
No 108
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=48.69 E-value=11 Score=23.90 Aligned_cols=23 Identities=17% Similarity=0.417 Sum_probs=16.7
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
+.|..|+.. |.. |.+|+|..|.-
T Consensus 1 I~CDgCg~~--PI~-----G~RykC~~C~d 23 (43)
T cd02342 1 IQCDGCGVL--PIT-----GPRYKSKVKED 23 (43)
T ss_pred CCCCCCCCC--ccc-----ccceEeCCCCC
Confidence 468888855 544 66899998864
No 109
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=47.41 E-value=20 Score=28.09 Aligned_cols=29 Identities=28% Similarity=0.665 Sum_probs=24.3
Q ss_pred ceecCCCCeEEccceEEEeCCceE--EEecCCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSF--VCNFCGLD 119 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w--~C~~C~~~ 119 (211)
=+-|..|+. |=..+..+++.| .|.-||..
T Consensus 97 yVlC~~C~s---PdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 97 YVICRECNR---PDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred eEECCCCCC---CCcEEEEeCCeEEEecccCCCC
Confidence 489999996 888888888876 79999984
No 110
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=47.02 E-value=11 Score=21.42 Aligned_cols=26 Identities=19% Similarity=0.611 Sum_probs=14.0
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~ 117 (211)
.|.+|+.++-.-.. .+...+.|+-|.
T Consensus 3 ~C~rC~~~~~~~~~--~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIGI--NGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEEE--TTEEEEE-TTTC
T ss_pred cCccCCCcceEeEe--cCCCCeECcCCc
Confidence 68999998543332 345568888885
No 111
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.52 E-value=12 Score=29.26 Aligned_cols=34 Identities=18% Similarity=0.429 Sum_probs=20.4
Q ss_pred CceecCCCCeEEccce-------------EEEeC--CceEEEecCCCCC
Q 028291 87 GLVRCCCCRGYRNPFM-------------EFVDN--GKSFVCNFCGLDG 120 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~-------------~~~~~--g~~w~C~~C~~~~ 120 (211)
...||..|+.....-- .+.+. ...+.|+-||...
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 4689999996533320 00000 3458899999743
No 112
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=46.17 E-value=9.7 Score=19.42 Aligned_cols=8 Identities=50% Similarity=1.377 Sum_probs=5.2
Q ss_pred EEEecCCC
Q 028291 111 FVCNFCGL 118 (211)
Q Consensus 111 w~C~~C~~ 118 (211)
|.|++|+.
T Consensus 1 ~~C~~C~~ 8 (24)
T PF13894_consen 1 FQCPICGK 8 (24)
T ss_dssp EE-SSTS-
T ss_pred CCCcCCCC
Confidence 78999987
No 113
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=44.57 E-value=6 Score=29.93 Aligned_cols=28 Identities=25% Similarity=0.477 Sum_probs=17.7
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDG 120 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~~ 120 (211)
.-.||..|+.-.. .....+.|+.||...
T Consensus 69 ~~~~C~~Cg~~~~------~~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 69 ARARCRDCGHEFE------PDEFDFSCPRCGSPD 96 (113)
T ss_dssp -EEEETTTS-EEE------CHHCCHH-SSSSSS-
T ss_pred CcEECCCCCCEEe------cCCCCCCCcCCcCCC
Confidence 4589999998743 333347799999854
No 114
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=44.51 E-value=8.8 Score=21.56 Aligned_cols=21 Identities=24% Similarity=0.537 Sum_probs=11.9
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
+|..|++-++-- .-.|+.||+
T Consensus 2 ~CP~C~~~V~~~--------~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPES--------AKFCPHCGY 22 (26)
T ss_pred cCCCCcCCchhh--------cCcCCCCCC
Confidence 466777665322 235677765
No 115
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.10 E-value=12 Score=32.14 Aligned_cols=23 Identities=35% Similarity=0.880 Sum_probs=18.8
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.-..|..||. ..++.|.|+-||.
T Consensus 308 tS~~C~~cg~---------~~~r~~~C~~cg~ 330 (364)
T COG0675 308 TSKTCPCCGH---------LSGRLFKCPRCGF 330 (364)
T ss_pred CcccccccCC---------ccceeEECCCCCC
Confidence 3478999998 3467899999998
No 116
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=43.83 E-value=12 Score=30.64 Aligned_cols=13 Identities=46% Similarity=1.165 Sum_probs=10.5
Q ss_pred CCceEEEecCCCC
Q 028291 107 NGKSFVCNFCGLD 119 (211)
Q Consensus 107 ~g~~w~C~~C~~~ 119 (211)
.|+.|+|+.||..
T Consensus 131 ~~~~~vC~vCGy~ 143 (166)
T COG1592 131 EGKVWVCPVCGYT 143 (166)
T ss_pred cCCEEEcCCCCCc
Confidence 4558999999984
No 117
>PHA00626 hypothetical protein
Probab=43.77 E-value=22 Score=23.91 Aligned_cols=11 Identities=36% Similarity=1.005 Sum_probs=9.6
Q ss_pred CceEEEecCCC
Q 028291 108 GKSFVCNFCGL 118 (211)
Q Consensus 108 g~~w~C~~C~~ 118 (211)
.+.|.|.-||.
T Consensus 21 snrYkCkdCGY 31 (59)
T PHA00626 21 SDDYVCCDCGY 31 (59)
T ss_pred CcceEcCCCCC
Confidence 56799999998
No 118
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=42.95 E-value=25 Score=20.29 Aligned_cols=25 Identities=24% Similarity=0.422 Sum_probs=13.3
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
-|.+|++= +....+|..-+|+-|+.
T Consensus 5 fC~~CG~~----t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 5 FCGRCGAP----TKPAPGGWARRCPSCGH 29 (32)
T ss_dssp B-TTT--B----EEE-SSSS-EEESSSS-
T ss_pred ccCcCCcc----ccCCCCcCEeECCCCcC
Confidence 47778775 44556677788888874
No 119
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=42.77 E-value=7.5 Score=25.14 Aligned_cols=31 Identities=23% Similarity=0.497 Sum_probs=11.5
Q ss_pred ceecCCCCeEE----ccceEEEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYR----NPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYi----Np~~~~~~~g~~w~C~~C~~ 118 (211)
|+|=.+|.=.- ..|.+.....+.|.|++|++
T Consensus 15 P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 15 PVRGKNCKHLQCFDLESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp EEEETT--SS--EEHHHHHHHHHHS---B-TTT--
T ss_pred CccCCcCcccceECHHHHHHHhhccCCeECcCCcC
Confidence 55555554331 12333333456799999985
No 120
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=42.54 E-value=3.7 Score=24.83 Aligned_cols=32 Identities=22% Similarity=0.430 Sum_probs=14.5
Q ss_pred CCceecCCCCeEEccceEE---EeCCceEEEecCC
Q 028291 86 SGLVRCCCCRGYRNPFMEF---VDNGKSFVCNFCG 117 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~---~~~g~~w~C~~C~ 117 (211)
..+++|++|+-.+...|-- ...+..|.|..|.
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--SS-----HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCCCCcEECCcCC
Confidence 3578999999988765531 2334459998773
No 121
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=42.48 E-value=21 Score=21.85 Aligned_cols=27 Identities=33% Similarity=0.854 Sum_probs=16.1
Q ss_pred ecCCCCeEEccceEEEe--CCceEEEecCCC
Q 028291 90 RCCCCRGYRNPFMEFVD--NGKSFVCNFCGL 118 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~--~g~~w~C~~C~~ 118 (211)
-|..|++- --|- |++ +...|+|+-|+.
T Consensus 5 pCP~CGG~-DrFr-~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 5 PCPNCGGS-DRFR-FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CCCCCCCc-cccc-cccCCCCcCEEeCCCCC
Confidence 36667661 2233 443 345699999975
No 122
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.93 E-value=12 Score=28.92 Aligned_cols=33 Identities=18% Similarity=0.218 Sum_probs=19.1
Q ss_pred CceecCCCCeEEccc-eEEEeCCceEEEecCCCCC
Q 028291 87 GLVRCCCCRGYRNPF-MEFVDNGKSFVCNFCGLDG 120 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~-~~~~~~g~~w~C~~C~~~~ 120 (211)
.-.|| +|+.+...- ...+.-...|.|+-||...
T Consensus 69 ~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~ 102 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKR 102 (124)
T ss_pred eeEEe-eCcCcccccccchhccccCCcCcCCCCCC
Confidence 45899 999764331 1111111137899999743
No 123
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=41.48 E-value=8.8 Score=31.53 Aligned_cols=31 Identities=35% Similarity=0.670 Sum_probs=12.0
Q ss_pred CCCceecCCCCe-EEccceEEEeCCceEEEecCCC
Q 028291 85 ESGLVRCCCCRG-YRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 85 ~~~p~RC~~C~a-YiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.-...+|.+|++ |+..- .+....+.|++|+-
T Consensus 131 ~l~l~~C~~C~~~fv~~~---~~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 131 MLQLAPCRRCGGHFVTHA---HDPRHSFVCPFCQP 162 (175)
T ss_dssp SEEEEE-TTT--EEEEES---S--SS----TT---
T ss_pred CccccCCCCCCCCeECcC---CCCCcCcCCCCCCC
Confidence 345799999997 44321 12256799999996
No 124
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=41.34 E-value=9.9 Score=23.74 Aligned_cols=9 Identities=33% Similarity=1.077 Sum_probs=7.8
Q ss_pred eecCCCCeE
Q 028291 89 VRCCCCRGY 97 (211)
Q Consensus 89 ~RC~~C~aY 97 (211)
+||.+|++|
T Consensus 2 ~kC~~CG~~ 10 (40)
T PF15288_consen 2 VKCKNCGAF 10 (40)
T ss_pred ccccccccc
Confidence 589999998
No 125
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=41.26 E-value=14 Score=21.93 Aligned_cols=9 Identities=44% Similarity=1.287 Sum_probs=8.3
Q ss_pred eEEEecCCC
Q 028291 110 SFVCNFCGL 118 (211)
Q Consensus 110 ~w~C~~C~~ 118 (211)
.|+|..||.
T Consensus 2 ~~~C~~CG~ 10 (34)
T cd00729 2 VWVCPVCGY 10 (34)
T ss_pred eEECCCCCC
Confidence 699999998
No 126
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=40.98 E-value=45 Score=26.17 Aligned_cols=64 Identities=16% Similarity=0.287 Sum_probs=37.7
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCCCCc--ccCCCCCCCCCCcceEEEechhhhccCCCCcEEEEEEEcc
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGR--CLDADERPELCRGTVEFAASREFMMRNVMPPVYFFLIDVS 161 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~~~--~~d~~~rpEL~~~tvE~~~p~~y~~r~~~pp~yvFvIDvS 161 (211)
--.||.+|+.+.=|= +-.|.-|+..+. -.....+=++..=|+-|..+..+ ...+|..+-+|+.-
T Consensus 28 ~g~kC~~CG~v~~PP--------r~~Cp~C~~~~~~E~vels~~G~V~t~Tv~~~~~~~~---~~~~P~viaiV~l~ 93 (140)
T COG1545 28 LGTKCKKCGRVYFPP--------RAYCPKCGSETELEWVELSGEGKVETYTVVYVKPPGF---SLEEPYVIAIVELE 93 (140)
T ss_pred EEEEcCCCCeEEcCC--------cccCCCCCCCCceEEEEeCCCeEEEEEEEEeeCCCCc---ccCCCEEEEEEEeC
Confidence 348999999984442 357899988642 11122222233345555555432 23478888888885
No 127
>PRK00420 hypothetical protein; Validated
Probab=40.86 E-value=19 Score=27.47 Aligned_cols=25 Identities=32% Similarity=0.761 Sum_probs=19.5
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
-.|..|++ |++++ .+| ...|+.||.
T Consensus 24 ~~CP~Cg~---pLf~l-k~g-~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGL---PLFEL-KDG-EVVCPVHGK 48 (112)
T ss_pred CCCCCCCC---cceec-CCC-ceECCCCCC
Confidence 57889993 77776 444 699999998
No 128
>PRK10997 yieM hypothetical protein; Provisional
Probab=40.34 E-value=45 Score=31.81 Aligned_cols=49 Identities=12% Similarity=0.102 Sum_probs=33.4
Q ss_pred cEEEEEEEcchhhHhhcHHHHHHHHHHHHHh--cCCCCCcEEEEEEeCCeEEEe
Q 028291 152 PVYFFLIDVSTDAVQTGATAAACSAIMQVIS--DLPINIFVVGLLKLKIWWMCI 203 (211)
Q Consensus 152 p~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~--~lp~~~~~Vg~Itfd~~i~~~ 203 (211)
-.++++||+|.. +. |.-+....++..+|- .+.+++ .+++|.|+..+..+
T Consensus 324 GpiII~VDtSGS-M~-G~ke~~AkalAaAL~~iAl~q~d-r~~li~Fs~~i~~~ 374 (487)
T PRK10997 324 GPFIVCVDTSGS-MG-GFNEQCAKAFCLALMRIALAENR-RCYIMLFSTEVVTY 374 (487)
T ss_pred CcEEEEEECCCC-CC-CCHHHHHHHHHHHHHHHHHhcCC-CEEEEEecCCceee
Confidence 458999999863 32 444455556555554 355664 89999999988764
No 129
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.33 E-value=24 Score=30.77 Aligned_cols=28 Identities=21% Similarity=0.386 Sum_probs=18.5
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
--|.+|++-|- .....+...|.|+-|..
T Consensus 245 ~pCprCG~~I~--~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 245 EPCLNCKTPIR--RVVVAGRSSHYCPHCQK 272 (272)
T ss_pred CcCCCCCCeeE--EEEECCCccEECcCCcC
Confidence 35888888762 22234567799998863
No 130
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=40.08 E-value=20 Score=28.20 Aligned_cols=24 Identities=29% Similarity=0.902 Sum_probs=18.6
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.-|..|++ |.++ .+|. -.|++|++
T Consensus 29 ~hCp~Cg~---PLF~--KdG~-v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGT---PLFR--KDGE-VFCPVCGY 52 (131)
T ss_pred hhCcccCC---ccee--eCCe-EECCCCCc
Confidence 46999997 5555 6674 99999996
No 131
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=39.95 E-value=10 Score=28.00 Aligned_cols=28 Identities=21% Similarity=0.175 Sum_probs=18.8
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.|.||++||=-.++ +.-+..-+|+.|+.
T Consensus 57 ~Pa~CkkCGfef~~----~~ik~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRD----DKIKKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCccccc----cccCCcccCCcchh
Confidence 48999999865444 12234467888886
No 132
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=38.29 E-value=1.3e+02 Score=30.26 Aligned_cols=105 Identities=15% Similarity=0.193 Sum_probs=58.1
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCCCCcccCCCCCCCCCCcceEEEech-hhhc-----cCCCCcEEEEEEEc
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGRCLDADERPELCRGTVEFAASR-EFMM-----RNVMPPVYFFLIDV 160 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~~~~~d~~~rpEL~~~tvE~~~p~-~y~~-----r~~~pp~yvFvIDv 160 (211)
.+.+|.+|-++ +.+-...+.-.|-.||+.... ....|+-.+...-+..+. +... -=|..+++.|--|+
T Consensus 443 ~v~~Cp~Cd~~----lt~H~~~~~L~CH~Cg~~~~~--p~~Cp~Cgs~~L~~~G~GterieeeL~~~FP~~rv~r~d~Dt 516 (730)
T COG1198 443 YIAECPNCDSP----LTLHKATGQLRCHYCGYQEPI--PQSCPECGSEHLRAVGPGTERIEEELKRLFPGARIIRIDSDT 516 (730)
T ss_pred CcccCCCCCcc----eEEecCCCeeEeCCCCCCCCC--CCCCCCCCCCeeEEecccHHHHHHHHHHHCCCCcEEEEcccc
Confidence 36677777766 345556788999999996322 345666555444444332 2111 12566666666666
Q ss_pred chhhHhhcHHHHHHHHHHHHH-------h------cCCCCCcEEEEEEeCCeEE
Q 028291 161 STDAVQTGATAAACSAIMQVI-------S------DLPINIFVVGLLKLKIWWM 201 (211)
Q Consensus 161 S~~a~~~g~l~~v~~sL~~~l-------~------~lp~~~~~Vg~Itfd~~i~ 201 (211)
+... |.++++++.+..-= + +.|+= ++||++-=|..+.
T Consensus 517 t~~k---~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~v-tLVgvl~aD~~L~ 566 (730)
T COG1198 517 TRRK---GALEDLLDQFANGEADILIGTQMIAKGHDFPNV-TLVGVLDADTGLG 566 (730)
T ss_pred ccch---hhHHHHHHHHhCCCCCeeecchhhhcCCCcccc-eEEEEEechhhhc
Confidence 5432 33444444433310 0 12333 8999998777655
No 133
>PF14581 SseB_C: SseB protein C-terminal domain
Probab=37.94 E-value=1.2e+02 Score=22.17 Aligned_cols=44 Identities=16% Similarity=0.185 Sum_probs=31.2
Q ss_pred CCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhc-CCCCCcEEEEEEeCC
Q 028291 149 VMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISD-LPINIFVVGLLKLKI 198 (211)
Q Consensus 149 ~~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~-lp~~~~~Vg~Itfd~ 198 (211)
...|.|+++||.... ..+.+.+.|..+... ++++ .-|-|++++.
T Consensus 46 ~~~~~~li~vd~~~~-----~~~~~~~~i~~~~~~~~~~~-~~vd~~~~~~ 90 (108)
T PF14581_consen 46 DEQPSLLIGVDFDGE-----DIEEIFQEIGRAARPYLPDG-WPVDFVLLDD 90 (108)
T ss_pred CCCceEEEEEeccCh-----hHHHHHHHHHHHhhhcCCCC-ceEEEEEccC
Confidence 678999999999861 234566666666654 5665 4788888875
No 134
>PF08879 WRC: WRC; InterPro: IPR014977 WRC is named after the conserved Trp-Arg-Cys motif, it contains two distinctive features: a putative nuclear localisation signal and a zinc-finger motif (C3H). It is suggested that WRC functions in DNA binding []. ; GO: 0005515 protein binding
Probab=37.54 E-value=15 Score=23.61 Aligned_cols=10 Identities=30% Similarity=0.846 Sum_probs=8.1
Q ss_pred eCCceEEEec
Q 028291 106 DNGKSFVCNF 115 (211)
Q Consensus 106 ~~g~~w~C~~ 115 (211)
.+|+.|.|.-
T Consensus 10 ~DGK~WrC~~ 19 (46)
T PF08879_consen 10 NDGKGWRCSR 19 (46)
T ss_pred CCCCccccCC
Confidence 5788999974
No 135
>PF05117 DUF695: Family of unknown function (DUF695) ; InterPro: IPR016097 This entry is found at the N terminus of a number of proteobacterial proteins of unknown function.
Probab=37.40 E-value=1.1e+02 Score=23.25 Aligned_cols=41 Identities=12% Similarity=0.026 Sum_probs=33.1
Q ss_pred hhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEEEeecCC
Q 028291 166 QTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWMCILYGN 207 (211)
Q Consensus 166 ~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~~~~~~~ 207 (211)
+...|..+-+.|...|...++. ..||-+|.+....++=|-+
T Consensus 57 e~~~L~~iEd~i~~~l~~~~~~-i~vG~~t~~g~r~~~fY~~ 97 (136)
T PF05117_consen 57 EYEELNDIEDAIIEALEADGNA-IYVGRITGNGRREFYFYCK 97 (136)
T ss_pred HHHHHHHHHHHHHHHhhcCCcc-eEEEEEEECCEEEEEEEEC
Confidence 3456788888999998888777 7999999999988776643
No 136
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=36.68 E-value=44 Score=22.64 Aligned_cols=28 Identities=25% Similarity=0.559 Sum_probs=21.7
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
-++|..|+.-- .-|........|..|++
T Consensus 11 ~VkCp~C~n~q---~vFsha~t~V~C~~Cg~ 38 (59)
T PRK00415 11 KVKCPDCGNEQ---VVFSHASTVVRCLVCGK 38 (59)
T ss_pred EEECCCCCCeE---EEEecCCcEEECcccCC
Confidence 38999999763 34455677899999999
No 137
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=36.20 E-value=16 Score=25.60 Aligned_cols=31 Identities=23% Similarity=0.365 Sum_probs=16.7
Q ss_pred ceecCCCCeEEccceE----EE-----eCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRNPFME----FV-----DNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~----~~-----~~g~~w~C~~C~~ 118 (211)
-.-|++|++++=|-.. +. .+.-.|.|..||+
T Consensus 46 r~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 46 RTICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp CTB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred cccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 3579999998876533 34 2344688988874
No 138
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=35.19 E-value=31 Score=26.20 Aligned_cols=27 Identities=22% Similarity=0.622 Sum_probs=19.2
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
.+.|.+|.+- |+- .+|..|+|+.|++.
T Consensus 2 lp~CP~C~se---ytY--~dg~~~iCpeC~~E 28 (109)
T TIGR00686 2 LPPCPKCNSE---YTY--HDGTQLICPSCLYE 28 (109)
T ss_pred CCcCCcCCCc---ceE--ecCCeeECcccccc
Confidence 4678888763 232 45678999999993
No 139
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.16 E-value=20 Score=33.48 Aligned_cols=74 Identities=22% Similarity=0.280 Sum_probs=41.8
Q ss_pred cCCceEEEEecCCCCCCCCC---CCceecc--CCCCceecCCCCeEEccceEEEeCCceEEEecCCCCCcccCCCCCC-C
Q 028291 57 SSMPSALMVQVLALPDPSED---PIPVVDF--GESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGRCLDADERP-E 130 (211)
Q Consensus 57 ~~iPlg~vv~Pf~~~~~~e~---~vP~v~~--~~~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~~~~~d~~~rp-E 130 (211)
.+|.-|-.|++....-+..- .+.++.. -...-++|.+|++-|..-=+ + -|+|.-||+.-...+...-| +
T Consensus 314 ~~L~pGD~i~~~G~~~~~~~n~ek~~v~~l~~~~~~~p~Cp~Cg~~m~S~G~----~-g~rC~kCg~~~~~~~~~~v~r~ 388 (421)
T COG1571 314 RKLIPGDEITVYGSVKPGTLNLEKFQVLKLARYERVNPVCPRCGGRMKSAGR----N-GFRCKKCGTRARETLIKEVPRD 388 (421)
T ss_pred HhcCCCCEEEEecCccccceeEEEEEEEEeeeeEEcCCCCCccCCchhhcCC----C-CcccccccccCCcccccccccc
Confidence 56777777777765433210 0111111 11345899999998765432 2 69999999953322222333 5
Q ss_pred CCCcc
Q 028291 131 LCRGT 135 (211)
Q Consensus 131 L~~~t 135 (211)
|..|.
T Consensus 389 l~~g~ 393 (421)
T COG1571 389 LEPGV 393 (421)
T ss_pred cCCCC
Confidence 66666
No 140
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=34.76 E-value=28 Score=23.22 Aligned_cols=25 Identities=40% Similarity=0.778 Sum_probs=19.1
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
..+..|.+|+.+.=| .-.|..||..
T Consensus 25 ~~l~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 25 PGLVECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred CcceECCCCCCccCC---------eEECCCCCcC
Confidence 457899999998655 4688888873
No 141
>PRK12496 hypothetical protein; Provisional
Probab=34.65 E-value=17 Score=29.41 Aligned_cols=25 Identities=24% Similarity=0.518 Sum_probs=16.6
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
-||..|+.+. +.+-..=.|++||+.
T Consensus 128 ~~C~gC~~~~------~~~~~~~~C~~CG~~ 152 (164)
T PRK12496 128 KVCKGCKKKY------PEDYPDDVCEICGSP 152 (164)
T ss_pred EECCCCCccc------cCCCCCCcCCCCCCh
Confidence 6899999763 222112379999984
No 142
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=33.85 E-value=26 Score=22.28 Aligned_cols=23 Identities=39% Similarity=0.925 Sum_probs=16.5
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
++|..|+.. |. .|.+|+|..|.-
T Consensus 1 V~Cd~C~~~--pI-----~G~RykC~~C~d 23 (45)
T cd02344 1 VTCDGCQMF--PI-----NGPRFKCRNCDD 23 (45)
T ss_pred CCCCCCCCC--CC-----ccCeEECCCCCC
Confidence 468888865 33 357899999985
No 143
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=33.17 E-value=20 Score=35.36 Aligned_cols=25 Identities=24% Similarity=0.491 Sum_probs=19.2
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
...-+|..|+ |+ .|..|.|+.||.+
T Consensus 624 ~~~~~C~~CG-~~--------~g~~~~CP~CG~~ 648 (656)
T PRK08270 624 PTFSICPKHG-YL--------SGEHEFCPKCGEE 648 (656)
T ss_pred CCCcccCCCC-Cc--------CCCCCCCcCCcCc
Confidence 4567999999 43 4667999999964
No 144
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=32.73 E-value=22 Score=18.74 Aligned_cols=8 Identities=38% Similarity=1.265 Sum_probs=6.8
Q ss_pred EEEecCCC
Q 028291 111 FVCNFCGL 118 (211)
Q Consensus 111 w~C~~C~~ 118 (211)
|.|.+|+.
T Consensus 1 ~~C~~C~~ 8 (25)
T PF12874_consen 1 FYCDICNK 8 (25)
T ss_dssp EEETTTTE
T ss_pred CCCCCCCC
Confidence 78999986
No 145
>PF06007 PhnJ: Phosphonate metabolism protein PhnJ; InterPro: IPR010306 This family consists of several bacterial phosphonate metabolism (PhnJ) sequences. The exact role that PhnJ plays in phosphonate utilisation is unknown.; GO: 0042916 alkylphosphonate transport
Probab=32.71 E-value=24 Score=30.70 Aligned_cols=26 Identities=27% Similarity=0.712 Sum_probs=20.4
Q ss_pred eecCCCCe---EEccceEEEeCCceEEEe
Q 028291 89 VRCCCCRG---YRNPFMEFVDNGKSFVCN 114 (211)
Q Consensus 89 ~RC~~C~a---YiNp~~~~~~~g~~w~C~ 114 (211)
-.|..|++ |+.-...-+.++++|+|+
T Consensus 236 ~~C~~CGs~~s~LdEvi~dd~G~~~~~CS 264 (277)
T PF06007_consen 236 GPCALCGSTDSFLDEVIDDDDGGRMFVCS 264 (277)
T ss_pred CcccccCCCceeceeeEEcCCCCEEEEEC
Confidence 37888876 777776667789999997
No 146
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=32.00 E-value=26 Score=27.28 Aligned_cols=31 Identities=23% Similarity=0.420 Sum_probs=23.0
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
...-+|..|+.-+-...+. ...++.|..|+.
T Consensus 121 ~~~~~C~~C~~~~~r~~~~--~~~~~~C~~C~~ 151 (157)
T PF10263_consen 121 KYVYRCPSCGREYKRHRRS--KRKRYRCGRCGG 151 (157)
T ss_pred ceEEEcCCCCCEeeeeccc--chhhEECCCCCC
Confidence 4578899999877666665 455689999974
No 147
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=31.83 E-value=41 Score=20.96 Aligned_cols=24 Identities=33% Similarity=0.836 Sum_probs=16.8
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~ 117 (211)
-.|..|+ .|.++ +.+| +-.|..|+
T Consensus 18 ~~Cp~C~---~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCG---TPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred CccCCCC---CeeEE-ecCC-CEECCCCC
Confidence 3577885 47777 4555 47899885
No 148
>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=31.50 E-value=33 Score=21.70 Aligned_cols=28 Identities=25% Similarity=0.603 Sum_probs=20.5
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
..+..|..|+..|-. .....+.|..|+.
T Consensus 9 ~~~~~C~~C~~~i~g-----~~~~g~~C~~C~~ 36 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWG-----LGKQGYRCSWCGL 36 (53)
T ss_dssp SSTEB-TTSSSBECS-----SSSCEEEETTTT-
T ss_pred CCCCCCcccCcccCC-----CCCCeEEECCCCC
Confidence 568899999999822 3456799999997
No 149
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=31.43 E-value=8.7 Score=25.33 Aligned_cols=29 Identities=34% Similarity=0.714 Sum_probs=23.1
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.|.+|++--.|..+-...+..-.||-|+.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl 29 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGL 29 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHH
Confidence 38899997777777666577789999998
No 150
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=31.38 E-value=56 Score=19.43 Aligned_cols=26 Identities=23% Similarity=0.530 Sum_probs=15.5
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
-|..|+..|=| +-+..++. .|.-|+.
T Consensus 3 FCp~C~nlL~p--~~~~~~~~-~C~~C~Y 28 (35)
T PF02150_consen 3 FCPECGNLLYP--KEDKEKRV-ACRTCGY 28 (35)
T ss_dssp BETTTTSBEEE--EEETTTTE-EESSSS-
T ss_pred eCCCCCccceE--cCCCccCc-CCCCCCC
Confidence 47778877643 33444444 7877775
No 151
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=31.21 E-value=27 Score=26.25 Aligned_cols=10 Identities=40% Similarity=1.076 Sum_probs=8.9
Q ss_pred ceEEEecCCC
Q 028291 109 KSFVCNFCGL 118 (211)
Q Consensus 109 ~~w~C~~C~~ 118 (211)
.+|+|-+||.
T Consensus 1 ~kWkC~iCg~ 10 (101)
T PF09943_consen 1 KKWKCYICGK 10 (101)
T ss_pred CceEEEecCC
Confidence 3799999998
No 152
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=31.16 E-value=29 Score=23.22 Aligned_cols=23 Identities=30% Similarity=0.736 Sum_probs=18.0
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
..+.+|.+|+.| .+ +-+|+.||.
T Consensus 3 s~mr~C~~CgvY-----TL-----k~~CP~CG~ 25 (56)
T PRK13130 3 SKIRKCPKCGVY-----TL-----KEICPVCGG 25 (56)
T ss_pred ccceECCCCCCE-----Ec-----cccCcCCCC
Confidence 357899999999 11 358999998
No 153
>PF12773 DZR: Double zinc ribbon
Probab=30.53 E-value=17 Score=22.83 Aligned_cols=29 Identities=17% Similarity=0.353 Sum_probs=20.7
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
.+-..|.+|++-+. ......++|.-|++.
T Consensus 10 ~~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP-----PPDQSKKICPNCGAE 38 (50)
T ss_pred ccccCChhhcCChh-----hccCCCCCCcCCcCC
Confidence 34577888888876 345556888888874
No 154
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=30.48 E-value=28 Score=22.77 Aligned_cols=26 Identities=31% Similarity=0.653 Sum_probs=17.4
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
..|.+|++= -|+- .-+.+|.|.-||.
T Consensus 20 ~~CPrCG~g--vfmA--~H~dR~~CGkCgy 45 (51)
T COG1998 20 RFCPRCGPG--VFMA--DHKDRWACGKCGY 45 (51)
T ss_pred ccCCCCCCc--chhh--hcCceeEeccccc
Confidence 579999942 2333 2334799999986
No 155
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=30.21 E-value=45 Score=29.00 Aligned_cols=26 Identities=19% Similarity=0.358 Sum_probs=18.0
Q ss_pred cCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 91 C~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
|.+|++-|-- ....+...|.|+-|..
T Consensus 248 C~~Cg~~I~~--~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 248 CRRCGTPIEK--IKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCeeEE--EEECCCCcEECcCCCC
Confidence 8889877632 2234567899999974
No 156
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=30.18 E-value=34 Score=30.13 Aligned_cols=28 Identities=18% Similarity=0.430 Sum_probs=20.2
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
--|.+|++-|---. ..+...|.|+-|.+
T Consensus 246 epC~~CGt~I~k~~--~~gR~t~~CP~CQ~ 273 (273)
T COG0266 246 EPCRRCGTPIEKIK--LGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCccCCEeEEEE--EcCCcCEeCCCCCC
Confidence 45889999875433 34556799999974
No 157
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=29.66 E-value=35 Score=21.85 Aligned_cols=23 Identities=30% Similarity=0.696 Sum_probs=16.1
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
++|..|+.. |.. |.+|+|..|.-
T Consensus 1 i~C~~C~~~--~i~-----g~R~~C~~C~d 23 (49)
T cd02338 1 VSCDGCGKS--NFT-----GRRYKCLICYD 23 (49)
T ss_pred CCCCCCcCC--CcE-----EeeEEeCCCCC
Confidence 478888852 222 56899999965
No 158
>KOG3886 consensus GTP-binding protein [Signal transduction mechanisms]
Probab=29.63 E-value=1.4e+02 Score=26.27 Aligned_cols=42 Identities=14% Similarity=0.256 Sum_probs=32.2
Q ss_pred cEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCCCCcEEEEEE
Q 028291 152 PVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLK 195 (211)
Q Consensus 152 p~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~lp~~~~~Vg~It 195 (211)
-+.+||.|++...++. .++...++|++.++.-|+. ..+.+++
T Consensus 83 ~vli~vFDves~e~~~-D~~~yqk~Le~ll~~SP~A-kiF~l~h 124 (295)
T KOG3886|consen 83 QVLIYVFDVESREMEK-DFHYYQKCLEALLQNSPEA-KIFCLLH 124 (295)
T ss_pred eeeeeeeeccchhhhh-hHHHHHHHHHHHHhcCCcc-eEEEEEe
Confidence 3577888998887764 4788888999999999888 4666654
No 159
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=28.72 E-value=42 Score=25.37 Aligned_cols=30 Identities=20% Similarity=0.281 Sum_probs=22.7
Q ss_pred eecCCCCeEEccceE----EEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFME----FVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~----~~~~g~~w~C~~C~~ 118 (211)
--|++|.+.|=|..+ +..+.-.|+|--||.
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~ 90 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGT 90 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCc
Confidence 459999997665544 455556899999998
No 160
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=28.63 E-value=40 Score=22.31 Aligned_cols=24 Identities=38% Similarity=0.823 Sum_probs=17.3
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
..+..|..|+.+.=| ..+|..||.
T Consensus 24 p~l~~C~~cG~~~~~---------H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEFKLP---------HRVCPSCGY 47 (55)
T ss_pred CcceECCCCCCcccC---------eeECCccCe
Confidence 457889999997443 357777775
No 161
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=28.51 E-value=89 Score=28.11 Aligned_cols=29 Identities=7% Similarity=-0.010 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHhcCCCCCcEEEEEEeCC
Q 028291 169 ATAAACSAIMQVISDLPINIFVVGLLKLKI 198 (211)
Q Consensus 169 ~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~ 198 (211)
-|..+.++|.++++.|..+ -++++|||.+
T Consensus 219 EL~~L~~~L~~a~~~L~~g-GRl~VIsFHS 247 (314)
T COG0275 219 ELEELEEALEAALDLLKPG-GRLAVISFHS 247 (314)
T ss_pred HHHHHHHHHHHHHHhhCCC-cEEEEEEecc
Confidence 4788999999999999988 5999999975
No 162
>PF06061 Baculo_ME53: Baculoviridae ME53; InterPro: IPR010336 ME53 is one of the major early-transcribed genes. The ME53 protein is reported to contain a putative zinc finger motif [].; GO: 0003677 DNA binding, 0008270 zinc ion binding
Probab=28.41 E-value=20 Score=32.36 Aligned_cols=87 Identities=17% Similarity=0.151 Sum_probs=52.2
Q ss_pred ceEEEecCCCCCc---ccC-CCCCCCCCCcceEEEechhhhccCCCCcEEEEEEEcchhhHh------hcHHHHHHHHHH
Q 028291 109 KSFVCNFCGLDGR---CLD-ADERPELCRGTVEFAASREFMMRNVMPPVYFFLIDVSTDAVQ------TGATAAACSAIM 178 (211)
Q Consensus 109 ~~w~C~~C~~~~~---~~d-~~~rpEL~~~tvE~~~p~~y~~r~~~pp~yvFvIDvS~~a~~------~g~l~~v~~sL~ 178 (211)
=++.|.-|..... ..| .+..|-|+..+|+-+.-.. ---.|+|=||.+..... .+ +.+-+.|+
T Consensus 91 fk~~C~~C~~~~~~~~~~dv~eLYP~l~L~~V~kL~~~g------f~~KyiFpi~~~~~~~~~~~~~~~~--~d~~~~~~ 162 (327)
T PF06061_consen 91 FKFCCLDCCNDYKDDDQMDVIELYPTLSLSNVKKLCYNG------FFKKYIFPIDLEYTVFYKKYIVIDH--HDVYKVFQ 162 (327)
T ss_pred EEEEhhhhhhhcccccceEEEEecCcccHHHHHHHHHcC------CeEEEEeeeecCcEEEEEEEEeecC--CCHHHHHH
Confidence 3577888887432 222 4566776665554433222 22358888888764332 21 24666667
Q ss_pred HHHhcCCCC-C-cEEEEEEeCCeEEEe
Q 028291 179 QVISDLPIN-I-FVVGLLKLKIWWMCI 203 (211)
Q Consensus 179 ~~l~~lp~~-~-~~Vg~Itfd~~i~~~ 203 (211)
++|+.-..+ . ..|.|.|++..|.-+
T Consensus 163 ~Ii~~K~~NEqI~~I~L~t~g~~v~~E 189 (327)
T PF06061_consen 163 DIIREKKPNEQIVKITLRTYGRVVFEE 189 (327)
T ss_pred HHHhcCCCCccEEEEEEEECCceeEEE
Confidence 777653333 3 889999999988744
No 163
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=28.01 E-value=41 Score=20.46 Aligned_cols=10 Identities=30% Similarity=0.760 Sum_probs=4.7
Q ss_pred ceecCCCCeE
Q 028291 88 LVRCCCCRGY 97 (211)
Q Consensus 88 p~RC~~C~aY 97 (211)
+-+|.+|++.
T Consensus 19 id~C~~C~G~ 28 (41)
T PF13453_consen 19 IDVCPSCGGI 28 (41)
T ss_pred EEECCCCCeE
Confidence 4445555443
No 164
>COG1773 Rubredoxin [Energy production and conversion]
Probab=27.77 E-value=34 Score=22.82 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=7.7
Q ss_pred CceEEEecCCC
Q 028291 108 GKSFVCNFCGL 118 (211)
Q Consensus 108 g~~w~C~~C~~ 118 (211)
-..|.|+.|+.
T Consensus 34 Pd~w~CP~Cg~ 44 (55)
T COG1773 34 PDDWVCPECGV 44 (55)
T ss_pred CCccCCCCCCC
Confidence 33488888876
No 165
>TIGR00006 S-adenosyl-methyltransferase MraW. Genetics paper in 1972 links mra cluster to peptidoglycan biosynthesis in E. coli. Seems to be common in proteobacteria.wn.
Probab=27.48 E-value=86 Score=28.03 Aligned_cols=31 Identities=6% Similarity=-0.052 Sum_probs=26.3
Q ss_pred hcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCC
Q 028291 167 TGATAAACSAIMQVISDLPINIFVVGLLKLKI 198 (211)
Q Consensus 167 ~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~ 198 (211)
++-|+.+.++|..+.+-|..+ -++++|||.+
T Consensus 213 N~EL~~L~~~L~~~~~~L~~g-Grl~VISfHS 243 (305)
T TIGR00006 213 NDELEELEEALQFAPNLLAPG-GRLSIISFHS 243 (305)
T ss_pred HHhHHHHHHHHHHHHHHhcCC-CEEEEEecCc
Confidence 556788889999999989888 5999999974
No 166
>PRK07218 replication factor A; Provisional
Probab=27.47 E-value=30 Score=32.37 Aligned_cols=23 Identities=22% Similarity=0.306 Sum_probs=18.7
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.-+-||..|+=.| .+|+|+.||.
T Consensus 295 gli~rCP~C~r~v----------~~~~C~~hG~ 317 (423)
T PRK07218 295 GLIERCPECGRVI----------QKGQCRSHGA 317 (423)
T ss_pred cceecCcCccccc----------cCCcCCCCCC
Confidence 4468999999887 2389999998
No 167
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=27.46 E-value=23 Score=24.36 Aligned_cols=21 Identities=24% Similarity=0.517 Sum_probs=15.6
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
.-|++|+...+ ++ +|+.||..
T Consensus 6 ~AC~~C~~i~~--------~~--~Cp~Cgs~ 26 (64)
T PRK06393 6 RACKKCKRLTP--------EK--TCPVHGDE 26 (64)
T ss_pred hhHhhCCcccC--------CC--cCCCCCCC
Confidence 45899998762 22 89999984
No 168
>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=26.79 E-value=45 Score=29.15 Aligned_cols=30 Identities=20% Similarity=0.573 Sum_probs=17.0
Q ss_pred CceecCCCCeEEccceEEEeC-----CceEEEecCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDN-----GKSFVCNFCGL 118 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~-----g~~w~C~~C~~ 118 (211)
.-..|.-||+. |.+.+..+ .+.-.|.+|++
T Consensus 171 ~~g~CPvCGs~--P~~s~l~~~~~~G~R~L~Cs~C~t 205 (290)
T PF04216_consen 171 QRGYCPVCGSP--PVLSVLRGGEREGKRYLHCSLCGT 205 (290)
T ss_dssp T-SS-TTT-----EEEEEEE------EEEEEETTT--
T ss_pred cCCcCCCCCCc--CceEEEecCCCCccEEEEcCCCCC
Confidence 34799999998 77776554 37789999999
No 169
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=26.77 E-value=48 Score=24.72 Aligned_cols=33 Identities=21% Similarity=0.419 Sum_probs=24.4
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
.....|.+|++. .--+.++.+...-.|..||..
T Consensus 19 pt~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGKV-SISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCCe-EeeeecCCCcceEECCCCCCc
Confidence 346889999963 444556667778899999983
No 170
>smart00400 ZnF_CHCC zinc finger.
Probab=26.57 E-value=88 Score=20.11 Aligned_cols=22 Identities=27% Similarity=0.560 Sum_probs=16.5
Q ss_pred cceEEEeCCceEEEecCCCCCc
Q 028291 100 PFMEFVDNGKSFVCNFCGLDGR 121 (211)
Q Consensus 100 p~~~~~~~g~~w~C~~C~~~~~ 121 (211)
|-+.++...+.|.|--|+..|.
T Consensus 13 pSf~v~~~kn~~~Cf~cg~gGd 34 (55)
T smart00400 13 PSFSVSPDKQFFHCFGCGAGGN 34 (55)
T ss_pred CCEEEECCCCEEEEeCCCCCCC
Confidence 4456666778899999998654
No 171
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=26.48 E-value=68 Score=26.75 Aligned_cols=29 Identities=28% Similarity=0.643 Sum_probs=23.6
Q ss_pred ceecCCCCeEEccceEEEeCCceE--EEecCCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSF--VCNFCGLD 119 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w--~C~~C~~~ 119 (211)
=+.|..|+. |=..+...++.| .|.-||..
T Consensus 98 yV~C~~C~~---pdT~l~k~~~~~~l~C~aCGa~ 128 (201)
T PRK12336 98 YVICSECGL---PDTRLVKEDRVLMLRCDACGAH 128 (201)
T ss_pred eEECCCCCC---CCcEEEEcCCeEEEEcccCCCC
Confidence 489999997 788887766665 69999994
No 172
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=26.42 E-value=43 Score=20.87 Aligned_cols=22 Identities=32% Similarity=0.685 Sum_probs=15.5
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
+.|..|+.. . .|.+|+|..|..
T Consensus 1 v~Cd~C~~~---i-----~G~ry~C~~C~d 22 (43)
T cd02340 1 VICDGCQGP---I-----VGVRYKCLVCPD 22 (43)
T ss_pred CCCCCCCCc---C-----cCCeEECCCCCC
Confidence 468888872 1 356799999964
No 173
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=26.28 E-value=30 Score=31.63 Aligned_cols=25 Identities=24% Similarity=0.523 Sum_probs=19.0
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
...-||.+|| |....-.|.|+-|+.
T Consensus 352 ~~~YRC~~CG--------F~a~~l~W~CPsC~~ 376 (389)
T COG2956 352 KPRYRCQNCG--------FTAHTLYWHCPSCRA 376 (389)
T ss_pred cCCceecccC--------CcceeeeeeCCCccc
Confidence 4568999997 233445799999998
No 174
>PF14353 CpXC: CpXC protein
Probab=25.84 E-value=62 Score=24.53 Aligned_cols=11 Identities=45% Similarity=0.920 Sum_probs=8.7
Q ss_pred ceEEEecCCCC
Q 028291 109 KSFVCNFCGLD 119 (211)
Q Consensus 109 ~~w~C~~C~~~ 119 (211)
..++|+-||+.
T Consensus 37 ~~~~CP~Cg~~ 47 (128)
T PF14353_consen 37 FSFTCPSCGHK 47 (128)
T ss_pred CEEECCCCCCc
Confidence 36899999984
No 175
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.84 E-value=55 Score=28.66 Aligned_cols=27 Identities=15% Similarity=0.239 Sum_probs=17.8
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
-|.+|++-|-- ....+...|.|+-|..
T Consensus 256 pC~~Cg~~I~~--~~~~gR~t~~CP~CQ~ 282 (282)
T PRK13945 256 PCRKCGTPIER--IKLAGRSTHWCPNCQK 282 (282)
T ss_pred CCCcCCCeeEE--EEECCCccEECCCCcC
Confidence 48888876642 2234567788888863
No 176
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=25.45 E-value=99 Score=27.47 Aligned_cols=31 Identities=6% Similarity=-0.007 Sum_probs=26.1
Q ss_pred hcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCC
Q 028291 167 TGATAAACSAIMQVISDLPINIFVVGLLKLKI 198 (211)
Q Consensus 167 ~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~ 198 (211)
++-++.+...|.++.+.|..+ -++++|||.+
T Consensus 209 N~El~~L~~~L~~~~~~L~~g-Grl~visfHS 239 (296)
T PRK00050 209 NDELEELERALEAALDLLKPG-GRLAVISFHS 239 (296)
T ss_pred HhhHHHHHHHHHHHHHHhcCC-CEEEEEecCc
Confidence 456788888899999889888 5999999974
No 177
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=25.42 E-value=24 Score=21.28 Aligned_cols=26 Identities=23% Similarity=0.361 Sum_probs=12.6
Q ss_pred cCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 91 C~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
|..|++.-|-... ......+|..||.
T Consensus 4 C~~Cg~~Yh~~~~--pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 4 CPKCGRIYHIEFN--PPKVEGVCDNCGG 29 (36)
T ss_dssp ETTTTEEEETTTB----SSTTBCTTTTE
T ss_pred cCCCCCccccccC--CCCCCCccCCCCC
Confidence 6666666664433 2233345555553
No 178
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=24.95 E-value=46 Score=18.16 Aligned_cols=12 Identities=33% Similarity=1.063 Sum_probs=8.8
Q ss_pred CCceEEEecCCC
Q 028291 107 NGKSFVCNFCGL 118 (211)
Q Consensus 107 ~g~~w~C~~C~~ 118 (211)
+.+.|.|..|+.
T Consensus 11 ~~k~~~C~~C~k 22 (26)
T PF13465_consen 11 GEKPYKCPYCGK 22 (26)
T ss_dssp SSSSEEESSSSE
T ss_pred CCCCCCCCCCcC
Confidence 456688888874
No 179
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=24.86 E-value=35 Score=21.20 Aligned_cols=26 Identities=35% Similarity=0.943 Sum_probs=12.4
Q ss_pred cCCCCeEEccceEEEe--CCceEEEecCC
Q 028291 91 CCCCRGYRNPFMEFVD--NGKSFVCNFCG 117 (211)
Q Consensus 91 C~~C~aYiNp~~~~~~--~g~~w~C~~C~ 117 (211)
|..|++ -.-|.-|+. ++..|+|+-|+
T Consensus 6 CP~CGG-~DrFri~~d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 6 CPICGG-KDRFRIFDDKDGRGTWICRQCG 33 (40)
T ss_dssp -TTTT--TTTEEEETT----S-EEETTTT
T ss_pred CCCCcC-ccccccCcCcccCCCEECCCCC
Confidence 566666 233333432 34579999994
No 180
>PRK10445 endonuclease VIII; Provisional
Probab=24.64 E-value=64 Score=27.96 Aligned_cols=26 Identities=19% Similarity=0.438 Sum_probs=14.0
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~ 117 (211)
.|.+|++-|- .....+...|.|+-|.
T Consensus 237 ~Cp~Cg~~I~--~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 237 ACERCGGIIE--KTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCEeE--EEEECCCCcEECCCCc
Confidence 3666666552 1122345567777665
No 181
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=24.21 E-value=32 Score=23.44 Aligned_cols=21 Identities=24% Similarity=0.624 Sum_probs=15.1
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGLDG 120 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~~ 120 (211)
-|++|+..+. .. +|+.||...
T Consensus 5 AC~~C~~i~~--------~~--~CP~Cgs~~ 25 (61)
T PRK08351 5 ACRHCHYITT--------ED--RCPVCGSRD 25 (61)
T ss_pred hhhhCCcccC--------CC--cCCCCcCCc
Confidence 5899988762 22 699999843
No 182
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=24.12 E-value=59 Score=34.49 Aligned_cols=26 Identities=31% Similarity=0.783 Sum_probs=22.0
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
---|..|+.| ++.++|..|+|.-||.
T Consensus 1190 g~~c~~cg~~-----~~vrngtc~~c~~cg~ 1215 (1220)
T PRK07562 1190 GEACSECGNF-----TLVRNGTCLKCDTCGS 1215 (1220)
T ss_pred CCcCCCcCCe-----EEEeCCeeeeccccCC
Confidence 3449999987 6778999999999997
No 183
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=23.68 E-value=75 Score=28.15 Aligned_cols=30 Identities=23% Similarity=0.568 Sum_probs=22.3
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
....+|..|++ +... .|....-.+|.-||.
T Consensus 9 ~~~~~Cp~Cg~--~~iv-~d~~~Ge~vC~~CG~ 38 (310)
T PRK00423 9 EEKLVCPECGS--DKLI-YDYERGEIVCADCGL 38 (310)
T ss_pred ccCCcCcCCCC--CCee-EECCCCeEeecccCC
Confidence 45678999997 3333 355666799999999
No 184
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=23.58 E-value=29 Score=23.83 Aligned_cols=23 Identities=22% Similarity=0.665 Sum_probs=16.0
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGLDG 120 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~~ 120 (211)
-|.+|+..++. ..=+|+.||.+.
T Consensus 6 AC~~Ck~l~~~--------d~e~CP~Cgs~~ 28 (64)
T COG2093 6 ACKNCKRLTPE--------DTEICPVCGSTD 28 (64)
T ss_pred HHhhccccCCC--------CCccCCCCCCcc
Confidence 48888877543 234899999853
No 185
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.43 E-value=33 Score=32.62 Aligned_cols=11 Identities=18% Similarity=0.389 Sum_probs=5.5
Q ss_pred ceecCCCCeEE
Q 028291 88 LVRCCCCRGYR 98 (211)
Q Consensus 88 p~RC~~C~aYi 98 (211)
..+|.+|.+.|
T Consensus 222 ~~~C~~C~~~l 232 (505)
T TIGR00595 222 ILCCPNCDVSL 232 (505)
T ss_pred ccCCCCCCCce
Confidence 34555555443
No 186
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=23.39 E-value=39 Score=26.26 Aligned_cols=29 Identities=17% Similarity=0.532 Sum_probs=19.4
Q ss_pred eecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
++|.=|+.. ....++...+.|.|.-|+..
T Consensus 1 v~C~fC~~~--s~~~~~~~~~~w~C~~C~q~ 29 (131)
T PF09779_consen 1 VNCWFCGQN--SKVPYDNRNSNWTCPHCEQY 29 (131)
T ss_pred CeeccCCCC--CCCCCCCCCCeeECCCCCCc
Confidence 467777765 33444445556999999993
No 187
>PRK04351 hypothetical protein; Provisional
Probab=23.27 E-value=59 Score=25.92 Aligned_cols=31 Identities=23% Similarity=0.339 Sum_probs=21.0
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.-.-||.+|+.-.--.-++ +..+++|.-|+.
T Consensus 110 ~y~Y~C~~Cg~~~~r~Rr~--n~~~yrCg~C~g 140 (149)
T PRK04351 110 NYLYECQSCGQQYLRKRRI--NTKRYRCGKCRG 140 (149)
T ss_pred eEEEECCCCCCEeeeeeec--CCCcEEeCCCCc
Confidence 3568999999754322332 446799999986
No 188
>PHA02942 putative transposase; Provisional
Probab=23.21 E-value=46 Score=30.55 Aligned_cols=27 Identities=26% Similarity=0.427 Sum_probs=20.0
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.--.|+.||...- ...++.|.|.-||.
T Consensus 324 TSq~Cs~CG~~~~-----~l~~r~f~C~~CG~ 350 (383)
T PHA02942 324 SSVSCPKCGHKMV-----EIAHRYFHCPSCGY 350 (383)
T ss_pred CCccCCCCCCccC-----cCCCCEEECCCCCC
Confidence 3467999998542 23467899999999
No 189
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=23.08 E-value=28 Score=23.79 Aligned_cols=13 Identities=31% Similarity=0.473 Sum_probs=10.2
Q ss_pred CceecCCCCeEEc
Q 028291 87 GLVRCCCCRGYRN 99 (211)
Q Consensus 87 ~p~RC~~C~aYiN 99 (211)
-|+||-.||..|.
T Consensus 3 iPiRCFsCGkvi~ 15 (63)
T COG1644 3 IPVRCFSCGKVIG 15 (63)
T ss_pred CceEeecCCCCHH
Confidence 4789999988764
No 190
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=22.99 E-value=68 Score=24.84 Aligned_cols=28 Identities=32% Similarity=0.762 Sum_probs=20.7
Q ss_pred ceecCCCCeEEccceEEEeCCceE--EEecCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSF--VCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w--~C~~C~~ 118 (211)
=+.|..|+ ||=..+...++.| .|.-||.
T Consensus 93 yVlC~~C~---spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 93 YVLCPECG---SPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp HSSCTSTS---SSSEEEEEETTCCEEEETTTSC
T ss_pred EEEcCCCC---CCccEEEEcCCEEEEEecccCC
Confidence 38999999 5677776655544 6888886
No 191
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.71 E-value=69 Score=27.87 Aligned_cols=27 Identities=19% Similarity=0.327 Sum_probs=18.5
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
-|.+|++-|-- ...-+...|.|+-|..
T Consensus 237 pC~~Cg~~I~~--~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 237 PCPRCGTPIEK--IVVGGRGTHFCPQCQP 263 (269)
T ss_pred CCCcCCCeeEE--EEECCCCcEECCCCcC
Confidence 48888876533 2234567899999876
No 192
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=22.61 E-value=34 Score=23.41 Aligned_cols=13 Identities=31% Similarity=0.439 Sum_probs=10.3
Q ss_pred CceecCCCCeEEc
Q 028291 87 GLVRCCCCRGYRN 99 (211)
Q Consensus 87 ~p~RC~~C~aYiN 99 (211)
-|+||-.||..|.
T Consensus 3 iPvRCFTCGkvi~ 15 (62)
T PRK04016 3 IPVRCFTCGKVIA 15 (62)
T ss_pred CCeEecCCCCChH
Confidence 3789999988764
No 193
>PRK10220 hypothetical protein; Provisional
Probab=22.58 E-value=69 Score=24.41 Aligned_cols=27 Identities=19% Similarity=0.620 Sum_probs=18.9
Q ss_pred ceecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
.+.|..|.+- |.- .+|..|+|+.|++.
T Consensus 3 lP~CP~C~se---ytY--~d~~~~vCpeC~hE 29 (111)
T PRK10220 3 LPHCPKCNSE---YTY--EDNGMYICPECAHE 29 (111)
T ss_pred CCcCCCCCCc---ceE--cCCCeEECCcccCc
Confidence 4678888753 222 45678999999983
No 194
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.54 E-value=1.3e+02 Score=21.77 Aligned_cols=32 Identities=16% Similarity=0.202 Sum_probs=21.5
Q ss_pred CCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhc
Q 028291 150 MPPVYFFLIDVSTDAVQTGATAAACSAIMQVISD 183 (211)
Q Consensus 150 ~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~ 183 (211)
....|.|.||+... +..-++.+++.|+..|..
T Consensus 53 ~~~~Y~FfVDieg~--~~~~~~~~l~~L~~~~~~ 84 (90)
T cd04931 53 NKDEYEFFINLDKK--SAPALDPIIKSLRNDIGA 84 (90)
T ss_pred CCceEEEEEEEEcC--CCHHHHHHHHHHHHHhCC
Confidence 34579999999864 223456677777776653
No 195
>PF00362 Integrin_beta: Integrin, beta chain; InterPro: IPR002369 Integrins are the major metazoan receptors for cell adhesion to extracellular matrix proteins and, in vertebrates, also play important roles in certain cell-cell adhesions, make transmembrane connections to the cytoskeleton and activate many intracellular signalling pathways [, ]. The integrin receptors are composed of alpha and beta subunit heterodimers. Each subunit crosses the membrane once, with most of the polypeptide residing in the extracellular space, and has two short cytoplasmic domains. Some members of this family have EGF repeats at the C terminus and also have a vWA domain inserted within the integrin domain at the N terminus. Most integrins recognise relatively short peptide motifs, and in general require an acidic amino acid to be present. Ligand specificity depends upon both the alpha and beta subunits []. There are at least 18 types of alpha and 8 types of beta subunits recognised in humans []. Each alpha subunit tends to associate only with one type of beta subunit, but there are exceptions to this rule []. Each association of alpha and beta subunits has its own binding specificity and signalling properties. Many integrins require activation on the cell surface before they can bind ligands. Integrins frequently intercommunicate, and binding at one integrin receptor activate or inhibit another. The structure of unliganded alphaV beta3 showed the molecule to be folded, with the head bent over towards the C termini of the legs which would normally be inserted into the membrane []. The head comprises a beta propeller domain at the end terminus of the alphaV subunit and an I/A domain inserted into a loop on the top of the hybrid domain in the beta subunit. The I/A domain consists of a Rossman fold with a core of beta parallel sheets surrounded by amphipathic alpha helices. Integrins are important therapeutic targets in conditions such as atherosclerosis, thrombosis, cancer and asthma []. At the N terminus of the beta subunit is a cysteine-containing domain reminiscent of that found in presenillins and semaphorins, which has hence been termed the PSI domain. C-terminal to the PSI domain is an A-domain, which has been predicted to adopt a Rossmann fold similar to that of the alpha subunit, but with additional loops between the second and third beta strands []. The murine gene Pactolus shares significant similarity with the beta subunit [], but lacks either one or both of the inserted loops. The C-terminal portion of the beta subunit extracellular domain contains an internally disulphide-bonded cysteine-rich region, while the intracellular tail contains putative sites of interaction with a variety of intracellular signalling and cytoskeletal proteins, such as focal adhesion kinase and alpha-actinin respectively []. Integrin cytoplasmic domains are normally less than 50 amino acids in length, with the beta-subunit sequences exhibiting greater homology to each other than the alpha-subunit sequences. This is consistent with current evidence that the beta subunit is the principal site for binding of cytoskeletal and signalling molecules, whereas the alpha subunit has a regulatory role. The first 20 amino acids of the beta-subunit cytoplasmic domain are also alpha helical, but the final 25 residues are disordered and, apart from a turn that follows a conserved NPxY motif, appear to lack defined structure, suggesting that this is adopted on effector binding. The two membrane-proximal helices mediate the link between the subunits via a series of hydrophobic and electrostatic contacts. This entry represents the N-terminal portion of the extracellular region of integrin beta subunits.; GO: 0005488 binding, 0007155 cell adhesion, 0007160 cell-matrix adhesion; PDB: 3VI4_B 3VI3_B 2VDQ_B 3IJE_B 1M1X_B 2VDR_B 3NIF_B 3NID_D 1TYE_F 2Q6W_F ....
Probab=22.00 E-value=1.4e+02 Score=27.85 Aligned_cols=48 Identities=15% Similarity=0.276 Sum_probs=32.2
Q ss_pred CCcEEEEEEEcchhhHh--hcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCe
Q 028291 150 MPPVYFFLIDVSTDAVQ--TGATAAACSAIMQVISDLPINIFVVGLLKLKIW 199 (211)
Q Consensus 150 ~pp~yvFvIDvS~~a~~--~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~ 199 (211)
.|--.-|++|+|. +++ -.-++.+-..|...|..+-.+ .++||=+|-..
T Consensus 101 yPvDLYyLmDlS~-Sm~ddl~~l~~lg~~l~~~~~~it~~-~~~GfGsfvdK 150 (426)
T PF00362_consen 101 YPVDLYYLMDLSY-SMKDDLENLKSLGQDLAEEMRNITSN-FRLGFGSFVDK 150 (426)
T ss_dssp --EEEEEEEE-SG-GGHHHHHHHCCCCHHHHHHHHTT-SS-EEEEEEEESSS
T ss_pred cceeEEEEeechh-hhhhhHHHHHHHHHHHHHHHHhcCcc-ceEechhhccc
Confidence 4566889999997 333 222445567888888889888 79999998543
No 196
>PRK11827 hypothetical protein; Provisional
Probab=21.98 E-value=69 Score=21.71 Aligned_cols=28 Identities=18% Similarity=0.587 Sum_probs=21.3
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
+++.|..|++=+- ++.++...+|..|+.
T Consensus 7 eILaCP~ckg~L~----~~~~~~~Lic~~~~l 34 (60)
T PRK11827 7 EIIACPVCNGKLW----YNQEKQELICKLDNL 34 (60)
T ss_pred hheECCCCCCcCe----EcCCCCeEECCccCe
Confidence 5789999998542 345566789999987
No 197
>PF11130 TraC_F_IV: F pilus assembly Type-IV secretion system for plasmid transfer
Probab=21.89 E-value=1.6e+02 Score=24.39 Aligned_cols=41 Identities=22% Similarity=0.288 Sum_probs=29.2
Q ss_pred EEEEEcchhhHhhcHHHHHHHHHHHHHh-cCCCCCcEEEEEEeCCe
Q 028291 155 FFLIDVSTDAVQTGATAAACSAIMQVIS-DLPINIFVVGLLKLKIW 199 (211)
Q Consensus 155 vFvIDvS~~a~~~g~l~~v~~sL~~~l~-~lp~~~~~Vg~Itfd~~ 199 (211)
=|+++++... |.-+.+.+.|.++|. .+|++ +.|=|+.|++.
T Consensus 29 Gf~~e~~Pl~---ga~~~~~~~L~~~l~~~lP~~-t~iQ~~l~~sp 70 (235)
T PF11130_consen 29 GFVFECSPLP---GADESTQEALESLLNDDLPEG-TVIQFYLFASP 70 (235)
T ss_pred EEEEEEechh---hcCHHHHHHHHHHHcccCCCC-CeEEEEEEeCC
Confidence 3555665543 333568899999998 89999 68888887753
No 198
>PF11524 SeleniumBinding: Selenium binding protein; InterPro: IPR021603 Selenium is an important nutrient which needs to be regulated since lack of the nutrient leads to cell abnormalities and high concentrations are toxic.SeBP regulates the level of free selenium in the cell by sequestering the nutrient during transport. SeBP acts as a pentamer and delivers the selenium to the selenophosphate synthetase enzyme []. Each subunit is composed of an alpha helix on top of a four stranded twisted ss sheet, stabilised by hydrogen bonds []. members of this entry are restricted to the archaeal Methanococcales.; PDB: 2JZ7_D.
Probab=21.75 E-value=43 Score=23.91 Aligned_cols=37 Identities=8% Similarity=-0.083 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHhcCCCCCcEEEEEEeCCeEEEeecCC
Q 028291 170 TAAACSAIMQVISDLPINIFVVGLLKLKIWWMCILYGN 207 (211)
Q Consensus 170 l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~~i~~~~~~~ 207 (211)
.+.+++.|+...++.... ..|||=+-....++.+||-
T Consensus 33 vd~li~~lee~vk~k~~~-giigFki~~~d~Kl~GYGt 69 (81)
T PF11524_consen 33 VDELIKKLEEKVKAKGGM-GIIGFKITAGDGKLMGYGT 69 (81)
T ss_dssp HHHHHHHHHHHHHHTT---EEES----SSSSSSBEEEE
T ss_pred HHHHHHHHHHHHHhCCCc-eEEEEEEEecCCcEEeeee
Confidence 578999999999988877 6888855444447777763
No 199
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=21.67 E-value=62 Score=20.11 Aligned_cols=20 Identities=30% Similarity=0.823 Sum_probs=14.9
Q ss_pred ecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
||..|+..- ..|.|-.|+.-
T Consensus 1 ~C~~C~~~~----------~l~~CL~C~~~ 20 (50)
T smart00290 1 RCSVCGTIE----------NLWLCLTCGQV 20 (50)
T ss_pred CcccCCCcC----------CeEEecCCCCc
Confidence 688888642 26999999873
No 200
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=21.61 E-value=42 Score=34.71 Aligned_cols=23 Identities=22% Similarity=0.508 Sum_probs=18.8
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.+.-||.+|+.| +-+++|+.||.
T Consensus 623 v~~RKCPkCG~y----------Tlk~rCP~CG~ 645 (1095)
T TIGR00354 623 IAIRKCPQCGKE----------SFWLKCPVCGE 645 (1095)
T ss_pred EEEEECCCCCcc----------cccccCCCCCC
Confidence 356899999999 34689999997
No 201
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=21.54 E-value=45 Score=21.71 Aligned_cols=13 Identities=23% Similarity=0.409 Sum_probs=10.9
Q ss_pred CCceecCCCCeEE
Q 028291 86 SGLVRCCCCRGYR 98 (211)
Q Consensus 86 ~~p~RC~~C~aYi 98 (211)
..+++|.+|+.+|
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 5799999999864
No 202
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=21.51 E-value=30 Score=23.09 Aligned_cols=14 Identities=36% Similarity=1.054 Sum_probs=5.3
Q ss_pred ceEEEecCCCCCcc
Q 028291 109 KSFVCNFCGLDGRC 122 (211)
Q Consensus 109 ~~w~C~~C~~~~~~ 122 (211)
+.++|++||.+|..
T Consensus 32 r~y~Cp~CgAtGd~ 45 (55)
T PF05741_consen 32 RKYVCPICGATGDN 45 (55)
T ss_dssp GG---TTT---GGG
T ss_pred hcCcCCCCcCcCcc
Confidence 45889999987653
No 203
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=21.44 E-value=97 Score=27.73 Aligned_cols=41 Identities=24% Similarity=0.367 Sum_probs=29.2
Q ss_pred CceeccCCCCceecCCCCeEEccceEEEeC----Cc-----------eEEEecCCC
Q 028291 78 IPVVDFGESGLVRCCCCRGYRNPFMEFVDN----GK-----------SFVCNFCGL 118 (211)
Q Consensus 78 vP~v~~~~~~p~RC~~C~aYiNp~~~~~~~----g~-----------~w~C~~C~~ 118 (211)
+.+|-+--.-.+||..|+.||---++|+-. |. +.+|..|+.
T Consensus 30 ~~~VRf~~Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~ 85 (324)
T PF04502_consen 30 ILTVRFMMPFNIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSN 85 (324)
T ss_pred ceEEEEcCCccCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCC
Confidence 445555445569999999998877777432 22 457999998
No 204
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=21.43 E-value=43 Score=31.64 Aligned_cols=34 Identities=21% Similarity=0.575 Sum_probs=19.9
Q ss_pred CCceecCCCCeEEccc-----------eEEEeCCceEEEecCCCC
Q 028291 86 SGLVRCCCCRGYRNPF-----------MEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~-----------~~~~~~g~~w~C~~C~~~ 119 (211)
...-+|..|+=.-+|- +.|+.--.-|.|+.|+..
T Consensus 423 ~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 423 GPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 3456788887555553 223333345788888763
No 205
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=21.41 E-value=34 Score=34.74 Aligned_cols=34 Identities=21% Similarity=0.371 Sum_probs=27.6
Q ss_pred CCCceecCCCCeEEccceEE------EeCCceEEEecCCC
Q 028291 85 ESGLVRCCCCRGYRNPFMEF------VDNGKSFVCNFCGL 118 (211)
Q Consensus 85 ~~~p~RC~~C~aYiNp~~~~------~~~g~~w~C~~C~~ 118 (211)
.....||+-|.-..+.+... ..+.+-|+||+||.
T Consensus 350 ~~~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~ 389 (958)
T KOG1074|consen 350 PFFKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGN 389 (958)
T ss_pred ccccchhhhhHhhcCchhhhhhhhhccCCCCCeeeccccc
Confidence 34578999999998887765 34678899999998
No 206
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=21.18 E-value=40 Score=17.29 Aligned_cols=8 Identities=38% Similarity=1.290 Sum_probs=6.0
Q ss_pred EEEecCCC
Q 028291 111 FVCNFCGL 118 (211)
Q Consensus 111 w~C~~C~~ 118 (211)
|+|..|+.
T Consensus 1 y~C~~C~~ 8 (23)
T PF00096_consen 1 YKCPICGK 8 (23)
T ss_dssp EEETTTTE
T ss_pred CCCCCCCC
Confidence 67888876
No 207
>KOG3768 consensus DEAD box RNA helicase [General function prediction only]
Probab=21.17 E-value=1.9e+02 Score=28.78 Aligned_cols=47 Identities=21% Similarity=0.177 Sum_probs=34.0
Q ss_pred cEEEEEEEcchhh-----HhhcHHHHHHHHHHHHHhcC---CCCC-cEEEEEEeCC
Q 028291 152 PVYFFLIDVSTDA-----VQTGATAAACSAIMQVISDL---PINI-FVVGLLKLKI 198 (211)
Q Consensus 152 p~yvFvIDvS~~a-----~~~g~l~~v~~sL~~~l~~l---p~~~-~~Vg~Itfd~ 198 (211)
|.++|+||+|..- .+..+|+.++.++...|+.- +.+. .+.=+.||..
T Consensus 2 pi~lFllDTS~SM~qrah~~~tylD~AKgaVEtFiK~R~r~~~~~gdryml~Tfee 57 (888)
T KOG3768|consen 2 PIFLFLLDTSGSMSQRAHPQFTYLDLAKGAVETFIKQRTRVGRETGDRYMLTTFEE 57 (888)
T ss_pred ceEEEEEecccchhhhccCCchhhHHHHHHHHHHHHHHhccccccCceEEEEeccc
Confidence 7899999998632 34678899999999988753 2222 4777778764
No 208
>PRK12366 replication factor A; Reviewed
Probab=21.13 E-value=64 Score=31.73 Aligned_cols=27 Identities=30% Similarity=0.641 Sum_probs=19.5
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 119 (211)
-..+|..|+--+ ..+.+.|.|.-|+..
T Consensus 531 ~y~aCp~CnkKv------~~~~g~~~C~~c~~~ 557 (637)
T PRK12366 531 ILYLCPNCRKRV------EEVDGEYICEFCGEV 557 (637)
T ss_pred EEecccccCeEe------EcCCCcEECCCCCCC
Confidence 358999996543 234567999999974
No 209
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=21.12 E-value=46 Score=22.51 Aligned_cols=22 Identities=27% Similarity=0.649 Sum_probs=16.5
Q ss_pred CceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 87 ~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
.+-+|.+|+.| .+ +=+|+.||.
T Consensus 4 ~~rkC~~cg~Y-----TL-----ke~Cp~CG~ 25 (59)
T COG2260 4 LIRKCPKCGRY-----TL-----KEKCPVCGG 25 (59)
T ss_pred hhhcCcCCCce-----ee-----cccCCCCCC
Confidence 35789999999 11 247999998
No 210
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=21.01 E-value=56 Score=28.84 Aligned_cols=15 Identities=33% Similarity=0.939 Sum_probs=14.2
Q ss_pred EEeCCceEEEecCCC
Q 028291 104 FVDNGKSFVCNFCGL 118 (211)
Q Consensus 104 ~~~~g~~w~C~~C~~ 118 (211)
|+.+|+.|+|+||..
T Consensus 136 w~hGGrif~CsfC~~ 150 (314)
T PF06524_consen 136 WDHGGRIFKCSFCDN 150 (314)
T ss_pred ccCCCeEEEeecCCC
Confidence 888999999999997
No 211
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=20.99 E-value=41 Score=22.85 Aligned_cols=10 Identities=30% Similarity=0.843 Sum_probs=3.4
Q ss_pred ceecCCCCeE
Q 028291 88 LVRCCCCRGY 97 (211)
Q Consensus 88 p~RC~~C~aY 97 (211)
-.+|.+|++|
T Consensus 48 g~KC~~C~SY 57 (61)
T PF14599_consen 48 GHKCSHCGSY 57 (61)
T ss_dssp ----TTTS--
T ss_pred hhcCCCCCCc
Confidence 3788888887
No 212
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=20.98 E-value=41 Score=23.64 Aligned_cols=13 Identities=31% Similarity=0.457 Sum_probs=10.4
Q ss_pred CceecCCCCeEEc
Q 028291 87 GLVRCCCCRGYRN 99 (211)
Q Consensus 87 ~p~RC~~C~aYiN 99 (211)
-|+||-.||..|.
T Consensus 3 iPVRCFTCGkvig 15 (71)
T PLN00032 3 IPVRCFTCGKVIG 15 (71)
T ss_pred CceeecCCCCCcH
Confidence 3789999998864
No 213
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=20.97 E-value=1.1e+02 Score=23.20 Aligned_cols=28 Identities=32% Similarity=0.755 Sum_probs=20.3
Q ss_pred ceecCCCCeEEccceEEEeCCceE--EEecCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKSF--VCNFCGL 118 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~w--~C~~C~~ 118 (211)
=+.|..|+. |=..+...++.| .|.-||.
T Consensus 80 yVlC~~C~s---pdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGS---PDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred cEECCCCCC---CCcEEEEeCCeEEEEccccCC
Confidence 388999985 667776655554 5888885
No 214
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=20.90 E-value=42 Score=21.35 Aligned_cols=12 Identities=33% Similarity=0.908 Sum_probs=10.3
Q ss_pred CCceecCCCCeE
Q 028291 86 SGLVRCCCCRGY 97 (211)
Q Consensus 86 ~~p~RC~~C~aY 97 (211)
.++-+|.+|++|
T Consensus 9 RGirkCp~CGt~ 20 (44)
T PF14952_consen 9 RGIRKCPKCGTY 20 (44)
T ss_pred hccccCCcCcCc
Confidence 468899999998
No 215
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.87 E-value=44 Score=33.47 Aligned_cols=24 Identities=29% Similarity=0.557 Sum_probs=18.0
Q ss_pred CCceecCCCCeEEccceEEEeCCceEEEecCCC
Q 028291 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (211)
Q Consensus 86 ~~p~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 118 (211)
...-+|..|+ |... -.|.|+.||.
T Consensus 678 ~~~~~C~~CG-~~~~--------~~~~CP~CG~ 701 (735)
T PRK07111 678 HPVDRCPVCG-YLGV--------IEDKCPKCGS 701 (735)
T ss_pred CCCeecCCCC-CCCC--------cCccCcCCCC
Confidence 4568999999 6332 3499999996
No 216
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=20.76 E-value=54 Score=28.43 Aligned_cols=18 Identities=28% Similarity=0.508 Sum_probs=14.0
Q ss_pred CceecCCCCe-EEccceEE
Q 028291 87 GLVRCCCCRG-YRNPFMEF 104 (211)
Q Consensus 87 ~p~RC~~C~a-YiNp~~~~ 104 (211)
.++||..|++ .|+|-+-|
T Consensus 145 ~~p~C~~Cg~~~lrP~VV~ 163 (250)
T COG0846 145 LIPRCPKCGGPVLRPDVVW 163 (250)
T ss_pred CCCcCccCCCccccCCEEE
Confidence 4788888888 77877765
No 217
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=20.58 E-value=1.1e+02 Score=24.07 Aligned_cols=29 Identities=28% Similarity=0.747 Sum_probs=23.2
Q ss_pred ceecCCCCeEEccceEEEeCCce--EEEecCCCC
Q 028291 88 LVRCCCCRGYRNPFMEFVDNGKS--FVCNFCGLD 119 (211)
Q Consensus 88 p~RC~~C~aYiNp~~~~~~~g~~--w~C~~C~~~ 119 (211)
=+.|..|+. |=..+...++. -.|.-||..
T Consensus 102 yVlC~~C~s---pdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGS---PDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCC---CCcEEEEcCCeEEEEcccCCCC
Confidence 589999997 77888777775 479999974
No 218
>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region). Portion of beta integrins that lies N-terminal to their EGF-like repeats. Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Beta integrins are proposed to have a von Willebrand factor type-A "insert" or "I" -like domain (although this remains to be confirmed).
Probab=20.55 E-value=3.5e+02 Score=25.41 Aligned_cols=48 Identities=17% Similarity=0.267 Sum_probs=34.2
Q ss_pred CCcEEEEEEEcchhhH-hhcHHHHHHHHHHHHHhcCCCCCcEEEEEEeCC
Q 028291 150 MPPVYFFLIDVSTDAV-QTGATAAACSAIMQVISDLPINIFVVGLLKLKI 198 (211)
Q Consensus 150 ~pp~yvFvIDvS~~a~-~~g~l~~v~~sL~~~l~~lp~~~~~Vg~Itfd~ 198 (211)
.|--..|+.|+|..-- +-.-++.+...|...|..+-.+ .++||-+|=.
T Consensus 98 yPvDLYyLMDlS~SM~ddl~~lk~lg~~L~~~m~~it~n-~rlGfGsFVD 146 (423)
T smart00187 98 YPVDLYYLMDLSYSMKDDLDNLKSLGDDLAREMKGLTSN-FRLGFGSFVD 146 (423)
T ss_pred CccceEEEEeCCccHHHHHHHHHHHHHHHHHHHHhcccC-ceeeEEEeec
Confidence 3556889999996422 2233666777777888888888 6999988753
No 219
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=20.54 E-value=57 Score=24.97 Aligned_cols=16 Identities=31% Similarity=0.441 Sum_probs=9.1
Q ss_pred cCCCCceecCCCCeEE
Q 028291 83 FGESGLVRCCCCRGYR 98 (211)
Q Consensus 83 ~~~~~p~RC~~C~aYi 98 (211)
-|...++||.+|+..+
T Consensus 15 rGhv~~V~C~nCgr~v 30 (113)
T PF01283_consen 15 RGHVQPVRCDNCGRCV 30 (113)
T ss_dssp SS---EEE-TTTB-EE
T ss_pred CCCCcCEeeCcccccC
Confidence 4567799999999875
No 220
>PF00025 Arf: ADP-ribosylation factor family The prints entry specific to Sar1 proteins The Prosite entry specific to Sar1 proteins; InterPro: IPR006689 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other. The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.; GO: 0005525 GTP binding; PDB: 2H57_B 2W83_B 3N5C_B 2J5X_A 3LVR_E 2BAO_A 3LVQ_E 2A5F_A 3PCR_B 1E0S_A ....
Probab=20.27 E-value=1.9e+02 Score=22.74 Aligned_cols=30 Identities=17% Similarity=0.252 Sum_probs=22.0
Q ss_pred CCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhc
Q 028291 150 MPPVYFFLIDVSTDAVQTGATAAACSAIMQVISD 183 (211)
Q Consensus 150 ~pp~yvFvIDvS~~a~~~g~l~~v~~sL~~~l~~ 183 (211)
..-..|||||.+-.. -++..++.|..+|..
T Consensus 81 ~~~~iIfVvDssd~~----~l~e~~~~L~~ll~~ 110 (175)
T PF00025_consen 81 NADGIIFVVDSSDPE----RLQEAKEELKELLND 110 (175)
T ss_dssp TESEEEEEEETTGGG----GHHHHHHHHHHHHTS
T ss_pred ccceeEEEEecccce----eecccccchhhhcch
Confidence 346899999998533 256678888888764
No 221
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=20.17 E-value=1e+02 Score=24.87 Aligned_cols=32 Identities=31% Similarity=0.677 Sum_probs=18.7
Q ss_pred ceecCCCCe------EEccceEEEeCC------ceEEEecCCCC
Q 028291 88 LVRCCCCRG------YRNPFMEFVDNG------KSFVCNFCGLD 119 (211)
Q Consensus 88 p~RC~~C~a------YiNp~~~~~~~g------~~w~C~~C~~~ 119 (211)
-++|.+|+- |||++-+.+..| =.|+|-+|++.
T Consensus 30 kvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re 73 (161)
T PF05907_consen 30 KVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRE 73 (161)
T ss_dssp EEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--
T ss_pred EEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCc
Confidence 489999995 788888776543 36889999884
Done!