Query 004238
Match_columns 766
No_of_seqs 187 out of 784
Neff 8.1
Searched_HMMs 46136
Date Thu Mar 28 19:57:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004238.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004238hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00162 transport protein sec 100.0 2E-166 4E-171 1455.5 77.7 751 4-766 1-761 (761)
2 KOG1986 Vesicle coat complex C 100.0 1E-164 2E-169 1332.5 65.5 734 5-766 2-744 (745)
3 COG5047 SEC23 Vesicle coat com 100.0 5E-156 1E-160 1230.9 51.4 743 4-765 1-753 (755)
4 KOG1985 Vesicle coat complex C 100.0 3E-127 7E-132 1054.4 51.3 664 9-765 167-887 (887)
5 KOG1984 Vesicle coat complex C 100.0 2E-121 5E-126 1008.7 53.9 676 1-765 272-1004(1007)
6 PTZ00395 Sec24-related protein 100.0 7E-113 1E-117 980.1 57.3 680 8-765 648-1555(1560)
7 COG5028 Vesicle coat complex C 100.0 1E-112 2E-117 931.9 52.2 651 8-764 146-860 (861)
8 cd01478 Sec23-like Sec23-like: 100.0 1.4E-55 3E-60 458.4 26.9 264 133-399 2-267 (267)
9 cd01479 Sec24-like Sec24-like: 100.0 2.9E-44 6.3E-49 370.9 21.8 228 133-403 2-242 (244)
10 cd01468 trunk_domain trunk dom 100.0 3.2E-44 7E-49 371.1 22.0 227 133-400 2-236 (239)
11 PF04811 Sec23_trunk: Sec23/Se 100.0 1.7E-42 3.7E-47 359.8 17.3 232 133-402 2-240 (243)
12 PF08033 Sec23_BS: Sec23/Sec24 99.8 3.1E-20 6.7E-25 163.7 11.7 92 411-508 1-96 (96)
13 PF04815 Sec23_helical: Sec23/ 99.7 6.1E-18 1.3E-22 151.0 10.1 101 523-623 1-103 (103)
14 PF04810 zf-Sec23_Sec24: Sec23 99.6 1.7E-16 3.6E-21 114.7 2.4 40 55-94 1-40 (40)
15 cd01465 vWA_subgroup VWA subgr 98.6 2.3E-06 5.1E-11 83.5 16.8 158 137-388 3-163 (170)
16 cd01463 vWA_VGCC_like VWA Volt 98.5 4.3E-06 9.3E-11 83.5 17.3 165 133-387 12-188 (190)
17 cd01451 vWA_Magnesium_chelatas 98.5 6E-06 1.3E-10 81.6 18.1 164 137-394 3-173 (178)
18 PRK13685 hypothetical protein; 98.5 4E-06 8.7E-11 91.0 18.2 162 133-387 87-275 (326)
19 cd01466 vWA_C3HC4_type VWA C3H 98.5 4.4E-06 9.6E-11 80.6 15.5 149 137-385 3-154 (155)
20 cd01456 vWA_ywmD_type VWA ywmD 98.5 3.6E-06 7.9E-11 85.2 15.2 169 133-382 19-196 (206)
21 cd01453 vWA_transcription_fact 98.4 6.3E-06 1.4E-10 81.8 14.8 152 136-387 5-167 (183)
22 PF00626 Gelsolin: Gelsolin re 98.3 1.1E-06 2.4E-11 73.7 5.9 71 636-722 5-76 (76)
23 cd01472 vWA_collagen von Wille 98.3 4.5E-05 9.7E-10 74.2 17.8 151 137-387 3-163 (164)
24 cd01470 vWA_complement_factors 98.2 5E-05 1.1E-09 76.3 16.1 167 137-388 3-190 (198)
25 cd01467 vWA_BatA_type VWA BatA 98.2 7.2E-05 1.6E-09 73.8 16.9 155 136-387 4-176 (180)
26 TIGR00868 hCaCC calcium-activa 98.2 7.1E-05 1.5E-09 89.1 18.8 155 133-387 303-462 (863)
27 TIGR03436 acidobact_VWFA VWFA- 98.1 0.00032 6.9E-09 75.3 22.1 49 133-181 52-102 (296)
28 cd01480 vWA_collagen_alpha_1-V 98.1 8.9E-05 1.9E-09 73.8 15.9 157 136-389 4-173 (186)
29 cd01452 VWA_26S_proteasome_sub 98.1 9E-05 1.9E-09 73.2 15.4 144 136-378 5-161 (187)
30 TIGR03788 marine_srt_targ mari 98.1 0.0032 7E-08 74.2 30.4 284 133-563 270-556 (596)
31 cd01461 vWA_interalpha_trypsin 98.0 0.00041 8.9E-09 67.6 17.6 159 134-388 2-162 (171)
32 PF13768 VWA_3: von Willebrand 98.0 0.00021 4.5E-09 68.8 15.2 151 137-383 3-154 (155)
33 cd01475 vWA_Matrilin VWA_Matri 98.0 0.00025 5.5E-09 72.8 16.4 155 135-389 3-170 (224)
34 PF13519 VWA_2: von Willebrand 98.0 9.2E-05 2E-09 71.8 12.3 150 137-386 2-159 (172)
35 cd01474 vWA_ATR ATR (Anthrax T 97.9 0.00033 7.2E-09 69.6 16.0 156 134-389 4-168 (185)
36 cd01482 vWA_collagen_alphaI-XI 97.9 0.00095 2E-08 64.9 17.9 45 137-181 3-52 (164)
37 cd01469 vWA_integrins_alpha_su 97.9 0.00078 1.7E-08 66.5 17.1 156 137-389 3-172 (177)
38 cd01450 vWFA_subfamily_ECM Von 97.7 0.0014 3E-08 62.9 16.2 145 137-379 3-156 (161)
39 cd01471 vWA_micronemal_protein 97.7 0.0011 2.4E-08 65.8 15.6 148 137-377 3-160 (186)
40 cd01481 vWA_collagen_alpha3-VI 97.6 0.0035 7.6E-08 61.0 17.1 45 137-181 3-52 (165)
41 TIGR02031 BchD-ChlD magnesium 97.6 0.003 6.6E-08 74.0 19.2 176 133-391 406-586 (589)
42 cd01476 VWA_integrin_invertebr 97.6 0.004 8.7E-08 60.2 17.1 41 137-177 3-47 (163)
43 cd01477 vWA_F09G8-8_type VWA F 97.6 0.0023 5.1E-08 63.9 15.4 49 133-181 18-77 (193)
44 PF00092 VWA: von Willebrand f 97.5 0.0024 5.3E-08 62.3 14.3 156 137-390 2-170 (178)
45 smart00327 VWA von Willebrand 97.5 0.0074 1.6E-07 58.6 17.6 154 135-384 2-164 (177)
46 PRK13406 bchD magnesium chelat 97.3 0.015 3.3E-07 67.6 20.2 172 133-394 400-576 (584)
47 PTZ00441 sporozoite surface pr 97.3 0.011 2.3E-07 67.3 17.5 164 133-389 41-217 (576)
48 TIGR02442 Cob-chelat-sub cobal 97.2 0.0068 1.5E-07 71.8 15.8 161 133-385 464-632 (633)
49 COG1240 ChlD Mg-chelatase subu 97.2 0.013 2.7E-07 59.8 15.2 168 134-393 78-252 (261)
50 cd00198 vWFA Von Willebrand fa 97.2 0.014 3E-07 55.1 15.0 148 136-378 2-155 (161)
51 cd01473 vWA_CTRP CTRP for CS 97.1 0.022 4.7E-07 57.0 16.1 146 137-377 3-161 (192)
52 smart00262 GEL Gelsolin homolo 97.0 0.0024 5.1E-08 55.4 7.3 69 638-722 15-84 (90)
53 cd01464 vWA_subfamily VWA subf 96.9 0.006 1.3E-07 60.0 9.7 45 137-181 6-58 (176)
54 PF04056 Ssl1: Ssl1-like; Int 96.8 0.017 3.8E-07 57.1 12.3 94 271-400 78-172 (193)
55 cd01454 vWA_norD_type norD typ 96.4 0.1 2.2E-06 51.0 14.9 43 136-178 2-48 (174)
56 cd01458 vWA_ku Ku70/Ku80 N-ter 96.3 0.1 2.2E-06 53.2 14.7 156 136-364 3-173 (218)
57 cd01462 VWA_YIEM_type VWA YIEM 95.9 0.28 6.1E-06 46.7 14.7 43 137-179 3-48 (152)
58 KOG2884 26S proteasome regulat 94.6 1.7 3.6E-05 43.2 15.3 84 273-387 85-175 (259)
59 KOG0443 Actin regulatory prote 94.2 0.064 1.4E-06 62.3 5.4 86 621-718 616-706 (827)
60 cd01460 vWA_midasin VWA_Midasi 94.2 2.6 5.7E-05 44.2 16.9 46 133-180 59-111 (266)
61 KOG0444 Cytoskeletal regulator 93.3 0.14 3E-06 58.2 5.9 90 626-731 623-717 (1255)
62 TIGR00578 ku70 ATP-dependent D 93.0 4.9 0.00011 47.3 18.5 73 272-369 116-190 (584)
63 smart00187 INB Integrin beta s 92.4 21 0.00046 39.7 24.5 280 134-468 99-391 (423)
64 COG4245 TerY Uncharacterized p 91.7 0.26 5.7E-06 47.8 4.8 47 135-182 5-59 (207)
65 COG5148 RPN10 26S proteasome r 91.3 6.3 0.00014 38.2 13.4 59 273-362 85-145 (243)
66 PF00362 Integrin_beta: Integr 90.5 35 0.00075 38.5 22.2 281 133-468 101-394 (426)
67 cd01457 vWA_ORF176_type VWA OR 89.8 3.4 7.4E-05 41.3 11.3 43 136-178 4-57 (199)
68 KOG0443 Actin regulatory prote 86.0 1.4 3E-05 51.7 6.2 93 624-732 254-358 (827)
69 TIGR01053 LSD1 zinc finger dom 81.9 1.4 3.1E-05 29.8 2.5 30 57-90 2-31 (31)
70 KOG2807 RNA polymerase II tran 81.9 31 0.00068 36.6 13.2 76 272-380 142-217 (378)
71 PF03850 Tfb4: Transcription f 81.5 74 0.0016 33.7 16.5 85 273-387 116-207 (276)
72 PF10058 DUF2296: Predicted in 79.9 1.2 2.5E-05 34.6 1.7 33 56-88 22-54 (54)
73 PRK00398 rpoP DNA-directed RNA 79.6 1.4 3E-05 32.9 2.0 30 56-89 3-32 (46)
74 PF09967 DUF2201: VWA-like dom 75.4 6.1 0.00013 36.5 5.5 42 138-181 2-45 (126)
75 TIGR00627 tfb4 transcription f 68.1 57 0.0012 34.5 11.3 85 272-386 118-208 (279)
76 smart00661 RPOL9 RNA polymeras 65.8 4 8.8E-05 31.0 1.7 32 58-91 2-33 (52)
77 cd00350 rubredoxin_like Rubred 63.1 4.4 9.5E-05 27.9 1.3 24 58-87 3-26 (33)
78 PF08271 TF_Zn_Ribbon: TFIIB z 61.1 11 0.00024 27.5 3.3 27 58-87 2-28 (43)
79 PF09723 Zn-ribbon_8: Zinc rib 60.8 4.2 9.2E-05 29.7 1.0 30 57-87 6-35 (42)
80 cd00730 rubredoxin Rubredoxin; 58.6 4.7 0.0001 30.7 0.9 30 58-87 3-43 (50)
81 PRK03954 ribonuclease P protei 57.2 6.8 0.00015 35.8 1.8 34 58-91 66-106 (121)
82 cd01455 vWA_F11C1-5a_type Von 57.2 2.1E+02 0.0045 28.5 12.3 111 249-402 75-187 (191)
83 PF13719 zinc_ribbon_5: zinc-r 56.6 7.2 0.00016 27.6 1.5 32 56-87 2-34 (37)
84 PF09082 DUF1922: Domain of un 56.2 6.1 0.00013 31.9 1.2 30 56-91 3-32 (68)
85 PF14803 Nudix_N_2: Nudix N-te 56.2 4.2 9.2E-05 28.2 0.3 30 58-87 2-31 (34)
86 PF10122 Mu-like_Com: Mu-like 56.2 5.5 0.00012 30.2 0.9 34 56-91 4-37 (51)
87 PRK12380 hydrogenase nickel in 55.4 6.6 0.00014 35.5 1.5 27 56-88 70-96 (113)
88 TIGR00100 hypA hydrogenase nic 53.4 7.7 0.00017 35.2 1.6 27 56-88 70-96 (115)
89 TIGR02605 CxxC_CxxC_SSSS putat 53.2 6.9 0.00015 29.8 1.1 31 57-88 6-36 (52)
90 PF00301 Rubredoxin: Rubredoxi 51.2 5.7 0.00012 29.8 0.3 30 58-87 3-43 (47)
91 PF03731 Ku_N: Ku70/Ku80 N-ter 50.8 21 0.00046 36.2 4.6 43 136-178 1-54 (224)
92 PF13240 zinc_ribbon_2: zinc-r 49.3 8.1 0.00018 24.3 0.7 21 58-86 1-21 (23)
93 smart00834 CxxC_CXXC_SSSS Puta 49.1 8.6 0.00019 27.5 1.0 29 57-86 6-34 (41)
94 PRK03681 hypA hydrogenase nick 48.8 10 0.00022 34.4 1.6 28 56-88 70-97 (114)
95 PF06943 zf-LSD1: LSD1 zinc fi 48.3 17 0.00037 23.4 2.1 24 59-86 1-24 (25)
96 COG1996 RPC10 DNA-directed RNA 47.5 9.9 0.00022 28.7 1.1 27 57-87 7-33 (49)
97 PF09779 Ima1_N: Ima1 N-termin 47.3 13 0.00029 34.5 2.2 34 57-92 1-34 (131)
98 PF13717 zinc_ribbon_4: zinc-r 47.1 13 0.00028 26.2 1.5 31 57-87 3-34 (36)
99 COG1096 Predicted RNA-binding 45.6 12 0.00027 36.5 1.7 26 56-87 149-174 (188)
100 PF07282 OrfB_Zn_ribbon: Putat 45.3 14 0.00031 29.9 1.8 27 57-87 29-55 (69)
101 PF08792 A2L_zn_ribbon: A2L zi 44.4 25 0.00054 24.3 2.6 29 56-88 3-31 (33)
102 PF02318 FYVE_2: FYVE-type zin 44.2 11 0.00024 34.3 1.2 32 56-87 71-103 (118)
103 KOG0444 Cytoskeletal regulator 43.1 47 0.001 38.7 5.9 49 621-669 730-787 (1255)
104 TIGR00686 phnA alkylphosphonat 41.3 22 0.00049 31.5 2.5 27 56-87 2-28 (109)
105 PRK00564 hypA hydrogenase nick 40.9 11 0.00024 34.4 0.5 28 56-88 71-98 (117)
106 cd01121 Sms Sms (bacterial rad 40.9 14 0.00031 40.8 1.6 27 58-92 2-28 (372)
107 PF01927 Mut7-C: Mut7-C RNAse 40.1 18 0.00038 34.4 1.9 33 56-88 91-134 (147)
108 PF05762 VWA_CoxE: VWA domain 39.9 50 0.0011 33.6 5.3 43 134-179 57-100 (222)
109 PRK12860 transcriptional activ 39.6 14 0.0003 36.5 1.0 28 55-85 133-161 (189)
110 PRK10997 yieM hypothetical pro 39.0 36 0.00078 38.9 4.3 51 135-185 324-377 (487)
111 PF10571 UPF0547: Uncharacteri 38.7 16 0.00034 23.8 0.9 22 58-87 2-23 (26)
112 PRK12722 transcriptional activ 38.7 14 0.00031 36.4 1.0 29 55-86 133-162 (187)
113 PF07754 DUF1610: Domain of un 38.6 22 0.00048 22.6 1.5 24 59-86 1-24 (24)
114 smart00659 RPOLCX RNA polymera 38.6 25 0.00055 26.0 2.1 25 58-87 4-28 (44)
115 PF12773 DZR: Double zinc ribb 38.4 18 0.0004 27.1 1.4 32 55-91 11-42 (50)
116 smart00401 ZnF_GATA zinc finge 38.2 21 0.00045 27.4 1.6 32 56-87 3-34 (52)
117 KOG3799 Rab3 effector RIM1 and 37.1 17 0.00037 33.2 1.1 31 55-89 88-118 (169)
118 TIGR00311 aIF-2beta translatio 36.0 35 0.00076 31.8 3.0 31 57-90 98-130 (133)
119 PF12760 Zn_Tnp_IS1595: Transp 35.2 44 0.00095 24.8 2.9 27 57-86 19-45 (46)
120 PF00641 zf-RanBP: Zn-finger i 35.1 14 0.00031 24.6 0.2 14 77-90 3-16 (30)
121 PRK00432 30S ribosomal protein 34.9 22 0.00048 27.1 1.3 25 57-87 21-46 (50)
122 PRK12286 rpmF 50S ribosomal pr 34.8 29 0.00063 27.2 1.9 26 55-89 26-51 (57)
123 PRK00762 hypA hydrogenase nick 34.6 17 0.00038 33.4 0.8 33 56-89 70-103 (124)
124 TIGR02098 MJ0042_CXXC MJ0042 f 33.8 25 0.00055 24.7 1.4 31 57-87 3-34 (38)
125 COG3357 Predicted transcriptio 33.7 21 0.00045 30.5 1.0 36 55-94 57-92 (97)
126 PRK03824 hypA hydrogenase nick 33.5 24 0.00053 33.0 1.6 33 56-88 70-117 (135)
127 PRK06393 rpoE DNA-directed RNA 33.4 23 0.0005 28.4 1.2 24 57-90 6-29 (64)
128 PF11781 RRN7: RNA polymerase 33.1 41 0.00088 23.7 2.3 27 56-87 8-34 (36)
129 COG5415 Predicted integral mem 32.5 25 0.00054 34.8 1.5 38 56-93 192-229 (251)
130 PF02891 zf-MIZ: MIZ/SP-RING z 32.3 16 0.00035 27.8 0.2 19 68-86 31-49 (50)
131 PF13894 zf-C2H2_4: C2H2-type 31.6 23 0.00049 21.4 0.8 11 79-89 1-11 (24)
132 PF01155 HypA: Hydrogenase exp 31.5 12 0.00026 33.8 -0.7 27 56-88 70-96 (113)
133 PF05280 FlhC: Flagellar trans 31.1 21 0.00045 35.0 0.7 29 55-86 133-162 (175)
134 COG2888 Predicted Zn-ribbon RN 31.0 40 0.00088 26.5 2.1 28 55-86 8-35 (61)
135 PRK08351 DNA-directed RNA poly 30.5 30 0.00064 27.6 1.4 23 58-90 5-27 (61)
136 PHA00626 hypothetical protein 30.4 46 0.001 25.8 2.3 30 58-89 2-34 (59)
137 TIGR01384 TFS_arch transcripti 30.1 33 0.00071 30.3 1.8 27 58-90 2-28 (104)
138 COG1198 PriA Primosomal protei 30.0 1.8E+02 0.0038 35.3 8.3 111 56-186 444-572 (730)
139 PRK10220 hypothetical protein; 29.9 44 0.00095 29.7 2.4 28 56-88 3-30 (111)
140 COG2051 RPS27A Ribosomal prote 29.8 46 0.00099 26.8 2.3 31 56-89 19-49 (67)
141 smart00132 LIM Zinc-binding do 29.7 41 0.00089 23.1 1.9 29 58-86 1-35 (39)
142 COG2425 Uncharacterized protei 29.7 1.7E+02 0.0037 33.0 7.6 41 137-177 275-318 (437)
143 PRK00420 hypothetical protein; 28.5 41 0.00088 30.3 2.1 29 57-90 24-52 (112)
144 PF08274 PhnA_Zn_Ribbon: PhnA 28.0 34 0.00075 23.1 1.1 27 56-87 2-28 (30)
145 COG0275 Predicted S-adenosylme 27.7 68 0.0015 34.2 3.9 29 148-176 218-246 (314)
146 COG1645 Uncharacterized Zn-fin 27.1 44 0.00094 30.9 2.0 25 57-87 29-53 (131)
147 PF00320 GATA: GATA zinc finge 26.9 22 0.00047 25.0 0.1 28 59-86 1-28 (36)
148 TIGR01031 rpmF_bact ribosomal 26.4 38 0.00082 26.4 1.3 25 55-88 25-49 (55)
149 KOG2846 Predicted membrane pro 25.9 34 0.00073 36.6 1.2 35 57-91 221-255 (328)
150 PF06707 DUF1194: Protein of u 25.9 7E+02 0.015 25.2 10.6 115 251-402 77-199 (205)
151 smart00547 ZnF_RBZ Zinc finger 25.8 29 0.00063 22.1 0.5 14 78-91 2-15 (26)
152 KOG2353 L-type voltage-depende 24.2 1.1E+02 0.0023 38.8 5.2 49 133-181 224-274 (1104)
153 smart00778 Prim_Zn_Ribbon Zinc 23.5 72 0.0016 22.7 2.1 27 58-86 5-33 (37)
154 PF03604 DNA_RNApol_7kD: DNA d 23.4 30 0.00065 23.7 0.2 10 55-64 16-25 (32)
155 COG0675 Transposase and inacti 23.4 43 0.00093 36.1 1.6 25 56-89 309-333 (364)
156 PF14353 CpXC: CpXC protein 23.3 74 0.0016 29.2 2.9 35 57-91 2-51 (128)
157 COG2260 Predicted Zn-ribbon RN 22.7 65 0.0014 25.3 1.9 30 56-95 5-36 (59)
158 COG1592 Rubrerythrin [Energy p 22.2 47 0.001 32.1 1.4 27 75-112 131-157 (166)
159 PRK07218 replication factor A; 21.9 41 0.00088 37.9 1.0 24 56-89 297-320 (423)
160 PRK12366 replication factor A; 21.8 62 0.0013 38.7 2.5 26 56-87 532-557 (637)
161 KOG0445 Actin regulatory prote 21.3 78 0.0017 37.0 3.1 30 640-669 362-391 (919)
162 cd00729 rubredoxin_SM Rubredox 21.1 52 0.0011 22.8 1.0 10 78-87 2-11 (34)
163 PF09297 zf-NADH-PPase: NADH p 21.0 94 0.002 21.0 2.3 26 58-87 5-30 (32)
164 TIGR00375 conserved hypothetic 20.9 32 0.00069 38.0 -0.1 30 54-87 238-267 (374)
165 PF02905 EBV-NA1: Epstein Barr 20.8 1.2E+02 0.0026 27.6 3.5 34 147-180 109-145 (146)
166 PRK08402 replication factor A; 20.8 71 0.0015 35.1 2.6 29 56-88 212-240 (355)
167 COG2956 Predicted N-acetylgluc 20.7 50 0.0011 35.4 1.3 28 55-90 353-380 (389)
168 COG1545 Predicted nucleic-acid 20.7 1.3E+02 0.0029 28.2 4.1 26 56-89 29-54 (140)
169 TIGR00354 polC DNA polymerase, 20.6 50 0.0011 40.3 1.4 26 55-90 624-649 (1095)
170 COG1773 Rubredoxin [Energy pro 20.4 48 0.001 25.8 0.8 11 76-86 34-44 (55)
171 PF06007 PhnJ: Phosphonate met 20.4 88 0.0019 32.0 2.9 27 56-82 235-264 (277)
172 PF04032 Rpr2: RNAse P Rpr2/Rp 20.3 58 0.0013 27.4 1.4 30 57-86 47-85 (85)
173 cd02342 ZZ_UBA_plant Zinc fing 20.1 78 0.0017 23.3 1.8 22 57-85 1-22 (43)
No 1
>PLN00162 transport protein sec23; Provisional
Probab=100.00 E-value=1.9e-166 Score=1455.50 Aligned_cols=751 Identities=74% Similarity=1.218 Sum_probs=694.9
Q ss_pred CCCCCcCCCCeeEeeccccCCCHHHhhhCCCceeEEEccCCCCCCCCCCCCCCcccCCCCceecCceeEEcCCceEEecC
Q 004238 4 MASTDPEGIDGVRMTWNVWPRTKVEASKCVIPLAASISPIRSHPDIPTLPYAPLRCKTCTAALNAFARVDFTAKIWICPF 83 (766)
Q Consensus 4 ~~~~~~~~~~~vR~t~~~~P~t~~~~~~~~iPlg~~v~P~~~~~~ip~~~~~p~RC~~C~ayiNp~~~~~~~~~~W~C~~ 83 (766)
|||.+.|+.++||+|||+||.|+.++++++|||||+|+||++.+++|+++++|+||++|+|||||||+|+.+|++|+|||
T Consensus 1 ~~~~~~e~~~gvR~s~n~~P~t~~~~~~~~iPlg~v~tPl~~~~~vp~v~~~pvRC~~CraylNPf~~~d~~~~~W~C~~ 80 (761)
T PLN00162 1 MDFAELEAIDGVRMSWNVWPSSKIEASKCVIPLAALYTPLKPLPELPVLPYDPLRCRTCRAVLNPYCRVDFQAKIWICPF 80 (761)
T ss_pred CchhhhcccCceEeeeecCCCCHHHHhcCCCCeEEEEecCCcCCCCCcCCCCCCccCCCcCEECCceEEecCCCEEEccC
Confidence 68999999999999999999999999999999999999999888899999999999999999999999999999999999
Q ss_pred CCCCCCCCcccccCCCCCCCccccCCCceEEEEecCCCCCCCCCCCCCCCCcEEEEEEEcccchHHHHHHHHHHHHHhcc
Q 004238 84 CYQRNHFPPHYAAISETNLPCELYPQYTTVEYTLPHSMQNPNNPNPDPRLSPVFVFVLDTCMIEEELGYARSELKRAIGL 163 (766)
Q Consensus 84 C~~~N~~p~~y~~~~~~~~~pEL~p~~~tvey~~~~~~~~~~~~~~~~~~~p~~vFvID~s~~~~~l~~~~~~l~~~l~~ 163 (766)
|++.|++|++|..+++.++||||+|+++||||.+|+ |+. ++| .||+|+||||+|..+++++.++++|+++|+.
T Consensus 81 C~~~N~~P~~Y~~~~~~~~p~EL~p~~~TvEY~~p~-~~~---~~~---~pp~fvFvID~s~~~~~l~~lk~sl~~~L~~ 153 (761)
T PLN00162 81 CFQRNHFPPHYSSISETNLPAELFPQYTTVEYTLPP-GSG---GAP---SPPVFVFVVDTCMIEEELGALKSALLQAIAL 153 (761)
T ss_pred CCCCCCCchHhcccCccCCChhhcCCceeEEEECCC-CCC---CCC---CCcEEEEEEecchhHHHHHHHHHHHHHHHHh
Confidence 999999999999888889999999999999999997 654 566 8999999999999999999999999999999
Q ss_pred CCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhccccCcccccCCCcccCCCCCCCCCC-ccccee
Q 004238 164 LPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLGLSASGRRAAGGYQKAAVPNAFPNSG-VSRFLL 242 (766)
Q Consensus 164 lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~~~d~~~~~~~g~~~~~~~~~~~~~p-~~~~l~ 242 (766)
||++++|||||||+.||||+|+.+.+++++||+|+++|+.+|+.+++++.+.+..++.+. +..+....+.| .++||+
T Consensus 154 LP~~a~VGlITF~s~V~~~~L~~~~~~~~~Vf~g~k~~t~~~l~~~l~l~~~~~~~~~~~--~~~~~~~~~~p~~~~fLv 231 (761)
T PLN00162 154 LPENALVGLITFGTHVHVHELGFSECSKSYVFRGNKEVSKDQILEQLGLGGKKRRPAGGG--IAGARDGLSSSGVNRFLL 231 (761)
T ss_pred CCCCCEEEEEEECCEEEEEEcCCCCCcceEEecCCccCCHHHHHHHhccccccccccccc--cccccccccCCCccceeE
Confidence 999999999999999999999988899999999999999999999998855322111000 00001113445 489999
Q ss_pred ehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccCCCCccEEEEEeCCCCCCCCcccccCCCCCCcc
Q 004238 243 PASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACLPGTGARIVALVGGPCTEGPGTIVSKDLSEPVR 322 (766)
Q Consensus 243 ~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~r 322 (766)
|++||+..|+++|++|+++.|++++++|+.||+|+||++|..+|+.+.++.||||++|++||||.|||+|+.++.++++|
T Consensus 232 pl~e~~~~i~~lLe~L~~~~~~~~~~~rp~r~tG~AL~vA~~lL~~~~~~~gGrI~~F~sgppT~GpG~v~~r~~~~~~r 311 (761)
T PLN00162 232 PASECEFTLNSALEELQKDPWPVPPGHRPARCTGAALSVAAGLLGACVPGTGARIMAFVGGPCTEGPGAIVSKDLSEPIR 311 (761)
T ss_pred EHHHHHHHHHHHHHhhhccccccCCCCCCCccHHHHHHHHHHHHhhccCCCceEEEEEeCCCCCCCCceeeccccccccc
Confidence 99999999999999999999999999999999999999999999988889999999999999999999999999999999
Q ss_pred CCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhhhhcccceEEEeCCCCchhhHHHHHHHHh
Q 004238 323 SHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVAEMKVAVEKTGGLVVLAESFGHSVFKDSFKRIFE 402 (766)
Q Consensus 323 s~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l~ 402 (766)
+|+|++++++++++++.+||++||.+|+++||+||+|+++.+|+|++||+.|++.|||.+++|++|+.+.|+++|+|+|+
T Consensus 312 sh~di~k~~~~~~~~a~~fY~~la~~~~~~gisvDlF~~s~dqvglaem~~l~~~TGG~v~~~~sF~~~~f~~~l~r~~~ 391 (761)
T PLN00162 312 SHKDLDKDAAPYYKKAVKFYEGLAKQLVAQGHVLDVFACSLDQVGVAEMKVAVERTGGLVVLAESFGHSVFKDSLRRVFE 391 (761)
T ss_pred CccccccchhhhcchHHHHHHHHHHHHHHcCceEEEEEccccccCHHHHhhhHhhcCcEEEEeCCcChHHHHHHHHHHhc
Confidence 99999999899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccc-ccceeeeEEEEEecCCceEEEEEcCcccccccc--------cCCCccceeeecCCCCceEEEEEEecCCCCCCC
Q 004238 403 DGEQS-LGLCFNGALEIICSKDIKIQGIIGPCTSLEKVR--------LRGEYYAWKMCGLDKSTCLTVFFDLSSSERLNT 473 (766)
Q Consensus 403 ~~~~~-~~~~~~a~l~vr~S~gl~v~~~~G~~~~~~~~~--------g~~~~~~~~l~~~~~~~s~~~~f~~~~~~~~~~ 473 (766)
+...+ +.+||+|+||||||+|++|++++||++...+++ |.++|+.|+++++++++||+|+|++++..+ ..
T Consensus 392 r~~~~~~~~gf~a~~~VrtS~glkv~g~~G~~~s~~~~~~~vsd~~iG~g~T~~w~l~~l~~~~t~av~f~~~~~~~-~~ 470 (761)
T PLN00162 392 RDGEGSLGLSFNGTFEVNCSKDVKVQGAIGPCASLEKKGPSVSDTEIGEGGTTAWKLCGLDKKTSLAVFFEVANSGQ-SN 470 (761)
T ss_pred ccccccccccceeEEEEEecCCeEEeeeEcCcccccccCCccccccccCCCCceeeecCcCcCCEEEEEEEEccccc-cC
Confidence 75322 468999999999999999999999998765442 788999999999999999999999998751 00
Q ss_pred CCCCCCcEEEEEEEEeecCCCcEEEEEEeeccccccCCCCHHHHHhccChhHHHHHHHHHHHHHhhcCChHHHHHHHHHH
Q 004238 474 PGTINPQLYLQFLTSFQSPEGRSVLRVTTVTRQWVDSAVSSEELVQGFDQESAAVVMARLTSLKMEMEEGFDATRWLDRS 553 (766)
Q Consensus 474 ~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~l~vt~~~~~~~~i~~~~D~~a~~~llak~a~~~~~~~~~~~~~~~l~~~ 553 (766)
+..+...+||||+++||+.+|+|||||||++++++..+ ++.+++++|||||++++|||+|+.++.+++..|+++||+++
T Consensus 471 ~~~~~~~~~iQ~a~lYt~~~G~rRiRV~T~~~~~~~~~-~~~~v~~~fDqeA~a~llaR~av~k~~~~~~~d~~r~ld~~ 549 (761)
T PLN00162 471 PQPPGQQFFLQFLTRYQHSNGQTRLRVTTVTRRWVEGS-SSEELVAGFDQEAAAVVMARLASHKMETEEEFDATRWLDRA 549 (761)
T ss_pred CCCCCceEEEEEEEEEEcCCCCEEEEEEccccCccCCC-CHHHHHHhcCHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHH
Confidence 11345779999999999999999999999999976422 56899999999999999999999999999999999999999
Q ss_pred HHHHHHHhcccccCCCCCccCCccccchHHHHHHhccccccCCCCCChHHHHHHHHHHccCCHHHHHHhhcccceeeccC
Q 004238 554 LIRLCSKFGDYRKDDPASFTLNPSFSLFPQFMFNLRRSQFVQVFNNSPDETAYFRMLLNRENITNAAVMIQPSLISYSFN 633 (766)
Q Consensus 554 l~~~~~~~~~y~~~~~~s~~lp~~l~~lP~~~~~L~ks~~l~~~~~s~Der~~~~~~l~~~~~~~~~~~iyP~L~~~~~~ 633 (766)
|++++++|+.|+|+++++|+||++|++||+|||+|+||++|+++|.|||||+|+|++++++++++++.||||+|++||++
T Consensus 550 li~~~~~f~~Yrk~~~~s~~Lp~~~~~lP~f~~~LrRS~~l~~~n~spDera~~r~~l~~~~~~~sl~mI~P~L~sy~~~ 629 (761)
T PLN00162 550 LIRLCSKFGDYRKDDPSSFRLSPNFSLYPQFMFNLRRSQFVQVFNNSPDETAYFRMMLNRENVTNSLVMIQPTLISYSFN 629 (761)
T ss_pred HHHHHHHHhhhcccCCccccCCHHHHHHHHHHHHHhhhhhccCCCCCchHHHHHHHHHhcCCHHHHHHhhCCeEEEecCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCcccccccccccCCeEEEEeCCcEEEEEECCchhHHhhcCCCCChhhhHHHHHhhCcHHHHHHHHhcCCCCcEEEEEe
Q 004238 634 SLPQPALLDVASIAADRILLLDTYFSVVIFHGMTIAQWRNMGYQNQPEHQAFAQLLRAPHDDAELIIRDRFPVPRLVVCD 713 (766)
Q Consensus 634 ~~p~~~~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~~~~~~g~~~~~~~~~~~~~l~~~~~~~~~i~~~R~p~p~~~~~~ 713 (766)
++|+|++||+++|++|+|||||+|++|+||+|++|++|+|+|||++|||++|+++|++|+++|++|+.+|||+||+++|+
T Consensus 630 ~~P~pv~Ld~~si~~d~ilLLD~~f~vvi~~G~~ia~w~~~~~~~~~~~~~~~~~l~~p~~~a~~~~~~Rfp~Pr~i~~~ 709 (761)
T PLN00162 630 GPPEPVLLDVASIAADRILLLDSYFSVVIFHGSTIAQWRKAGYHNQPEHEAFAQLLEAPQADAQAIIKERFPVPRLVVCD 709 (761)
T ss_pred CCCcceecchhhccCCceEEEeCCCEEEEEecCcccchhhcCCCCCcchhhHHHHHHhHHHHHHHHHhcCCCCCeEEEeC
Confidence 88999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCChHHHHHHhhcCCCCcCCcccccCCCcccccCCchHHHHHHHHHHHHhcC
Q 004238 714 QHGSQARFLLAKLNPSATYNNANEIAAGSDIIFTDDVSLQVFIEHLQRLAVQS 766 (766)
Q Consensus 714 ~g~s~~r~l~s~L~p~~~~~~~~~~~~~~~~~~t~~~Sy~~f~~~L~~~i~~~ 766 (766)
||+||||||++||||+++|++.+ ++.+++.|+|||+||+.||+||+|++|++
T Consensus 710 ~~~SqaRfl~~klnPs~~~~~~~-~~~~~~~~~tdd~sl~~f~~~l~~~~v~~ 761 (761)
T PLN00162 710 QHGSQARFLLAKLNPSATYNSAN-AMGGSDIIFTDDVSLQVFMEHLQRLAVQS 761 (761)
T ss_pred CCCcHHHHHHHhcCCcccccCCC-CCCCCCeeecCCcCHHHHHHHHHHHhcCC
Confidence 99999999999999999985532 23467899999999999999999999974
No 2
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=9.6e-165 Score=1332.51 Aligned_cols=734 Identities=62% Similarity=1.064 Sum_probs=694.3
Q ss_pred CCCCcCCCCeeEeeccccCCCHHHhhhCCCceeEEEccCCCCCCCCCCCCCCcccCCCCceecCceeEEcCCceEEecCC
Q 004238 5 ASTDPEGIDGVRMTWNVWPRTKVEASKCVIPLAASISPIRSHPDIPTLPYAPLRCKTCTAALNAFARVDFTAKIWICPFC 84 (766)
Q Consensus 5 ~~~~~~~~~~vR~t~~~~P~t~~~~~~~~iPlg~~v~P~~~~~~ip~~~~~p~RC~~C~ayiNp~~~~~~~~~~W~C~~C 84 (766)
.++++|+.++||+|||+||.++.+..++++|++|+|+||++...+|+++|+|+||++|+||+||||++|.+.+.|.|+||
T Consensus 2 ~~~~~e~~dGvR~twnvwPs~~~~~~~~vvPla~lytPl~e~~~~~~~~y~P~~C~~C~AvlNPyc~vd~~a~~W~CpfC 81 (745)
T KOG1986|consen 2 FIEDIEEIDGVRFTWNVWPSTRAEASRTVVPLACLYTPLKERPDLPPIQYDPLRCSKCGAVLNPYCSVDFRAKSWICPFC 81 (745)
T ss_pred cccccccCCCcccccccCCCcccccccccccHHHhccccccCCCCCccCCCCchhccchhhcCcceeecccCceEecccc
Confidence 45679999999999999999999999999999999999998777899999999999999999999999999999999999
Q ss_pred CCCCCCCcccccCCCCCCCccccCCCceEEEEecCCCCCCCCCCCCCCCCcEEEEEEEcccchHHHHHHHHHHHHHhccC
Q 004238 85 YQRNHFPPHYAAISETNLPCELYPQYTTVEYTLPHSMQNPNNPNPDPRLSPVFVFVLDTCMIEEELGYARSELKRAIGLL 164 (766)
Q Consensus 85 ~~~N~~p~~y~~~~~~~~~pEL~p~~~tvey~~~~~~~~~~~~~~~~~~~p~~vFvID~s~~~~~l~~~~~~l~~~l~~l 164 (766)
+++|.+|++|..+++.|.|+||+|+++||||.++++ .. .||+|+||||+|..+++|+.+|++|+.+|+.|
T Consensus 82 ~qrN~~p~~Y~~is~~n~P~el~Pq~stvEy~l~~~-------~~---~ppvf~fVvDtc~~eeeL~~LkssL~~~l~lL 151 (745)
T KOG1986|consen 82 NQRNPFPPHYSGISENNLPPELLPQYSTVEYTLSPG-------RV---SPPVFVFVVDTCMDEEELQALKSSLKQSLSLL 151 (745)
T ss_pred ccCCCCChhhcccCccCCChhhcCCcceeEEecCCC-------CC---CCceEEEEEeeccChHHHHHHHHHHHHHHhhC
Confidence 999999999999999999999999999999999855 23 68999999999999999999999999999999
Q ss_pred CCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhccccCcccccCCCcccCCCCCCCCCCcccceeeh
Q 004238 165 PDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPA 244 (766)
Q Consensus 165 p~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~ 244 (766)
|++++||||||++.|++|+++...+++++||+|+|||+.++++++++.+..... | .....+..+||.|+
T Consensus 152 P~~alvGlItfg~~v~v~el~~~~~sk~~VF~G~ke~s~~q~~~~L~~~~~~~~---~--------~~~~~~~~rFL~P~ 220 (745)
T KOG1986|consen 152 PENALVGLITFGTMVQVHELGFEECSKSYVFSGNKEYSAKQLLDLLGLSGGAGK---G--------SENQSASNRFLLPA 220 (745)
T ss_pred CCcceEEEEEecceEEEEEcCCCcccceeEEeccccccHHHHHHHhcCCccccc---C--------CcccccchhhhccH
Confidence 999999999999999999999999999999999999999999999987541100 1 01112357999999
Q ss_pred hhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccCCCCccEEEEEeCCCCCCCCcccccCCCCCCccCC
Q 004238 245 SECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACLPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSH 324 (766)
Q Consensus 245 ~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~ 324 (766)
++|...+.++|++|++++|+++.++|+.||||+||++|+.||++|++++|+||++|++||||.|||++++++.++++|+|
T Consensus 221 ~~c~~~L~~lle~L~~d~wpV~~g~Rp~RcTG~Al~iA~~Ll~~c~p~~g~rIv~f~gGPcT~GpG~vv~~el~~piRsh 300 (745)
T KOG1986|consen 221 QECEFKLTNLLEELQPDPWPVPPGHRPLRCTGVALSIASGLLEGCFPNTGARIVLFAGGPCTRGPGTVVSRELKEPIRSH 300 (745)
T ss_pred HHHHHHHHHHHHHhcCCCCCCCCCCCcccchhHHHHHHHHHhcccCCCCcceEEEeccCCCCcCCceecchhhcCCCcCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhhhhcccceEEEeCCCCchhhHHHHHHHHhhc
Q 004238 325 KDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVAEMKVAVEKTGGLVVLAESFGHSVFKDSFKRIFEDG 404 (766)
Q Consensus 325 ~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l~~~ 404 (766)
+|+++++++|++++.+||++||++++++|+++|+|+++.||+|+++|++|++.|||.+.+.++|+.+.|+++++|+|.++
T Consensus 301 hdi~~d~a~y~kKa~KfY~~La~r~~~~ghvlDifa~~lDQvGi~EMk~l~~~TGG~lvl~dsF~~s~Fk~sfqR~f~~d 380 (745)
T KOG1986|consen 301 HDIEKDNAPYYKKAIKFYEKLAERLANQGHVLDIFAAALDQVGILEMKPLVESTGGVLVLGDSFNTSIFKQSFQRIFTRD 380 (745)
T ss_pred ccccCcchHHHHHHHHHHHHHHHHHHhCCceEeeeeeeccccchHHHHHHhhcCCcEEEEecccchHHHHHHHHHHhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999965
Q ss_pred ccc-ccceeeeEEEEEecCCceEEEEEcCcccccccc--------cCCCccceeeecCCCCceEEEEEEecCCCCCCCCC
Q 004238 405 EQS-LGLCFNGALEIICSKDIKIQGIIGPCTSLEKVR--------LRGEYYAWKMCGLDKSTCLTVFFDLSSSERLNTPG 475 (766)
Q Consensus 405 ~~~-~~~~~~a~l~vr~S~gl~v~~~~G~~~~~~~~~--------g~~~~~~~~l~~~~~~~s~~~~f~~~~~~~~~~~~ 475 (766)
..+ +.+||+|+|+|+||++++|++++|++.+.++|+ |.++|..|+++.+++.+++++.|++..... .
T Consensus 381 ~~~~l~~~fn~~leV~tSkdlkI~g~IGp~~Sl~~k~~~vsdt~ig~g~t~~wkm~~ls~~t~~s~~fei~~~~~----~ 456 (745)
T KOG1986|consen 381 GEGDLKMGFNGTLEVKTSKDLKIQGVIGPCVSLNKKGPNVSDTEIGEGNTSAWKMCGLSPSTTLSLFFEISNQHN----I 456 (745)
T ss_pred cccchhhhcCceEEEEecCCcEEEecccccccccCCCCccccceeccccccceeeeccCCCceEEEEEEeccccC----C
Confidence 443 789999999999999999999999999998765 999999999999999999999999998653 1
Q ss_pred CCCCcEEEEEEEEeecCCCcEEEEEEeeccccccCCCCHHHHHhccChhHHHHHHHHHHHHHhhcCChHHHHHHHHHHHH
Q 004238 476 TINPQLYLQFLTSFQSPEGRSVLRVTTVTRQWVDSAVSSEELVQGFDQESAAVVMARLTSLKMEMEEGFDATRWLDRSLI 555 (766)
Q Consensus 476 ~~~~~~~iQ~al~Yt~~~G~rriRV~T~~l~vt~~~~~~~~i~~~~D~~a~~~llak~a~~~~~~~~~~~~~~~l~~~l~ 555 (766)
..+..+||||+++|.+++|++|+||+|+++++++.. . .++.++|||||++++|||+++.++.+++..|+++|+|+.|+
T Consensus 457 ~~~~~~~iQFiT~Yq~s~g~~riRVtT~~r~~~d~~-~-~~i~~~FDqEaaAV~mAR~~~~kae~e~~~d~~rwlDr~Li 534 (745)
T KOG1986|consen 457 PQSGQGYIQFITQYQHSSGQKRIRVTTLARPWADSG-S-PEISQSFDQEAAAVLMARLALLKAETEDGPDVLRWLDRNLI 534 (745)
T ss_pred CCCCeeEEEEEEEEEcCCCcEEEEEEEeehhhcccc-c-hHhhhccchHHHHHHHHHHHHHhhhccccchHHHHHHHHHH
Confidence 346799999999999999999999999999999822 2 68999999999999999999999999999999999999999
Q ss_pred HHHHHhcccccCCCCCccCCccccchHHHHHHhccccccCCCCCChHHHHHHHHHHccCCHHHHHHhhcccceeeccCCC
Q 004238 556 RLCSKFGDYRKDDPASFTLNPSFSLFPQFMFNLRRSQFVQVFNNSPDETAYFRMLLNRENITNAAVMIQPSLISYSFNSL 635 (766)
Q Consensus 556 ~~~~~~~~y~~~~~~s~~lp~~l~~lP~~~~~L~ks~~l~~~~~s~Der~~~~~~l~~~~~~~~~~~iyP~L~~~~~~~~ 635 (766)
++|++|+.|+|++|++|.|+++|+++|+|||+||||++|+++|.|||||+|+||+|++.++.+++.||+|+|++|++++.
T Consensus 535 rlc~kFg~y~k~dPssf~l~~~fsl~PQfmfhLRRS~fLqvfNnSPDEt~~yrhll~~e~v~~sliMIqP~L~sySf~g~ 614 (745)
T KOG1986|consen 535 RLCQKFGDYRKDDPSSFRLSPNFSLYPQFMFHLRRSPFLQVFNNSPDETAYYRHLLNREDVDNSLIMIQPTLLSYSFNGP 614 (745)
T ss_pred HHHHHHhccCCCCchhhcCChhhhhhHHHHHhhccchhhhccCCCcchHHHHHHHHhhccchhhhheecceeeeeecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccccccccCCeEEEEeCCcEEEEEECCchhHHhhcCCCCChhhhHHHHHhhCcHHHHHHHHhcCCCCcEEEEEeCC
Q 004238 636 PQPALLDVASIAADRILLLDTYFSVVIFHGMTIAQWRNMGYQNQPEHQAFAQLLRAPHDDAELIIRDRFPVPRLVVCDQH 715 (766)
Q Consensus 636 p~~~~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~~~~~~g~~~~~~~~~~~~~l~~~~~~~~~i~~~R~p~p~~~~~~~g 715 (766)
|+|++||..||.+|.|+|||++++|+||+|++++||+++|||++|||++|+++|++|+.+|++|..+|||+||+++|+||
T Consensus 615 ~epvlLD~~Si~~D~iLLlDt~f~i~i~hG~tIaqWR~~gy~~~pe~~~f~~LL~ap~~dA~el~~~RFP~PR~v~~~q~ 694 (745)
T KOG1986|consen 615 PEPVLLDVASILADRILLLDTYFTIVIFHGSTIAQWRKAGYHEQPEYENFKELLEAPREDAQELLLERFPMPRYVVTDQG 694 (745)
T ss_pred CceeEecccccCCceEEEeecceEEEEECCchHHHHHhcccccChhhHHHHHHHHhHHHHHHHHHHhhCCCCeEEEecCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHhhcCCCCcCCcccccCCCcccccCCchHHHHHHHHHHHHhcC
Q 004238 716 GSQARFLLAKLNPSATYNNANEIAAGSDIIFTDDVSLQVFIEHLQRLAVQS 766 (766)
Q Consensus 716 ~s~~r~l~s~L~p~~~~~~~~~~~~~~~~~~t~~~Sy~~f~~~L~~~i~~~ 766 (766)
+||||||++|+||+.++++... +++++.|+|||+||++||+||+|++|++
T Consensus 695 GSQARFLlsklnPS~t~~~~~~-~~~s~~I~TDDvSlq~fm~hLkklav~~ 744 (745)
T KOG1986|consen 695 GSQARFLLSKLNPSETHNNLTA-HGGSSIILTDDVSLQVFMEHLKKLAVSS 744 (745)
T ss_pred ccHHHhhhhhcCcchhccchhh-ccCCCeeeeccccHHHHHHHHHhhcCCC
Confidence 9999999999999999877533 3447899999999999999999999873
No 3
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=100.00 E-value=4.9e-156 Score=1230.90 Aligned_cols=743 Identities=47% Similarity=0.858 Sum_probs=693.1
Q ss_pred CCCCCcCCCCeeEeeccccCCCHHHhhhCCCceeEEEccCCCCCCCCCCCCCCcccCC-CCceecCceeEEcCCceEEec
Q 004238 4 MASTDPEGIDGVRMTWNVWPRTKVEASKCVIPLAASISPIRSHPDIPTLPYAPLRCKT-CTAALNAFARVDFTAKIWICP 82 (766)
Q Consensus 4 ~~~~~~~~~~~vR~t~~~~P~t~~~~~~~~iPlg~~v~P~~~~~~ip~~~~~p~RC~~-C~ayiNp~~~~~~~~~~W~C~ 82 (766)
|+|+.+|+.++||+|||+||.|+.++.++.+|++|+|+|+++.+++++..|+|+.|.. |+||+||||.+|.+++.|.|+
T Consensus 1 m~fe~iee~dgir~twnvfpat~~da~~~~iPia~lY~Pl~e~~~~~v~~yepv~C~~pC~avlnpyC~id~r~~~W~Cp 80 (755)
T COG5047 1 MNFEIIEENDGIRLTWNVFPATRGDATRTVIPIACLYTPLHEDDALTVNYYEPVKCTAPCKAVLNPYCHIDERNQSWICP 80 (755)
T ss_pred CchhhhccccceEEEEecccCCccccccccccHHHhccccccccccCcccCCCceecccchhhcCcceeeccCCceEecc
Confidence 7899999999999999999999999999999999999999988889999999999999 999999999999999999999
Q ss_pred CCCCCCCCCcccccCCCCCCCccccCCCceEEEEecCCCCCCCCCCCCCCCCcEEEEEEEcccchHHHHHHHHHHHHHhc
Q 004238 83 FCYQRNHFPPHYAAISETNLPCELYPQYTTVEYTLPHSMQNPNNPNPDPRLSPVFVFVLDTCMIEEELGYARSELKRAIG 162 (766)
Q Consensus 83 ~C~~~N~~p~~y~~~~~~~~~pEL~p~~~tvey~~~~~~~~~~~~~~~~~~~p~~vFvID~s~~~~~l~~~~~~l~~~l~ 162 (766)
||+.+|.+|++|..+++.++++||.|+++||||+++++ +. .||+|+||||++++.++|.++|++|+..|+
T Consensus 81 fCnqrn~lp~qy~~iS~~~LplellpqssTiey~lskp-------~~---~ppvf~fvvD~~~D~e~l~~Lkdslivsls 150 (755)
T COG5047 81 FCNQRNTLPPQYRDISNANLPLELLPQSSTIEYTLSKP-------VI---LPPVFFFVVDACCDEEELTALKDSLIVSLS 150 (755)
T ss_pred eecCCCCCChhhcCCCcccCCccccCCCceEEEEccCC-------cc---CCceEEEEEEeecCHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999976 33 789999999999999999999999999999
Q ss_pred cCCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhccccCcccccCCCcccCCCCCCCCCCccccee
Q 004238 163 LLPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLL 242 (766)
Q Consensus 163 ~lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~ 242 (766)
.+|+++.||||||++.|++|+++....++++||+|+++|+.++|++|+..+.. ..+. |+. ...+....+ ...+|+.
T Consensus 151 llppeaLvglItygt~i~v~el~ae~~~r~~VF~g~~eyt~~~L~~ll~~~~~-~~~~-~~e-s~is~~~~~-~~~rFl~ 226 (755)
T COG5047 151 LLPPEALVGLITYGTSIQVHELNAENHRRSYVFSGNKEYTKENLQELLALSKP-TKSG-GFE-SKISGIGQF-ASSRFLL 226 (755)
T ss_pred cCCccceeeEEEecceeEEEeccccccCcceeecchHHHHHHHHHHHhcccCC-CCcc-hhh-hhccccccc-chhhhhc
Confidence 99999999999999999999999998999999999999999999999977521 1110 100 000000011 1257999
Q ss_pred ehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccCCCCccEEEEEeCCCCCCCCcccccCCCCCCcc
Q 004238 243 PASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACLPGTGARIVALVGGPCTEGPGTIVSKDLSEPVR 322 (766)
Q Consensus 243 ~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~r 322 (766)
|+++|+..+.++|++|++++|+++.++||.||||+||++|+.||+.|+++.|+||++|++||||.|||+|++++.+++||
T Consensus 227 p~q~ce~~L~n~le~L~pd~~~v~~~~Rp~RCTGsAl~ias~Ll~~~~p~~~~~i~lF~~GPcTvGpG~Vvs~elkEpmR 306 (755)
T COG5047 227 PTQQCEFKLLNILEQLQPDPWPVPAGKRPLRCTGSALNIASSLLEQCFPNAGCHIVLFAGGPCTVGPGTVVSTELKEPMR 306 (755)
T ss_pred cHHHHHHHHHHHHHHhCCCCccCCCCCCCccccchhHHHHHHHHHhhccCcceeEEEEcCCCccccCceeeehhhccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhhhhcccceEEEeCCCCchhhHHHHHHHHh
Q 004238 323 SHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVAEMKVAVEKTGGLVVLAESFGHSVFKDSFKRIFE 402 (766)
Q Consensus 323 s~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l~ 402 (766)
+||+++++.+++.+++.+||++|+++.+++|+++|+|+++.+|+|+.+|++|+..|||.+.+.++|+.++|+++++|+|.
T Consensus 307 shH~ie~d~aqh~kka~KFY~~laeR~a~~gh~~DifagcldqIGI~eM~~L~~sTgg~lvlsdsF~t~ifkqSfqrif~ 386 (755)
T COG5047 307 SHHDIESDSAQHSKKATKFYKGLAERVANQGHALDIFAGCLDQIGIMEMEPLTTSTGGALVLSDSFTTSIFKQSFQRIFN 386 (755)
T ss_pred ccccccccchhhccchHHHHHHHHHHHhccchhHHHHHHHHHhhhhhcchhhccCCcceEEEeccccHHHHHHHHHHHhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccc-ccceeeeEEEEEecCCceEEEEEcCcccccccc--------cCCCccceeeecCCCCceEEEEEEecCCCCCCC
Q 004238 403 DGEQS-LGLCFNGALEIICSKDIKIQGIIGPCTSLEKVR--------LRGEYYAWKMCGLDKSTCLTVFFDLSSSERLNT 473 (766)
Q Consensus 403 ~~~~~-~~~~~~a~l~vr~S~gl~v~~~~G~~~~~~~~~--------g~~~~~~~~l~~~~~~~s~~~~f~~~~~~~~~~ 473 (766)
++..+ +.+||+|.|+|.||+++++++++|+....++|+ |++.|+.|++++++|.+++++.||+......+
T Consensus 387 ~d~~g~l~~gfNa~m~V~TsKnl~~~g~ig~a~~~~k~~~ni~~~eigi~~t~swkm~slsPk~nyal~fei~~~~~~~- 465 (755)
T COG5047 387 RDSEGYLKMGFNANMEVKTSKNLKIKGLIGHAVSVKKKANNISDSEIGIGATNSWKMASLSPKSNYALYFEIALGAASG- 465 (755)
T ss_pred cCcccchhhhhccceeEeeccCceeeeeecceeeecccccccccccccccccccccccccCCCcceEEEEEeccccCCC-
Confidence 87765 779999999999999999999999999887654 89999999999999999999999998765311
Q ss_pred CCCCCCcEEEEEEEEeecCCCcEEEEEEeeccccccCCCCHHHHHhccChhHHHHHHHHHHHHHhhcCChHHHHHHHHHH
Q 004238 474 PGTINPQLYLQFLTSFQSPEGRSVLRVTTVTRQWVDSAVSSEELVQGFDQESAAVVMARLTSLKMEMEEGFDATRWLDRS 553 (766)
Q Consensus 474 ~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~l~vt~~~~~~~~i~~~~D~~a~~~llak~a~~~~~~~~~~~~~~~l~~~ 553 (766)
+.+....+||||.+.|.+++|..||||+|++..+++ .....++++|||||+++++||+++.++..++..|+.+|+|+.
T Consensus 466 ~~~~~~~a~iQfiT~yQhss~t~riRVtTvar~f~~--~~~p~i~~SFdqEaaaV~~aR~a~~K~~~ed~~Dv~rw~dr~ 543 (755)
T COG5047 466 SAQRPAEAYIQFITTYQHSSGTYRIRVTTVARMFTD--GGLPKINRSFDQEAAAVFMARIAAFKAETEDIIDVFRWIDRN 543 (755)
T ss_pred ccCCcccchhhhhhhhhccCCcEEEEEeehhhhhcc--CCChhhhhcchhhHHHHHHHHHHHhhcccccchhHHHHHHHH
Confidence 113457899999999999999999999999999987 344789999999999999999999999999999999999999
Q ss_pred HHHHHHHhcccccCCCCCccCCccccchHHHHHHhccccccCCCCCChHHHHHHHHHHccCCHHHHHHhhcccceeeccC
Q 004238 554 LIRLCSKFGDYRKDDPASFTLNPSFSLFPQFMFNLRRSQFVQVFNNSPDETAYFRMLLNRENITNAAVMIQPSLISYSFN 633 (766)
Q Consensus 554 l~~~~~~~~~y~~~~~~s~~lp~~l~~lP~~~~~L~ks~~l~~~~~s~Der~~~~~~l~~~~~~~~~~~iyP~L~~~~~~ 633 (766)
++++|++|+.|+|++|++|.|++++.++|+|||+|+|||+|+++|.|||||++|+|++.+.++++++.||+|+|++||++
T Consensus 544 lirlcq~fa~y~k~dpssfrl~~~f~lypqf~y~lrRSpfL~vfNnSPDEt~fyrh~l~~~dv~~sLimiqPtL~Sys~~ 623 (755)
T COG5047 544 LIRLCQKFADYRKDDPSSFRLDPNFTLYPQFMYHLRRSPFLSVFNNSPDETAFYRHMLNNADVNDSLIMIQPTLQSYSFE 623 (755)
T ss_pred HHHHHHHHHhcCCCCchhhcCCcchhhhhHHHhhhhccceeeccCCCcchHHHHHHHHhcccccchhhhhcchheeeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCcccccccccccCCeEEEEeCCcEEEEEECCchhHHhhcCCCCChhhhHHHHHhhCcHHHHHHHHhcCCCCcEEEEEe
Q 004238 634 SLPQPALLDVASIAADRILLLDTYFSVVIFHGMTIAQWRNMGYQNQPEHQAFAQLLRAPHDDAELIIRDRFPVPRLVVCD 713 (766)
Q Consensus 634 ~~p~~~~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~~~~~~g~~~~~~~~~~~~~l~~~~~~~~~i~~~R~p~p~~~~~~ 713 (766)
+.+.||.||+-++++|.|+|+|++++|+||+|+.++||+++|||++|||..++.+|++|+.+|.+++.+|||.|++++|+
T Consensus 624 ~~~~pVlLDs~svkpdviLLlDtff~Ili~hG~~iaqwr~agyq~qpey~~lK~Ll~~p~~ea~ell~dRfP~Prfi~te 703 (755)
T COG5047 624 KGGVPVLLDSVSVKPDVILLLDTFFHILIFHGSYIAQWRNAGYQEQPEYLNLKELLEAPRLEAAELLQDRFPIPRFIVTE 703 (755)
T ss_pred CCCceEEEeccccCCCeEEEeeceeEEEEECChHHHHHHhhhhhcCchhhhHHHHhhchhhHHHHHHHhhCCCCeEEEec
Confidence 77999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCChHHHHHHhhcCCCCcCCcccccCCCcccccCCchHHHHHHHHHHHHhc
Q 004238 714 QHGSQARFLLAKLNPSATYNNANEIAAGSDIIFTDDVSLQVFIEHLQRLAVQ 765 (766)
Q Consensus 714 ~g~s~~r~l~s~L~p~~~~~~~~~~~~~~~~~~t~~~Sy~~f~~~L~~~i~~ 765 (766)
||+||+|||++|+||+.+++.+ +| +|++.+.|||++|++||.||++++|.
T Consensus 704 qggSQaRfLlskinPsd~~~~~-~~-~~s~tilTddv~lq~fm~hl~~lav~ 753 (755)
T COG5047 704 QGGSQARFLLSKINPSDITNKM-SG-GGSETILTDDVNLQKFMNHLRKLAVS 753 (755)
T ss_pred CCccHHHHHHhhcCcccccccc-cc-CccceeeecccCHHHHHHHHHHHhcc
Confidence 9999999999999999877543 22 34678999999999999999999986
No 4
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.2e-127 Score=1054.45 Aligned_cols=664 Identities=21% Similarity=0.296 Sum_probs=588.6
Q ss_pred cCCCCeeEeeccccCCCHHHhhhCCCceeEEEccCCCC---CCCCCC-CCCCcccCCCCceecCceeEEcCCceEEecCC
Q 004238 9 PEGIDGVRMTWNVWPRTKVEASKCVIPLAASISPIRSH---PDIPTL-PYAPLRCKTCTAALNAFARVDFTAKIWICPFC 84 (766)
Q Consensus 9 ~~~~~~vR~t~~~~P~t~~~~~~~~iPlg~~v~P~~~~---~~ip~~-~~~p~RC~~C~ayiNp~~~~~~~~~~W~C~~C 84 (766)
|++|+|+|+|++++|.+.+++++++||||++|+||++. ++.|++ +..|+||++||+||||||.|++.|++|+||+|
T Consensus 167 nc~p~y~RsTl~~iP~t~sLl~kskLPlglvv~Pf~~~~d~~~~p~~~~~~IvRCr~CRtYiNPFV~fid~gr~WrCNlC 246 (887)
T KOG1985|consen 167 NCSPSYVRSTLSAIPQTQSLLKKSKLPLGLVVHPFAHLDDIDPLPVITSTLIVRCRRCRTYINPFVEFIDQGRRWRCNLC 246 (887)
T ss_pred CCCHHHHHHHHHhCCccHHHHHhcCCCceEEEeecccccccCCCCcccCCceeeehhhhhhcCCeEEecCCCceeeechh
Confidence 88999999999999999999999999999999999954 455654 45899999999999999999999999999999
Q ss_pred CCCCCCCcccccC------CCCCCCccccCCCceEEEEecCCCCCCCCCCCCCCCCcEEEEEEEcccchHH---HHHHHH
Q 004238 85 YQRNHFPPHYAAI------SETNLPCELYPQYTTVEYTLPHSMQNPNNPNPDPRLSPVFVFVLDTCMIEEE---LGYARS 155 (766)
Q Consensus 85 ~~~N~~p~~y~~~------~~~~~~pEL~p~~~tvey~~~~~~~~~~~~~~~~~~~p~~vFvID~s~~~~~---l~~~~~ 155 (766)
+..|++|.+|..- .+...|||+ ++++|||++|.|||. |+| +|++|||+||||.++++ |+++++
T Consensus 247 ~~~NdvP~~f~~~~~t~~~~~~~~RpEl--~~s~vE~iAP~eYml---R~P---~Pavy~FliDVS~~a~ksG~L~~~~~ 318 (887)
T KOG1985|consen 247 GRVNDVPDDFDWDPLTGAYGDPYSRPEL--TSSVVEFIAPSEYML---RPP---QPAVYVFLIDVSISAIKSGYLETVAR 318 (887)
T ss_pred hhhcCCcHHhhcCccccccCCcccCccc--cceeEEEecCccccc---CCC---CCceEEEEEEeehHhhhhhHHHHHHH
Confidence 9999999998642 244579999 999999999999999 788 99999999999999988 899999
Q ss_pred HHHHHhccCC--CCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhccccCcccccCCCcccCCCCCCC
Q 004238 156 ELKRAIGLLP--DNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLGLSASGRRAAGGYQKAAVPNAFP 233 (766)
Q Consensus 156 ~l~~~l~~lp--~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~~~d~~~~~~~g~~~~~~~~~~~ 233 (766)
+|+..|+.|| ++++|||||||+.||||++..+. .+ ++|++++|.+ |.
T Consensus 319 slL~~LD~lpgd~Rt~igfi~fDs~ihfy~~~~~~---------------~q-p~mm~vsdl~---------------d~ 367 (887)
T KOG1985|consen 319 SLLENLDALPGDPRTRIGFITFDSTIHFYSVQGDL---------------NQ-PQMMIVSDLD---------------DP 367 (887)
T ss_pred HHHHhhhcCCCCCcceEEEEEeeceeeEEecCCCc---------------CC-Cceeeecccc---------------cc
Confidence 9999999999 67999999999999999997653 23 5788888764 36
Q ss_pred CCC-cccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccCCCCccEEEEEeCCCCCCCCccc
Q 004238 234 NSG-VSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACLPGTGARIVALVGGPCTEGPGTI 312 (766)
Q Consensus 234 ~~p-~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~gGrIi~f~sg~pt~GpG~l 312 (766)
|.| .++||+|++|||+.|..+|+.|+++ +..++..++|+|+||++|..+|+ ..||||++|.+++|+.|.|+|
T Consensus 368 flp~pd~lLv~L~~ck~~i~~lL~~lp~~---F~~~~~t~~alGpALkaaf~li~----~~GGri~vf~s~lPnlG~G~L 440 (887)
T KOG1985|consen 368 FLPMPDSLLVPLKECKDLIETLLKTLPEM---FQDTRSTGSALGPALKAAFNLIG----STGGRISVFQSTLPNLGAGKL 440 (887)
T ss_pred ccCCchhheeeHHHHHHHHHHHHHHHHHH---HhhccCcccccCHHHHHHHHHHh----hcCCeEEEEeccCCCCCcccc
Confidence 666 3999999999999999999999997 67777889999999999999998 899999999999999999999
Q ss_pred ccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhhhhcccceEEEeCCCCch-
Q 004238 313 VSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVAEMKVAVEKTGGLVVLAESFGHS- 391 (766)
Q Consensus 313 ~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~- 391 (766)
+.||+.+..++ ++..+++.+++.|||+||.+|++.||+||+|+++.+|.|+|+|+.|++.|||.+|+|++|+.+
T Consensus 441 ~~rEdp~~~~s-----~~~~qlL~~~t~FYK~~a~~cs~~qI~VDlFl~s~qY~DlAsLs~LskySgG~~y~YP~f~~s~ 515 (887)
T KOG1985|consen 441 KPREDPNVRSS-----DEDSQLLSPATDFYKDLALECSKSQICVDLFLFSEQYTDLASLSCLSKYSGGQVYYYPSFDGSN 515 (887)
T ss_pred ccccccccccc-----hhhhhccCCCchHHHHHHHHhccCceEEEEEeecccccchhhhhccccccCceeEEccCCCCCC
Confidence 99977655432 333678999999999999999999999999999999999999999999999999999999876
Q ss_pred -----hhHHHHHHHHhhccccccceeeeEEEEEecCCceEEEEEcCcccccccccCCCccceeeecCCCCceEEEEEEec
Q 004238 392 -----VFKDSFKRIFEDGEQSLGLCFNGALEIICSKDIKIQGIIGPCTSLEKVRLRGEYYAWKMCGLDKSTCLTVFFDLS 466 (766)
Q Consensus 392 -----~~~~~l~~~l~~~~~~~~~~~~a~l~vr~S~gl~v~~~~G~~~~~~~~~g~~~~~~~~l~~~~~~~s~~~~f~~~ 466 (766)
+|.++|.|+|++ ++||+|+||||||+|++++.+||||+. ++++++.++++.+|++++++++++
T Consensus 516 p~~~~Kf~~el~r~Ltr-----~~~feaVmRiR~S~gl~~~~f~GnFF~-------RStDLla~~~v~~D~sy~~qisiE 583 (887)
T KOG1985|consen 516 PHDVLKFARELARYLTR-----KIGFEAVMRIRCSTGLRMSSFFGNFFV-------RSTDLLALPNVNPDQSYAFQISIE 583 (887)
T ss_pred HHHHHHHHHHHHHHhhh-----hhhhheeEEeeccccccccceeccccc-------CcHHHhcccCCCCCccceEEEEee
Confidence 466777777774 799999999999999999999999995 689999999999999999999999
Q ss_pred CCCCCCCCCCCCCcEEEEEEEEeecCCCcEEEEEEeeccccccCCCCHHHHHhccChhHHHHHHHHHHHHHhhcCChHHH
Q 004238 467 SSERLNTPGTINPQLYLQFLTSFQSPEGRSVLRVTTVTRQWVDSAVSSEELVQGFDQESAAVVMARLTSLKMEMEEGFDA 546 (766)
Q Consensus 467 ~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~l~vt~~~~~~~~i~~~~D~~a~~~llak~a~~~~~~~~~~~~ 546 (766)
+.+ .....+||.|++||...|||||||||+++|++. ++.++|.++|++|++.+++++|++++++..+.|+
T Consensus 584 esl-------~~~~~~fQvAlLyT~~~GERRIRV~T~~lpt~~---sl~evY~saD~~AI~~lla~~Av~ksl~ssL~da 653 (887)
T KOG1985|consen 584 ESL-------TTGFCVFQVALLYTLSKGERRIRVHTLCLPTVS---SLNEVYASADQEAIASLLAKKAVEKSLSSSLSDA 653 (887)
T ss_pred hhc-------CCceeEEEeeeeecccCCceeEEEEEeeccccc---cHHHHHhhcCHHHHHHHHHHHHHHHHHHhhhhhH
Confidence 987 367788999999999999999999999999999 8899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcccccCCCC------CccCCccccchHHHHHHhccccccCC-CCCChHHHHHHHHHHccCCHHHH
Q 004238 547 TRWLDRSLIRLCSKFGDYRKDDPA------SFTLNPSFSLFPQFMFNLRRSQFVQV-FNNSPDETAYFRMLLNRENITNA 619 (766)
Q Consensus 547 ~~~l~~~l~~~~~~~~~y~~~~~~------s~~lp~~l~~lP~~~~~L~ks~~l~~-~~~s~Der~~~~~~l~~~~~~~~ 619 (766)
|+.|.+.++++ ++.|++.... .+.+|.+|++||+|+++|+|+++|+. ..+++|+|+|++.++..+++..+
T Consensus 654 rdal~~~~~D~---l~aYk~~~~~~~~~~~~l~~p~~LrllPllvlALlK~~~fr~g~~~~lD~R~~a~~~~~~lpl~~L 730 (887)
T KOG1985|consen 654 RDALTNAVVDI---LNAYKKLVSNQNGQGITLSLPASLRLLPLLVLALLKHPAFRPGTGTRLDYRAYAMCLMSTLPLKYL 730 (887)
T ss_pred HHHHHHHHHHH---HHHHHHHhcccccCCcceecCcchhhhHHHHHHHhcCCcccCCCCCCchHHHHHHHHhhcCCHHHH
Confidence 99999999999 7778876433 69999999999999999999999996 48999999999999999999999
Q ss_pred HHhhcccceeecc----------CC---CCcccccccccccCCeEEEEeCCcEEEEEECCchh-HHhhc--CCC------
Q 004238 620 AVMIQPSLISYSF----------NS---LPQPALLDVASIAADRILLLDTYFSVVIFHGMTIA-QWRNM--GYQ------ 677 (766)
Q Consensus 620 ~~~iyP~L~~~~~----------~~---~p~~~~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~-~~~~~--g~~------ 677 (766)
+++|||+||++|. |+ +|++++|+++.+++.|+||||+|..+++|+|+++. ++... |..
T Consensus 731 ~k~IYP~Lysl~~l~~ea~~~~~d~~~~~p~~L~ltae~l~~~GlyL~D~g~~lfl~vg~~a~P~ll~~vfg~~~~adi~ 810 (887)
T KOG1985|consen 731 MKYIYPTLYSLHDLDDEAGLPIHDQTVVLPPPLNLTAELLSRRGLYLMDTGTTLFLWVGSNADPSLLFDVFGVSTLADIP 810 (887)
T ss_pred HhhhcccceeccccccccCcccccccccCCCccchHHHHhccCceEEEecCcEEEEEEcCCCCccccccccCcchHhhcc
Confidence 9999999999983 11 37889999999999999999999999999999986 44333 221
Q ss_pred ----CChhhhHHHHHhhCcHHHHHHHHhcCCCCcEEEEEeCCC-ChH-HHHHHhhcCCCCcCCcccccCCCcccccCCch
Q 004238 678 ----NQPEHQAFAQLLRAPHDDAELIIRDRFPVPRLVVCDQHG-SQA-RFLLAKLNPSATYNNANEIAAGSDIIFTDDVS 751 (766)
Q Consensus 678 ----~~~~~~~~~~~l~~~~~~~~~i~~~R~p~p~~~~~~~g~-s~~-r~l~s~L~p~~~~~~~~~~~~~~~~~~t~~~S 751 (766)
+.++.++ ...+...++++++|.+|...|.++++|+++ +.+ -+|+++|+||+++ ...|
T Consensus 811 ~~~~~lp~~~n--~~s~r~~~fI~~lR~d~~~~p~~~ivr~~~~s~~k~~f~~~lvEDrs~---------------~~~S 873 (887)
T KOG1985|consen 811 IGKYTLPELDN--EESDRVRRFIKKLRDDRTYFPNLYIVRGDDNSPLKAWFFSRLVEDRSE---------------NSPS 873 (887)
T ss_pred cccccCccccc--chhHHHHHHHHHhhcCCcccceEEEEecCCCchHHHHHHHHHHhhhhc---------------CcHH
Confidence 1122111 011223457779999999999999999763 334 4667999999975 3499
Q ss_pred HHHHHHHHHHHHhc
Q 004238 752 LQVFIEHLQRLAVQ 765 (766)
Q Consensus 752 y~~f~~~L~~~i~~ 765 (766)
|.||++|||++|.+
T Consensus 874 Y~efLq~lk~qv~~ 887 (887)
T KOG1985|consen 874 YYEFLQHLKAQVSK 887 (887)
T ss_pred HHHHHHHHHHHhcC
Confidence 99999999999863
No 5
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.1e-121 Score=1008.66 Aligned_cols=676 Identities=22% Similarity=0.279 Sum_probs=598.6
Q ss_pred CCCCCCC----CcCCCCeeEeeccccCCCHHHhhhCCCceeEEEccCCCC----CCCCCCCC---CCcccCCCCceecCc
Q 004238 1 MSEMAST----DPEGIDGVRMTWNVWPRTKVEASKCVIPLAASISPIRSH----PDIPTLPY---APLRCKTCTAALNAF 69 (766)
Q Consensus 1 ~~~~~~~----~~~~~~~vR~t~~~~P~t~~~~~~~~iPlg~~v~P~~~~----~~ip~~~~---~p~RC~~C~ayiNp~ 69 (766)
++|.||. .|++|+|||+|+|++|.|.++++.++||||++|+||+.. +++|+++. +|+||+||+||+|||
T Consensus 272 l~TTd~~~~DqGN~sPr~mr~T~Y~iP~T~Dl~~as~iPLalvIqPfa~l~p~E~~~~vVd~g~sgPvRC~RCkaYinPF 351 (1007)
T KOG1984|consen 272 LVTTDFFIQDQGNCSPRFMRCTMYTIPCTNDLLKASQIPLALVIQPFATLTPNEAPVPVVDLGESGPVRCNRCKAYINPF 351 (1007)
T ss_pred CcccceEEeccCCCCcchheeecccCCccHhHHHhcCCcceeEecccccCCcccCCCceecCCCCCCcchhhhhhhcCcc
Confidence 3566643 399999999999999999999999999999999999954 35677653 799999999999999
Q ss_pred eeEEcCCceEEecCCCCCCCCCccccc-CC------CCCCCccccCCCceEEEEecCCCCCCCCCCCCCCCCcEEEEEEE
Q 004238 70 ARVDFTAKIWICPFCYQRNHFPPHYAA-IS------ETNLPCELYPQYTTVEYTLPHSMQNPNNPNPDPRLSPVFVFVLD 142 (766)
Q Consensus 70 ~~~~~~~~~W~C~~C~~~N~~p~~y~~-~~------~~~~~pEL~p~~~tvey~~~~~~~~~~~~~~~~~~~p~~vFvID 142 (766)
++|.++|++|+||||+..|++|++|++ ++ +.+.|||| ..|||||+++++|+.+. .+| +||+|||+||
T Consensus 352 mqF~~~gr~f~Cn~C~~~n~vp~~yf~~L~~~grr~D~~erpEL--~~Gt~dfvatk~Y~~~~-k~p---~ppafvFmID 425 (1007)
T KOG1984|consen 352 MQFIDGGRKFICNFCGSKNQVPDDYFNHLGPTGRRVDVEERPEL--CLGTVDFVATKDYCRKT-KPP---KPPAFVFMID 425 (1007)
T ss_pred eEEecCCceEEecCCCccccCChhhcccCCCcccccccccCchh--cccccceeeehhhhhcC-CCC---CCceEEEEEE
Confidence 999999999999999999999999986 43 34679999 89999999999999854 356 9999999999
Q ss_pred cccchHH---HHHHHHHHHHHhccCC---CCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhccccCc
Q 004238 143 TCMIEEE---LGYARSELKRAIGLLP---DNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLGLSASG 216 (766)
Q Consensus 143 ~s~~~~~---l~~~~~~l~~~l~~lp---~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~~~d~~ 216 (766)
||+++++ +.+++++|++.|+.+| ++.+|||||||+.|||||+++.+ +| ++|++++|.+
T Consensus 426 VSy~Ai~~G~~~a~ce~ik~~l~~lp~~~p~~~Vgivtfd~tvhFfnl~s~L---------------~q-p~mliVsdv~ 489 (1007)
T KOG1984|consen 426 VSYNAISNGAVKAACEAIKSVLEDLPREEPNIRVGIVTFDKTVHFFNLSSNL---------------AQ-PQMLIVSDVD 489 (1007)
T ss_pred eehhhhhcchHHHHHHHHHHHHhhcCccCCceEEEEEEecceeEeeccCccc---------------cC-ceEEEeeccc
Confidence 9999998 8999999999999998 37999999999999999999876 45 6899898764
Q ss_pred ccccCCCcccCCCCCCCCCCc-ccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccCCCCcc
Q 004238 217 RRAAGGYQKAAVPNAFPNSGV-SRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACLPGTGA 295 (766)
Q Consensus 217 ~~~~~g~~~~~~~~~~~~~p~-~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~gG 295 (766)
|.|+|+ +++||+..|++..|+.+|++|+.+ +..++.++.|+|+||++|..+|++ ..||
T Consensus 490 ---------------dvfvPf~~g~~V~~~es~~~i~~lLd~Ip~m---f~~sk~pes~~g~alqaa~lalk~---~~gG 548 (1007)
T KOG1984|consen 490 ---------------DVFVPFLDGLFVNPNESRKVIELLLDSIPTM---FQDSKIPESVFGSALQAAKLALKA---ADGG 548 (1007)
T ss_pred ---------------ccccccccCeeccchHHHHHHHHHHHHhhhh---hccCCCCchhHHHHHHHHHHHHhc---cCCc
Confidence 489995 899999999999999999999997 677888999999999999999995 2399
Q ss_pred EEEEEeCCCCCCCCc-ccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhh
Q 004238 296 RIVALVGGPCTEGPG-TIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVAEMKVA 374 (766)
Q Consensus 296 rIi~f~sg~pt~GpG-~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~~l~~l 374 (766)
|+++|++..||.|.| +++.+++...+. .+|| +.++.++++.|++||++|++.|+|||||++...|+|+|+++.+
T Consensus 549 Kl~vF~s~Lpt~g~g~kl~~r~D~~l~~----t~ke-k~l~~pq~~~y~~LA~e~v~~g~svDlF~t~~ayvDvAtlg~v 623 (1007)
T KOG1984|consen 549 KLFVFHSVLPTAGAGGKLSNRDDRRLIG----TDKE-KNLLQPQDKTYTTLAKEFVESGCSVDLFLTPNAYVDVATLGVV 623 (1007)
T ss_pred eEEEEecccccccCcccccccchhhhhc----ccch-hhccCcchhHHHHHHHHHHHhCceEEEEEcccceeeeeeeccc
Confidence 999999999999988 888888776654 3555 4789999999999999999999999999999999999999999
Q ss_pred hhcccceEEEeCCCCchh----hHHHHHHHHhhccccccceeeeEEEEEecCCceEEEEEcCcccccccccCCCccceee
Q 004238 375 VEKTGGLVVLAESFGHSV----FKDSFKRIFEDGEQSLGLCFNGALEIICSKDIKIQGIIGPCTSLEKVRLRGEYYAWKM 450 (766)
Q Consensus 375 ~~~TGG~v~~~~~f~~~~----~~~~l~~~l~~~~~~~~~~~~a~l~vr~S~gl~v~~~~G~~~~~~~~~g~~~~~~~~l 450 (766)
++.|||.+|+|.+|.... +.++|.+.++ ++.||+|+||||||.||++.+|+||+.. +.+++.++
T Consensus 624 ~~~TgG~vy~Y~~F~a~~D~~rl~nDL~~~vt-----k~~gf~a~mrvRtStGirv~~f~Gnf~~-------~~~tDiel 691 (1007)
T KOG1984|consen 624 PALTGGQVYKYYPFQALTDGPRLLNDLVRNVT-----KKQGFDAVMRVRTSTGIRVQDFYGNFLM-------RNPTDIEL 691 (1007)
T ss_pred ccccCceeEEecchhhcccHHHHHHHHHHhcc-----cceeeeeEEEEeecCceeeeeeechhhh-------cCCCCccc
Confidence 999999999999998764 5556655555 4789999999999999999999999984 57889999
Q ss_pred ecCCCCceEEEEEEecCCCCCCCCCCCCCcEEEEEEEEeecCCCcEEEEEEeeccccccCCCCHHHHHhccChhHHHHHH
Q 004238 451 CGLDKSTCLTVFFDLSSSERLNTPGTINPQLYLQFLTSFQSPEGRSVLRVTTVTRQWVDSAVSSEELVQGFDQESAAVVM 530 (766)
Q Consensus 451 ~~~~~~~s~~~~f~~~~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~l~vt~~~~~~~~i~~~~D~~a~~~ll 530 (766)
+.+|+|++++++|++++++ +....++||+|++||+.+|+||+||+|+++++++ ++.++|+++|+|+++++|
T Consensus 692 a~lD~dkt~~v~fkhDdkL------q~~s~~~fQ~AlLYTti~G~RR~Rv~Nlsl~~ts---~l~~lyr~~~~d~l~a~m 762 (1007)
T KOG1984|consen 692 AALDCDKTLTVEFKHDDKL------QDGSDVHFQTALLYTTIDGQRRLRVLNLSLAVTS---QLSELYRSADTDPLIAIM 762 (1007)
T ss_pred cccccCceeEEEEeccccc------cCCcceeEEEEEEEeccCCceeEEEEecchhhhh---hHHHHHHhcCccHHHHHH
Confidence 9999999999999999998 4678899999999999999999999999999999 889999999999999999
Q ss_pred HHHHHHHhhcCChHHHHHHHHHHHHHHHHHhcccccCCC-----CCccCCccccchHHHHHHhccccccCCCCCChHHHH
Q 004238 531 ARLTSLKMEMEEGFDATRWLDRSLIRLCSKFGDYRKDDP-----ASFTLNPSFSLFPQFMFNLRRSQFVQVFNNSPDETA 605 (766)
Q Consensus 531 ak~a~~~~~~~~~~~~~~~l~~~l~~~~~~~~~y~~~~~-----~s~~lp~~l~~lP~~~~~L~ks~~l~~~~~s~Der~ 605 (766)
+|.|+..+..+.+.++|+.|.+.++++ |+.||+.|+ +||+|||+||+||+|+++|+||.+|++..++-|+|+
T Consensus 763 aK~a~~~i~~~~lk~vre~l~~~~~~i---L~~YRk~cas~~ssgQLILPeslKLlPly~la~lKs~~l~~~~~~~DdRi 839 (1007)
T KOG1984|consen 763 AKQAAKAILDKPLKEVREQLVSQCAQI---LASYRKNCASPASSGQLILPESLKLLPLYMLALLKSSALRPQEIRTDDRI 839 (1007)
T ss_pred HHHHHHhcccccHHHHHHHHHHHHHHH---HHHHHHhhcCCCCcccEechhhhHHHHHHHHHHHHhhcccccccccchhH
Confidence 999999999999999999999999999 777888764 589999999999999999999999999899999999
Q ss_pred HHHHHHccCCHHHHHHhhcccceeecc---C-----CCCcccccccccccCCeEEEEeCCcEEEEEECCchh-HHhhc--
Q 004238 606 YFRMLLNRENITNAAVMIQPSLISYSF---N-----SLPQPALLDVASIAADRILLLDTYFSVVIFHGMTIA-QWRNM-- 674 (766)
Q Consensus 606 ~~~~~l~~~~~~~~~~~iyP~L~~~~~---~-----~~p~~~~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~-~~~~~-- 674 (766)
|.+.++.++++++++.++||+|+++|. + ..|.+|+++.+.|..+||||||+|..+|||+|++++ .|+++
T Consensus 840 ~~~~~v~sl~v~~~~~~~YPrl~p~hdl~i~dtl~~~~p~~VraS~e~l~negiYll~nG~~~ylwvg~sv~~~llQ~lf 919 (1007)
T KOG1984|consen 840 YQLQLVTSLSVEQLMPFFYPRLLPFHDLDIEDTLEFVLPKAVRASSEFLSNEGIYLLDNGQKIYLWVGESVDPDLLQDLF 919 (1007)
T ss_pred HHHHHhhcccHHhhhhhhccceeeeeccccccccccccccceecchhhccCCceEEEecCcEEEEEecCCCCHHHHHHHh
Confidence 999999999999999999999999993 1 258899999999999999999999999999999998 57776
Q ss_pred CCCCC----------hhhhHHHHHhhCcHHHHHHHHhcCCCCcEEEEEeCCCChH-HHHHHhhcCCCCcCCcccccCCCc
Q 004238 675 GYQNQ----------PEHQAFAQLLRAPHDDAELIIRDRFPVPRLVVCDQHGSQA-RFLLAKLNPSATYNNANEIAAGSD 743 (766)
Q Consensus 675 g~~~~----------~~~~~~~~~l~~~~~~~~~i~~~R~p~p~~~~~~~g~s~~-r~l~s~L~p~~~~~~~~~~~~~~~ 743 (766)
++... ||+.+ .+-+..++.+..+++.|....+++++++|..+. -++.+.|+||+.-
T Consensus 920 ~V~s~~~i~s~~~~Lpe~dn--~lS~k~r~~i~~i~~~r~~~l~v~~~k~g~~~~~~~~~~~lved~~~----------- 986 (1007)
T KOG1984|consen 920 SVSSFEQIDSQSGVLPELDN--PLSRKVRNVISLIRRQRSSELPVVLVKQGLDGSEVEFSEYLVEDRGR----------- 986 (1007)
T ss_pred cCccccccccccccccccCc--HHHHHHHHHHHHHHhccccccccEEEecCCCchhhhhhhhhhccccc-----------
Confidence 33222 22211 000112334556777788888899999997775 7788899999852
Q ss_pred ccccCCchHHHHHHHHHHHHhc
Q 004238 744 IIFTDDVSLQVFIEHLQRLAVQ 765 (766)
Q Consensus 744 ~~~t~~~Sy~~f~~~L~~~i~~ 765 (766)
+..||.+||+.||+.|++
T Consensus 987 ----~~~sY~dyL~~~H~ki~~ 1004 (1007)
T KOG1984|consen 987 ----NISSYVDYLCELHKKIQQ 1004 (1007)
T ss_pred ----CccccchHHHHHHHHHHh
Confidence 459999999999999975
No 6
>PTZ00395 Sec24-related protein; Provisional
Probab=100.00 E-value=6.7e-113 Score=980.08 Aligned_cols=680 Identities=15% Similarity=0.184 Sum_probs=556.6
Q ss_pred CcCCCCeeEeeccccCCCHHHhhhCCCceeEEEccCCCC---CCCCCCC-----------CCCcccCCCCceecCceeEE
Q 004238 8 DPEGIDGVRMTWNVWPRTKVEASKCVIPLAASISPIRSH---PDIPTLP-----------YAPLRCKTCTAALNAFARVD 73 (766)
Q Consensus 8 ~~~~~~~vR~t~~~~P~t~~~~~~~~iPlg~~v~P~~~~---~~ip~~~-----------~~p~RC~~C~ayiNp~~~~~ 73 (766)
.++||++||+||+.+|.+.++++.+.||||++++||+.+ ++||.++ .+|+||.+|++|+|+++.++
T Consensus 648 gn~dP~~~r~tmY~iP~~~~~~~~~~iP~gi~v~Pfa~~~~~e~~~~~~~~~~~~d~~~~~~~~rc~~c~~y~~~~~~~~ 727 (1560)
T PTZ00395 648 GKADPRFLKSTLYQIPLFSETLKLSQIPFGIIVNPFACLNEGEGIDKIDMKDIINDKEENIEILRCPKCLGYLHATILED 727 (1560)
T ss_pred CCCChhhhhhhhhcCcchHHHHHhcCCCceeecchhhhcCCCCCCcccchhhcccchhhccceeecchhHhhhcchheec
Confidence 389999999999999999999999999999999999975 4566532 37999999999999999999
Q ss_pred cCCceEEecCCCCCCCCCcc-------ccc-CC----CCC-----CCccccCCCceEEEEecCCCCCCC-----------
Q 004238 74 FTAKIWICPFCYQRNHFPPH-------YAA-IS----ETN-----LPCELYPQYTTVEYTLPHSMQNPN----------- 125 (766)
Q Consensus 74 ~~~~~W~C~~C~~~N~~p~~-------y~~-~~----~~~-----~~pEL~p~~~tvey~~~~~~~~~~----------- 125 (766)
.. +++.|+||++.+.+... |.. +. +.+ .-| | ..|+||+++|+.|....
T Consensus 728 ~~-~~~~c~~c~~~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 803 (1560)
T PTZ00395 728 IS-SSVQCVFCDTDFLINENVLFDIFQYNEKIGHKESDHNEHGNSLSP-L--LKGSVDIIIPPIYYHNVNKFKLTYTYLN 803 (1560)
T ss_pred cc-ceEEEEecCCcchhhHHHHHHHHHHhhhhccccccccccccccch-h--hcCceeEEccchhhccCCccceeeehhh
Confidence 76 89999999999988432 211 11 111 113 3 37888888776432110
Q ss_pred --------------------------------------------------------------------------------
Q 004238 126 -------------------------------------------------------------------------------- 125 (766)
Q Consensus 126 -------------------------------------------------------------------------------- 125 (766)
T Consensus 804 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 883 (1560)
T PTZ00395 804 KNINQTAFMITNKIMSFTKHISNSLVANDSKGGNKATSASAFGDSGDANFLAGGGYTNYGGAGGYNTYDNQSGYNNHDVV 883 (1560)
T ss_pred cchhhhhhhhhhhhhhhhhhhcchheecccccccccchhhhccccccccccccccccccccccccccccccccccccccc
Confidence
Q ss_pred ----------------------------------------------------CC-------CC-CCCCCcEEEEEEEccc
Q 004238 126 ----------------------------------------------------NP-------NP-DPRLSPVFVFVLDTCM 145 (766)
Q Consensus 126 ----------------------------------------------------~~-------~~-~~~~~p~~vFvID~s~ 145 (766)
.| +. ...+||+|+||||||.
T Consensus 884 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~PP~YvFLIDVS~ 963 (1560)
T PTZ00395 884 NNRGGSGAGNHLYGKDHDVQNFDNVMDNANFTIHDMKNLICEKNGEPDSAKIRRNSFLAKYPQVKNMLPPYFVFVVECSY 963 (1560)
T ss_pred ccccccCcCcccccCcccccchhhhccCCceeeecchhhhhcccCCchhhhhhccchhhccccccCCCCCEEEEEEECCH
Confidence 00 00 0037899999999999
Q ss_pred chHH---HHHHHHHHHHHhccCC-CCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhccccCcccccC
Q 004238 146 IEEE---LGYARSELKRAIGLLP-DNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLGLSASGRRAAG 221 (766)
Q Consensus 146 ~~~~---l~~~~~~l~~~l~~lp-~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~~~d~~~~~~~ 221 (766)
.+++ +.+++++|+.+|+.|+ ++++|||||||+.||||+|+++.-..-. .++..-..++ +||++|+|+|
T Consensus 964 ~AVkSGLl~tacesIK~sLDsL~dpRTRVGIITFDSsLHFYNLks~l~~~~~--~~~~~~~l~q-PQMLVVSDLD----- 1035 (1560)
T PTZ00395 964 NAIYNNITYTILEGIRYAVQNVKCPQTKIAIITFNSSIYFYHCKGGKGVSGE--EGDGGGGSGN-HQVIVMSDVD----- 1035 (1560)
T ss_pred HHHhhChHHHHHHHHHHHHhcCCCCCcEEEEEEecCcEEEEecCcccccccc--cccccccCCC-ceEEeecCCc-----
Confidence 9998 8999999999999997 5799999999999999999753100000 0111111234 6899998875
Q ss_pred CCcccCCCCCCCCCCc--ccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccCCCCccEEEE
Q 004238 222 GYQKAAVPNAFPNSGV--SRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACLPGTGARIVA 299 (766)
Q Consensus 222 g~~~~~~~~~~~~~p~--~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~gGrIi~ 299 (766)
|+|+|+ +++||++.|+++.|+.+|+.|+.+ +.....+..|+|+||++|..+|+. .+.||||++
T Consensus 1036 ----------DPFLPlP~ddLLVnL~ESRevIe~LLDkLPem---Ft~t~~~esCLGSALqAA~~aLk~--~GGGGKIiV 1100 (1560)
T PTZ00395 1036 ----------DPFLPLPLEDLFFGCVEEIDKINTLIDTIKSV---STTMQSYGSCGNSALKIAMDMLKE--RNGLGSICM 1100 (1560)
T ss_pred ----------cCcCCCCccCeeechHHHHHHHHHHHHHHHHH---hhccCCCcccHHHHHHHHHHHHHh--cCCCceEEE
Confidence 478885 789999999999999999999885 455566789999999999999992 123599999
Q ss_pred EeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccC--hhcchhhhhc
Q 004238 300 LVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVG--VAEMKVAVEK 377 (766)
Q Consensus 300 f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~--l~~l~~l~~~ 377 (766)
|++++|++|||+|+.++. ..++ ..++.++.+||++||.+|++.+|+||||+++..++| +++|+.|++.
T Consensus 1101 F~SSLPniGpGaLK~Re~---------~~KE-k~Ll~pqd~FYK~LA~ECsk~qISVDLFLfSsqYvDVDVATLg~Lsr~ 1170 (1560)
T PTZ00395 1101 FYTTTPNCGIGAIKELKK---------DLQE-NFLEVKQKIFYDSLLLDLYAFNISVDIFIISSNNVRVCVPSLQYVAQN 1170 (1560)
T ss_pred EEcCCCCCCCCccccccc---------cccc-ccccccchHHHHHHHHHHHhcCCceEEEEccCcccccccccccchhcc
Confidence 999999999999987542 1133 356788899999999999999999999999998876 7999999999
Q ss_pred ccceEEEeCCCCchhhH----HHHHHHHhhccccccceeeeEEEEEecCCceEEEEEc--CcccccccccCCCccceeee
Q 004238 378 TGGLVVLAESFGHSVFK----DSFKRIFEDGEQSLGLCFNGALEIICSKDIKIQGIIG--PCTSLEKVRLRGEYYAWKMC 451 (766)
Q Consensus 378 TGG~v~~~~~f~~~~~~----~~l~~~l~~~~~~~~~~~~a~l~vr~S~gl~v~~~~G--~~~~~~~~~g~~~~~~~~l~ 451 (766)
|||.+++|+.|+..+.. .+|.+.|++ +.+||+|+||||||+||+|+.+|| +++.. .++++++.+|
T Consensus 1171 TGGqlyyYPnFna~rD~~KL~~DL~r~LTr----e~iGyEAVMRVRCS~GLrVs~fyG~GnnF~s-----~rStDLLaLP 1241 (1560)
T PTZ00395 1171 TGGKILFVENFLWQKDYKEIYMNIMDTLTS----EDIAYCCELKLRYSHHMSVKKLFCCNNNFNS-----IISVDTIKIP 1241 (1560)
T ss_pred cceeEEEeCCCcccccHHHHHHHHHHHhhc----cceeeEEEEEEECCCCeEEEEEeccCCcccc-----cccccccccc
Confidence 99999999999876544 455555553 248999999999999999999994 44421 2467899999
Q ss_pred cCCCCceEEEEEEecCCCCCCCCCCCCCcEEEEEEEEeecCCCcEEEEEEeeccccccCCCCHHHHHhccChhHHHHHHH
Q 004238 452 GLDKSTCLTVFFDLSSSERLNTPGTINPQLYLQFLTSFQSPEGRSVLRVTTVTRQWVDSAVSSEELVQGFDQESAAVVMA 531 (766)
Q Consensus 452 ~~~~~~s~~~~f~~~~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~l~vt~~~~~~~~i~~~~D~~a~~~lla 531 (766)
.+++|++|+|+|++++.+ .....+|||+|++||+.+|+|||||||+++||+. ++.++|+++|++|++.+|+
T Consensus 1242 ~Id~DqSfaVeLk~DEkL------~~~~~AYFQaALLYTSssGERRIRVHTLALPVTS---sLseVFrsADqdAIvslLA 1312 (1560)
T PTZ00395 1242 KIRHDQTFAFLLNYSDIS------ESKKQIYFQCACIYTNLWGDRFVRLHTTHMNLTS---SLSTVFRYTDAEALMNILI 1312 (1560)
T ss_pred ccCCCceEEEEEEecccc------CCCCcEEEEEEEeeccCCCcEEEEEEeeeecccC---CHHHHHHhhcHHHHHHHHH
Confidence 999999999999999988 3567899999999999999999999999999999 8899999999999999999
Q ss_pred HHHHHHhhcCChHHHHHHHHHHHHHHHHHhcccccCC-----CCCccCCccccchHHHHHHhccccccCCCCCChHHHHH
Q 004238 532 RLTSLKMEMEEGFDATRWLDRSLIRLCSKFGDYRKDD-----PASFTLNPSFSLFPQFMFNLRRSQFVQVFNNSPDETAY 606 (766)
Q Consensus 532 k~a~~~~~~~~~~~~~~~l~~~l~~~~~~~~~y~~~~-----~~s~~lp~~l~~lP~~~~~L~ks~~l~~~~~s~Der~~ 606 (766)
|+|+.+++++. ++|+.|.+.++++ |..||+.| +++|+||++||+||+|+++|+||++|+ ..+++|+|++
T Consensus 1313 K~AV~~aLsss--dARe~L~dklVdI---LtaYRK~CAsssssgQLILPESLKLLPLYILSLLKS~AfR-t~I~sDeRVy 1386 (1560)
T PTZ00395 1313 KQLCTNILHND--NYSKIIIDNLAAI---LFSYRINCASSAHSGQLILPDTLKLLPLFTSSLLKHNVTK-KEILHDLKVY 1386 (1560)
T ss_pred HHHHHHhcccH--HHHHHHHHHHHHH---HHHHHHHhhccCCCccccchhHHHHHHHHHHHHhcccccc-CCCCccHHHH
Confidence 99999999874 8999999999999 66777765 358999999999999999999999998 4789999999
Q ss_pred HHHHHccCCHHHHHHhhcccceeecc-------C-----C---CCcccccccccccCCeEEEEeCCcEEEEEECCchh-H
Q 004238 607 FRMLLNRENITNAAVMIQPSLISYSF-------N-----S---LPQPALLDVASIAADRILLLDTYFSVVIFHGMTIA-Q 670 (766)
Q Consensus 607 ~~~~l~~~~~~~~~~~iyP~L~~~~~-------~-----~---~p~~~~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~-~ 670 (766)
.++.++++++..++.++||+||++|. + + +|.+++||.+.|.++|+||||+|..+|||+|++|+ +
T Consensus 1387 aL~rL~SmPI~~Li~yLYPRLYpLHdL~~e~e~d~~d~d~~ivLPp~LrLS~ErLesdGIYLLDNGe~IyLWVG~~V~Pq 1466 (1560)
T PTZ00395 1387 SLIKLLSMPIISSLLYVYPVMYVIHIKGKTNEIDSMDVDDDLFIPKTIPSSAEKIYSNGIYLLDACTHFYLYFGFHSDAN 1466 (1560)
T ss_pred HHHHHhCCCHHHHHhhhcCceEEcccccccccCCccCCCCccccCCcccchHHHhcCCcEEEEECCCEEEEEECCCCCHH
Confidence 99999999999999999999999984 0 1 48899999999999999999999999999999998 7
Q ss_pred Hhhc--CCCCC-------hhhhHHHHHhhCcHHHHHHHHhcC--CCCcEEEEEeCCCChHHHHHHhhcCCCCcCCccccc
Q 004238 671 WRNM--GYQNQ-------PEHQAFAQLLRAPHDDAELIIRDR--FPVPRLVVCDQHGSQARFLLAKLNPSATYNNANEIA 739 (766)
Q Consensus 671 ~~~~--g~~~~-------~~~~~~~~~l~~~~~~~~~i~~~R--~p~p~~~~~~~g~s~~r~l~s~L~p~~~~~~~~~~~ 739 (766)
|+++ |.... |+.+. .+=+..+..++.|++.| .+++++++++++++.+-+|++.|+||++.
T Consensus 1467 LLqDLFGv~~~~~~~~eLPelDT--~iS~RVrnII~~LR~~r~~~~Y~pL~IVRqgDp~E~~F~s~LVEDRs~------- 1537 (1560)
T PTZ00395 1467 FAKEIVGDIPTEKNAHELNLTDT--PNAQKVQRIIKNLSRIHHFNKYVPLVMVAPKSNEEEHLISLCVEDKAD------- 1537 (1560)
T ss_pred HHHHHcCCCccccccccccCCCC--HHHHHHHHHHHHHHHhccCCCcceEEEEeCCCchHHHHHHhCeecCCC-------
Confidence 8876 53211 11100 00011233455777765 46788899999988888899999999952
Q ss_pred CCCcccccCCchHHHHHHHHHHHHhc
Q 004238 740 AGSDIIFTDDVSLQVFIEHLQRLAVQ 765 (766)
Q Consensus 740 ~~~~~~~t~~~Sy~~f~~~L~~~i~~ 765 (766)
+.+||.+||++|||+|++
T Consensus 1538 --------g~~SYvDFLc~LHKqIq~ 1555 (1560)
T PTZ00395 1538 --------KEYSYVNFLCFIHKLVHK 1555 (1560)
T ss_pred --------CCCCHHHHHHHHHHHHHH
Confidence 359999999999999976
No 7
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=100.00 E-value=9.9e-113 Score=931.88 Aligned_cols=651 Identities=19% Similarity=0.306 Sum_probs=576.8
Q ss_pred CcCCCCeeEeeccccCCCHHHhhhCCCceeEEEccCCCCC----CCCCC-CCCCcccCCCCceecCceeEEcCCceEEec
Q 004238 8 DPEGIDGVRMTWNVWPRTKVEASKCVIPLAASISPIRSHP----DIPTL-PYAPLRCKTCTAALNAFARVDFTAKIWICP 82 (766)
Q Consensus 8 ~~~~~~~vR~t~~~~P~t~~~~~~~~iPlg~~v~P~~~~~----~ip~~-~~~p~RC~~C~ayiNp~~~~~~~~~~W~C~ 82 (766)
.|++|+|+|+|++++|.+.++.++++||||++++||.++. .+|+. +..|+||++||+|+|||.+|.++|++|+||
T Consensus 146 ~n~~p~yvrsT~yaiP~t~dl~~~skiPfgLVI~Pf~~l~~e~~~vpl~~d~~ivRCrrCrsYiNPfv~fi~~g~kw~CN 225 (861)
T COG5028 146 SNCSPKYVRSTMYAIPETNDLLKKSKIPFGLVIRPFLELYPEEDPVPLVEDGSIVRCRRCRSYINPFVQFIEQGRKWRCN 225 (861)
T ss_pred CCCCHHHHHHHHhhCCCchhHHHhcCCCceEEeehhhhcCccCCCCccCCCCcchhhhhhHhhcCceEEEecCCcEEEEe
Confidence 3889999999999999999999999999999999999762 34543 345899999999999999999999999999
Q ss_pred CCCCCCCCCccccc-------CCCCCCCccccCCCceEEEEecCCCCCCCCCCCCCCCCcEEEEEEEcccchHH---HHH
Q 004238 83 FCYQRNHFPPHYAA-------ISETNLPCELYPQYTTVEYTLPHSMQNPNNPNPDPRLSPVFVFVLDTCMIEEE---LGY 152 (766)
Q Consensus 83 ~C~~~N~~p~~y~~-------~~~~~~~pEL~p~~~tvey~~~~~~~~~~~~~~~~~~~p~~vFvID~s~~~~~---l~~ 152 (766)
+|+..|++|..+.+ .++.+.|+|| .+++|||.+|++|++ |.| .||+|||+||||.++.+ +.+
T Consensus 226 iC~~kN~vp~~~~~~~~~~~~r~d~~~r~El--~~~vvdf~ap~~Y~~---~~p---~P~~yvFlIDVS~~a~~~g~~~a 297 (861)
T COG5028 226 ICRSKNDVPEGFDNPSGPNDPRSDRYSRPEL--KSGVVDFLAPKEYSL---RQP---PPPVYVFLIDVSFEAIKNGLVKA 297 (861)
T ss_pred eccccccCcccccCcCCCCCccccccccchh--hceeeEEecccceee---ccC---CCCEEEEEEEeehHhhhcchHHH
Confidence 99999999998873 1235689999 899999999999998 566 79999999999999987 789
Q ss_pred HHHHHHHHhccCC---CCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhccccCcccccCCCcccCCC
Q 004238 153 ARSELKRAIGLLP---DNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLGLSASGRRAAGGYQKAAVP 229 (766)
Q Consensus 153 ~~~~l~~~l~~lp---~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~~~d~~~~~~~g~~~~~~~ 229 (766)
+.++|+..|+.+| +++||+||.||+.||+++++.+. + .+|++++|.|
T Consensus 298 ~~r~Il~~l~~~~~~dpr~kIaii~fD~sl~ffk~s~d~---------------~--~~~~~vsdld------------- 347 (861)
T COG5028 298 AIRAILENLDQIPNFDPRTKIAIICFDSSLHFFKLSPDL---------------D--EQMLIVSDLD------------- 347 (861)
T ss_pred HHHHHHhhccCCCCCCCcceEEEEEEcceeeEEecCCCC---------------c--cceeeecccc-------------
Confidence 9999999999886 58999999999999999997653 1 2678787654
Q ss_pred CCCCCCCc--ccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccCCCCccEEEEEeCCCCCC
Q 004238 230 NAFPNSGV--SRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACLPGTGARIVALVGGPCTE 307 (766)
Q Consensus 230 ~~~~~~p~--~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~gGrIi~f~sg~pt~ 307 (766)
++|+|. +.|++|+++|+..++.||+.++.+ +..++.++.|+|+||++|..+++ .+||||++|.+..||.
T Consensus 348 --~pFlPf~s~~fv~pl~~~k~~~etLl~~~~~I---f~d~~~pk~~~G~aLk~a~~l~g----~~GGkii~~~stlPn~ 418 (861)
T COG5028 348 --EPFLPFPSGLFVLPLKSCKQIIETLLDRVPRI---FQDNKSPKNALGPALKAAKSLIG----GTGGKIIVFLSTLPNM 418 (861)
T ss_pred --cccccCCcchhcccHHHHHHHHHHHHHHhhhh---hcccCCCccccCHHHHHHHHHhh----ccCceEEEEeecCCCc
Confidence 378884 589999999999988999999986 56788899999999999999998 8999999999999999
Q ss_pred CCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhhhhcccceEEEeCC
Q 004238 308 GPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVAEMKVAVEKTGGLVVLAES 387 (766)
Q Consensus 308 GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~ 387 (766)
|.|+|..|+++ + ..++++.+.||++++.+|++.||+||+|+++.+|+|+++++.|++.|||..++|+.
T Consensus 419 G~Gkl~~r~d~-----------e-~~ll~c~d~fYk~~a~e~~k~gIsvd~Flt~~~yidvaTls~l~~~T~G~~~~Yp~ 486 (861)
T COG5028 419 GIGKLQLREDK-----------E-SSLLSCKDSFYKEFAIECSKVGISVDLFLTSEDYIDVATLSHLCRYTGGQTYFYPN 486 (861)
T ss_pred ccccccccccc-----------h-hhhccccchHHHHHHHHHHHhcceEEEEeccccccchhhhcchhhccCcceEEcCC
Confidence 99999988652 2 23788999999999999999999999999999999999999999999999999999
Q ss_pred CCchh------hHHHHHHHHhhccccccceeeeEEEEEecCCceEEEEEcCcccccccccCCCccceeeecCCCCceEEE
Q 004238 388 FGHSV------FKDSFKRIFEDGEQSLGLCFNGALEIICSKDIKIQGIIGPCTSLEKVRLRGEYYAWKMCGLDKSTCLTV 461 (766)
Q Consensus 388 f~~~~------~~~~l~~~l~~~~~~~~~~~~a~l~vr~S~gl~v~~~~G~~~~~~~~~g~~~~~~~~l~~~~~~~s~~~ 461 (766)
|+.++ |.++|.+.+. ++.||+++||||||+|++++++|||++. ++.++..++.+++|+|+.|
T Consensus 487 f~~~~~~d~~kl~~dL~~~ls-----~~~gy~~~~rvR~S~glr~s~fyGnf~~-------rs~dl~~F~tm~rd~Sl~~ 554 (861)
T COG5028 487 FSATRPNDATKLANDLVSHLS-----MEIGYEAVMRVRCSTGLRVSSFYGNFFN-------RSSDLCAFSTMPRDTSLLV 554 (861)
T ss_pred cccCCchhHHHHHHHHHHhhh-----hhhhhheeeEeeccCceehhhhhccccc-------cCcccccccccCCCceEEE
Confidence 99887 6666666666 4789999999999999999999999996 4789999999999999999
Q ss_pred EEEecCCCCCCCCCCCCCcEEEEEEEEeecCCCcEEEEEEeeccccccCCCCHHHHHhccChhHHHHHHHHHHHHHhhcC
Q 004238 462 FFDLSSSERLNTPGTINPQLYLQFLTSFQSPEGRSVLRVTTVTRQWVDSAVSSEELVQGFDQESAAVVMARLTSLKMEME 541 (766)
Q Consensus 462 ~f~~~~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~l~vt~~~~~~~~i~~~~D~~a~~~llak~a~~~~~~~ 541 (766)
+|++++++. ...+|||.|++||..+|+|||||.|+++++++ ++.++|+++||+|++.+|+|+|+.++..+
T Consensus 555 ~~sid~~l~-------~~~v~fQvAlL~T~~~GeRRiRVvn~s~~~ss---~~~evyasadq~aIa~~lak~a~~~~~~~ 624 (861)
T COG5028 555 EFSIDEKLM-------TSDVYFQVALLYTLNDGERRIRVVNLSLPTSS---SIREVYASADQLAIACILAKKASTKALNS 624 (861)
T ss_pred EEEeccccc-------CCceEEEEEEEeeccCCceEEEEEEeccccch---hHHHHHHhccHHHHHHHHHHHHHHHhhhh
Confidence 999999983 58999999999999999999999999999998 88999999999999999999999999999
Q ss_pred ChHHHHHHHHHHHHHHHHHhcccccC-----CCCCccCCccccchHHHHHHhccccccCCCCCChHHHHHHHHHHccCCH
Q 004238 542 EGFDATRWLDRSLIRLCSKFGDYRKD-----DPASFTLNPSFSLFPQFMFNLRRSQFVQVFNNSPDETAYFRMLLNRENI 616 (766)
Q Consensus 542 ~~~~~~~~l~~~l~~~~~~~~~y~~~-----~~~s~~lp~~l~~lP~~~~~L~ks~~l~~~~~s~Der~~~~~~l~~~~~ 616 (766)
...++|+.|++.++++ +..|||. .++++.||++|++||++|++|.||.+|+...++.|.|++....+.++++
T Consensus 625 s~~~~r~~i~~s~~~I---L~~Ykk~~~~snt~tql~Lp~nL~lLPll~lal~Ks~~~rs~~~~sD~r~~~L~~l~~~p~ 701 (861)
T COG5028 625 SLKEARVLINKSMVDI---LKAYKKELVKSNTSTQLPLPANLKLLPLLMLALLKSSAFRSGSTPSDIRISALNRLTSLPL 701 (861)
T ss_pred hHHHHHHHHHHHHHHH---HHHHHHHHhhccCCccccchhhhHHHHHHHHHHhhhcccccCCCccchhHHHHHHhhcCCH
Confidence 9999999999999999 6667763 3568999999999999999999999999888899999999999999999
Q ss_pred HHHHHhhcccceeecc----CC--------CCcccccccccccCCeEEEEeCCcEEEEEECCchh-HHhhc--CCCC---
Q 004238 617 TNAAVMIQPSLISYSF----NS--------LPQPALLDVASIAADRILLLDTYFSVVIFHGMTIA-QWRNM--GYQN--- 678 (766)
Q Consensus 617 ~~~~~~iyP~L~~~~~----~~--------~p~~~~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~-~~~~~--g~~~--- 678 (766)
.++++.|||+||++|. .+ .|+++.++.+.+.++|+||+|+|.++|+|+|+++. +++.+ |..+
T Consensus 702 ~~l~~~iYP~lyalHdm~~e~~l~~~~~~~~~~piNaT~s~le~~GlYLidtg~~iflw~g~d~~p~Ll~dlf~~~~~~~ 781 (861)
T COG5028 702 KQLMRNIYPTLYALHDMPIEAGLPDEGLLVLPSPINATSSLLESGGLYLIDTGQKIFLWFGKDAVPSLLQDLFGVDSLSD 781 (861)
T ss_pred HHHHHhhccceeeecccccccCCCcccccccccchhhhHHHHhcCCeEEEEcCCEEEEEecCCCCHHHHHHhcCcchhhh
Confidence 9999999999999992 11 47889999999999999999999999999999976 55554 3321
Q ss_pred ------------ChhhhHHHHHhhCcHHHHHHHHh-cCCCCcEEEEEeCCCChH--HHHHHhhcCCCCcCCcccccCCCc
Q 004238 679 ------------QPEHQAFAQLLRAPHDDAELIIR-DRFPVPRLVVCDQHGSQA--RFLLAKLNPSATYNNANEIAAGSD 743 (766)
Q Consensus 679 ------------~~~~~~~~~~l~~~~~~~~~i~~-~R~p~p~~~~~~~g~s~~--r~l~s~L~p~~~~~~~~~~~~~~~ 743 (766)
++..++++ +.+.++|+ .+..++.++++|+|+.+. -++++.|+||+++
T Consensus 782 I~~~k~~~p~~~n~~n~~v~-------~iI~~lrs~~~~~tl~lvlVR~~~d~s~~~~~~s~lVEDk~~----------- 843 (861)
T COG5028 782 IPSGKFTLPPTGNEFNERVR-------NIIGELRSVNDDSTLPLVLVRGGGDPSLRLWFFSTLVEDKTL----------- 843 (861)
T ss_pred ccccccccCCcCCHHHHHHH-------HHHHHHHhhCCCCccceEEEecCCCcchhhheehheeccccc-----------
Confidence 12222333 34458886 677777799999997775 4668999999975
Q ss_pred ccccCCchHHHHHHHHHHHHh
Q 004238 744 IIFTDDVSLQVFIEHLQRLAV 764 (766)
Q Consensus 744 ~~~t~~~Sy~~f~~~L~~~i~ 764 (766)
+-.||.+|++.||..|.
T Consensus 844 ----n~~SY~~yL~~lh~ki~ 860 (861)
T COG5028 844 ----NIPSYLDYLQILHEKIK 860 (861)
T ss_pred ----CCccHHHHHHHHHHHhc
Confidence 34999999999999875
No 8
>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=100.00 E-value=1.4e-55 Score=458.38 Aligned_cols=264 Identities=57% Similarity=0.982 Sum_probs=240.2
Q ss_pred CCcEEEEEEEcccchHHHHHHHHHHHHHhccCCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhcc
Q 004238 133 LSPVFVFVLDTCMIEEELGYARSELKRAIGLLPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLGL 212 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~~l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~~ 212 (766)
.||+|+||||+|.++++++.++++|+++|+.||++++|||||||++||||+|+...+++++||+|+++|+.+++++|+++
T Consensus 2 ~pp~~vFviDvs~~~~el~~l~~sl~~~L~~lP~~a~VGlITfd~~V~~~~L~~~~~~~~~vf~g~~~~~~~~~~~~l~~ 81 (267)
T cd01478 2 SPPVFLFVVDTCMDEEELDALKESLIMSLSLLPPNALVGLITFGTMVQVHELGFEECSKSYVFRGNKDYTAKQIQDMLGL 81 (267)
T ss_pred CCCEEEEEEECccCHHHHHHHHHHHHHHHHhCCCCCEEEEEEECCEEEEEEcCCCcCceeeeccCCccCCHHHHHHHhcc
Confidence 78999999999999999999999999999999999999999999999999999888999999999999999999999987
Q ss_pred ccCcccccCCCcccCCCCCCCCCC--cccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccC
Q 004238 213 SASGRRAAGGYQKAAVPNAFPNSG--VSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACL 290 (766)
Q Consensus 213 ~d~~~~~~~g~~~~~~~~~~~~~p--~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~ 290 (766)
++..... .+.......+.+.| .++||+|++||++.|+++|++|+++.|++++++++.||+|+||++|..+|+.++
T Consensus 82 ~~~~~~~---~~~~~~~~~~~~~p~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~r~~r~~G~Al~~A~~ll~~~~ 158 (267)
T cd01478 82 GGPAMRP---SASQHPGAGNPLPSAAASRFLLPVSQCEFTLTDLLEQLQPDPWPVPAGHRPLRCTGVALSIAVGLLEACF 158 (267)
T ss_pred ccccccc---cccCcCCccccccccccccEEEEHHHHHHHHHHHHHhCcccccccCCCCCCCCchHHHHHHHHHHHHhhc
Confidence 6431100 00000001235555 379999999999999999999999999999999999999999999999999888
Q ss_pred CCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChhc
Q 004238 291 PGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVAE 370 (766)
Q Consensus 291 ~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~~ 370 (766)
++.||||++|++||||.|||+|+.++.++++|+|.|++++++++++++.+||++||.+|+++||+||+|+++.+|+|+++
T Consensus 159 ~~~gGki~~F~sg~pT~GpG~l~~r~~~~~~r~~~d~~~~~~~~~~~a~~fY~~la~~~~~~~vsvDlF~~s~d~vglae 238 (267)
T cd01478 159 PNTGARIMLFAGGPCTVGPGAVVSTELKDPIRSHHDIDKDNAKYYKKAVKFYDSLAKRLAANGHAVDIFAGCLDQVGLLE 238 (267)
T ss_pred CCCCcEEEEEECCCCCCCCceeeccccccccccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEEeccccccCHHH
Confidence 88999999999999999999999999999999999999988889999999999999999999999999999999999999
Q ss_pred chhhhhcccceEEEeCCCCchhhHHHHHH
Q 004238 371 MKVAVEKTGGLVVLAESFGHSVFKDSFKR 399 (766)
Q Consensus 371 l~~l~~~TGG~v~~~~~f~~~~~~~~l~~ 399 (766)
|++|++.|||.+++|++|+.+.|+++++|
T Consensus 239 m~~l~~~TGG~v~~~~~f~~~~f~~s~~~ 267 (267)
T cd01478 239 MKVLVNSTGGHVVLSDSFTTSIFKQSFQR 267 (267)
T ss_pred HHHHHHhcCcEEEEeCCcchHHHHHHhcC
Confidence 99999999999999999999999998764
No 9
>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=100.00 E-value=2.9e-44 Score=370.95 Aligned_cols=228 Identities=25% Similarity=0.328 Sum_probs=198.0
Q ss_pred CCcEEEEEEEcccchHH---HHHHHHHHHHHhccCCCC---cEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhH
Q 004238 133 LSPVFVFVLDTCMIEEE---LGYARSELKRAIGLLPDN---AMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQV 206 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~~---l~~~~~~l~~~l~~lp~~---~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l 206 (766)
+||+|+||||+|..+++ +++++++|+++|+.||++ ++|||||||+.||||+++++. ++
T Consensus 2 ~pp~~~FvIDvs~~a~~~g~~~~~~~si~~~L~~lp~~~~~~~VgiITfd~~v~~y~l~~~~---------------~~- 65 (244)
T cd01479 2 QPAVYVFLIDVSYNAIKSGLLATACEALLSNLDNLPGDDPRTRVGFITFDSTLHFFNLKSSL---------------EQ- 65 (244)
T ss_pred CCCEEEEEEEccHHHHhhChHHHHHHHHHHHHHhcCCCCCCeEEEEEEECCeEEEEECCCCC---------------CC-
Confidence 79999999999999986 999999999999999977 999999999999999998653 23
Q ss_pred HhhhccccCcccccCCCcccCCCCCCCCCCc-ccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHH
Q 004238 207 LEQLGLSASGRRAAGGYQKAAVPNAFPNSGV-SRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGL 285 (766)
Q Consensus 207 ~~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~-~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~l 285 (766)
++|++++|.+ ++++|+ ++||+|++||++.|+++|++|+.. +.+++++.+|+|+||++|..+
T Consensus 66 ~q~~vv~dl~---------------d~f~P~~~~~lv~l~e~~~~i~~lL~~L~~~---~~~~~~~~~c~G~Al~~A~~l 127 (244)
T cd01479 66 PQMMVVSDLD---------------DPFLPLPDGLLVNLKESRQVIEDLLDQIPEM---FQDTKETESALGPALQAAFLL 127 (244)
T ss_pred CeEEEeeCcc---------------cccCCCCcceeecHHHHHHHHHHHHHHHHHH---HhcCCCCcccHHHHHHHHHHH
Confidence 3567676653 367774 889999999999999999999763 567788999999999999999
Q ss_pred hhccCCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCc
Q 004238 286 LGACLPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQ 365 (766)
Q Consensus 286 l~~~~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~ 365 (766)
|+ +.||||++|++|+||.|||+++.++.++ +++|+ ++ +++++++++||++||.+|+++||+||+|+++.++
T Consensus 128 L~----~~GGkIi~f~s~~pt~GpG~l~~~~~~~-~~~~~---~e-~~~~~p~~~fY~~la~~~~~~~isvDlF~~~~~~ 198 (244)
T cd01479 128 LK----ETGGKIIVFQSSLPTLGAGKLKSREDPK-LLSTD---KE-KQLLQPQTDFYKKLALECVKSQISVDLFLFSNQY 198 (244)
T ss_pred HH----hcCCEEEEEeCCCCCcCCcccccCcccc-ccCch---hh-hhhcCcchHHHHHHHHHHHHcCeEEEEEEccCcc
Confidence 99 8999999999999999999999998655 44432 33 4789999999999999999999999999999999
Q ss_pred cChhcchhhhhcccceEEEeC--CCCchh----hHHHHHHHHhh
Q 004238 366 VGVAEMKVAVEKTGGLVVLAE--SFGHSV----FKDSFKRIFED 403 (766)
Q Consensus 366 ~~l~~l~~l~~~TGG~v~~~~--~f~~~~----~~~~l~~~l~~ 403 (766)
+|+++|+.|++.|||.+++|+ .|+..+ +..+|.|.++|
T Consensus 199 ~dla~l~~l~~~TGG~v~~y~~~~~~~~~d~~kl~~dl~~~ltr 242 (244)
T cd01479 199 VDVATLGCLSRLTGGQVYYYPSFNFSAPNDVEKLVNELARYLTR 242 (244)
T ss_pred cChhhhhhhhhhcCceEEEECCccCCchhhHHHHHHHHHHHhcc
Confidence 999999999999999999999 666543 44555565554
No 10
>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=100.00 E-value=3.2e-44 Score=371.08 Aligned_cols=227 Identities=41% Similarity=0.607 Sum_probs=197.8
Q ss_pred CCcEEEEEEEcccchH---HHHHHHHHHHHHhccCC--CCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHH
Q 004238 133 LSPVFVFVLDTCMIEE---ELGYARSELKRAIGLLP--DNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVL 207 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~---~l~~~~~~l~~~l~~lp--~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~ 207 (766)
+||+|+||||+|.+++ +++.++++|+++|+.|| ++++|||||||++||||++++... + +
T Consensus 2 ~pp~~vFvID~s~~ai~~~~l~~~~~sl~~~l~~lp~~~~~~igiITf~~~V~~~~~~~~~~---------------~-~ 65 (239)
T cd01468 2 QPPVFVFVIDVSYEAIKEGLLQALKESLLASLDLLPGDPRARVGLITYDSTVHFYNLSSDLA---------------Q-P 65 (239)
T ss_pred CCCEEEEEEEcchHhccccHHHHHHHHHHHHHHhCCCCCCcEEEEEEeCCeEEEEECCCCCC---------------C-C
Confidence 7999999999999954 49999999999999999 999999999999999999976541 1 3
Q ss_pred hhhccccCcccccCCCcccCCCCCCCCCCc-ccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHh
Q 004238 208 EQLGLSASGRRAAGGYQKAAVPNAFPNSGV-SRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLL 286 (766)
Q Consensus 208 ~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~-~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll 286 (766)
+|++++|.+ |.++|. ++++++++|+++.|.++|++|+++.++. .++++.||+|+||++|..+|
T Consensus 66 ~~~v~~dl~---------------d~f~p~~~~~l~~~~e~~~~i~~~l~~l~~~~~~~-~~~~~~~~~G~Al~~A~~ll 129 (239)
T cd01468 66 KMYVVSDLK---------------DVFLPLPDRFLVPLSECKKVIHDLLEQLPPMFWPV-PTHRPERCLGPALQAAFLLL 129 (239)
T ss_pred eEEEeCCCc---------------cCcCCCcCceeeeHHHHHHHHHHHHHhhhhhcccc-CCCCCcccHHHHHHHHHHHH
Confidence 456665543 366774 7899999999999999999999975432 36788999999999999999
Q ss_pred hccCCCC--ccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCC
Q 004238 287 GACLPGT--GARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALD 364 (766)
Q Consensus 287 ~~~~~~~--gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~ 364 (766)
+ .. ||||++|++|+||.|||+|+.++.++++|+|. ++++++++.+||++||.+|+++||+||+|+++.+
T Consensus 130 ~----~~~~gGkI~~f~sg~pt~GpG~l~~~~~~~~~~~~~-----e~~~~~~a~~fY~~la~~~~~~~isvdlF~~~~~ 200 (239)
T cd01468 130 K----GTFAGGRIIVFQGGLPTVGPGKLKSREDKEPIRSHD-----EAQLLKPATKFYKSLAKECVKSGICVDLFAFSLD 200 (239)
T ss_pred h----hcCCCceEEEEECCCCCCCCCccccCcccccCCCcc-----chhcccccHHHHHHHHHHHHHcCeEEEEEecccc
Confidence 9 45 99999999999999999999999999999862 3689999999999999999999999999999999
Q ss_pred ccChhcchhhhhcccceEEEeCCCCchhhHHHHHHH
Q 004238 365 QVGVAEMKVAVEKTGGLVVLAESFGHSVFKDSFKRI 400 (766)
Q Consensus 365 ~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~ 400 (766)
++|+++|++|++.|||.+++|++|+..+..+.|...
T Consensus 201 ~~dl~~l~~l~~~TGG~v~~y~~f~~~~~~~~~~~~ 236 (239)
T cd01468 201 YVDVATLKQLAKSTGGQVYLYDSFQAPNDGSKFKQD 236 (239)
T ss_pred ccCHHHhhhhhhcCCceEEEeCCCCCcccHHHHHHH
Confidence 999999999999999999999999655444444333
No 11
>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=100.00 E-value=1.7e-42 Score=359.75 Aligned_cols=232 Identities=32% Similarity=0.492 Sum_probs=179.2
Q ss_pred CCcEEEEEEEcccchHH---HHHHHHHHHHHhccCC--CCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHH
Q 004238 133 LSPVFVFVLDTCMIEEE---LGYARSELKRAIGLLP--DNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVL 207 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~~---l~~~~~~l~~~l~~lp--~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~ 207 (766)
+||+|+||||+|.++++ ++.++++|+++|+.|| ++++|||||||+.||+|+++.+. ++ .
T Consensus 2 ~pp~y~FvID~s~~av~~g~~~~~~~sl~~~l~~l~~~~~~~vgiitfd~~V~~y~l~~~~---------------~~-~ 65 (243)
T PF04811_consen 2 QPPVYVFVIDVSYEAVQSGLLQSLIESLKSALDSLPGDERTRVGIITFDSSVHFYNLSSSL---------------SQ-P 65 (243)
T ss_dssp S--EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTSSTSTT-EEEEEEESSSEEEEETTTTS---------------SS-T
T ss_pred CCCEEEEEEECchhhhhccHHHHHHHHHHHHHHhccCCCCcEEEEEEeCCEEEEEECCCCc---------------CC-C
Confidence 79999999999999765 9999999999999999 89999999999999999998654 11 3
Q ss_pred hhhccccCcccccCCCcccCCCCCCCCCCc-ccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHh
Q 004238 208 EQLGLSASGRRAAGGYQKAAVPNAFPNSGV-SRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLL 286 (766)
Q Consensus 208 ~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~-~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll 286 (766)
++++++|.+ +++.|. ++|+++++|+++.|.++|++|++. |+...++++.||+|+||++|..+|
T Consensus 66 ~~~v~~dl~---------------~~~~p~~~~llv~~~e~~~~i~~ll~~L~~~-~~~~~~~~~~~c~G~Al~~A~~ll 129 (243)
T PF04811_consen 66 QMIVVSDLD---------------DPFIPLPDGLLVPLSECRDAIEELLESLPSI-FPETAGKRPERCLGSALSAALSLL 129 (243)
T ss_dssp EEEEEHHTT---------------SHHSSTSSSSSEETTTCHHHHHHHHHHHHHH-STT-TTB-----HHHHHHHHHHHH
T ss_pred cccchHHHh---------------hcccCCcccEEEEhHHhHHHHHHHHHHhhhh-cccccccCccccHHHHHHHHHHHH
Confidence 455565543 245553 899999999999999999999873 333334788999999999999999
Q ss_pred hccCCCCccEEEEEeCCCCCCCC-cccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCc
Q 004238 287 GACLPGTGARIVALVGGPCTEGP-GTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQ 365 (766)
Q Consensus 287 ~~~~~~~gGrIi~f~sg~pt~Gp-G~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~ 365 (766)
+.. +.||||++|++|+||.|| |++..++.. ++.+++++++.+++++.+||++||.+|+++||+||+|+++.++
T Consensus 130 ~~~--~~gGkI~~F~s~~pt~G~Gg~l~~~~~~----~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~ 203 (243)
T PF04811_consen 130 SSR--NTGGKILVFTSGPPTYGPGGSLKKREDS----SHYDTEKEKALLLPPANEFYKKLAEECSKQGISVDLFVFSSDY 203 (243)
T ss_dssp HHH--TS-EEEEEEESS---SSSTTSS-SBTTS----CCCCHCTTHHCHSHSSSHHHHHHHHHHHHCTEEEEEEEECSS-
T ss_pred hcc--ccCCEEEEEeccCCCCCCCceecccccc----cccccccchhhhccccchHHHHHHHHHHhcCCEEEEEeecCCC
Confidence 842 589999999999999999 666666543 4556777777888999999999999999999999999999999
Q ss_pred cChhcchhhhhcccceEEEeCCCCchhhHHHHHHHHh
Q 004238 366 VGVAEMKVAVEKTGGLVVLAESFGHSVFKDSFKRIFE 402 (766)
Q Consensus 366 ~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l~ 402 (766)
+|+++|+.|++.|||.+++|++|+.+++.+.|++.|.
T Consensus 204 ~~l~tl~~l~~~TGG~l~~y~~f~~~~~~~~l~~dl~ 240 (243)
T PF04811_consen 204 VDLATLGPLARYTGGSLYYYPNFNAERDGEKLRQDLK 240 (243)
T ss_dssp -SHHHHTHHHHCTT-EEEEETTTTCHHHHHHHHHHHH
T ss_pred CCcHhHHHHHHhCceeEEEeCCCCCchhHHHHHHHHH
Confidence 9999999999999999999999996554444444443
No 12
>PF08033 Sec23_BS: Sec23/Sec24 beta-sandwich domain; InterPro: IPR012990 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 (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes part of the Sec23/24 beta-barrel domain, which is formed from approximately 180 residues from three segments of the polypeptide. The strands of the barrel are oriented roughly parallel to the membrane such that one end of the barrel forms part of the inner surface of the coat and the other end part of the membrane-distal surface. The barrel is constructed from two opposed sheets: a six-stranded beta sheet facing partly towards the zinc finger domain and partly towards the solvent, and a five-stranded beta sheet facing the helical domain.; PDB: 3EFO_B 3EG9_B 1PD0_A 1PD1_A 1M2V_B 1PCX_A 3EH2_C 3EGD_A 2NUP_A 3EGX_A ....
Probab=99.83 E-value=3.1e-20 Score=163.70 Aligned_cols=92 Identities=30% Similarity=0.556 Sum_probs=80.0
Q ss_pred eeeeEEEEEecCCceEEEEEcCcccccc----cccCCCccceeeecCCCCceEEEEEEecCCCCCCCCCCCCCcEEEEEE
Q 004238 411 CFNGALEIICSKDIKIQGIIGPCTSLEK----VRLRGEYYAWKMCGLDKSTCLTVFFDLSSSERLNTPGTINPQLYLQFL 486 (766)
Q Consensus 411 ~~~a~l~vr~S~gl~v~~~~G~~~~~~~----~~g~~~~~~~~l~~~~~~~s~~~~f~~~~~~~~~~~~~~~~~~~iQ~a 486 (766)
||+|+||||||+|++|++++||+..... .-|.++++.|++++++++++++|+|++++++ ...+.+||||+
T Consensus 1 g~~~~l~vr~S~gl~v~~~~G~~~~~~~~s~~~~g~~~~~~~~~~~l~~~~s~~~~~~~~~~~------~~~~~~~iQ~~ 74 (96)
T PF08033_consen 1 GFNAVLRVRCSKGLKVSGVIGPCFNRSSVSDNEIGEGDTTRWKLPSLDPDTSFAFEFEIDEDL------PNGSQAYIQFA 74 (96)
T ss_dssp EEEEEEEEEE-TTEEEEEEESSSEESSTBESSECSBSSCSEEEEEEEETT--EEEEEEESSBT------BTTSEEEEEEE
T ss_pred CceEEEEEEECCCeEEEEEEcCccccccccceeeccCCccEEEecccCCCCEEEEEEEECCCC------CCCCeEEEEEE
Confidence 7999999999999999999999998741 1155677789999999999999999999886 45789999999
Q ss_pred EEeecCCCcEEEEEEeeccccc
Q 004238 487 TSFQSPEGRSVLRVTTVTRQWV 508 (766)
Q Consensus 487 l~Yt~~~G~rriRV~T~~l~vt 508 (766)
++||+.+|+|||||+|+++|+|
T Consensus 75 ~~Yt~~~G~r~iRV~T~~l~vt 96 (96)
T PF08033_consen 75 LLYTDSNGERRIRVTTLSLPVT 96 (96)
T ss_dssp EEEEETTSEEEEEEEEEEEEEE
T ss_pred EEEECCCCCEEEEEEeeccccC
Confidence 9999999999999999999986
No 13
>PF04815 Sec23_helical: Sec23/Sec24 helical domain; InterPro: IPR006900 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 (IPR006896 from INTERPRO), an all-helical region, and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes the all-helical domain, which forms an approximately 105-residue segment with the C-terminal 30 residues. The linker between alpha-M and alpha-N contacts Sar1.; GO: 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EGD_B 2NUP_B 2NUT_B 3EGX_B 3EH2_C 3EH1_A 3EFO_B 3EG9_B 2QTV_A 1M2O_C ....
Probab=99.74 E-value=6.1e-18 Score=151.05 Aligned_cols=101 Identities=25% Similarity=0.301 Sum_probs=89.2
Q ss_pred hhHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHhcccccCCC--CCccCCccccchHHHHHHhccccccCCCCCC
Q 004238 523 QESAAVVMARLTSLKMEMEEGFDATRWLDRSLIRLCSKFGDYRKDDP--ASFTLNPSFSLFPQFMFNLRRSQFVQVFNNS 600 (766)
Q Consensus 523 ~~a~~~llak~a~~~~~~~~~~~~~~~l~~~l~~~~~~~~~y~~~~~--~s~~lp~~l~~lP~~~~~L~ks~~l~~~~~s 600 (766)
|||++++++|+++.++.++++.++|+++++++++++..|+.+....+ ++++|||+||+||+|+++|+||++|++.+++
T Consensus 1 Qda~~~llak~ai~~~~~~~l~~~r~~l~~~~v~il~~Yr~~~~~~~~~~qLilPe~lklLPly~l~llKs~alr~~~v~ 80 (103)
T PF04815_consen 1 QDAITSLLAKQAIDKALSSSLKDARESLDNRLVDILAAYRKNCASSSSSGQLILPESLKLLPLYILALLKSPALRPTNVS 80 (103)
T ss_dssp HHHHHHHHHHHHHHHHCCS-HHHHHHHHHHHHHHHHHHHHHHCTTECCCTEEEEEGGGTTHHHHHHHHHTSTTTSCSTS-
T ss_pred CHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHhhccCCCCchhhhCCHHHHHHHHHHHHHHcchhhcCCCCC
Confidence 79999999999999999999999999999999999655555544433 5799999999999999999999999999999
Q ss_pred hHHHHHHHHHHccCCHHHHHHhh
Q 004238 601 PDETAYFRMLLNRENITNAAVMI 623 (766)
Q Consensus 601 ~Der~~~~~~l~~~~~~~~~~~i 623 (766)
+|||+|+++++++++++.++.||
T Consensus 81 ~D~R~~~~~~~~~~~~~~~~~~i 103 (103)
T PF04815_consen 81 PDERAYAMHLLLSMPVDSLLRMI 103 (103)
T ss_dssp HHHHHHHHHHHHHS-HHHHHHHH
T ss_pred CcHHHHHHHHHHCCCHHHHHhhC
Confidence 99999999999999999999876
No 14
>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=99.61 E-value=1.7e-16 Score=114.66 Aligned_cols=40 Identities=50% Similarity=1.158 Sum_probs=29.2
Q ss_pred CCcccCCCCceecCceeEEcCCceEEecCCCCCCCCCccc
Q 004238 55 APLRCKTCTAALNAFARVDFTAKIWICPFCYQRNHFPPHY 94 (766)
Q Consensus 55 ~p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~p~~y 94 (766)
+|+||++|+||||||++|+.++++|+|+||++.|++|++|
T Consensus 1 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp~~Y 40 (40)
T PF04810_consen 1 GPVRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLPPHY 40 (40)
T ss_dssp -S-B-TTT--BS-TTSEEETTTTEEEETTT--EEE--GGG
T ss_pred CccccCCCCCEECCcceEcCCCCEEECcCCCCcCCCCCCC
Confidence 5899999999999999999999999999999999999887
No 15
>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=98.58 E-value=2.3e-06 Score=83.50 Aligned_cols=158 Identities=18% Similarity=0.188 Sum_probs=109.4
Q ss_pred EEEEEEcccchHH--HHHHHHHHHHHhccCCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhcccc
Q 004238 137 FVFVLDTCMIEEE--LGYARSELKRAIGLLPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLGLSA 214 (766)
Q Consensus 137 ~vFvID~s~~~~~--l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~~~d 214 (766)
++||+|+|.++.. ++.+++++...+..++++.+||+++|++..+..- ...
T Consensus 3 ~~~vlD~S~SM~~~~~~~~k~a~~~~~~~l~~~~~v~li~f~~~~~~~~-~~~--------------------------- 54 (170)
T cd01465 3 LVFVIDRSGSMDGPKLPLVKSALKLLVDQLRPDDRLAIVTYDGAAETVL-PAT--------------------------- 54 (170)
T ss_pred EEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEecCCccEEe-cCc---------------------------
Confidence 6899999999743 7888999999999999888999999997654420 000
Q ss_pred CcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccCC-CC
Q 004238 215 SGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACLP-GT 293 (766)
Q Consensus 215 ~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~-~~ 293 (766)
+ ...+..+...|+.++. ...+.++.||..|...+..... ..
T Consensus 55 ---------------------~--------~~~~~~l~~~l~~~~~---------~g~T~~~~al~~a~~~~~~~~~~~~ 96 (170)
T cd01465 55 ---------------------P--------VRDKAAILAAIDRLTA---------GGSTAGGAGIQLGYQEAQKHFVPGG 96 (170)
T ss_pred ---------------------c--------cchHHHHHHHHHcCCC---------CCCCCHHHHHHHHHHHHHhhcCCCC
Confidence 0 0011223444555443 1235789999999888863221 11
Q ss_pred ccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchh
Q 004238 294 GARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVAEMKV 373 (766)
Q Consensus 294 gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~~l~~ 373 (766)
-.+|++|++|.++.|+... +-+.+....+.+.++.|+.+.++ +..+...|..
T Consensus 97 ~~~ivl~TDG~~~~~~~~~---------------------------~~~~~~~~~~~~~~v~i~~i~~g-~~~~~~~l~~ 148 (170)
T cd01465 97 VNRILLATDGDFNVGETDP---------------------------DELARLVAQKRESGITLSTLGFG-DNYNEDLMEA 148 (170)
T ss_pred eeEEEEEeCCCCCCCCCCH---------------------------HHHHHHHHHhhcCCeEEEEEEeC-CCcCHHHHHH
Confidence 2679999999988764110 11233444556789999999998 6788899999
Q ss_pred hhhcccceEEEeCCC
Q 004238 374 AVEKTGGLVVLAESF 388 (766)
Q Consensus 374 l~~~TGG~v~~~~~f 388 (766)
++..++|..++.++.
T Consensus 149 ia~~~~g~~~~~~~~ 163 (170)
T cd01465 149 IADAGNGNTAYIDNL 163 (170)
T ss_pred HHhcCCceEEEeCCH
Confidence 999999998876553
No 16
>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=98.52 E-value=4.3e-06 Score=83.54 Aligned_cols=165 Identities=16% Similarity=0.112 Sum_probs=107.2
Q ss_pred CCcEEEEEEEcccchH--HHHHHHHHHHHHhccCCCCcEEEEEEECCeEEEEE-cCCCCCcceeEecCCcccchhhHHhh
Q 004238 133 LSPVFVFVLDTCMIEE--ELGYARSELKRAIGLLPDNAMVGLVTFGTQAHVHE-LGFSDMSKVYVFRGNKEISKDQVLEQ 209 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~--~l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~~~-l~~~~~~~~~v~~g~~~~~~~~l~~~ 209 (766)
.|-..+||||+|.++. .++.++++++..++.++++.+||||+|++.++..- ....
T Consensus 12 ~p~~vv~llD~SgSM~~~~l~~ak~~~~~ll~~l~~~d~v~lv~F~~~~~~~~~~~~~---------------------- 69 (190)
T cd01463 12 SPKDIVILLDVSGSMTGQRLHLAKQTVSSILDTLSDNDFFNIITFSNEVNPVVPCFND---------------------- 69 (190)
T ss_pred CCceEEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCCCEEEEEEeCCCeeEEeeeccc----------------------
Confidence 5678999999999974 38999999999999999999999999999877641 1100
Q ss_pred hccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhcc
Q 004238 210 LGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGAC 289 (766)
Q Consensus 210 l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 289 (766)
.++....+.+..+...|+.|+.. ..+.++.||..|...+...
T Consensus 70 -----------------------------~~~~~~~~~~~~~~~~l~~l~~~---------G~T~~~~al~~a~~~l~~~ 111 (190)
T cd01463 70 -----------------------------TLVQATTSNKKVLKEALDMLEAK---------GIANYTKALEFAFSLLLKN 111 (190)
T ss_pred -----------------------------ceEecCHHHHHHHHHHHhhCCCC---------CcchHHHHHHHHHHHHHHh
Confidence 00000111233344555555432 2367899999999888731
Q ss_pred C--------CCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHH-HHHHcCcEEEEEE
Q 004238 290 L--------PGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAK-QLVSQGHVLDLFA 360 (766)
Q Consensus 290 ~--------~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~-~~~~~~isvdlf~ 360 (766)
. +.....|+++|+|.++.+.-. ...+.. .....++.|..|.
T Consensus 112 ~~~~~~~~~~~~~~~iillTDG~~~~~~~~------------------------------~~~~~~~~~~~~~v~i~tig 161 (190)
T cd01463 112 LQSNHSGSRSQCNQAIMLITDGVPENYKEI------------------------------FDKYNWDKNSEIPVRVFTYL 161 (190)
T ss_pred hhcccccccCCceeEEEEEeCCCCCcHhHH------------------------------HHHhcccccCCCcEEEEEEe
Confidence 0 112346899999976532100 011100 0011246666666
Q ss_pred ecCCccChhcchhhhhcccceEEEeCC
Q 004238 361 SALDQVGVAEMKVAVEKTGGLVVLAES 387 (766)
Q Consensus 361 ~~~~~~~l~~l~~l~~~TGG~v~~~~~ 387 (766)
++.+..|...|..|+..+||..++.++
T Consensus 162 iG~~~~d~~~L~~lA~~~~G~~~~i~~ 188 (190)
T cd01463 162 IGREVTDRREIQWMACENKGYYSHIQS 188 (190)
T ss_pred cCCccccchHHHHHHhhcCCeEEEccc
Confidence 666656888999999999999988765
No 17
>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=98.52 E-value=6e-06 Score=81.58 Aligned_cols=164 Identities=17% Similarity=0.137 Sum_probs=110.0
Q ss_pred EEEEEEcccchH---HHHHHHHHHHHHhcc-CCCCcEEEEEEECCe-EEEEEcCCCCCcceeEecCCcccchhhHHhhhc
Q 004238 137 FVFVLDTCMIEE---ELGYARSELKRAIGL-LPDNAMVGLVTFGTQ-AHVHELGFSDMSKVYVFRGNKEISKDQVLEQLG 211 (766)
Q Consensus 137 ~vFvID~s~~~~---~l~~~~~~l~~~l~~-lp~~~~VglItf~~~-V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~ 211 (766)
++|+||+|.++. .++.+++++...+.. ++++.+||+|+|++. .++. +...
T Consensus 3 v~lvlD~SgSM~~~~rl~~ak~a~~~~~~~~~~~~d~v~lv~F~~~~~~~~-~~~t------------------------ 57 (178)
T cd01451 3 VIFVVDASGSMAARHRMAAAKGAVLSLLRDAYQRRDKVALIAFRGTEAEVL-LPPT------------------------ 57 (178)
T ss_pred EEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCceEE-eCCC------------------------
Confidence 679999999975 488888888887754 567789999999864 2221 0000
Q ss_pred cccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccCC
Q 004238 212 LSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACLP 291 (766)
Q Consensus 212 ~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~ 291 (766)
..+..+...|+.++. ...+.++.||..|...++....
T Consensus 58 ----------------------------------~~~~~~~~~l~~l~~---------~G~T~l~~aL~~a~~~l~~~~~ 94 (178)
T cd01451 58 ----------------------------------RSVELAKRRLARLPT---------GGGTPLAAGLLAAYELAAEQAR 94 (178)
T ss_pred ----------------------------------CCHHHHHHHHHhCCC---------CCCCcHHHHHHHHHHHHHHHhc
Confidence 001123344555543 2346899999999998821111
Q ss_pred CC--ccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChh
Q 004238 292 GT--GARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVA 369 (766)
Q Consensus 292 ~~--gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~ 369 (766)
.. ...|+++++|.++.|.... ..+ -.+++.++...||.+..+....+..+-.
T Consensus 95 ~~~~~~~ivliTDG~~~~g~~~~-----------------------~~~---~~~~~~~l~~~gi~v~~I~~~~~~~~~~ 148 (178)
T cd01451 95 DPGQRPLIVVITDGRANVGPDPT-----------------------ADR---ALAAARKLRARGISALVIDTEGRPVRRG 148 (178)
T ss_pred CCCCceEEEEECCCCCCCCCCch-----------------------hHH---HHHHHHHHHhcCCcEEEEeCCCCccCcc
Confidence 22 2578999999888764100 000 1456777788899887776666666777
Q ss_pred cchhhhhcccceEEEeCCCCchhhH
Q 004238 370 EMKVAVEKTGGLVVLAESFGHSVFK 394 (766)
Q Consensus 370 ~l~~l~~~TGG~v~~~~~f~~~~~~ 394 (766)
.|..+++.|||..++.++.+...|.
T Consensus 149 ~l~~iA~~tgG~~~~~~d~~~~~~~ 173 (178)
T cd01451 149 LAKDLARALGGQYVRLPDLSADAIA 173 (178)
T ss_pred HHHHHHHHcCCeEEEcCcCCHHHHH
Confidence 8999999999999999888765543
No 18
>PRK13685 hypothetical protein; Provisional
Probab=98.51 E-value=4e-06 Score=91.05 Aligned_cols=162 Identities=22% Similarity=0.184 Sum_probs=113.1
Q ss_pred CCcEEEEEEEcccchH-------HHHHHHHHHHHHhccCCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhh
Q 004238 133 LSPVFVFVLDTCMIEE-------ELGYARSELKRAIGLLPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQ 205 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~-------~l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~ 205 (766)
.+...+||||+|.++. .++.++++++..++.++++.+||+|+|++..++. ..
T Consensus 87 ~~~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l~~~d~vglv~Fa~~a~~~--~p------------------- 145 (326)
T PRK13685 87 NRAVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELTPGINLGLIAFAGTATVL--VS------------------- 145 (326)
T ss_pred CCceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhCCCCCeEEEEEEcCceeec--CC-------------------
Confidence 3446899999999974 3899999999999999888899999999875531 00
Q ss_pred HHhhhccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHH
Q 004238 206 VLEQLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGL 285 (766)
Q Consensus 206 l~~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~l 285 (766)
+...++.+...|+.|... ..++.|.|+..|...
T Consensus 146 --------------------------------------~t~d~~~l~~~l~~l~~~---------~~T~~g~al~~A~~~ 178 (326)
T PRK13685 146 --------------------------------------PTTNREATKNAIDKLQLA---------DRTATGEAIFTALQA 178 (326)
T ss_pred --------------------------------------CCCCHHHHHHHHHhCCCC---------CCcchHHHHHHHHHH
Confidence 001223466677777642 235788999999888
Q ss_pred hhcc-------CCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEE
Q 004238 286 LGAC-------LPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDL 358 (766)
Q Consensus 286 l~~~-------~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdl 358 (766)
+... .....++|+++++|-.+.|.... +. ... .+.+..+.+.||.|..
T Consensus 179 l~~~~~~~~~~~~~~~~~IILlTDG~~~~~~~~~-------------~~--------~~~----~~aa~~a~~~gi~i~~ 233 (326)
T PRK13685 179 IATVGAVIGGGDTPPPARIVLMSDGKETVPTNPD-------------NP--------RGA----YTAARTAKDQGVPIST 233 (326)
T ss_pred HHhhhcccccccCCCCCEEEEEcCCCCCCCCCCC-------------Cc--------ccH----HHHHHHHHHcCCeEEE
Confidence 7521 01234789999999877653110 00 000 1345566788999999
Q ss_pred EEecCCc-------------cChhcchhhhhcccceEEEeCC
Q 004238 359 FASALDQ-------------VGVAEMKVAVEKTGGLVVLAES 387 (766)
Q Consensus 359 f~~~~~~-------------~~l~~l~~l~~~TGG~v~~~~~ 387 (766)
+.++.+. .|-..|..+++.|||..++.++
T Consensus 234 Ig~G~~~g~~~~~g~~~~~~~d~~~L~~iA~~tgG~~~~~~~ 275 (326)
T PRK13685 234 ISFGTPYGSVEINGQRQPVPVDDESLKKIAQLSGGEFYTAAS 275 (326)
T ss_pred EEECCCCCCcCcCCceeeecCCHHHHHHHHHhcCCEEEEcCC
Confidence 9988642 5778899999999998887654
No 19
>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=98.48 E-value=4.4e-06 Score=80.57 Aligned_cols=149 Identities=22% Similarity=0.203 Sum_probs=103.8
Q ss_pred EEEEEEcccchHH--HHHHHHHHHHHhccCCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhcccc
Q 004238 137 FVFVLDTCMIEEE--LGYARSELKRAIGLLPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLGLSA 214 (766)
Q Consensus 137 ~vFvID~s~~~~~--l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~~~d 214 (766)
.+|+||+|.++.. ++.+++++...++.|+++.+||||+|++..+... . ++
T Consensus 3 v~~vlD~S~SM~~~rl~~ak~a~~~l~~~l~~~~~~~li~F~~~~~~~~-~--------------------------~~- 54 (155)
T cd01466 3 LVAVLDVSGSMAGDKLQLVKHALRFVISSLGDADRLSIVTFSTSAKRLS-P--------------------------LR- 54 (155)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcceEEEEEecCCccccC-C--------------------------Cc-
Confidence 5799999999763 8889999999999999989999999998654320 0 00
Q ss_pred CcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccC-CCC
Q 004238 215 SGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACL-PGT 293 (766)
Q Consensus 215 ~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~-~~~ 293 (766)
+. -...+..+.++++.+.+ ...++++.||..|..++.... .+.
T Consensus 55 ---------------------~~------~~~~~~~~~~~i~~~~~---------~g~T~~~~al~~a~~~~~~~~~~~~ 98 (155)
T cd01466 55 ---------------------RM------TAKGKRSAKRVVDGLQA---------GGGTNVVGGLKKALKVLGDRRQKNP 98 (155)
T ss_pred ---------------------cc------CHHHHHHHHHHHHhccC---------CCCccHHHHHHHHHHHHhhcccCCC
Confidence 00 00123345566666543 234789999999999987321 123
Q ss_pred ccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchh
Q 004238 294 GARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVAEMKV 373 (766)
Q Consensus 294 gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~~l~~ 373 (766)
...|+++++|.++.|+.. . ++.+.++.|..+.++. ..+..+|..
T Consensus 99 ~~~iillTDG~~~~~~~~---------~--------------------------~~~~~~v~v~~igig~-~~~~~~l~~ 142 (155)
T cd01466 99 VASIMLLSDGQDNHGAVV---------L--------------------------RADNAPIPIHTFGLGA-SHDPALLAF 142 (155)
T ss_pred ceEEEEEcCCCCCcchhh---------h--------------------------cccCCCceEEEEecCC-CCCHHHHHH
Confidence 468999999987765100 0 0123578888887764 467789999
Q ss_pred hhhcccceEEEe
Q 004238 374 AVEKTGGLVVLA 385 (766)
Q Consensus 374 l~~~TGG~v~~~ 385 (766)
++..|||..++.
T Consensus 143 iA~~t~G~~~~~ 154 (155)
T cd01466 143 IAEITGGTFSYV 154 (155)
T ss_pred HHhccCceEEEe
Confidence 999999998864
No 20
>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=98.46 E-value=3.6e-06 Score=85.23 Aligned_cols=169 Identities=27% Similarity=0.335 Sum_probs=108.7
Q ss_pred CCcEEEEEEEcccchH--------HHHHHHHHHHHHhccCCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchh
Q 004238 133 LSPVFVFVLDTCMIEE--------ELGYARSELKRAIGLLPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKD 204 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~--------~l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~ 204 (766)
.+..++||||+|.++. .++.+++++...++.++++.+|||++|++.++-. .. +
T Consensus 19 ~~~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~l~~~~~v~lv~F~~~~~~~----~~------------~--- 79 (206)
T cd01456 19 LPPNVAIVLDNSGSMREVDGGGETRLDNAKAALDETANALPDGTRLGLWTFSGDGDNP----LD------------V--- 79 (206)
T ss_pred CCCcEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHhCCCCceEEEEEecCCCCCC----cc------------c---
Confidence 6788999999999976 3899999999999999989999999999854210 00 0
Q ss_pred hHHhhhccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHH
Q 004238 205 QVLEQLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATG 284 (766)
Q Consensus 205 ~l~~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ 284 (766)
... +. ... ...+...+ ....+..+...|+.+.. + ...+.++.||..|..
T Consensus 80 ---~~~-~p-~~~---------------~~~~~~~~---~~~~~~~l~~~i~~i~~-----~---~G~T~l~~aL~~a~~ 128 (206)
T cd01456 80 ---RVL-VP-KGC---------------LTAPVNGF---PSAQRSALDAALNSLQT-----P---TGWTPLAAALAEAAA 128 (206)
T ss_pred ---ccc-cc-ccc---------------cccccCCC---CcccHHHHHHHHHhhcC-----C---CCcChHHHHHHHHHH
Confidence 000 00 000 00000000 00234456677777751 1 124689999999999
Q ss_pred HhhccCCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHH-HHcCcEEEEEEecC
Q 004238 285 LLGACLPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQL-VSQGHVLDLFASAL 363 (766)
Q Consensus 285 ll~~~~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~-~~~~isvdlf~~~~ 363 (766)
.+. ......|+++++|.++.|+.. .+..+++.... ...+|.|+.+.++.
T Consensus 129 ~l~---~~~~~~iillTDG~~~~~~~~---------------------------~~~~~~~~~~~~~~~~i~i~~igiG~ 178 (206)
T cd01456 129 YVD---PGRVNVVVLITDGEDTCGPDP---------------------------CEVARELAKRRTPAPPIKVNVIDFGG 178 (206)
T ss_pred HhC---CCCcceEEEEcCCCccCCCCH---------------------------HHHHHHHHHhcCCCCCceEEEEEecC
Confidence 985 133378999999987665300 00111222110 12589999999876
Q ss_pred CccChhcchhhhhcccceE
Q 004238 364 DQVGVAEMKVAVEKTGGLV 382 (766)
Q Consensus 364 ~~~~l~~l~~l~~~TGG~v 382 (766)
+ .+...|..+++.|||..
T Consensus 179 ~-~~~~~l~~iA~~tgG~~ 196 (206)
T cd01456 179 D-ADRAELEAIAEATGGTY 196 (206)
T ss_pred c-ccHHHHHHHHHhcCCeE
Confidence 5 67889999999999987
No 21
>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=98.40 E-value=6.3e-06 Score=81.77 Aligned_cols=152 Identities=13% Similarity=0.076 Sum_probs=99.2
Q ss_pred EEEEEEEcccchH-------HHHHHHHHHHHHhccC---CCCcEEEEEEE-CCeEEEEEcCCCCCcceeEecCCcccchh
Q 004238 136 VFVFVLDTCMIEE-------ELGYARSELKRAIGLL---PDNAMVGLVTF-GTQAHVHELGFSDMSKVYVFRGNKEISKD 204 (766)
Q Consensus 136 ~~vFvID~s~~~~-------~l~~~~~~l~~~l~~l---p~~~~VglItf-~~~V~~~~l~~~~~~~~~v~~g~~~~~~~ 204 (766)
..+++||+|.++. .++.+++.+...++.+ .++.+||||+| ++.-++- .+
T Consensus 5 ~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~a~~~--~P------------------ 64 (183)
T cd01453 5 HLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKL--TD------------------ 64 (183)
T ss_pred EEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCccEEE--EC------------------
Confidence 4689999999975 3899999998887754 34579999999 4433331 00
Q ss_pred hHHhhhccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHH
Q 004238 205 QVLEQLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATG 284 (766)
Q Consensus 205 ~l~~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ 284 (766)
+ ....+.+...|+.+ +. + ...+.++.||..|..
T Consensus 65 -------l--------------------------------T~D~~~~~~~L~~~--~~---~---~G~t~l~~aL~~A~~ 97 (183)
T cd01453 65 -------L--------------------------------TGNPRKHIQALKTA--RE---C---SGEPSLQNGLEMALE 97 (183)
T ss_pred -------C--------------------------------CCCHHHHHHHhhcc--cC---C---CCchhHHHHHHHHHH
Confidence 0 00001123333333 10 1 124789999999999
Q ss_pred HhhccCCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCC
Q 004238 285 LLGACLPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALD 364 (766)
Q Consensus 285 ll~~~~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~ 364 (766)
.++..-....++|++++++.-+.+|+ -+.++++.+.+.||.|++..++.
T Consensus 98 ~l~~~~~~~~~~iiil~sd~~~~~~~------------------------------~~~~~~~~l~~~~I~v~~IgiG~- 146 (183)
T cd01453 98 SLKHMPSHGSREVLIIFSSLSTCDPG------------------------------NIYETIDKLKKENIRVSVIGLSA- 146 (183)
T ss_pred HHhcCCccCceEEEEEEcCCCcCChh------------------------------hHHHHHHHHHHcCcEEEEEEech-
Confidence 99731112246788887753222110 02456788889999999999864
Q ss_pred ccChhcchhhhhcccceEEEeCC
Q 004238 365 QVGVAEMKVAVEKTGGLVVLAES 387 (766)
Q Consensus 365 ~~~l~~l~~l~~~TGG~v~~~~~ 387 (766)
+...|+.+|+.|||+.|...+
T Consensus 147 --~~~~L~~ia~~tgG~~~~~~~ 167 (183)
T cd01453 147 --EMHICKEICKATNGTYKVILD 167 (183)
T ss_pred --HHHHHHHHHHHhCCeeEeeCC
Confidence 467899999999999987644
No 22
>PF00626 Gelsolin: Gelsolin repeat; InterPro: IPR007123 Gelsolin is a cytoplasmic, calcium-regulated, actin-modulating protein that binds to the barbed ends of actin filaments, preventing monomer exchange (end-blocking or capping) []. It can promote nucleation (the assembly of monomers into filaments), as well as sever existing filaments. In addition, this protein binds with high affinity to fibronectin. Plasma gelsolin and cytoplasmic gelsolin are derived from a single gene by alternate initiation sites and differential splicing. Sequence comparisons indicate an evolutionary relationship between gelsolin, villin, fragmin and severin []. Six large repeating segments occur in gelsolin and villin, and 3 similar segments in severin and fragmin. While the multiple repeats have yet to be related to any known function of the actin-severing proteins, the superfamily appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues [].; PDB: 3FG6_F 1RGI_G 2FGH_A 1D0N_B 3EGD_B 2NUP_B 2NUT_B 3EGX_B 1JHW_A 1J72_A ....
Probab=98.30 E-value=1.1e-06 Score=73.65 Aligned_cols=71 Identities=21% Similarity=0.411 Sum_probs=57.0
Q ss_pred CcccccccccccCCeEEEEeCCcEEEEEECCchhHHhhcCCCCChhhhHHHHHhhCcHHHHHHHH-hcCCCCcEEEEEeC
Q 004238 636 PQPALLDVASIAADRILLLDTYFSVVIFHGMTIAQWRNMGYQNQPEHQAFAQLLRAPHDDAELII-RDRFPVPRLVVCDQ 714 (766)
Q Consensus 636 p~~~~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~~~~~~g~~~~~~~~~~~~~l~~~~~~~~~i~-~~R~p~p~~~~~~~ 714 (766)
|++++++.++|.++++||||+|..||+|+|++... .+ . . .....|+++. .+|.+.|+++++.+
T Consensus 5 ~~~~~~s~~~L~s~~~yIld~~~~i~vW~G~~~~~---------~e--~---~--~a~~~a~~~~~~~~~~~~~~~~~~e 68 (76)
T PF00626_consen 5 PEQVPLSQSSLNSDDCYILDCGYEIFVWVGKKSSP---------EE--K---A--FAAQLAQELLSEERPPLPEVIRVEE 68 (76)
T ss_dssp EEEESSSGGGEETTSEEEEEESSEEEEEEHTTSHH---------HH--H---H--HHHHHHHHHHHHHTTTTSEEEEEET
T ss_pred CCcCCCCHHHcCCCCEEEEEeCCCcEEEEeccCCH---------HH--H---H--HHHHHHHHhhhhcCCCCCEEEEecC
Confidence 66789999999999999999999999999997321 11 1 1 1224567787 78999999999999
Q ss_pred CCChHHHH
Q 004238 715 HGSQARFL 722 (766)
Q Consensus 715 g~s~~r~l 722 (766)
|+..++|+
T Consensus 69 g~E~~~F~ 76 (76)
T PF00626_consen 69 GKEPAEFL 76 (76)
T ss_dssp THHHHHHH
T ss_pred CCCChHHC
Confidence 99888875
No 23
>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=98.29 E-value=4.5e-05 Score=74.18 Aligned_cols=151 Identities=17% Similarity=0.161 Sum_probs=95.9
Q ss_pred EEEEEEcccchHH--HHHHHHHHHHHhccCC---CCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhc
Q 004238 137 FVFVLDTCMIEEE--LGYARSELKRAIGLLP---DNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLG 211 (766)
Q Consensus 137 ~vFvID~s~~~~~--l~~~~~~l~~~l~~lp---~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~ 211 (766)
.+|+||+|.+... ++.++++++..+..+. ++.++|+|+|++..+.. ..
T Consensus 3 vv~vlD~SgSm~~~~~~~~k~~~~~~~~~l~~~~~~~~~giv~Fs~~~~~~-~~-------------------------- 55 (164)
T cd01472 3 IVFLVDGSESIGLSNFNLVKDFVKRVVERLDIGPDGVRVGVVQYSDDPRTE-FY-------------------------- 55 (164)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHhhcccCCCCeEEEEEEEcCceeEE-Ee--------------------------
Confidence 5899999998754 7888888888887764 46799999999876652 10
Q ss_pred cccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhcc--
Q 004238 212 LSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGAC-- 289 (766)
Q Consensus 212 ~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~-- 289 (766)
+... ..+..+...|+.++.. ...+.+|.||..|...+...
T Consensus 56 ~~~~------------------------------~~~~~~~~~l~~l~~~--------~g~T~~~~al~~a~~~l~~~~~ 97 (164)
T cd01472 56 LNTY------------------------------RSKDDVLEAVKNLRYI--------GGGTNTGKALKYVRENLFTEAS 97 (164)
T ss_pred cCCC------------------------------CCHHHHHHHHHhCcCC--------CCCchHHHHHHHHHHHhCCccc
Confidence 0000 0112244455565531 22468999999999988731
Q ss_pred --CCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccC
Q 004238 290 --LPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVG 367 (766)
Q Consensus 290 --~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~ 367 (766)
.++....|+++++|.++.+. ...+..+.+.||.+..+..+. .|
T Consensus 98 ~~~~~~~~~iiliTDG~~~~~~---------------------------------~~~~~~l~~~gv~i~~ig~g~--~~ 142 (164)
T cd01472 98 GSREGVPKVLVVITDGKSQDDV---------------------------------EEPAVELKQAGIEVFAVGVKN--AD 142 (164)
T ss_pred CCCCCCCEEEEEEcCCCCCchH---------------------------------HHHHHHHHHCCCEEEEEECCc--CC
Confidence 12334567888888432110 011233455777666555544 48
Q ss_pred hhcchhhhhcccc-eEEEeCC
Q 004238 368 VAEMKVAVEKTGG-LVVLAES 387 (766)
Q Consensus 368 l~~l~~l~~~TGG-~v~~~~~ 387 (766)
...|..++..++| .++.+.+
T Consensus 143 ~~~L~~ia~~~~~~~~~~~~~ 163 (164)
T cd01472 143 EEELKQIASDPKELYVFNVAD 163 (164)
T ss_pred HHHHHHHHCCCchheEEeccC
Confidence 9999999999987 5555544
No 24
>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=98.19 E-value=5e-05 Score=76.35 Aligned_cols=167 Identities=13% Similarity=0.121 Sum_probs=100.5
Q ss_pred EEEEEEcccchH--HHHHHHHHHHHHhccCC---CCcEEEEEEECCeEEEE-EcCCCCCcceeEecCCcccchhhHHhhh
Q 004238 137 FVFVLDTCMIEE--ELGYARSELKRAIGLLP---DNAMVGLVTFGTQAHVH-ELGFSDMSKVYVFRGNKEISKDQVLEQL 210 (766)
Q Consensus 137 ~vFvID~s~~~~--~l~~~~~~l~~~l~~lp---~~~~VglItf~~~V~~~-~l~~~~~~~~~v~~g~~~~~~~~l~~~l 210 (766)
++||||+|.++. .++.+++++...++.|+ .+.+||+|+|++..+.. .+....
T Consensus 3 i~~vlD~SgSM~~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~~~~~~~~~~~---------------------- 60 (198)
T cd01470 3 IYIALDASDSIGEEDFDEAKNAIKTLIEKISSYEVSPRYEIISYASDPKEIVSIRDFN---------------------- 60 (198)
T ss_pred EEEEEECCCCccHHHHHHHHHHHHHHHHHccccCCCceEEEEEecCCceEEEecccCC----------------------
Confidence 689999999975 38899999999998876 36799999999876542 221100
Q ss_pred ccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccC
Q 004238 211 GLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACL 290 (766)
Q Consensus 211 ~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~ 290 (766)
...+..+...|+.++... ......+.++.||..|...+...-
T Consensus 61 ----------------------------------~~~~~~~~~~l~~~~~~~----~~~~ggT~~~~Al~~~~~~l~~~~ 102 (198)
T cd01470 61 ----------------------------------SNDADDVIKRLEDFNYDD----HGDKTGTNTAAALKKVYERMALEK 102 (198)
T ss_pred ----------------------------------CCCHHHHHHHHHhCCccc----ccCccchhHHHHHHHHHHHHHHHH
Confidence 001112344455554321 111235678999988877663100
Q ss_pred -C------CCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHH------HHHHcCcEEE
Q 004238 291 -P------GTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAK------QLVSQGHVLD 357 (766)
Q Consensus 291 -~------~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~------~~~~~~isvd 357 (766)
. ...-.|+++|+|.++.|... ..+.+.++++.. .+...++.|.
T Consensus 103 ~~~~~~~~~~~~~iillTDG~~~~g~~~------------------------~~~~~~~~~~~~~~~~~~~~~~~~v~i~ 158 (198)
T cd01470 103 VRNKEAFNETRHVIILFTDGKSNMGGSP------------------------LPTVDKIKNLVYKNNKSDNPREDYLDVY 158 (198)
T ss_pred hcCccchhhcceEEEEEcCCCcCCCCCh------------------------hHHHHHHHHHHhcccccccchhcceeEE
Confidence 0 01124789999998876310 011112222211 1234466666
Q ss_pred EEEecCCccChhcchhhhhcccc--eEEEeCCC
Q 004238 358 LFASALDQVGVAEMKVAVEKTGG--LVVLAESF 388 (766)
Q Consensus 358 lf~~~~~~~~l~~l~~l~~~TGG--~v~~~~~f 388 (766)
.+..+ +.++-.+|..++..||| .+|...+|
T Consensus 159 ~iGvG-~~~~~~~L~~iA~~~~g~~~~f~~~~~ 190 (198)
T cd01470 159 VFGVG-DDVNKEELNDLASKKDNERHFFKLKDY 190 (198)
T ss_pred EEecC-cccCHHHHHHHhcCCCCCceEEEeCCH
Confidence 66554 35788999999999999 46766665
No 25
>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=98.19 E-value=7.2e-05 Score=73.80 Aligned_cols=155 Identities=22% Similarity=0.219 Sum_probs=101.7
Q ss_pred EEEEEEEcccchH--------HHHHHHHHHHHHhccCCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHH
Q 004238 136 VFVFVLDTCMIEE--------ELGYARSELKRAIGLLPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVL 207 (766)
Q Consensus 136 ~~vFvID~s~~~~--------~l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~ 207 (766)
-++|+||+|.++. .++.++..+...+...| +.+||+|+|++.++.. +.
T Consensus 4 ~vv~vlD~S~SM~~~~~~~~~r~~~a~~~~~~~~~~~~-~~~v~lv~f~~~~~~~-~~---------------------- 59 (180)
T cd01467 4 DIMIALDVSGSMLAQDFVKPSRLEAAKEVLSDFIDRRE-NDRIGLVVFAGAAFTQ-AP---------------------- 59 (180)
T ss_pred eEEEEEECCcccccccCCCCCHHHHHHHHHHHHHHhCC-CCeEEEEEEcCCeeec-cC----------------------
Confidence 4789999999863 25777777777666554 6799999998866532 00
Q ss_pred hhhccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhh
Q 004238 208 EQLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLG 287 (766)
Q Consensus 208 ~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~ 287 (766)
+ ...+..+..+|+.|... .. ...+.++.||..|...+.
T Consensus 60 ----~--------------------------------~~~~~~~~~~l~~l~~~---~~---~g~T~l~~al~~a~~~l~ 97 (180)
T cd01467 60 ----L--------------------------------TLDRESLKELLEDIKIG---LA---GQGTAIGDAIGLAIKRLK 97 (180)
T ss_pred ----C--------------------------------CccHHHHHHHHHHhhhc---cc---CCCCcHHHHHHHHHHHHH
Confidence 0 00112234455555421 11 234678999999999886
Q ss_pred ccCCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCC---
Q 004238 288 ACLPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALD--- 364 (766)
Q Consensus 288 ~~~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~--- 364 (766)
.. ......|+++++|.++.|+ . . ..+.+..+.+.||.|+.+.++..
T Consensus 98 ~~-~~~~~~iiliTDG~~~~g~--~-----------------------~-----~~~~~~~~~~~gi~i~~i~ig~~~~~ 146 (180)
T cd01467 98 NS-EAKERVIVLLTDGENNAGE--I-----------------------D-----PATAAELAKNKGVRIYTIGVGKSGSG 146 (180)
T ss_pred hc-CCCCCEEEEEeCCCCCCCC--C-----------------------C-----HHHHHHHHHHCCCEEEEEEecCCCCC
Confidence 31 2234678999999876542 0 0 01123345568999999988762
Q ss_pred -------ccChhcchhhhhcccceEEEeCC
Q 004238 365 -------QVGVAEMKVAVEKTGGLVVLAES 387 (766)
Q Consensus 365 -------~~~l~~l~~l~~~TGG~v~~~~~ 387 (766)
..+...|..|++.|||.+++..+
T Consensus 147 ~~~~~~~~~~~~~l~~la~~tgG~~~~~~~ 176 (180)
T cd01467 147 PKPDGSTILDEDSLVEIADKTGGRIFRALD 176 (180)
T ss_pred cCCCCcccCCHHHHHHHHHhcCCEEEEecC
Confidence 46778899999999999998754
No 26
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=98.16 E-value=7.1e-05 Score=89.13 Aligned_cols=155 Identities=19% Similarity=0.247 Sum_probs=103.6
Q ss_pred CCcEEEEEEEcccchH---HHHHHHHHHHHHh-ccCCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHh
Q 004238 133 LSPVFVFVLDTCMIEE---ELGYARSELKRAI-GLLPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLE 208 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~---~l~~~~~~l~~~l-~~lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~ 208 (766)
.+...++|||+|.++. .++.++++++..+ +.++++.+||||+|++..++.. .
T Consensus 303 ~~r~VVLVLDvSGSM~g~dRL~~lkqAA~~fL~~~l~~~DrVGLVtFsssA~vl~---p--------------------- 358 (863)
T TIGR00868 303 RQRIVCLVLDKSGSMTVEDRLKRMNQAAKLFLLQTVEKGSWVGMVTFDSAAYIKN---E--------------------- 358 (863)
T ss_pred CCceEEEEEECCccccccCHHHHHHHHHHHHHHHhCCCCCEEEEEEECCceeEee---c---------------------
Confidence 3456999999999985 3888888877665 4578889999999999866521 0
Q ss_pred hhccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhc
Q 004238 209 QLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGA 288 (766)
Q Consensus 209 ~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~ 288 (766)
+..+++ ...+ ..++..|+. .+ ...++++.||..|..+|..
T Consensus 359 Lt~Its------------------------------~~dr---~aL~~~L~~----~A---~GGT~I~~GL~~Alq~L~~ 398 (863)
T TIGR00868 359 LIQITS------------------------------SAER---DALTANLPT----AA---SGGTSICSGLKAAFQVIKK 398 (863)
T ss_pred cccCCc------------------------------HHHH---HHHHHhhcc----cc---CCCCcHHHHHHHHHHHHHh
Confidence 000000 0011 222233321 11 2358999999999999984
Q ss_pred cC-CCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccC
Q 004238 289 CL-PGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVG 367 (766)
Q Consensus 289 ~~-~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~ 367 (766)
.. +..++.|+++++|-.+.+ ..+...+.+.|+.|..+.++.+.-
T Consensus 399 ~~~~~~~~~IILLTDGedn~~----------------------------------~~~l~~lk~~gVtI~TIg~G~dad- 443 (863)
T TIGR00868 399 SYQSTDGSEIVLLTDGEDNTI----------------------------------SSCFEEVKQSGAIIHTIALGPSAA- 443 (863)
T ss_pred cccccCCCEEEEEeCCCCCCH----------------------------------HHHHHHHHHcCCEEEEEEeCCChH-
Confidence 32 135678999998854321 113344566899999999886642
Q ss_pred hhcchhhhhcccceEEEeCC
Q 004238 368 VAEMKVAVEKTGGLVVLAES 387 (766)
Q Consensus 368 l~~l~~l~~~TGG~v~~~~~ 387 (766)
..|..||+.|||..++.++
T Consensus 444 -~~L~~IA~~TGG~~f~asd 462 (863)
T TIGR00868 444 -KELEELSDMTGGLRFYASD 462 (863)
T ss_pred -HHHHHHHHhcCCEEEEeCC
Confidence 4699999999999988864
No 27
>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=98.14 E-value=0.00032 Score=75.27 Aligned_cols=49 Identities=31% Similarity=0.281 Sum_probs=42.1
Q ss_pred CCcEEEEEEEcccchHH-HHHHHHHHHHHhcc-CCCCcEEEEEEECCeEEE
Q 004238 133 LSPVFVFVLDTCMIEEE-LGYARSELKRAIGL-LPDNAMVGLVTFGTQAHV 181 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~~-l~~~~~~l~~~l~~-lp~~~~VglItf~~~V~~ 181 (766)
.|...+||||+|.++.. +..+++++...++. ++++.+||||+|++.+++
T Consensus 52 ~p~~vvlvlD~SgSM~~~~~~a~~a~~~~l~~~l~~~d~v~lv~f~~~~~~ 102 (296)
T TIGR03436 52 LPLTVGLVIDTSGSMRNDLDRARAAAIRFLKTVLRPNDRVFVVTFNTRLRL 102 (296)
T ss_pred CCceEEEEEECCCCchHHHHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeE
Confidence 47889999999999765 77888888888876 788899999999987765
No 28
>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=98.12 E-value=8.9e-05 Score=73.78 Aligned_cols=157 Identities=17% Similarity=0.128 Sum_probs=99.9
Q ss_pred EEEEEEEcccchH--HHHHHHHHHHHHhccC---------CCCcEEEEEEECCeEEEE-EcCCCCCcceeEecCCcccch
Q 004238 136 VFVFVLDTCMIEE--ELGYARSELKRAIGLL---------PDNAMVGLVTFGTQAHVH-ELGFSDMSKVYVFRGNKEISK 203 (766)
Q Consensus 136 ~~vFvID~s~~~~--~l~~~~~~l~~~l~~l---------p~~~~VglItf~~~V~~~-~l~~~~~~~~~v~~g~~~~~~ 203 (766)
-.+|+||.|.+.. .++.+++.++..++.+ +++.+||+|+|++..++. .+..
T Consensus 4 dvv~vlD~S~Sm~~~~~~~~k~~~~~~~~~l~~~~~~~i~~~~~rvglv~fs~~~~~~~~l~~----------------- 66 (186)
T cd01480 4 DITFVLDSSESVGLQNFDITKNFVKRVAERFLKDYYRKDPAGSWRVGVVQYSDQQEVEAGFLR----------------- 66 (186)
T ss_pred eEEEEEeCCCccchhhHHHHHHHHHHHHHHHhhhhccCCCCCceEEEEEEecCCceeeEeccc-----------------
Confidence 4689999999975 3777777777777766 446899999999865442 1100
Q ss_pred hhHHhhhccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHH
Q 004238 204 DQVLEQLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVAT 283 (766)
Q Consensus 204 ~~l~~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~ 283 (766)
. ...+..+.+.|++++.. ...+.+|.||..|.
T Consensus 67 -----------------------------~-----------~~~~~~l~~~i~~l~~~--------gg~T~~~~AL~~a~ 98 (186)
T cd01480 67 -----------------------------D-----------IRNYTSLKEAVDNLEYI--------GGGTFTDCALKYAT 98 (186)
T ss_pred -----------------------------c-----------cCCHHHHHHHHHhCccC--------CCCccHHHHHHHHH
Confidence 0 00123355666666531 12478999999999
Q ss_pred HHhhcc-CCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEec
Q 004238 284 GLLGAC-LPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASA 362 (766)
Q Consensus 284 ~ll~~~-~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~ 362 (766)
..+... .+.....|+++|+|.++.++. .-..+.+..+.+.||.+-.+..+
T Consensus 99 ~~l~~~~~~~~~~~iillTDG~~~~~~~-----------------------------~~~~~~~~~~~~~gi~i~~vgig 149 (186)
T cd01480 99 EQLLEGSHQKENKFLLVITDGHSDGSPD-----------------------------GGIEKAVNEADHLGIKIFFVAVG 149 (186)
T ss_pred HHHhccCCCCCceEEEEEeCCCcCCCcc-----------------------------hhHHHHHHHHHHCCCEEEEEecC
Confidence 988631 123345678888886532210 00123455666788886666654
Q ss_pred CCccChhcchhhhhcccceEEEeCCCC
Q 004238 363 LDQVGVAEMKVAVEKTGGLVVLAESFG 389 (766)
Q Consensus 363 ~~~~~l~~l~~l~~~TGG~v~~~~~f~ 389 (766)
. .+...|..++...+|. ++.++|.
T Consensus 150 ~--~~~~~L~~IA~~~~~~-~~~~~~~ 173 (186)
T cd01480 150 S--QNEEPLSRIACDGKSA-LYRENFA 173 (186)
T ss_pred c--cchHHHHHHHcCCcch-hhhcchh
Confidence 4 7888899999888775 4445543
No 29
>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=98.11 E-value=9e-05 Score=73.17 Aligned_cols=144 Identities=19% Similarity=0.187 Sum_probs=96.0
Q ss_pred EEEEEEEcccchHH-------HHHHHHHHHHHh----ccCCCCcEEEEEEECC-eEEEEEcCCCCCcceeEecCCcccch
Q 004238 136 VFVFVLDTCMIEEE-------LGYARSELKRAI----GLLPDNAMVGLVTFGT-QAHVHELGFSDMSKVYVFRGNKEISK 203 (766)
Q Consensus 136 ~~vFvID~s~~~~~-------l~~~~~~l~~~l----~~lp~~~~VglItf~~-~V~~~~l~~~~~~~~~v~~g~~~~~~ 203 (766)
+.+++||+|..+.+ +++.++.+...+ +..|++ +||||+|.. .-.+. .
T Consensus 5 a~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np~~-~vGlv~fag~~a~v~--~------------------ 63 (187)
T cd01452 5 ATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPEN-NVGLMTMAGNSPEVL--V------------------ 63 (187)
T ss_pred EEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCCCc-cEEEEEecCCceEEE--E------------------
Confidence 56899999999753 888888887664 656644 999999986 33221 0
Q ss_pred hhHHhhhccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHH
Q 004238 204 DQVLEQLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVAT 283 (766)
Q Consensus 204 ~~l~~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~ 283 (766)
|+......+...|+.+... ....+|.||+.|.
T Consensus 64 ---------------------------------------plT~D~~~~~~~L~~i~~~---------g~~~l~~AL~~A~ 95 (187)
T cd01452 64 ---------------------------------------TLTNDQGKILSKLHDVQPK---------GKANFITGIQIAQ 95 (187)
T ss_pred ---------------------------------------CCCCCHHHHHHHHHhCCCC---------CcchHHHHHHHHH
Confidence 0111123355566665431 2457999999999
Q ss_pred HHhhccCCC-CccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEec
Q 004238 284 GLLGACLPG-TGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASA 362 (766)
Q Consensus 284 ~ll~~~~~~-~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~ 362 (766)
..|+..-.. ...||++|.+++.+.-|| + ..++++++.++||.||++.++
T Consensus 96 ~~L~~~~~~~~~~rivi~v~S~~~~d~~-----------------------------~-i~~~~~~lkk~~I~v~vI~~G 145 (187)
T cd01452 96 LALKHRQNKNQKQRIVAFVGSPIEEDEK-----------------------------D-LVKLAKRLKKNNVSVDIINFG 145 (187)
T ss_pred HHHhcCCCcCCcceEEEEEecCCcCCHH-----------------------------H-HHHHHHHHHHcCCeEEEEEeC
Confidence 999742222 335999999876432111 1 235788999999999999998
Q ss_pred CCccChhcchhhhhcc
Q 004238 363 LDQVGVAEMKVAVEKT 378 (766)
Q Consensus 363 ~~~~~l~~l~~l~~~T 378 (766)
...-+..-|..+.+..
T Consensus 146 ~~~~~~~~l~~~~~~~ 161 (187)
T cd01452 146 EIDDNTEKLTAFIDAV 161 (187)
T ss_pred CCCCCHHHHHHHHHHh
Confidence 7766666666666555
No 30
>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=98.07 E-value=0.0032 Score=74.23 Aligned_cols=284 Identities=14% Similarity=0.058 Sum_probs=159.7
Q ss_pred CCcEEEEEEEcccchH--HHHHHHHHHHHHhccCCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhh
Q 004238 133 LSPVFVFVLDTCMIEE--ELGYARSELKRAIGLLPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQL 210 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~--~l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l 210 (766)
.|.-++||||+|.++. .++.+++++..+|..|+++.+++||+|++.++.+. ... .
T Consensus 270 ~p~~vvfvlD~SgSM~g~~i~~ak~al~~~l~~L~~~d~~~ii~F~~~~~~~~--~~~---------------------~ 326 (596)
T TIGR03788 270 LPRELVFVIDTSGSMAGESIEQAKSALLLALDQLRPGDRFNIIQFDSDVTLLF--PVP---------------------V 326 (596)
T ss_pred CCceEEEEEECCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEECCcceEec--ccc---------------------c
Confidence 5667999999999975 38889999999999999999999999999877641 100 0
Q ss_pred ccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccC
Q 004238 211 GLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACL 290 (766)
Q Consensus 211 ~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~ 290 (766)
..+ .+....+...|+.|... ..+.+..||..|........
T Consensus 327 ~~~-------------------------------~~~~~~a~~~i~~l~a~---------GgT~l~~aL~~a~~~~~~~~ 366 (596)
T TIGR03788 327 PAT-------------------------------AHNLARARQFVAGLQAD---------GGTEMAGALSAALRDDGPES 366 (596)
T ss_pred cCC-------------------------------HHHHHHHHHHHhhCCCC---------CCccHHHHHHHHHHhhcccC
Confidence 000 01112234455555432 24678999999987653211
Q ss_pred CCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChhc
Q 004238 291 PGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVAE 370 (766)
Q Consensus 291 ~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~~ 370 (766)
.....+|+++|+|..+. .....+.+. ....++.+..|.++.+ .+-..
T Consensus 367 ~~~~~~iillTDG~~~~------------------------------~~~~~~~~~--~~~~~~ri~tvGiG~~-~n~~l 413 (596)
T TIGR03788 367 SGALRQVVFLTDGAVGN------------------------------EDALFQLIR--TKLGDSRLFTVGIGSA-PNSYF 413 (596)
T ss_pred CCceeEEEEEeCCCCCC------------------------------HHHHHHHHH--HhcCCceEEEEEeCCC-cCHHH
Confidence 12234799999985210 001122221 1234567777776643 57788
Q ss_pred chhhhhcccceEEEeCCCCchhhHHHHHHHHhhccccccceeeeEEEEEecCCceEEEEEcCcccccccccCCCccceee
Q 004238 371 MKVAVEKTGGLVVLAESFGHSVFKDSFKRIFEDGEQSLGLCFNGALEIICSKDIKIQGIIGPCTSLEKVRLRGEYYAWKM 450 (766)
Q Consensus 371 l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l~~~~~~~~~~~~a~l~vr~S~gl~v~~~~G~~~~~~~~~g~~~~~~~~l 450 (766)
|..+|+.+||..++..+ .+...+.+.+++.+.. .+...+..+++.. ..+..++ --.+
T Consensus 414 L~~lA~~g~G~~~~i~~--~~~~~~~~~~~l~~~~--~p~l~~v~v~~~~---~~~~~v~----------------P~~~ 470 (596)
T TIGR03788 414 MRKAAQFGRGSFTFIGS--TDEVQRKMSQLFAKLE--QPALTDIALTFDN---GNAADVY----------------PSPI 470 (596)
T ss_pred HHHHHHcCCCEEEECCC--HHHHHHHHHHHHHhhc--CeEEEEEEEEEcC---Cccceec----------------cCCC
Confidence 99999999998776543 3344555666666532 2445555555532 2222221 1135
Q ss_pred ecCCCCceEEEEEEecCCCCCCCCCCCCCcEEEEEEEEeecCCCcEEEEEEeeccccccCCCCHHHHHhccChhHHHHHH
Q 004238 451 CGLDKSTCLTVFFDLSSSERLNTPGTINPQLYLQFLTSFQSPEGRSVLRVTTVTRQWVDSAVSSEELVQGFDQESAAVVM 530 (766)
Q Consensus 451 ~~~~~~~s~~~~f~~~~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~l~vt~~~~~~~~i~~~~D~~a~~~ll 530 (766)
+.+-....+.+...+... ...+ .+.....++... ..+++.. . -+-..+-.+.
T Consensus 471 p~L~~g~~l~v~g~~~~~---------~~~i----~v~g~~~~~~~~-----~~~~~~~---~-------~~~~~l~~lw 522 (596)
T TIGR03788 471 PDLYRGEPLQIAIKLQQA---------AGEL----QLTGRTGSQPWS-----QQLDLDS---A-------APGKGIDKLW 522 (596)
T ss_pred ccccCCCEEEEEEEecCC---------CCeE----EEEEEcCCceEE-----EEEecCC---C-------CCcchHHHHH
Confidence 566667777777664321 1222 233333333322 2223322 1 1223355577
Q ss_pred HHHHHHHhhcCChH-HHHHHHHHHHHHHHHHhcc
Q 004238 531 ARLTSLKMEMEEGF-DATRWLDRSLIRLCSKFGD 563 (766)
Q Consensus 531 ak~a~~~~~~~~~~-~~~~~l~~~l~~~~~~~~~ 563 (766)
||.-+..+...... .-.+.+.+.++++..+|+-
T Consensus 523 A~~~I~~L~~~~~~~~~~~~~~~~Ii~Lsl~y~l 556 (596)
T TIGR03788 523 ARRKIDSLEDSLRYGANEEKVKDQVTALALNHHL 556 (596)
T ss_pred HHHHHHHHHHHHhhcCCcHHHHHHHHHHHHHhCC
Confidence 77777766532110 0123466778888666543
No 31
>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=97.99 E-value=0.00041 Score=67.58 Aligned_cols=159 Identities=19% Similarity=0.199 Sum_probs=102.6
Q ss_pred CcEEEEEEEcccchH--HHHHHHHHHHHHhccCCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhc
Q 004238 134 SPVFVFVLDTCMIEE--ELGYARSELKRAIGLLPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLG 211 (766)
Q Consensus 134 ~p~~vFvID~s~~~~--~l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~ 211 (766)
|.-++||+|+|.++. .++.+++++...+..++++.+|++++|++.++.+ .... .
T Consensus 2 ~~~v~~vlD~S~SM~~~~~~~~~~al~~~l~~l~~~~~~~l~~Fs~~~~~~--~~~~---------------------~- 57 (171)
T cd01461 2 PKEVVFVIDTSGSMSGTKIEQTKEALLTALKDLPPGDYFNIIGFSDTVEEF--SPSS---------------------V- 57 (171)
T ss_pred CceEEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEeCCCceee--cCcc---------------------e-
Confidence 456899999999984 3888999999999999988899999999876543 1000 0
Q ss_pred cccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccCC
Q 004238 212 LSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACLP 291 (766)
Q Consensus 212 ~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~ 291 (766)
+.+ .+....+.+.|+.+.+ ...+.++.||..|...+.. .+
T Consensus 58 ------------------------~~~------~~~~~~~~~~l~~~~~---------~g~T~l~~al~~a~~~l~~-~~ 97 (171)
T cd01461 58 ------------------------SAT------AENVAAAIEYVNRLQA---------LGGTNMNDALEAALELLNS-SP 97 (171)
T ss_pred ------------------------eCC------HHHHHHHHHHHHhcCC---------CCCcCHHHHHHHHHHhhcc-CC
Confidence 000 0011112334444433 1235789999999988862 12
Q ss_pred CCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChhcc
Q 004238 292 GTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVAEM 371 (766)
Q Consensus 292 ~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~~l 371 (766)
.....|++|++|.++. ..+.+ +...++.+.++.|..+.++. ..+-..|
T Consensus 98 ~~~~~iillTDG~~~~------------------------------~~~~~-~~~~~~~~~~i~i~~i~~g~-~~~~~~l 145 (171)
T cd01461 98 GSVPQIILLTDGEVTN------------------------------ESQIL-KNVREALSGRIRLFTFGIGS-DVNTYLL 145 (171)
T ss_pred CCccEEEEEeCCCCCC------------------------------HHHHH-HHHHHhcCCCceEEEEEeCC-ccCHHHH
Confidence 3446788888875211 01222 23333444577777777653 4566789
Q ss_pred hhhhhcccceEEEeCCC
Q 004238 372 KVAVEKTGGLVVLAESF 388 (766)
Q Consensus 372 ~~l~~~TGG~v~~~~~f 388 (766)
..++..|||..++..+-
T Consensus 146 ~~ia~~~gG~~~~~~~~ 162 (171)
T cd01461 146 ERLAREGRGIARRIYET 162 (171)
T ss_pred HHHHHcCCCeEEEecCh
Confidence 99999999999887653
No 32
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=97.99 E-value=0.00021 Score=68.76 Aligned_cols=151 Identities=17% Similarity=0.177 Sum_probs=100.6
Q ss_pred EEEEEEcccchHH-HHHHHHHHHHHhccCCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhhccccC
Q 004238 137 FVFVLDTCMIEEE-LGYARSELKRAIGLLPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQLGLSAS 215 (766)
Q Consensus 137 ~vFvID~s~~~~~-l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l~~~d~ 215 (766)
.+||||+|.++.. .+.++++|+..++.|+++.++.||+|++.+..+. +. +...+
T Consensus 3 vvilvD~S~Sm~g~~~~~k~al~~~l~~L~~~d~fnii~f~~~~~~~~--~~---------------------~~~~~-- 57 (155)
T PF13768_consen 3 VVILVDTSGSMSGEKELVKDALRAILRSLPPGDRFNIIAFGSSVRPLF--PG---------------------LVPAT-- 57 (155)
T ss_pred EEEEEeCCCCCCCcHHHHHHHHHHHHHhCCCCCEEEEEEeCCEeeEcc--hh---------------------HHHHh--
Confidence 6899999999754 4889999999999999999999999999777542 11 01000
Q ss_pred cccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccCCCCcc
Q 004238 216 GRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACLPGTGA 295 (766)
Q Consensus 216 ~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~gG 295 (766)
.+.++.....|+.++.. ...+.++.||+.|...+. .++..-
T Consensus 58 -----------------------------~~~~~~a~~~I~~~~~~--------~G~t~l~~aL~~a~~~~~--~~~~~~ 98 (155)
T PF13768_consen 58 -----------------------------EENRQEALQWIKSLEAN--------SGGTDLLAALRAALALLQ--RPGCVR 98 (155)
T ss_pred -----------------------------HHHHHHHHHHHHHhccc--------CCCccHHHHHHHHHHhcc--cCCCcc
Confidence 01222234455555441 234789999999998862 125567
Q ss_pred EEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhhh
Q 004238 296 RIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVAEMKVAV 375 (766)
Q Consensus 296 rIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~~l~~l~ 375 (766)
.|+++++|.++.++ ....+.+. .+ ...+.++.|.++. ..+-..|..|+
T Consensus 99 ~IilltDG~~~~~~-----------------------------~~i~~~v~-~~-~~~~~i~~~~~g~-~~~~~~L~~LA 146 (155)
T PF13768_consen 99 AIILLTDGQPVSGE-----------------------------EEILDLVR-RA-RGHIRIFTFGIGS-DADADFLRELA 146 (155)
T ss_pred EEEEEEeccCCCCH-----------------------------HHHHHHHH-hc-CCCceEEEEEECC-hhHHHHHHHHH
Confidence 89999998763332 11111121 11 1457777777765 45668899999
Q ss_pred hcccceEE
Q 004238 376 EKTGGLVV 383 (766)
Q Consensus 376 ~~TGG~v~ 383 (766)
+.|||..+
T Consensus 147 ~~~~G~~~ 154 (155)
T PF13768_consen 147 RATGGSFH 154 (155)
T ss_pred HcCCCEEE
Confidence 99999865
No 33
>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=97.97 E-value=0.00025 Score=72.77 Aligned_cols=155 Identities=18% Similarity=0.243 Sum_probs=96.9
Q ss_pred cEEEEEEEcccchH--HHHHHHHHHHHHhccC---CCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhh
Q 004238 135 PVFVFVLDTCMIEE--ELGYARSELKRAIGLL---PDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQ 209 (766)
Q Consensus 135 p~~vFvID~s~~~~--~l~~~~~~l~~~l~~l---p~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~ 209 (766)
.-.+|+||.|.+.. +++.+++.++..++.+ |+..+||+|+|++.+++. +.
T Consensus 3 ~DlvfllD~S~Sm~~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~~~~-~~------------------------ 57 (224)
T cd01475 3 TDLVFLIDSSRSVRPENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTVKQE-FP------------------------ 57 (224)
T ss_pred ccEEEEEeCCCCCCHHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCceeEE-ec------------------------
Confidence 34799999999964 4888999998888876 356899999999977652 11
Q ss_pred hccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhcc
Q 004238 210 LGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGAC 289 (766)
Q Consensus 210 l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 289 (766)
+.+ + ..++.+...|+.++.. ...+.+|.||..|...+-..
T Consensus 58 --l~~-------------------~-----------~~~~~l~~~i~~i~~~--------~~~t~tg~AL~~a~~~~~~~ 97 (224)
T cd01475 58 --LGR-------------------F-----------KSKADLKRAVRRMEYL--------ETGTMTGLAIQYAMNNAFSE 97 (224)
T ss_pred --ccc-------------------c-----------CCHHHHHHHHHhCcCC--------CCCChHHHHHHHHHHHhCCh
Confidence 000 0 0112244555665542 12357899999888653210
Q ss_pred ----CCCC---ccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEec
Q 004238 290 ----LPGT---GARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASA 362 (766)
Q Consensus 290 ----~~~~---gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~ 362 (766)
.+.. ...|+++++|.++. + ..+.+.++...||.|-.+ +
T Consensus 98 ~~g~r~~~~~~~kvvillTDG~s~~------------------~---------------~~~~a~~lk~~gv~i~~V--g 142 (224)
T cd01475 98 AEGARPGSERVPRVGIVVTDGRPQD------------------D---------------VSEVAAKARALGIEMFAV--G 142 (224)
T ss_pred hcCCCCCCCCCCeEEEEEcCCCCcc------------------c---------------HHHHHHHHHHCCcEEEEE--e
Confidence 0111 22457888875321 0 234566777788765444 4
Q ss_pred CCccChhcchhhhhccc-ceEEEeCCCC
Q 004238 363 LDQVGVAEMKVAVEKTG-GLVVLAESFG 389 (766)
Q Consensus 363 ~~~~~l~~l~~l~~~TG-G~v~~~~~f~ 389 (766)
....+..+|..++..++ +.++..++|+
T Consensus 143 vG~~~~~~L~~ias~~~~~~~f~~~~~~ 170 (224)
T cd01475 143 VGRADEEELREIASEPLADHVFYVEDFS 170 (224)
T ss_pred CCcCCHHHHHHHhCCCcHhcEEEeCCHH
Confidence 44568889999998765 4667766665
No 34
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=97.96 E-value=9.2e-05 Score=71.83 Aligned_cols=150 Identities=24% Similarity=0.257 Sum_probs=96.1
Q ss_pred EEEEEEcccchHH-------HHHHHHHHHHHhccCCCCcEEEEEEECCeEEEE-EcCCCCCcceeEecCCcccchhhHHh
Q 004238 137 FVFVLDTCMIEEE-------LGYARSELKRAIGLLPDNAMVGLVTFGTQAHVH-ELGFSDMSKVYVFRGNKEISKDQVLE 208 (766)
Q Consensus 137 ~vFvID~s~~~~~-------l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~~-~l~~~~~~~~~v~~g~~~~~~~~l~~ 208 (766)
++||||+|.++.. ++.+++++...++.+|++ +|||++|++..++. ++.
T Consensus 2 vv~v~D~SgSM~~~~~~~~~~~~~~~~~~~~~~~~~~~-~v~l~~f~~~~~~~~~~t----------------------- 57 (172)
T PF13519_consen 2 VVFVLDNSGSMNGYDGNRTRIDQAKDALNELLANLPGD-RVGLVSFSDSSRTLSPLT----------------------- 57 (172)
T ss_dssp EEEEEE-SGGGGTTTSSS-HHHHHHHHHHHHHHHHTTS-EEEEEEESTSCEEEEEEE-----------------------
T ss_pred EEEEEECCcccCCCCCCCcHHHHHHHHHHHHHHHCCCC-EEEEEEeccccccccccc-----------------------
Confidence 6899999999742 788899999999888855 99999999753221 010
Q ss_pred hhccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhc
Q 004238 209 QLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGA 288 (766)
Q Consensus 209 ~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~ 288 (766)
..+..+.+.++++.... ......+++.|+..|..++..
T Consensus 58 -------------------------------------~~~~~~~~~l~~~~~~~-----~~~~~t~~~~al~~a~~~~~~ 95 (172)
T PF13519_consen 58 -------------------------------------SDKDELKNALNKLSPQG-----MPGGGTNLYDALQEAAKMLAS 95 (172)
T ss_dssp -------------------------------------SSHHHHHHHHHTHHHHG-------SSS--HHHHHHHHHHHHHC
T ss_pred -------------------------------------ccHHHHHHHhhcccccc-----cCccCCcHHHHHHHHHHHHHh
Confidence 01122333444443210 012346899999999999984
Q ss_pred cCCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccCh
Q 004238 289 CLPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGV 368 (766)
Q Consensus 289 ~~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l 368 (766)
. +.....|++|++|.++. . ..+.+..+.+.+|.+..+.++.+...-
T Consensus 96 ~-~~~~~~iv~iTDG~~~~-------------------------~--------~~~~~~~~~~~~i~i~~v~~~~~~~~~ 141 (172)
T PF13519_consen 96 S-DNRRRAIVLITDGEDNS-------------------------S--------DIEAAKALKQQGITIYTVGIGSDSDAN 141 (172)
T ss_dssp --SSEEEEEEEEES-TTHC-------------------------H--------HHHHHHHHHCTTEEEEEEEES-TT-EH
T ss_pred C-CCCceEEEEecCCCCCc-------------------------c--------hhHHHHHHHHcCCeEEEEEECCCccHH
Confidence 2 12345677777774330 0 012566778899999999998877656
Q ss_pred hcchhhhhcccceEEEeC
Q 004238 369 AEMKVAVEKTGGLVVLAE 386 (766)
Q Consensus 369 ~~l~~l~~~TGG~v~~~~ 386 (766)
..|..+++.|||..+...
T Consensus 142 ~~l~~la~~tgG~~~~~~ 159 (172)
T PF13519_consen 142 EFLQRLAEATGGRYFHVD 159 (172)
T ss_dssp HHHHHHHHHTEEEEEEE-
T ss_pred HHHHHHHHhcCCEEEEec
Confidence 789999999999988873
No 35
>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=97.93 E-value=0.00033 Score=69.59 Aligned_cols=156 Identities=15% Similarity=0.069 Sum_probs=88.9
Q ss_pred CcEEEEEEEcccchHH-HHHHHHHHHHHhccC-CCCcEEEEEEECCeEEEE-EcCCCCCcceeEecCCcccchhhHHhhh
Q 004238 134 SPVFVFVLDTCMIEEE-LGYARSELKRAIGLL-PDNAMVGLVTFGTQAHVH-ELGFSDMSKVYVFRGNKEISKDQVLEQL 210 (766)
Q Consensus 134 ~p~~vFvID~s~~~~~-l~~~~~~l~~~l~~l-p~~~~VglItf~~~V~~~-~l~~~~~~~~~v~~g~~~~~~~~l~~~l 210 (766)
+.-.+|+||.|.+... ....++.++..++.+ .++.+||+|+|++..++. .+...
T Consensus 4 ~~Dvv~llD~SgSm~~~~~~~~~~~~~l~~~~~~~~~rvglv~Fs~~~~~~~~l~~~----------------------- 60 (185)
T cd01474 4 HFDLYFVLDKSGSVAANWIEIYDFVEQLVDRFNSPGLRFSFITFSTRATKILPLTDD----------------------- 60 (185)
T ss_pred ceeEEEEEeCcCchhhhHHHHHHHHHHHHHHcCCCCcEEEEEEecCCceEEEecccc-----------------------
Confidence 4457999999999754 323334444444433 356899999999865442 11100
Q ss_pred ccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccC
Q 004238 211 GLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACL 290 (766)
Q Consensus 211 ~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~ 290 (766)
. ..+...++.|.... + ...+++|.||..|...+...
T Consensus 61 ----------------------------------~---~~~~~~l~~l~~~~---~---~g~T~~~~aL~~a~~~l~~~- 96 (185)
T cd01474 61 ----------------------------------S---SAIIKGLEVLKKVT---P---SGQTYIHEGLENANEQIFNR- 96 (185)
T ss_pred ----------------------------------H---HHHHHHHHHHhccC---C---CCCCcHHHHHHHHHHHHHhh-
Confidence 0 01223333444321 1 23578999999999877310
Q ss_pred CCCc-----cEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCc
Q 004238 291 PGTG-----ARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQ 365 (766)
Q Consensus 291 ~~~g-----GrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~ 365 (766)
..| ..|+++|+|.++...+. + -...+..+.+.|+.|..+.. ..
T Consensus 97 -~~~~r~~~~~villTDG~~~~~~~~--------------~---------------~~~~a~~l~~~gv~i~~vgv--~~ 144 (185)
T cd01474 97 -NGGGRETVSVIIALTDGQLLLNGHK--------------Y---------------PEHEAKLSRKLGAIVYCVGV--TD 144 (185)
T ss_pred -ccCCCCCCeEEEEEcCCCcCCCCCc--------------c---------------hHHHHHHHHHcCCEEEEEee--ch
Confidence 222 34788888876421100 0 01123455667886655554 56
Q ss_pred cChhcchhhhhcccceEE-EeCCCC
Q 004238 366 VGVAEMKVAVEKTGGLVV-LAESFG 389 (766)
Q Consensus 366 ~~l~~l~~l~~~TGG~v~-~~~~f~ 389 (766)
.+..+|..++..++ .+| ...+|.
T Consensus 145 ~~~~~L~~iA~~~~-~~f~~~~~~~ 168 (185)
T cd01474 145 FLKSQLINIADSKE-YVFPVTSGFQ 168 (185)
T ss_pred hhHHHHHHHhCCCC-eeEecCccHH
Confidence 78889999998775 444 334444
No 36
>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=97.88 E-value=0.00095 Score=64.90 Aligned_cols=45 Identities=27% Similarity=0.463 Sum_probs=36.3
Q ss_pred EEEEEEcccchH--HHHHHHHHHHHHhccC---CCCcEEEEEEECCeEEE
Q 004238 137 FVFVLDTCMIEE--ELGYARSELKRAIGLL---PDNAMVGLVTFGTQAHV 181 (766)
Q Consensus 137 ~vFvID~s~~~~--~l~~~~~~l~~~l~~l---p~~~~VglItf~~~V~~ 181 (766)
.+|++|.|.+.. .++.+++.++..+..+ +++.+||+|+|++..++
T Consensus 3 v~~vlD~S~Sm~~~~~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~~~ 52 (164)
T cd01482 3 IVFLVDGSWSIGRSNFNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDPRT 52 (164)
T ss_pred EEEEEeCCCCcChhhHHHHHHHHHHHHhheeeCCCceEEEEEEECCCeeE
Confidence 689999999975 3888888888777765 46799999999987544
No 37
>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=97.86 E-value=0.00078 Score=66.45 Aligned_cols=156 Identities=16% Similarity=0.131 Sum_probs=99.4
Q ss_pred EEEEEEcccchH--HHHHHHHHHHHHhccCC---CCcEEEEEEECCeEEEE-EcCCCCCcceeEecCCcccchhhHHhhh
Q 004238 137 FVFVLDTCMIEE--ELGYARSELKRAIGLLP---DNAMVGLVTFGTQAHVH-ELGFSDMSKVYVFRGNKEISKDQVLEQL 210 (766)
Q Consensus 137 ~vFvID~s~~~~--~l~~~~~~l~~~l~~lp---~~~~VglItf~~~V~~~-~l~~~~~~~~~v~~g~~~~~~~~l~~~l 210 (766)
.+|+||.|.+.. +++.+++.++..++.+. +++|||+|+|++..++. ++.
T Consensus 3 i~fvlD~S~S~~~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~~~~~~l~------------------------- 57 (177)
T cd01469 3 IVFVLDGSGSIYPDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESFRTEFTLN------------------------- 57 (177)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCceeEEEecC-------------------------
Confidence 589999999964 48888888888887765 46899999999876542 111
Q ss_pred ccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhc--
Q 004238 211 GLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGA-- 288 (766)
Q Consensus 211 ~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~-- 288 (766)
+. . +...+...++.++.. .+ .+.+|.||..|...+-.
T Consensus 58 ---~~-------------------~-----------~~~~~~~~i~~~~~~-----~g---~T~~~~AL~~a~~~l~~~~ 96 (177)
T cd01469 58 ---EY-------------------R-----------TKEEPLSLVKHISQL-----LG---LTNTATAIQYVVTELFSES 96 (177)
T ss_pred ---cc-------------------C-----------CHHHHHHHHHhCccC-----CC---CccHHHHHHHHHHHhcCcc
Confidence 00 0 011133445555431 12 37899999999887621
Q ss_pred --cCCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCc-
Q 004238 289 --CLPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQ- 365 (766)
Q Consensus 289 --~~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~- 365 (766)
..++....++++|+|..+.|+- .++.+..+...||.|-.+..+.+.
T Consensus 97 ~g~R~~~~kv~illTDG~~~~~~~-------------------------------~~~~~~~~k~~gv~v~~Vgvg~~~~ 145 (177)
T cd01469 97 NGARKDATKVLVVITDGESHDDPL-------------------------------LKDVIPQAEREGIIRYAIGVGGHFQ 145 (177)
T ss_pred cCCCCCCCeEEEEEeCCCCCCccc-------------------------------cHHHHHHHHHCCcEEEEEEeccccc
Confidence 0112233578888887654320 022455566788887777776542
Q ss_pred --cChhcchhhhhcccc-eEEEeCCCC
Q 004238 366 --VGVAEMKVAVEKTGG-LVVLAESFG 389 (766)
Q Consensus 366 --~~l~~l~~l~~~TGG-~v~~~~~f~ 389 (766)
.+..+|..++..+++ ++|..++|+
T Consensus 146 ~~~~~~~L~~ias~p~~~h~f~~~~~~ 172 (177)
T cd01469 146 RENSREELKTIASKPPEEHFFNVTDFA 172 (177)
T ss_pred ccccHHHHHHHhcCCcHHhEEEecCHH
Confidence 346888899988764 666667664
No 38
>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=97.73 E-value=0.0014 Score=62.89 Aligned_cols=145 Identities=19% Similarity=0.174 Sum_probs=96.7
Q ss_pred EEEEEEcccchHH--HHHHHHHHHHHhccCC---CCcEEEEEEECCeEEEE-EcCCCCCcceeEecCCcccchhhHHhhh
Q 004238 137 FVFVLDTCMIEEE--LGYARSELKRAIGLLP---DNAMVGLVTFGTQAHVH-ELGFSDMSKVYVFRGNKEISKDQVLEQL 210 (766)
Q Consensus 137 ~vFvID~s~~~~~--l~~~~~~l~~~l~~lp---~~~~VglItf~~~V~~~-~l~~~~~~~~~v~~g~~~~~~~~l~~~l 210 (766)
++|++|+|.++.. ++.+++.+...+..+. ++.++||++|++..... ++...
T Consensus 3 i~~llD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~~~~~~~~~----------------------- 59 (161)
T cd01450 3 IVFLLDGSESVGPENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVRVEFSLNDY----------------------- 59 (161)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCceEEEECCCC-----------------------
Confidence 5799999999754 7778888888777665 47899999999854331 11000
Q ss_pred ccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccC
Q 004238 211 GLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACL 290 (766)
Q Consensus 211 ~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~ 290 (766)
. .+..+.+.++.+... .+ ..+.++.||..|...+....
T Consensus 60 ---------------------------~--------~~~~~~~~i~~~~~~-----~~--~~t~~~~al~~a~~~~~~~~ 97 (161)
T cd01450 60 ---------------------------K--------SKDDLLKAVKNLKYL-----GG--GGTNTGKALQYALEQLFSES 97 (161)
T ss_pred ---------------------------C--------CHHHHHHHHHhcccC-----CC--CCccHHHHHHHHHHHhcccc
Confidence 0 112244455554431 11 35789999999999987321
Q ss_pred ---CCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccC
Q 004238 291 ---PGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVG 367 (766)
Q Consensus 291 ---~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~ 367 (766)
......|++|++|.++.++ -..++.+++.+.++.+..+..+. .+
T Consensus 98 ~~~~~~~~~iiliTDG~~~~~~-------------------------------~~~~~~~~~~~~~v~v~~i~~g~--~~ 144 (161)
T cd01450 98 NARENVPKVIIVLTDGRSDDGG-------------------------------DPKEAAAKLKDEGIKVFVVGVGP--AD 144 (161)
T ss_pred cccCCCCeEEEEECCCCCCCCc-------------------------------chHHHHHHHHHCCCEEEEEeccc--cC
Confidence 2344578999999876643 01334556667788888887765 68
Q ss_pred hhcchhhhhccc
Q 004238 368 VAEMKVAVEKTG 379 (766)
Q Consensus 368 l~~l~~l~~~TG 379 (766)
...|..++..+|
T Consensus 145 ~~~l~~la~~~~ 156 (161)
T cd01450 145 EEELREIASCPS 156 (161)
T ss_pred HHHHHHHhCCCC
Confidence 888999998883
No 39
>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=97.71 E-value=0.0011 Score=65.83 Aligned_cols=148 Identities=18% Similarity=0.083 Sum_probs=91.8
Q ss_pred EEEEEEcccchH--H-HHHHHHHHHHHhccCC---CCcEEEEEEECCeEEE-EEcCCCCCcceeEecCCcccchhhHHhh
Q 004238 137 FVFVLDTCMIEE--E-LGYARSELKRAIGLLP---DNAMVGLVTFGTQAHV-HELGFSDMSKVYVFRGNKEISKDQVLEQ 209 (766)
Q Consensus 137 ~vFvID~s~~~~--~-l~~~~~~l~~~l~~lp---~~~~VglItf~~~V~~-~~l~~~~~~~~~v~~g~~~~~~~~l~~~ 209 (766)
++|+||.|.++. + ++.+++.+...++.++ ++.+||+|+|++..+. +++....
T Consensus 3 v~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~~~~~l~~~~--------------------- 61 (186)
T cd01471 3 LYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAKELIRLSSPN--------------------- 61 (186)
T ss_pred EEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCceEEEECCCcc---------------------
Confidence 689999999964 3 7888888888888774 5789999999987664 2222100
Q ss_pred hccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhcc
Q 004238 210 LGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGAC 289 (766)
Q Consensus 210 l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 289 (766)
...+..+..+++.|.... .+ ...++++.||..|...+...
T Consensus 62 -----------------------------------~~~~~~~~~~i~~l~~~~--~~---~G~T~l~~aL~~a~~~l~~~ 101 (186)
T cd01471 62 -----------------------------------STNKDLALNAIRALLSLY--YP---NGSTNTTSALLVVEKHLFDT 101 (186)
T ss_pred -----------------------------------ccchHHHHHHHHHHHhCc--CC---CCCccHHHHHHHHHHHhhcc
Confidence 001111233444443321 11 23478999999999988631
Q ss_pred ---CCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCcc
Q 004238 290 ---LPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQV 366 (766)
Q Consensus 290 ---~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~ 366 (766)
.++....|+++|+|.++.++. . .+.++++...|+.+-++.++ ...
T Consensus 102 ~~~r~~~~~~villTDG~~~~~~~---------------------------~----~~~a~~l~~~gv~v~~igiG-~~~ 149 (186)
T cd01471 102 RGNRENAPQLVIIMTDGIPDSKFR---------------------------T----LKEARKLRERGVIIAVLGVG-QGV 149 (186)
T ss_pred CCCcccCceEEEEEccCCCCCCcc---------------------------h----hHHHHHHHHCCCEEEEEEee-hhh
Confidence 112234688888887653210 0 02355566778877777665 356
Q ss_pred Chhcchhhhhc
Q 004238 367 GVAEMKVAVEK 377 (766)
Q Consensus 367 ~l~~l~~l~~~ 377 (766)
+...|..++..
T Consensus 150 d~~~l~~ia~~ 160 (186)
T cd01471 150 NHEENRSLVGC 160 (186)
T ss_pred CHHHHHHhcCC
Confidence 77777777765
No 40
>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=97.61 E-value=0.0035 Score=61.04 Aligned_cols=45 Identities=22% Similarity=0.302 Sum_probs=37.0
Q ss_pred EEEEEEcccchH--HHHHHHHHHHHHhccCC---CCcEEEEEEECCeEEE
Q 004238 137 FVFVLDTCMIEE--ELGYARSELKRAIGLLP---DNAMVGLVTFGTQAHV 181 (766)
Q Consensus 137 ~vFvID~s~~~~--~l~~~~~~l~~~l~~lp---~~~~VglItf~~~V~~ 181 (766)
.+|+||.|.+.- +++.+++.++..++.++ +.++||+|+|++..+.
T Consensus 3 ivfllD~S~Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~~ 52 (165)
T cd01481 3 IVFLIDGSDNVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPRP 52 (165)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCeeE
Confidence 589999999854 58889988888888774 5699999999986544
No 41
>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=97.59 E-value=0.003 Score=73.96 Aligned_cols=176 Identities=16% Similarity=0.094 Sum_probs=115.2
Q ss_pred CCcEEEEEEEcccchH--HHHHHHHHHHHHhccC-CCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhh
Q 004238 133 LSPVFVFVLDTCMIEE--ELGYARSELKRAIGLL-PDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQ 209 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~--~l~~~~~~l~~~l~~l-p~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~ 209 (766)
..-.++||||+|.++. .++.+|+++...+... .+.-+||||+|++...-+-+...
T Consensus 406 ~~~~v~fvvD~SGSM~~~rl~~aK~av~~Ll~~~~~~~D~v~Li~F~~~~a~~~lp~t---------------------- 463 (589)
T TIGR02031 406 SGRLLIFVVDASGSAAVARMSEAKGAVELLLGEAYVHRDQVSLIAFRGTAAEVLLPPS---------------------- 463 (589)
T ss_pred cCceEEEEEECCCCCChHHHHHHHHHHHHHHHhhccCCCEEEEEEECCCCceEECCCC----------------------
Confidence 4566889999999985 3899999988888753 45569999999754311101100
Q ss_pred hccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhcc
Q 004238 210 LGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGAC 289 (766)
Q Consensus 210 l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 289 (766)
.....+...|+.|+. ...+.++.||..|...+...
T Consensus 464 ------------------------------------~~~~~~~~~L~~l~~---------gGgTpL~~gL~~A~~~~~~~ 498 (589)
T TIGR02031 464 ------------------------------------RSVEQAKRRLDVLPG---------GGGTPLAAGLAAAFQTALQA 498 (589)
T ss_pred ------------------------------------CCHHHHHHHHhcCCC---------CCCCcHHHHHHHHHHHHHHh
Confidence 011112344555543 12467999999999998732
Q ss_pred CCCCc--cEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccC
Q 004238 290 LPGTG--ARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVG 367 (766)
Q Consensus 290 ~~~~g--GrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~ 367 (766)
.. .+ -.|+++|+|.+|.|-+.....+ + .-..+..+-...++..+...||.+-++-+...+.+
T Consensus 499 ~~-~~~~~~ivllTDG~~nv~~~~~~~~~------------~---~~~~~~~~~~~~~a~~~~~~gi~~~vid~~~~~~~ 562 (589)
T TIGR02031 499 RS-SGGTPTIVLITDGRGNIPLDGDPESI------------K---ADREQAAEEALALARKIREAGMPALVIDTAMRFVS 562 (589)
T ss_pred cc-cCCceEEEEECCCCCCCCCCcccccc------------c---ccchhHHHHHHHHHHHHHhcCCeEEEEeCCCCCcc
Confidence 22 23 3699999999998753110000 0 00122334445678888899988877777766666
Q ss_pred hhcchhhhhcccceEEEeCCCCch
Q 004238 368 VAEMKVAVEKTGGLVVLAESFGHS 391 (766)
Q Consensus 368 l~~l~~l~~~TGG~v~~~~~f~~~ 391 (766)
...+..||+..||..++.++-+.+
T Consensus 563 ~~~~~~lA~~~~g~y~~l~~~~a~ 586 (589)
T TIGR02031 563 TGFAQKLARKMGAHYIYLPNATAA 586 (589)
T ss_pred chHHHHHHHhcCCcEEeCCCCChh
Confidence 666889999999999998876653
No 42
>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=97.58 E-value=0.004 Score=60.23 Aligned_cols=41 Identities=22% Similarity=0.324 Sum_probs=32.9
Q ss_pred EEEEEEcccchHH-HHHHHHHHHHHhccCC---CCcEEEEEEECC
Q 004238 137 FVFVLDTCMIEEE-LGYARSELKRAIGLLP---DNAMVGLVTFGT 177 (766)
Q Consensus 137 ~vFvID~s~~~~~-l~~~~~~l~~~l~~lp---~~~~VglItf~~ 177 (766)
++|++|+|.+... ++..++.++..+..+. +..+||+|+|++
T Consensus 3 v~~llD~S~Sm~~~~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~~ 47 (163)
T cd01476 3 LLFVLDSSGSVRGKFEKYKKYIERIVEGLEIGPTATRVALITYSG 47 (163)
T ss_pred EEEEEeCCcchhhhHHHHHHHHHHHHHhcCCCCCCcEEEEEEEcC
Confidence 6899999998755 6666777777777664 478999999988
No 43
>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=97.56 E-value=0.0023 Score=63.92 Aligned_cols=49 Identities=33% Similarity=0.394 Sum_probs=38.3
Q ss_pred CCcEEEEEEEcccchH--HHHHHHHHHHHHhccC---------CCCcEEEEEEECCeEEE
Q 004238 133 LSPVFVFVLDTCMIEE--ELGYARSELKRAIGLL---------PDNAMVGLVTFGTQAHV 181 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~--~l~~~~~~l~~~l~~l---------p~~~~VglItf~~~V~~ 181 (766)
.+.=.||+||.|.+.- +++.+++.++..+..+ |..+|||+|+|++..++
T Consensus 18 ~~~DivfvlD~S~Sm~~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a~~ 77 (193)
T cd01477 18 LWLDIVFVVDNSKGMTQGGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNATV 77 (193)
T ss_pred ceeeEEEEEeCCCCcchhhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCceEE
Confidence 4556899999999964 4888888887766543 34589999999987665
No 44
>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=97.49 E-value=0.0024 Score=62.30 Aligned_cols=156 Identities=22% Similarity=0.274 Sum_probs=94.7
Q ss_pred EEEEEEcccchHH--HHHHHHHHHHHhccC---CCCcEEEEEEECCeEEEE-EcCCCCCcceeEecCCcccchhhHHhhh
Q 004238 137 FVFVLDTCMIEEE--LGYARSELKRAIGLL---PDNAMVGLVTFGTQAHVH-ELGFSDMSKVYVFRGNKEISKDQVLEQL 210 (766)
Q Consensus 137 ~vFvID~s~~~~~--l~~~~~~l~~~l~~l---p~~~~VglItf~~~V~~~-~l~~~~~~~~~v~~g~~~~~~~~l~~~l 210 (766)
.+|+||.|..... ++.+++.+...++.+ +++.+||+|+|++..+.+ ++....
T Consensus 2 ivflvD~S~sm~~~~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~~~~~~~~~~---------------------- 59 (178)
T PF00092_consen 2 IVFLVDTSGSMSGDNFEKAKQFVKSIISRLSISNNGTRVGIVTFSDSARVLFSLTDYQ---------------------- 59 (178)
T ss_dssp EEEEEE-STTSCHHHHHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEEEEEETTSHS----------------------
T ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHHhhhccccccccceeeeeccccccccccccc----------------------
Confidence 5899999999754 888888888888754 568999999999877643 111100
Q ss_pred ccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHH-HhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhcc
Q 004238 211 GLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLL-DELQPDQWPVAPRTRPSRCTGVALSVATGLLGAC 289 (766)
Q Consensus 211 ~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL-~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 289 (766)
....+...+ ..++. ....+.+|.||..|...+...
T Consensus 60 ------------------------------------~~~~~~~~i~~~~~~--------~~g~t~~~~aL~~a~~~l~~~ 95 (178)
T PF00092_consen 60 ------------------------------------SKNDLLNAINDSIPS--------SGGGTNLGAALKFAREQLFSS 95 (178)
T ss_dssp ------------------------------------SHHHHHHHHHTTGGC--------CBSSB-HHHHHHHHHHHTTSG
T ss_pred ------------------------------------ccccccccccccccc--------cchhhhHHHHHhhhhhccccc
Confidence 001112222 23322 123567999999999998632
Q ss_pred ----CCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCc
Q 004238 290 ----LPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQ 365 (766)
Q Consensus 290 ----~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~ 365 (766)
.+....-|+++++|.++.++- ... .+..+.+. ..|.+|+.+.+.
T Consensus 96 ~~~~r~~~~~~iiliTDG~~~~~~~--------------------------~~~-----~~~~~~~~-~~i~~~~ig~~~ 143 (178)
T PF00092_consen 96 NNGGRPNSPKVIILITDGNSNDSDS--------------------------PSE-----EAANLKKS-NGIKVIAIGIDN 143 (178)
T ss_dssp GGTTGTTSEEEEEEEESSSSSSHSG--------------------------HHH-----HHHHHHHH-CTEEEEEEEESC
T ss_pred ccccccccccceEEEEeecccCCcc--------------------------hHH-----HHHHHHHh-cCcEEEEEecCc
Confidence 122334578888887655420 000 11111111 556667666667
Q ss_pred cChhcchhhhhc--ccceEEEeCCCCc
Q 004238 366 VGVAEMKVAVEK--TGGLVVLAESFGH 390 (766)
Q Consensus 366 ~~l~~l~~l~~~--TGG~v~~~~~f~~ 390 (766)
.+..+|..|+.. .+|.+++..+++.
T Consensus 144 ~~~~~l~~la~~~~~~~~~~~~~~~~~ 170 (178)
T PF00092_consen 144 ADNEELRELASCPTSEGHVFYLADFSD 170 (178)
T ss_dssp CHHHHHHHHSHSSTCHHHEEEESSHHH
T ss_pred CCHHHHHHHhCCCCCCCcEEEcCCHHH
Confidence 888889999965 4477887777654
No 45
>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=97.48 E-value=0.0074 Score=58.62 Aligned_cols=154 Identities=24% Similarity=0.208 Sum_probs=100.7
Q ss_pred cEEEEEEEcccch-HH-HHHHHHHHHHHhccCCC---CcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhh
Q 004238 135 PVFVFVLDTCMIE-EE-LGYARSELKRAIGLLPD---NAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQ 209 (766)
Q Consensus 135 p~~vFvID~s~~~-~~-l~~~~~~l~~~l~~lp~---~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~ 209 (766)
.-++|+||+|.++ .. ++.+++.+...+..+.. +.+||+++|++..+.+- .
T Consensus 2 ~~v~l~vD~S~SM~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ii~f~~~~~~~~-~------------------------ 56 (177)
T smart00327 2 LDVVFLLDGSGSMGPNRFEKAKEFVLKLVEQLDIGPDGDRVGLVTFSDDATVLF-P------------------------ 56 (177)
T ss_pred ccEEEEEeCCCccchHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeCCCceEEE-c------------------------
Confidence 3478999999998 33 78888888888877765 88999999998443321 0
Q ss_pred hccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhcc
Q 004238 210 LGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGAC 289 (766)
Q Consensus 210 l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 289 (766)
+.+ ......+...++.+... ......++.||..|...+...
T Consensus 57 --~~~------------------------------~~~~~~~~~~i~~~~~~-------~~~~~~~~~al~~~~~~~~~~ 97 (177)
T smart00327 57 --LND------------------------------SRSKDALLEALASLSYK-------LGGGTNLGAALQYALENLFSK 97 (177)
T ss_pred --ccc------------------------------cCCHHHHHHHHHhcCCC-------CCCCchHHHHHHHHHHHhcCc
Confidence 000 00112244555555431 123457889999999887521
Q ss_pred CCC----CccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCc
Q 004238 290 LPG----TGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQ 365 (766)
Q Consensus 290 ~~~----~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~ 365 (766)
... ..-.|++|++|.++.+ ..+.+...++.+.+|.+..+.++.+.
T Consensus 98 ~~~~~~~~~~~iviitDg~~~~~-------------------------------~~~~~~~~~~~~~~i~i~~i~~~~~~ 146 (177)
T smart00327 98 SAGSRRGAPKVLILITDGESNDG-------------------------------GDLLKAAKELKRSGVKVFVVGVGNDV 146 (177)
T ss_pred CCCCCCCCCeEEEEEcCCCCCCC-------------------------------ccHHHHHHHHHHCCCEEEEEEccCcc
Confidence 111 1346788888876543 11345566777888888888877543
Q ss_pred cChhcchhhhhcccceEEE
Q 004238 366 VGVAEMKVAVEKTGGLVVL 384 (766)
Q Consensus 366 ~~l~~l~~l~~~TGG~v~~ 384 (766)
+-..|..++..++|...+
T Consensus 147 -~~~~l~~~~~~~~~~~~~ 164 (177)
T smart00327 147 -DEEELKKLASAPGGVYVF 164 (177)
T ss_pred -CHHHHHHHhCCCcceEEe
Confidence 777899999999987654
No 46
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=97.31 E-value=0.015 Score=67.61 Aligned_cols=172 Identities=15% Similarity=0.112 Sum_probs=111.3
Q ss_pred CCcEEEEEEEcccchH--HHHHHHHHHHHHhcc-CCCCcEEEEEEECCe-EEEEEcCCCCCcceeEecCCcccchhhHHh
Q 004238 133 LSPVFVFVLDTCMIEE--ELGYARSELKRAIGL-LPDNAMVGLVTFGTQ-AHVHELGFSDMSKVYVFRGNKEISKDQVLE 208 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~--~l~~~~~~l~~~l~~-lp~~~~VglItf~~~-V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~ 208 (766)
.+-.++||||+|.++. .+..+|.++...|.. +.++-+||||+|++. ..+- +..+
T Consensus 400 ~~~~vvfvvD~SGSM~~~rl~~aK~a~~~ll~~ay~~rD~v~lI~F~g~~a~~~-lppT--------------------- 457 (584)
T PRK13406 400 SETTTIFVVDASGSAALHRLAEAKGAVELLLAEAYVRRDQVALVAFRGRGAELL-LPPT--------------------- 457 (584)
T ss_pred CCccEEEEEECCCCCcHhHHHHHHHHHHHHHHhhcCCCCEEEEEEECCCceeEE-cCCC---------------------
Confidence 4578999999999984 388999998888855 456779999999653 3220 1000
Q ss_pred hhccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhc
Q 004238 209 QLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGA 288 (766)
Q Consensus 209 ~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~ 288 (766)
.+...+...|+.|+. ...+.++.||..|..++..
T Consensus 458 -------------------------------------~~~~~~~~~L~~l~~---------gGgTpL~~gL~~A~~~l~~ 491 (584)
T PRK13406 458 -------------------------------------RSLVRAKRSLAGLPG---------GGGTPLAAGLDAAAALALQ 491 (584)
T ss_pred -------------------------------------cCHHHHHHHHhcCCC---------CCCChHHHHHHHHHHHHHH
Confidence 011123344455543 1347899999999998863
Q ss_pred cC-CCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccC
Q 004238 289 CL-PGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVG 367 (766)
Q Consensus 289 ~~-~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~ 367 (766)
.. ++.--.|+++|+|-+|.|-+.-..+. .....+ ..++..+...||.+-++-+....
T Consensus 492 ~~~~~~~~~iVLlTDG~~n~~~~~~~~~~----------------~~~~~~----~~~a~~~~~~gi~~~vId~g~~~-- 549 (584)
T PRK13406 492 VRRKGMTPTVVLLTDGRANIARDGTAGRA----------------QAEEDA----LAAARALRAAGLPALVIDTSPRP-- 549 (584)
T ss_pred hccCCCceEEEEEeCCCCCCCcccccccc----------------chhhHH----HHHHHHHHhcCCeEEEEecCCCC--
Confidence 22 12235889999999988653211110 000111 34577777888877666665443
Q ss_pred hhcchhhhhcccceEEEeCCCCchhhH
Q 004238 368 VAEMKVAVEKTGGLVVLAESFGHSVFK 394 (766)
Q Consensus 368 l~~l~~l~~~TGG~v~~~~~f~~~~~~ 394 (766)
...+..||+.+||..+..+.-+.+...
T Consensus 550 ~~~~~~LA~~~gg~y~~l~~~~a~~~~ 576 (584)
T PRK13406 550 QPQARALAEAMGARYLPLPRADAGRLS 576 (584)
T ss_pred cHHHHHHHHhcCCeEEECCCCCHHHHH
Confidence 345789999999999999988775543
No 47
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=97.26 E-value=0.011 Score=67.33 Aligned_cols=164 Identities=9% Similarity=-0.030 Sum_probs=95.9
Q ss_pred CCcEEEEEEEcccchHH---HHHHHHHHHHHhccCC---CCcEEEEEEECCeEEE-EEcCCCCCcceeEecCCcccchhh
Q 004238 133 LSPVFVFVLDTCMIEEE---LGYARSELKRAIGLLP---DNAMVGLVTFGTQAHV-HELGFSDMSKVYVFRGNKEISKDQ 205 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~~---l~~~~~~l~~~l~~lp---~~~~VglItf~~~V~~-~~l~~~~~~~~~v~~g~~~~~~~~ 205 (766)
...-.+||||.|.+... ++.++..+...+..+. +..+||+++|++..+. +.+.... .+
T Consensus 41 ~~lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~r~vfpL~s~~-----------s~---- 105 (576)
T PTZ00441 41 EEVDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNTTELIRLGSGA-----------SK---- 105 (576)
T ss_pred CCceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCceEEEecCCCc-----------cc----
Confidence 45668999999999743 4667777777777663 5689999999986543 2332110 00
Q ss_pred HHhhhccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHH
Q 004238 206 VLEQLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGL 285 (766)
Q Consensus 206 l~~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~l 285 (766)
.+..+...|..|.... .+ ...+.+|.||..|...
T Consensus 106 -----------------------------------------Dk~~aL~~I~sL~~~~--~p---gGgTnig~AL~~Aae~ 139 (576)
T PTZ00441 106 -----------------------------------------DKEQALIIVKSLRKTY--LP---YGKTNMTDALLEVRKH 139 (576)
T ss_pred -----------------------------------------cHHHHHHHHHHHHhhc--cC---CCCccHHHHHHHHHHH
Confidence 0011222233332210 11 1246799999988887
Q ss_pred hhcc--CCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecC
Q 004238 286 LGAC--LPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASAL 363 (766)
Q Consensus 286 l~~~--~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~ 363 (766)
+... ..+..+.||+||+|.++.+. + -.+.+.++...||.|-++.++.
T Consensus 140 L~sr~~R~nvpKVVILLTDG~sns~~----------------d---------------vleaAq~LR~~GVeI~vIGVG~ 188 (576)
T PTZ00441 140 LNDRVNRENAIQLVILMTDGIPNSKY----------------R---------------ALEESRKLKDRNVKLAVIGIGQ 188 (576)
T ss_pred HhhcccccCCceEEEEEecCCCCCcc----------------c---------------HHHHHHHHHHCCCEEEEEEeCC
Confidence 7521 11233678999988743210 0 0123556677888777777653
Q ss_pred CccChhcchhhh----hcccceEEEeCCCC
Q 004238 364 DQVGVAEMKVAV----EKTGGLVVLAESFG 389 (766)
Q Consensus 364 ~~~~l~~l~~l~----~~TGG~v~~~~~f~ 389 (766)
..+...+..++ ..++|.+|...+|.
T Consensus 189 -g~n~e~LrlIAgC~p~~g~c~~Y~vadf~ 217 (576)
T PTZ00441 189 -GINHQFNRLLAGCRPREGKCKFYSDADWE 217 (576)
T ss_pred -CcCHHHHHHHhccCCCCCCCceEEeCCHH
Confidence 45655566566 33556777777774
No 48
>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=97.18 E-value=0.0068 Score=71.82 Aligned_cols=161 Identities=17% Similarity=0.169 Sum_probs=104.0
Q ss_pred CCcEEEEEEEcccchH---HHHHHHHHHHHHhcc-CCCCcEEEEEEECCe-EEEEEcCCCCCcceeEecCCcccchhhHH
Q 004238 133 LSPVFVFVLDTCMIEE---ELGYARSELKRAIGL-LPDNAMVGLVTFGTQ-AHVHELGFSDMSKVYVFRGNKEISKDQVL 207 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~---~l~~~~~~l~~~l~~-lp~~~~VglItf~~~-V~~~~l~~~~~~~~~v~~g~~~~~~~~l~ 207 (766)
....++|+||+|.++. .++.++.++...+.. ...+.+||+|+|+.. ..+. +..
T Consensus 464 ~~~~vv~vvD~SgSM~~~~rl~~ak~a~~~ll~~a~~~~D~v~lI~F~g~~a~~~-~p~--------------------- 521 (633)
T TIGR02442 464 AGNLVIFVVDASGSMAARGRMAAAKGAVLSLLRDAYQKRDKVALITFRGEEAEVL-LPP--------------------- 521 (633)
T ss_pred CCceEEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCceEE-cCC---------------------
Confidence 3457889999999974 477788887777654 445789999999743 2211 000
Q ss_pred hhhccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhh
Q 004238 208 EQLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLG 287 (766)
Q Consensus 208 ~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~ 287 (766)
......+...|+.|+. ...+.++.||..|..++.
T Consensus 522 -------------------------------------t~~~~~~~~~L~~l~~---------gG~Tpl~~aL~~A~~~l~ 555 (633)
T TIGR02442 522 -------------------------------------TSSVELAARRLEELPT---------GGRTPLAAGLLKAAEVLS 555 (633)
T ss_pred -------------------------------------CCCHHHHHHHHHhCCC---------CCCCCHHHHHHHHHHHHH
Confidence 0011223345555543 124678999999999887
Q ss_pred cc---CCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCC
Q 004238 288 AC---LPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALD 364 (766)
Q Consensus 288 ~~---~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~ 364 (766)
.. .+...+.|+++++|.+|.|.+. . + + ... -..++..+...||.+.++-+...
T Consensus 556 ~~~~~~~~~~~~vvliTDG~~n~~~~~--~-~---~--------------~~~----~~~~a~~l~~~~i~~~vIdt~~~ 611 (633)
T TIGR02442 556 NELLRDDDGRPLLVVITDGRANVADGG--E-P---P--------------TDD----ARTIAAKLAARGILFVVIDTESG 611 (633)
T ss_pred HhhccCCCCceEEEEECCCCCCCCCCC--C-C---h--------------HHH----HHHHHHHHHhcCCeEEEEeCCCC
Confidence 21 1234567999999998886211 0 0 0 011 13456677777887777766666
Q ss_pred ccChhcchhhhhcccceEEEe
Q 004238 365 QVGVAEMKVAVEKTGGLVVLA 385 (766)
Q Consensus 365 ~~~l~~l~~l~~~TGG~v~~~ 385 (766)
.++...+..||+.+||..+..
T Consensus 612 ~~~~~~~~~lA~~~gg~y~~l 632 (633)
T TIGR02442 612 FVRLGLAEDLARALGGEYVRL 632 (633)
T ss_pred CcchhHHHHHHHhhCCeEEec
Confidence 677778999999999998764
No 49
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=97.17 E-value=0.013 Score=59.78 Aligned_cols=168 Identities=15% Similarity=0.118 Sum_probs=111.2
Q ss_pred CcEEEEEEEcccchHH---HHHHHHHHHHHhccCC-CCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhh
Q 004238 134 SPVFVFVLDTCMIEEE---LGYARSELKRAIGLLP-DNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQ 209 (766)
Q Consensus 134 ~p~~vFvID~s~~~~~---l~~~~~~l~~~l~~lp-~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~ 209 (766)
..-+|||||.|.++.- .+.+|-++.+.|..=. ..-+|++|+|... . .+.
T Consensus 78 g~lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~dAYq~RdkvavI~F~G~--------~-------------------A~l 130 (261)
T COG1240 78 GNLIVFVVDASGSMAARRRMAAAKGAALSLLRDAYQRRDKVAVIAFRGE--------K-------------------AEL 130 (261)
T ss_pred CCcEEEEEeCcccchhHHHHHHHHHHHHHHHHHHHHccceEEEEEecCC--------c-------------------ceE
Confidence 4568999999999753 7888888777775433 3569999998631 0 011
Q ss_pred hccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhcc
Q 004238 210 LGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGAC 289 (766)
Q Consensus 210 l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 289 (766)
+ + |...+-+.+...|+.|+. .+ .+=+..||..|..++.-+
T Consensus 131 l-l------------------------------~pT~sv~~~~~~L~~l~~------GG---~TPL~~aL~~a~ev~~r~ 170 (261)
T COG1240 131 L-L------------------------------PPTSSVELAERALERLPT------GG---KTPLADALRQAYEVLARE 170 (261)
T ss_pred E-e------------------------------CCcccHHHHHHHHHhCCC------CC---CCchHHHHHHHHHHHHHh
Confidence 1 1 111122335566667664 22 245899999999999854
Q ss_pred CC---CCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCcc
Q 004238 290 LP---GTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQV 366 (766)
Q Consensus 290 ~~---~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~ 366 (766)
.. ..--.+++.|+|.||.+.+.=+. ... ...+.++...|+-+=+.-+-..++
T Consensus 171 ~r~~p~~~~~~vviTDGr~n~~~~~~~~---------------------~e~----~~~a~~~~~~g~~~lvid~e~~~~ 225 (261)
T COG1240 171 KRRGPDRRPVMVVITDGRANVPIPLGPK---------------------AET----LEAASKLRLRGIQLLVIDTEGSEV 225 (261)
T ss_pred hccCCCcceEEEEEeCCccCCCCCCchH---------------------HHH----HHHHHHHhhcCCcEEEEecCCccc
Confidence 32 23457899999998876522100 011 134555666777666666666777
Q ss_pred ChhcchhhhhcccceEEEeCCCCchhh
Q 004238 367 GVAEMKVAVEKTGGLVVLAESFGHSVF 393 (766)
Q Consensus 367 ~l~~l~~l~~~TGG~v~~~~~f~~~~~ 393 (766)
.+.-...+|..+||..++.+..+....
T Consensus 226 ~~g~~~~iA~~~Gg~~~~L~~l~~~~i 252 (261)
T COG1240 226 RLGLAEEIARASGGEYYHLDDLSDDSI 252 (261)
T ss_pred cccHHHHHHHHhCCeEEecccccchHH
Confidence 777788999999999999998877544
No 50
>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=97.15 E-value=0.014 Score=55.14 Aligned_cols=148 Identities=28% Similarity=0.339 Sum_probs=95.5
Q ss_pred EEEEEEEcccch--HHHHHHHHHHHHHhccCCC---CcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHhhh
Q 004238 136 VFVFVLDTCMIE--EELGYARSELKRAIGLLPD---NAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLEQL 210 (766)
Q Consensus 136 ~~vFvID~s~~~--~~l~~~~~~l~~~l~~lp~---~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~~l 210 (766)
.++|+||+|.++ ..++.+++.+...+..++. ..+||++.|+...+.+- .
T Consensus 2 ~v~~viD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~f~~~~~~~~-~------------------------- 55 (161)
T cd00198 2 DIVFLLDVSGSMGGEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARVVL-P------------------------- 55 (161)
T ss_pred cEEEEEeCCCCcCcchHHHHHHHHHHHHHhcccCCCCcEEEEEEecCccceee-c-------------------------
Confidence 378999999987 3388888888888888875 78999999997433220 0
Q ss_pred ccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccC
Q 004238 211 GLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACL 290 (766)
Q Consensus 211 ~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~ 290 (766)
+.+ . ...+.+...++.+.. .......+..|+..|...+....
T Consensus 56 -~~~-------------------~-----------~~~~~~~~~~~~~~~-------~~~~~t~~~~al~~~~~~~~~~~ 97 (161)
T cd00198 56 -LTT-------------------D-----------TDKADLLEAIDALKK-------GLGGGTNIGAALRLALELLKSAK 97 (161)
T ss_pred -ccc-------------------c-----------CCHHHHHHHHHhccc-------CCCCCccHHHHHHHHHHHhcccC
Confidence 000 0 011223444555442 11234678899999999987321
Q ss_pred -CCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCccChh
Q 004238 291 -PGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQVGVA 369 (766)
Q Consensus 291 -~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~~l~ 369 (766)
+.....+++|++|.++.++ . + ..+....+.+.++.+.++.++. ..+-.
T Consensus 98 ~~~~~~~lvvitDg~~~~~~-----~----------~---------------~~~~~~~~~~~~v~v~~v~~g~-~~~~~ 146 (161)
T cd00198 98 RPNARRVIILLTDGEPNDGP-----E----------L---------------LAEAARELRKLGITVYTIGIGD-DANED 146 (161)
T ss_pred CCCCceEEEEEeCCCCCCCc-----c----------h---------------hHHHHHHHHHcCCEEEEEEcCC-CCCHH
Confidence 2356678888888765543 0 0 1234555667799999888876 34556
Q ss_pred cchhhhhcc
Q 004238 370 EMKVAVEKT 378 (766)
Q Consensus 370 ~l~~l~~~T 378 (766)
.+..++..+
T Consensus 147 ~l~~l~~~~ 155 (161)
T cd00198 147 ELKEIADKT 155 (161)
T ss_pred HHHHHhccc
Confidence 788888877
No 51
>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=97.09 E-value=0.022 Score=56.96 Aligned_cols=146 Identities=12% Similarity=0.067 Sum_probs=89.4
Q ss_pred EEEEEEcccchHH--HH-HHHHHHHHHhccC---CCCcEEEEEEECCeEEEE-EcCCCCCcceeEecCCcccchhhHHhh
Q 004238 137 FVFVLDTCMIEEE--LG-YARSELKRAIGLL---PDNAMVGLVTFGTQAHVH-ELGFSDMSKVYVFRGNKEISKDQVLEQ 209 (766)
Q Consensus 137 ~vFvID~s~~~~~--l~-~~~~~l~~~l~~l---p~~~~VglItf~~~V~~~-~l~~~~~~~~~v~~g~~~~~~~~l~~~ 209 (766)
.+|+||.|.+..+ ++ .+++.++..++.+ ++++|||+|+|++..+++ .+....
T Consensus 3 i~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~~~~~~~~~~--------------------- 61 (192)
T cd01473 3 LTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNRDVVPFSDEE--------------------- 61 (192)
T ss_pred EEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCceeEEecCccc---------------------
Confidence 5899999999743 55 4677777777766 457999999999876543 121100
Q ss_pred hccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhcc
Q 004238 210 LGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGAC 289 (766)
Q Consensus 210 l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 289 (766)
...+..+...++++.... .. ...+.+|.||..|...+..
T Consensus 62 -----------------------------------~~~~~~l~~~i~~l~~~~---~~--~g~T~~~~AL~~a~~~~~~- 100 (192)
T cd01473 62 -----------------------------------RYDKNELLKKINDLKNSY---RS--GGETYIVEALKYGLKNYTK- 100 (192)
T ss_pred -----------------------------------ccCHHHHHHHHHHHHhcc---CC--CCcCcHHHHHHHHHHHhcc-
Confidence 001122445555665321 11 2356899999999887752
Q ss_pred CCCCcc-----E-EEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecC
Q 004238 290 LPGTGA-----R-IVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASAL 363 (766)
Q Consensus 290 ~~~~gG-----r-Ii~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~ 363 (766)
..|+ | ++++|+|..+.+- + .--.+.++.+.+.||.+-.+..+.
T Consensus 101 --~~~~r~~~~kv~IllTDG~s~~~~--------------------~---------~~~~~~a~~lk~~gV~i~~vGiG~ 149 (192)
T cd01473 101 --HGNRRKDAPKVTMLFTDGNDTSAS--------------------K---------KELQDISLLYKEENVKLLVVGVGA 149 (192)
T ss_pred --CCCCcccCCeEEEEEecCCCCCcc--------------------h---------hhHHHHHHHHHHCCCEEEEEEecc
Confidence 2222 2 6788887533210 0 001245677788899888887764
Q ss_pred CccChhcchhhhhc
Q 004238 364 DQVGVAEMKVAVEK 377 (766)
Q Consensus 364 ~~~~l~~l~~l~~~ 377 (766)
.+-.++..++..
T Consensus 150 --~~~~el~~ia~~ 161 (192)
T cd01473 150 --ASENKLKLLAGC 161 (192)
T ss_pred --ccHHHHHHhcCC
Confidence 356778777764
No 52
>smart00262 GEL Gelsolin homology domain. Gelsolin/severin/villin homology domain. Calcium-binding and actin-binding. Both intra- and extracellular domains.
Probab=97.00 E-value=0.0024 Score=55.39 Aligned_cols=69 Identities=16% Similarity=0.125 Sum_probs=48.9
Q ss_pred ccccccccccCCeEEEEeCCcEEEEEECCchhHHhhcCCCCChhhhHHHHHhhCcHHHHHHHHh-cCCCCcEEEEEeCCC
Q 004238 638 PALLDVASIAADRILLLDTYFSVVIFHGMTIAQWRNMGYQNQPEHQAFAQLLRAPHDDAELIIR-DRFPVPRLVVCDQHG 716 (766)
Q Consensus 638 ~~~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~~~~~~g~~~~~~~~~~~~~l~~~~~~~~~i~~-~R~p~p~~~~~~~g~ 716 (766)
.++++.++|.++.+||||+|..||+|+|+.++ ..+-. .....++.+.+ .|.+..++++++||.
T Consensus 15 ~~~~~~~~L~s~d~fild~~~~iyvW~G~~as---------~~ek~-------~A~~~a~~~~~~~~~~~~~i~~v~eg~ 78 (90)
T smart00262 15 EVPFSQGSLNSGDCYILDTGSEIYVWVGKKSS---------QDEKK-------KAAELAVELDDTLGPGPVQVRVVDEGK 78 (90)
T ss_pred EcCCCHHHCCCCCEEEEECCCEEEEEECCCCC---------HHHHH-------HHHHHHHHHHHhcCCCCceEEEEeCCC
Confidence 35678889999999999999999999999854 11211 11234555554 355677888999998
Q ss_pred ChHHHH
Q 004238 717 SQARFL 722 (766)
Q Consensus 717 s~~r~l 722 (766)
....|+
T Consensus 79 E~~~F~ 84 (90)
T smart00262 79 EPPEFW 84 (90)
T ss_pred CCHHHH
Confidence 666555
No 53
>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=96.86 E-value=0.006 Score=59.98 Aligned_cols=45 Identities=20% Similarity=0.242 Sum_probs=35.9
Q ss_pred EEEEEEcccchH--HHHHHHHHHHHHhccCCC------CcEEEEEEECCeEEE
Q 004238 137 FVFVLDTCMIEE--ELGYARSELKRAIGLLPD------NAMVGLVTFGTQAHV 181 (766)
Q Consensus 137 ~vFvID~s~~~~--~l~~~~~~l~~~l~~lp~------~~~VglItf~~~V~~ 181 (766)
++||||+|.++. .++.++++++..++.+.+ +.+||+|+|++..+.
T Consensus 6 v~~llD~SgSM~~~~~~~~k~a~~~~~~~l~~~~~~~~~~~v~ii~F~~~a~~ 58 (176)
T cd01464 6 IYLLLDTSGSMAGEPIEALNQGLQMLQSELRQDPYALESVEISVITFDSAARV 58 (176)
T ss_pred EEEEEECCCCCCChHHHHHHHHHHHHHHHHhcChhhccccEEEEEEecCCceE
Confidence 579999999974 378888888888877753 569999999987654
No 54
>PF04056 Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like proteins are 40 kDa subunits of the transcription factor II H complex. This domain is often found associated with the C2H2 type Zn-finger (IPR007087 from INTERPRO).; GO: 0008270 zinc ion binding, 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent
Probab=96.81 E-value=0.017 Score=57.12 Aligned_cols=94 Identities=20% Similarity=0.225 Sum_probs=65.3
Q ss_pred CCcchhHHHHHHHHHhhccCCCCcc-EEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHH
Q 004238 271 PSRCTGVALSVATGLLGACLPGTGA-RIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQL 349 (766)
Q Consensus 271 ~~~~~G~AL~~A~~ll~~~~~~~gG-rIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~ 349 (766)
....+-.||+.|...|+..- ..+. .|+++.++.-|..||.+ .+..+.+
T Consensus 78 G~~SLqN~Le~A~~~L~~~p-~~~srEIlvi~gSl~t~Dp~di------------------------------~~ti~~l 126 (193)
T PF04056_consen 78 GEPSLQNGLEMARSSLKHMP-SHGSREILVIFGSLTTCDPGDI------------------------------HETIESL 126 (193)
T ss_pred CChhHHHHHHHHHHHHhhCc-cccceEEEEEEeecccCCchhH------------------------------HHHHHHH
Confidence 35689999999999998532 2333 56666677766666533 2456678
Q ss_pred HHcCcEEEEEEecCCccChhcchhhhhcccceEEEeCCCCchhhHHHHHHH
Q 004238 350 VSQGHVLDLFASALDQVGVAEMKVAVEKTGGLVVLAESFGHSVFKDSFKRI 400 (766)
Q Consensus 350 ~~~~isvdlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~ 400 (766)
.+.+|-|++...+. .+...+.+|+.|||.... ..++..|++.|...
T Consensus 127 ~~~~IrvsvI~laa---Ev~I~k~i~~~T~G~y~V--~lde~H~~~lL~~~ 172 (193)
T PF04056_consen 127 KKENIRVSVISLAA---EVYICKKICKETGGTYGV--ILDEDHFKELLMEH 172 (193)
T ss_pred HHcCCEEEEEEEhH---HHHHHHHHHHhhCCEEEE--ecCHHHHHHHHHhh
Confidence 89999999999875 567789999999994432 33445566554433
No 55
>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=96.40 E-value=0.1 Score=51.04 Aligned_cols=43 Identities=14% Similarity=0.122 Sum_probs=35.1
Q ss_pred EEEEEEEcccchH---HHHHHHHHHHHHhccCCC-CcEEEEEEECCe
Q 004238 136 VFVFVLDTCMIEE---ELGYARSELKRAIGLLPD-NAMVGLVTFGTQ 178 (766)
Q Consensus 136 ~~vFvID~s~~~~---~l~~~~~~l~~~l~~lp~-~~~VglItf~~~ 178 (766)
.++|+||+|.++. .++.+++++...++.+.+ +.++|+++|++.
T Consensus 2 ~v~~llD~SgSM~~~~kl~~ak~a~~~l~~~l~~~~d~~~l~~F~~~ 48 (174)
T cd01454 2 AVTLLLDLSGSMRSDRRIDVAKKAAVLLAEALEACGVPHAILGFTTD 48 (174)
T ss_pred EEEEEEECCCCCCCCcHHHHHHHHHHHHHHHHHHcCCcEEEEEecCC
Confidence 4789999999974 478888888877777764 789999999875
No 56
>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=96.28 E-value=0.1 Score=53.19 Aligned_cols=156 Identities=16% Similarity=0.115 Sum_probs=88.3
Q ss_pred EEEEEEEcccchH---------HHHHHHHHHHHHhccC---CCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccch
Q 004238 136 VFVFVLDTCMIEE---------ELGYARSELKRAIGLL---PDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISK 203 (766)
Q Consensus 136 ~~vFvID~s~~~~---------~l~~~~~~l~~~l~~l---p~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~ 203 (766)
..+|+||+|.++. .|+.+++.+...+... -++.+||+|.|++.-+-.. .. |
T Consensus 3 ~ivf~iDvS~SM~~~~~~~~~s~l~~a~~~i~~~~~~ki~~~~~D~vGlilf~t~~~~~~---~~------------~-- 65 (218)
T cd01458 3 SVVFLVDVSPSMFESKDGEYESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTEESKNP---VG------------Y-- 65 (218)
T ss_pred EEEEEEeCCHHHcCCCCCCCCChHHHHHHHHHHHHHhceeCCCCCeEEEEEEcccCCCCc---CC------------C--
Confidence 4699999999763 2788888888888752 3466999999986432100 00 0
Q ss_pred hhHHhhhccccCcccccCCCcccCCCCCCCCCCcccceeehhhhHHHHHHHHHhcCCCCCC--CCCCCCCCcchhHHHHH
Q 004238 204 DQVLEQLGLSASGRRAAGGYQKAAVPNAFPNSGVSRFLLPASECEYTLNSLLDELQPDQWP--VAPRTRPSRCTGVALSV 281 (766)
Q Consensus 204 ~~l~~~l~~~d~~~~~~~g~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~lL~~L~~~~~~--~~~~~~~~~~~G~AL~~ 281 (766)
+++.++.+.+ .| ..+.+..+++.+.+.... ...+......++.||.+
T Consensus 66 ---~~i~v~~~l~------------------~~----------~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~l~~aL~~ 114 (218)
T cd01458 66 ---ENIYVLLDLD------------------TP----------GAERVEDLKELIEPGGLSFAGQVGDSGQVSLSDALWV 114 (218)
T ss_pred ---CceEEeecCC------------------CC----------CHHHHHHHHHHhhcchhhhcccCCCCCCccHHHHHHH
Confidence 1111111100 00 112233343333221000 00112346789999999
Q ss_pred HHHHhhccCC-CCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHHcCcEEEEEE
Q 004238 282 ATGLLGACLP-GTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFA 360 (766)
Q Consensus 282 A~~ll~~~~~-~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~ 360 (766)
|..++..+.+ ...-+|++||+|--..|.. .....-...++.++.+.||.+.+|.
T Consensus 115 a~~~~~~~~~~~~~k~IvL~TDg~~p~~~~-------------------------~~~~~~~~~~a~~l~~~gI~i~~i~ 169 (218)
T cd01458 115 CLDLFSKGKKKKSHKRIFLFTNNDDPHGGD-------------------------SIKDSQAAVKAEDLKDKGIELELFP 169 (218)
T ss_pred HHHHHHhccccccccEEEEECCCCCCCCCC-------------------------HHHHHHHHHHHHHHHhCCcEEEEEe
Confidence 9999984212 2345799999875333210 0012224567888888999999998
Q ss_pred ecCC
Q 004238 361 SALD 364 (766)
Q Consensus 361 ~~~~ 364 (766)
.+.+
T Consensus 170 i~~~ 173 (218)
T cd01458 170 LSSP 173 (218)
T ss_pred cCCC
Confidence 7544
No 57
>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=95.85 E-value=0.28 Score=46.65 Aligned_cols=43 Identities=12% Similarity=0.088 Sum_probs=32.3
Q ss_pred EEEEEEcccchHH--HHHHHHHHHHHhccCC-CCcEEEEEEECCeE
Q 004238 137 FVFVLDTCMIEEE--LGYARSELKRAIGLLP-DNAMVGLVTFGTQA 179 (766)
Q Consensus 137 ~vFvID~s~~~~~--l~~~~~~l~~~l~~lp-~~~~VglItf~~~V 179 (766)
++|+||+|.++.. ++..+..+...+..+. ++.+|++|+|++..
T Consensus 3 v~illD~SgSM~~~k~~~a~~~~~~l~~~~~~~~~~v~li~F~~~~ 48 (152)
T cd01462 3 VILLVDQSGSMYGAPEEVAKAVALALLRIALAENRDTYLILFDSEF 48 (152)
T ss_pred EEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHcCCcEEEEEeCCCc
Confidence 6899999999864 5556666666666554 46799999999873
No 58
>KOG2884 consensus 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=94.65 E-value=1.7 Score=43.18 Aligned_cols=84 Identities=20% Similarity=0.201 Sum_probs=58.4
Q ss_pred cchhHHHHHHHHHhhccCCCCc--cEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHH
Q 004238 273 RCTGVALSVATGLLGACLPGTG--ARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLV 350 (766)
Q Consensus 273 ~~~G~AL~~A~~ll~~~~~~~g--GrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~ 350 (766)
--++.+|++|...|+.- .+.+ -||++|.++|... ..+-.-++|+++.
T Consensus 85 ~~~~~~i~iA~lalkhR-qnk~~~~riVvFvGSpi~e------------------------------~ekeLv~~akrlk 133 (259)
T KOG2884|consen 85 ANFMTGIQIAQLALKHR-QNKNQKQRIVVFVGSPIEE------------------------------SEKELVKLAKRLK 133 (259)
T ss_pred ccHHHHHHHHHHHHHhh-cCCCcceEEEEEecCcchh------------------------------hHHHHHHHHHHHH
Confidence 46889999999999842 1333 7999999987321 1112456899999
Q ss_pred HcCcEEEEEEecCCccChhcchhhhhcccce-----EEEeCC
Q 004238 351 SQGHVLDLFASALDQVGVAEMKVAVEKTGGL-----VVLAES 387 (766)
Q Consensus 351 ~~~isvdlf~~~~~~~~l~~l~~l~~~TGG~-----v~~~~~ 387 (766)
+++|.||++.++-...+-.-+......++|. +...++
T Consensus 134 k~~Vaidii~FGE~~~~~e~l~~fida~N~~~~gshlv~Vpp 175 (259)
T KOG2884|consen 134 KNKVAIDIINFGEAENNTEKLFEFIDALNGKGDGSHLVSVPP 175 (259)
T ss_pred hcCeeEEEEEeccccccHHHHHHHHHHhcCCCCCceEEEeCC
Confidence 9999999999987665544455555555554 555544
No 59
>KOG0443 consensus Actin regulatory proteins (gelsolin/villin family) [Cytoskeleton]
Probab=94.18 E-value=0.064 Score=62.31 Aligned_cols=86 Identities=21% Similarity=0.241 Sum_probs=53.2
Q ss_pred HhhcccceeeccC-CC---CcccccccccccCCeEEEEeCCcEEEEEECCchhHHhhcCCCCChhhhHHHHHhhCcHHHH
Q 004238 621 VMIQPSLISYSFN-SL---PQPALLDVASIAADRILLLDTYFSVVIFHGMTIAQWRNMGYQNQPEHQAFAQLLRAPHDDA 696 (766)
Q Consensus 621 ~~iyP~L~~~~~~-~~---p~~~~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~~~~~~g~~~~~~~~~~~~~l~~~~~~~ 696 (766)
.-..|+||..+.. +. -+-...+.+-|..+-|||||++..||||+|++++. .+.. ..|.......
T Consensus 616 ~~~~PrLF~Cs~~~g~f~~~EI~~F~QdDL~tdDi~lLDt~~evfvWvG~~a~~--------~eK~----~Al~~~~~yl 683 (827)
T KOG0443|consen 616 PERDPRLFSCSNKTGSFVVEEIYNFTQDDLMTDDIMLLDTWSEVFVWVGQEANE--------KEKE----EALTIGQKYL 683 (827)
T ss_pred CCCCCcEEEEEecCCcEEEEEecCcchhhccccceEEEecCceEEEEecCCCCh--------hHHH----HHHHHHHHHH
Confidence 4567888887743 21 12235667888999999999999999999998651 1111 1222111111
Q ss_pred HH-HHhcCCCCcEEEEEeCCCCh
Q 004238 697 EL-IIRDRFPVPRLVVCDQHGSQ 718 (766)
Q Consensus 697 ~~-i~~~R~p~p~~~~~~~g~s~ 718 (766)
+. +...|-|.-.+++++||+..
T Consensus 684 ~~~~p~gr~~~TPI~vV~qG~EP 706 (827)
T KOG0443|consen 684 ETDLPEGRDPRTPIYVVKQGHEP 706 (827)
T ss_pred hccCcccCCCCCceEEecCCCCC
Confidence 11 23567775556778888655
No 60
>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=94.17 E-value=2.6 Score=44.19 Aligned_cols=46 Identities=20% Similarity=0.316 Sum_probs=36.1
Q ss_pred CCcEEEEEEEcccchHH-------HHHHHHHHHHHhccCCCCcEEEEEEECCeEE
Q 004238 133 LSPVFVFVLDTCMIEEE-------LGYARSELKRAIGLLPDNAMVGLVTFGTQAH 180 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~~-------l~~~~~~l~~~l~~lp~~~~VglItf~~~V~ 180 (766)
....++++||.|.++.+ ++ .+..|..+++.++. .+||++.|+..+.
T Consensus 59 r~~qIvlaID~S~SM~~~~~~~~ale-ak~lIs~al~~Le~-g~vgVv~Fg~~~~ 111 (266)
T cd01460 59 RDYQILIAIDDSKSMSENNSKKLALE-SLCLVSKALTLLEV-GQLGVCSFGEDVQ 111 (266)
T ss_pred cCceEEEEEecchhcccccccccHHH-HHHHHHHHHHhCcC-CcEEEEEeCCCce
Confidence 57789999999999854 55 45577777777774 5899999998654
No 61
>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]
Probab=93.31 E-value=0.14 Score=58.17 Aligned_cols=90 Identities=24% Similarity=0.255 Sum_probs=66.1
Q ss_pred cceeeccCC---CCcccccccccccCCeEEEEeCCcEEEEEECCchhHHhhcCCCCChhhhHHHHHhhCcHHHHHHHH-h
Q 004238 626 SLISYSFNS---LPQPALLDVASIAADRILLLDTYFSVVIFHGMTIAQWRNMGYQNQPEHQAFAQLLRAPHDDAELII-R 701 (766)
Q Consensus 626 ~L~~~~~~~---~p~~~~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~~~~~~g~~~~~~~~~~~~~l~~~~~~~~~i~-~ 701 (766)
|||.++..+ .-+||+|+..|+++.-++|||.|..||||.|...- . ... ...+-+|+.|. .
T Consensus 623 RlYrv~~~g~~i~lEPVpl~~tSLDPRf~FlLD~G~~IyiW~G~~s~------~----t~~------~KARLfAEkinK~ 686 (1255)
T KOG0444|consen 623 RLYRVGVNGTAIELEPVPLSVTSLDPRFCFLLDAGETIYIWSGYKSR------I----TVS------NKARLFAEKINKR 686 (1255)
T ss_pred hhheeccccceeEeeccCccccccCcceEEEEeCCceEEEEeccchh------c----ccc------hHHHHHHHHhhhh
Confidence 556666544 35799999999999999999999999999987521 0 000 11233566665 4
Q ss_pred cCCCCcEEEEEeCCCChHHHHHHh-hcCCCC
Q 004238 702 DRFPVPRLVVCDQHGSQARFLLAK-LNPSAT 731 (766)
Q Consensus 702 ~R~p~p~~~~~~~g~s~~r~l~s~-L~p~~~ 731 (766)
+|--.-.+-.++||.-...||-+- .+|+..
T Consensus 687 eRKgK~EI~l~rQg~e~pEFWqaLgg~p~e~ 717 (1255)
T KOG0444|consen 687 ERKGKSEIELCRQGREPPEFWQALGGNPDEP 717 (1255)
T ss_pred hccCceeeehhhhcCCCHHHHHHhCCCCccc
Confidence 688888999999999889999765 666663
No 62
>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=92.99 E-value=4.9 Score=47.32 Aligned_cols=73 Identities=18% Similarity=0.149 Sum_probs=43.8
Q ss_pred CcchhHHHHHHHHHhhccCCCCcc-EEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHH
Q 004238 272 SRCTGVALSVATGLLGACLPGTGA-RIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLV 350 (766)
Q Consensus 272 ~~~~G~AL~~A~~ll~~~~~~~gG-rIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~ 350 (766)
...+..||.+|..++..+.++.+. ||++||+--.-.|. + + . ...-=...+..+.
T Consensus 116 ~~~l~daL~~~~~~f~~~~~k~~~kRI~lfTd~D~P~~~----------------~--~---~----~~~~a~~~a~dl~ 170 (584)
T TIGR00578 116 DYSLSEVLWVCANLFSDVQFRMSHKRIMLFTNEDNPHGN----------------D--S---A----KASRARTKAGDLR 170 (584)
T ss_pred CCcHHHHHHHHHHHHHhcchhhcCcEEEEECCCCCCCCC----------------c--h---h----HHHHHHHHHHHHH
Confidence 347899999999999854444444 69999964221110 0 0 0 0000122477888
Q ss_pred HcCcEEEEEEec-CCccChh
Q 004238 351 SQGHVLDLFASA-LDQVGVA 369 (766)
Q Consensus 351 ~~~isvdlf~~~-~~~~~l~ 369 (766)
..||.+++|..+ .+.+|..
T Consensus 171 ~~gi~ielf~l~~~~~Fd~s 190 (584)
T TIGR00578 171 DTGIFLDLMHLKKPGGFDIS 190 (584)
T ss_pred hcCeEEEEEecCCCCCCChh
Confidence 899999999654 2334444
No 63
>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=92.45 E-value=21 Score=39.75 Aligned_cols=280 Identities=12% Similarity=0.088 Sum_probs=139.8
Q ss_pred CcEEEEEEEcccchHH----HHHHHHHHHHHhccCCCCcEEEEEEECCe-EEEEEcCCCCCcceeEecCCcccchhhHHh
Q 004238 134 SPVFVFVLDTCMIEEE----LGYARSELKRAIGLLPDNAMVGLVTFGTQ-AHVHELGFSDMSKVYVFRGNKEISKDQVLE 208 (766)
Q Consensus 134 ~p~~vFvID~s~~~~~----l~~~~~~l~~~l~~lp~~~~VglItf~~~-V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~ 208 (766)
|-=..|+.|+|.++.+ ++.+...|...|..+..+.|+||=+|=+. |.=|- . .. .+++..
T Consensus 99 PvDLYyLMDlS~SM~ddl~~lk~lg~~L~~~m~~it~n~rlGfGsFVDK~v~P~~-~-t~--------------p~~l~~ 162 (423)
T smart00187 99 PVDLYYLMDLSYSMKDDLDNLKSLGDDLAREMKGLTSNFRLGFGSFVDKTVSPFV-S-TR--------------PEKLEN 162 (423)
T ss_pred ccceEEEEeCCccHHHHHHHHHHHHHHHHHHHHhcccCceeeEEEeecCccCCcc-c-CC--------------HHHhcC
Confidence 4456799999999865 66677777778888888999999988543 32221 1 00 011100
Q ss_pred hhccccCcccccCCCcccCCCCCCCCCC-c-ccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHh
Q 004238 209 QLGLSASGRRAAGGYQKAAVPNAFPNSG-V-SRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLL 286 (766)
Q Consensus 209 ~l~~~d~~~~~~~g~~~~~~~~~~~~~p-~-~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll 286 (766)
.. .. .. ..-.| . =+-.+++.+.-....+.+.+..-. .+...|+-.+-+-+++|+--=
T Consensus 163 PC--~~--~~-------------~~c~p~f~f~~~L~LT~~~~~F~~~V~~~~iS----gN~D~PEgG~DAimQaaVC~~ 221 (423)
T smart00187 163 PC--PN--YN-------------LTCEPPYGFKHVLSLTDDTDEFNEEVKKQRIS----GNLDAPEGGFDAIMQAAVCTE 221 (423)
T ss_pred CC--cC--CC-------------CCcCCCcceeeeccCCCCHHHHHHHHhhceee----cCCcCCcccHHHHHHHHhhcc
Confidence 00 00 00 00111 0 011234454433344445443321 122345666666667774321
Q ss_pred hccCCCCccEEEEEeCCCCC--CCCcccccCCCCCCccCCCCCCcCcCccchh---HHHHHHHHHHHHHHcCcEEEEEEe
Q 004238 287 GACLPGTGARIVALVGGPCT--EGPGTIVSKDLSEPVRSHKDLDKDAAPFFKK---AVKFYDGLAKQLVSQGHVLDLFAS 361 (766)
Q Consensus 287 ~~~~~~~gGrIi~f~sg~pt--~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~---a~~fY~~la~~~~~~~isvdlf~~ 361 (766)
+...+...-|+++|++-.+. -|-|+|...-.++-.+.|-+-.. .|... ...--.+|++++.+++|.+ ||+.
T Consensus 222 ~IGWR~~a~rllv~~TDa~fH~AGDGkLaGIv~PNDg~CHL~~~g---~Yt~s~~~DYPSi~ql~~kL~e~nI~~-IFAV 297 (423)
T smart00187 222 QIGWREDARRLLVFSTDAGFHFAGDGKLAGIVQPNDGQCHLDNNG---EYTMSTTQDYPSIGQLNQKLAENNINP-IFAV 297 (423)
T ss_pred ccccCCCceEEEEEEcCCCccccCCcceeeEecCCCCcceeCCCC---CcCccCcCCCCCHHHHHHHHHhcCceE-EEEE
Confidence 11123445689999866554 57777655533343444533110 11111 1112356778888888865 7887
Q ss_pred cCCccChhcchhhhhcccceEEEeCCCCchhhHHHHHHHHhhccccccceeeeEEEEEe-cCCceEEEEEcCcccccccc
Q 004238 362 ALDQVGVAEMKVAVEKTGGLVVLAESFGHSVFKDSFKRIFEDGEQSLGLCFNGALEIIC-SKDIKIQGIIGPCTSLEKVR 440 (766)
Q Consensus 362 ~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l~~~~~~~~~~~~a~l~vr~-S~gl~v~~~~G~~~~~~~~~ 440 (766)
+..+.+++ ..|+++-.|...=-=+=+.+...+-+..... +.....+|+... +.+++++-.- .|....
T Consensus 298 T~~~~~~Y--~~Ls~lipgs~vg~Ls~DSsNIv~LI~~aY~------~i~S~V~l~~~~~p~~v~~~y~s-~C~~g~--- 365 (423)
T smart00187 298 TKKQVSLY--KELSALIPGSSVGVLSEDSSNVVELIKDAYN------KISSRVELEDNSLPEGVSVTYTS-SCPGGV--- 365 (423)
T ss_pred cccchhHH--HHHHHhcCcceeeecccCcchHHHHHHHHHH------hhceEEEEecCCCCCcEEEEEEe-eCCCCC---
Confidence 77777664 4455444444331111112222222222222 234555665553 6777776333 332211
Q ss_pred cCCCccceeeecCCCCceEEEEEEecCC
Q 004238 441 LRGEYYAWKMCGLDKSTCLTVFFDLSSS 468 (766)
Q Consensus 441 g~~~~~~~~l~~~~~~~s~~~~f~~~~~ 468 (766)
.....-+..++.....+.|..+++..
T Consensus 366 --~~~~~~~C~~v~iG~~V~F~v~vta~ 391 (423)
T smart00187 366 --VGPGTRKCEGVKIGDTVSFEVTVTAT 391 (423)
T ss_pred --cccCCcccCCcccCCEEEEEEEEEeC
Confidence 11111145567777788888777743
No 64
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=91.71 E-value=0.26 Score=47.77 Aligned_cols=47 Identities=28% Similarity=0.328 Sum_probs=37.6
Q ss_pred cEEEEEEEcccchHH--HHHHHHHHHHHhccCCC------CcEEEEEEECCeEEEE
Q 004238 135 PVFVFVLDTCMIEEE--LGYARSELKRAIGLLPD------NAMVGLVTFGTQAHVH 182 (766)
Q Consensus 135 p~~vFvID~s~~~~~--l~~~~~~l~~~l~~lp~------~~~VglItf~~~V~~~ 182 (766)
|+ ++++|+|.++.- .+++..+|+..++.|.. .+.++|||||+.+++|
T Consensus 5 P~-~lllDtSgSM~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~~a~~~ 59 (207)
T COG4245 5 PC-YLLLDTSGSMIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGPARVI 59 (207)
T ss_pred CE-EEEEecCcccccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecCcceEE
Confidence 44 589999999854 78888888888877753 4799999999877776
No 65
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=91.28 E-value=6.3 Score=38.23 Aligned_cols=59 Identities=31% Similarity=0.298 Sum_probs=42.9
Q ss_pred cchhHHHHHHHHHhhccCCCCc--cEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHH
Q 004238 273 RCTGVALSVATGLLGACLPGTG--ARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLV 350 (766)
Q Consensus 273 ~~~G~AL~~A~~ll~~~~~~~g--GrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~ 350 (766)
--.+-+|+.|..+++. ..+.| -||++|.++|... + .+-.-.+++++.
T Consensus 85 a~~~~~lqiaql~lkh-R~nk~q~qriVaFvgSpi~e---------------------s---------edeLirlak~lk 133 (243)
T COG5148 85 ADIMRCLQIAQLILKH-RDNKGQRQRIVAFVGSPIQE---------------------S---------EDELIRLAKQLK 133 (243)
T ss_pred chHHHHHHHHHHHHhc-ccCCccceEEEEEecCcccc---------------------c---------HHHHHHHHHHHH
Confidence 3578899999999984 22344 7999999987321 0 111235789999
Q ss_pred HcCcEEEEEEec
Q 004238 351 SQGHVLDLFASA 362 (766)
Q Consensus 351 ~~~isvdlf~~~ 362 (766)
+++|+||++-++
T Consensus 134 knnVAidii~fG 145 (243)
T COG5148 134 KNNVAIDIIFFG 145 (243)
T ss_pred hcCeeEEEEehh
Confidence 999999999876
No 66
>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=90.54 E-value=35 Score=38.54 Aligned_cols=281 Identities=11% Similarity=0.094 Sum_probs=130.7
Q ss_pred CCcEEEEEEEcccchHH----HHHHHHHHHHHhccCCCCcEEEEEEECCeEEEEEcCCCCCcceeEecCCcccchhhHHh
Q 004238 133 LSPVFVFVLDTCMIEEE----LGYARSELKRAIGLLPDNAMVGLVTFGTQAHVHELGFSDMSKVYVFRGNKEISKDQVLE 208 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~~----l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~~~l~~~~~~~~~v~~g~~~~~~~~l~~ 208 (766)
.|-=..|++|+|.++.. ++.+-..|...|..+..+.|+||=+|=+..-. .+.... .+.+..
T Consensus 101 yPvDLYyLmDlS~Sm~ddl~~l~~lg~~l~~~~~~it~~~~~GfGsfvdK~~~-P~~~~~--------------p~~l~~ 165 (426)
T PF00362_consen 101 YPVDLYYLMDLSYSMKDDLENLKSLGQDLAEEMRNITSNFRLGFGSFVDKPVM-PFVSTT--------------PEKLKN 165 (426)
T ss_dssp --EEEEEEEE-SGGGHHHHHHHCCCCHHHHHHHHTT-SSEEEEEEEESSSSST-TTST-S--------------SHCHHS
T ss_pred cceeEEEEeechhhhhhhHHHHHHHHHHHHHHHHhcCccceEechhhcccccC-CcccCC--------------hhhhcC
Confidence 34557899999999865 55566778888889999999999988543211 011000 011111
Q ss_pred hhccccCcccccCCCcccCCCCCCCCCC-c-ccceeehhhhHHHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHh
Q 004238 209 QLGLSASGRRAAGGYQKAAVPNAFPNSG-V-SRFLLPASECEYTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLL 286 (766)
Q Consensus 209 ~l~~~d~~~~~~~g~~~~~~~~~~~~~p-~-~~~l~~~~e~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll 286 (766)
.. .... ..-.| . =+-.+++.+........+.+..- . .+-..|+..+=+-+++|+--=
T Consensus 166 pc--~~~~---------------~~c~~~~~f~~~l~Lt~~~~~F~~~v~~~~i-s---~n~D~PEgg~dal~Qa~vC~~ 224 (426)
T PF00362_consen 166 PC--PSKN---------------PNCQPPFSFRHVLSLTDDITEFNEEVNKQKI-S---GNLDAPEGGLDALMQAAVCQE 224 (426)
T ss_dssp TS--CCTT---------------S--B---SEEEEEEEES-HHHHHHHHHTS---B-----SSSSBSHHHHHHHHHH-HH
T ss_pred cc--cccC---------------CCCCCCeeeEEeecccchHHHHHHhhhhccc-c---CCCCCCccccchheeeeeccc
Confidence 11 0000 01111 1 12234566554445555554321 1 122346666667777765422
Q ss_pred hccCCCCccEEEEEeCCC--CCCCCcccccCCCCCCccCCCCCCcCcCccc---hhHHHHHHHHHHHHHHcCcEEEEEEe
Q 004238 287 GACLPGTGARIVALVGGP--CTEGPGTIVSKDLSEPVRSHKDLDKDAAPFF---KKAVKFYDGLAKQLVSQGHVLDLFAS 361 (766)
Q Consensus 287 ~~~~~~~gGrIi~f~sg~--pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~---~~a~~fY~~la~~~~~~~isvdlf~~ 361 (766)
....+...-|+++|++-. -.-|-|++...-.++-.+.|-+-.. .|. .....-..+|.+.+.+++|.+ ||+.
T Consensus 225 ~igWr~~a~~llv~~TD~~fH~agDg~l~gi~~pnd~~Chl~~~~---~y~~~~~~DYPSv~ql~~~l~e~~i~~-IFAV 300 (426)
T PF00362_consen 225 EIGWRNEARRLLVFSTDAGFHFAGDGKLAGIVKPNDGKCHLDDNG---MYTASTEQDYPSVGQLVRKLSENNINP-IFAV 300 (426)
T ss_dssp HHT--STSEEEEEEEESS-B--TTGGGGGT--S---SS--BSTTS---BBGGGGCS----HHHHHHHHHHTTEEE-EEEE
T ss_pred ccCcccCceEEEEEEcCCccccccccccceeeecCCCceEECCCC---cccccccccCCCHHHHHHHHHHcCCEE-EEEE
Confidence 211335567898888554 3478888877655555556643221 221 223445667778888877765 7777
Q ss_pred cCCccChhcchhhhhcc-cceEEEeCCCCchhhHHHHHHHHhhccccccceeeeEEEEEe-cCCceEEEEEcCccccccc
Q 004238 362 ALDQVGVAEMKVAVEKT-GGLVVLAESFGHSVFKDSFKRIFEDGEQSLGLCFNGALEIIC-SKDIKIQGIIGPCTSLEKV 439 (766)
Q Consensus 362 ~~~~~~l~~l~~l~~~T-GG~v~~~~~f~~~~~~~~l~~~l~~~~~~~~~~~~a~l~vr~-S~gl~v~~~~G~~~~~~~~ 439 (766)
.....+++ ..|+..- |+.+-.... +.+...+-+.....+ ......++... ++++++ .+..+|.....
T Consensus 301 t~~~~~~Y--~~L~~~i~~s~vg~L~~-dSsNIv~LI~~aY~~------i~s~V~L~~~~~p~~v~v-~y~s~C~~~~~- 369 (426)
T PF00362_consen 301 TKDVYSIY--EELSNLIPGSSVGELSS-DSSNIVQLIKEAYNK------ISSKVELKHDNAPDGVKV-SYTSNCPNGST- 369 (426)
T ss_dssp EGGGHHHH--HHHHHHSTTEEEEEEST-TSHTHHHHHHHHHHH------HCTEEEEEECS--TTEEE-EEEEEESSSEE-
T ss_pred chhhhhHH--HHHhhcCCCceeccccc-CchhHHHHHHHHHHH------HhheEEEEecCCCCcEEE-EEEEEccCCcc-
Confidence 77666544 3444433 344434333 223333333332222 33445555333 456666 44445543110
Q ss_pred ccCCCccceeeecCCCCceEEEEEEecCC
Q 004238 440 RLRGEYYAWKMCGLDKSTCLTVFFDLSSS 468 (766)
Q Consensus 440 ~g~~~~~~~~l~~~~~~~s~~~~f~~~~~ 468 (766)
....-...++....++.|.+.++-.
T Consensus 370 ----~~~~~~C~~V~iG~~V~F~VtVta~ 394 (426)
T PF00362_consen 370 ----VPGTNECSNVKIGDTVTFNVTVTAK 394 (426)
T ss_dssp ----EECCEEECSE-TT-EEEEEEEEEES
T ss_pred ----cCcCccccCEecCCEEEEEEEEEEe
Confidence 1112345556677777777766654
No 67
>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=89.77 E-value=3.4 Score=41.29 Aligned_cols=43 Identities=9% Similarity=0.088 Sum_probs=30.7
Q ss_pred EEEEEEEcccchH---------HHHHHHHHHHHHhccCC--CCcEEEEEEECCe
Q 004238 136 VFVFVLDTCMIEE---------ELGYARSELKRAIGLLP--DNAMVGLVTFGTQ 178 (766)
Q Consensus 136 ~~vFvID~s~~~~---------~l~~~~~~l~~~l~~lp--~~~~VglItf~~~ 178 (766)
-++|+||.|.++. .++.+++++...+..++ +...+++++|++.
T Consensus 4 dvv~~ID~SgSM~~~~~~~~~~k~~~ak~~~~~l~~~~~~~D~d~i~l~~f~~~ 57 (199)
T cd01457 4 DYTLLIDKSGSMAEADEAKERSRWEEAQESTRALARKCEEYDSDGITVYLFSGD 57 (199)
T ss_pred CEEEEEECCCcCCCCCCCCCchHHHHHHHHHHHHHHHHHhcCCCCeEEEEecCC
Confidence 4789999999984 36777777777666543 2346888877544
No 68
>KOG0443 consensus Actin regulatory proteins (gelsolin/villin family) [Cytoskeleton]
Probab=85.98 E-value=1.4 Score=51.69 Aligned_cols=93 Identities=16% Similarity=0.172 Sum_probs=60.5
Q ss_pred cccceeecc--CCC--C--cccccccccccCCeEEEEeCC-cEEEEEECCchhHHhhcCCCCChhhhHHHHHhhCcHHHH
Q 004238 624 QPSLISYSF--NSL--P--QPALLDVASIAADRILLLDTY-FSVVIFHGMTIAQWRNMGYQNQPEHQAFAQLLRAPHDDA 696 (766)
Q Consensus 624 yP~L~~~~~--~~~--p--~~~~Ls~~~l~~~~i~llD~g-~~i~i~~G~~v~~~~~~g~~~~~~~~~~~~~l~~~~~~~ 696 (766)
.++||.++. .++ + ..-+|+-+-|+.+.+|+||+| ..||||.|+.+. ..|. +. ....|
T Consensus 254 ~~kLYkVsd~~g~l~v~~va~~~l~qdlLd~~dCYILD~g~~~IfVW~Gr~as---------~~ER---ka----Am~~A 317 (827)
T KOG0443|consen 254 AAKLYKVSDASGGLKVPVVADGPLTKDLLDTEDCYILDCGGGEIFVWKGRQAS---------LDER---KA----AMSSA 317 (827)
T ss_pred ccEEEEEeccCCCccccccccchhhHHhhccCCeEEEecCCceEEEEeCCCCC---------HHHH---HH----HHHHH
Confidence 468888873 111 1 111277788899999999999 999999999854 2231 12 22345
Q ss_pred HHHHh--cCCCCcEEEEEeCCCChH---HHHHHhhcCCCCc
Q 004238 697 ELIIR--DRFPVPRLVVCDQHGSQA---RFLLAKLNPSATY 732 (766)
Q Consensus 697 ~~i~~--~R~p~p~~~~~~~g~s~~---r~l~s~L~p~~~~ 732 (766)
++.++ .|.+.-.+.++.+|...+ ++|.+=..++++.
T Consensus 318 eeFlk~k~yP~~TqV~rv~EG~Esa~FKq~F~~W~~~~~t~ 358 (827)
T KOG0443|consen 318 EEFLKKKKYPPNTQVVRVLEGAESAPFKQLFDSWPDKDQTN 358 (827)
T ss_pred HHHHHhccCCCCceEEEecCCCcchhHHHHHhhCccccccc
Confidence 55553 466678888888886665 4455556666653
No 69
>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=81.89 E-value=1.4 Score=29.83 Aligned_cols=30 Identities=23% Similarity=0.388 Sum_probs=23.5
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCCCCCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCYQRNHF 90 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~ 90 (766)
+.|..|++.|- .-.+..+++|..|...|.+
T Consensus 2 ~~C~~C~t~L~----yP~gA~~vrCs~C~~vt~v 31 (31)
T TIGR01053 2 VVCGGCRTLLM----YPRGASSVRCALCQTVNLV 31 (31)
T ss_pred cCcCCCCcEee----cCCCCCeEECCCCCeEecC
Confidence 57999998764 3367789999999988753
No 70
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=81.89 E-value=31 Score=36.56 Aligned_cols=76 Identities=18% Similarity=0.161 Sum_probs=51.8
Q ss_pred CcchhHHHHHHHHHhhccCCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHHHHHHHH
Q 004238 272 SRCTGVALSVATGLLGACLPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGLAKQLVS 351 (766)
Q Consensus 272 ~~~~G~AL~~A~~ll~~~~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~la~~~~~ 351 (766)
...+-.||+.|...|+..-.+..--|++..++..|.-||.+-. . -+.+.+
T Consensus 142 ~fSLqNaLe~a~~~Lk~~p~H~sREVLii~sslsT~DPgdi~~-----------------------------t-I~~lk~ 191 (378)
T KOG2807|consen 142 DFSLQNALELAREVLKHMPGHVSREVLIIFSSLSTCDPGDIYE-----------------------------T-IDKLKA 191 (378)
T ss_pred ChHHHHHHHHHHHHhcCCCcccceEEEEEEeeecccCcccHHH-----------------------------H-HHHHHh
Confidence 3578889999999998311111124566667778887765532 2 234667
Q ss_pred cCcEEEEEEecCCccChhcchhhhhcccc
Q 004238 352 QGHVLDLFASALDQVGVAEMKVAVEKTGG 380 (766)
Q Consensus 352 ~~isvdlf~~~~~~~~l~~l~~l~~~TGG 380 (766)
..|-|.++..+. .+..-+.||+.|||
T Consensus 192 ~kIRvsvIgLsa---Ev~icK~l~kaT~G 217 (378)
T KOG2807|consen 192 YKIRVSVIGLSA---EVFICKELCKATGG 217 (378)
T ss_pred hCeEEEEEeech---hHHHHHHHHHhhCC
Confidence 788899887764 45566899999999
No 71
>PF03850 Tfb4: Transcription factor Tfb4; InterPro: IPR004600 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p34 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0000439 core TFIIH complex
Probab=81.51 E-value=74 Score=33.65 Aligned_cols=85 Identities=16% Similarity=0.132 Sum_probs=55.8
Q ss_pred cchhHHHHHHHHHhhccC-------CCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHH
Q 004238 273 RCTGVALSVATGLLGACL-------PGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGL 345 (766)
Q Consensus 273 ~~~G~AL~~A~~ll~~~~-------~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~l 345 (766)
..+..||..|+-.+.-.. ....+||+++.++-+.. ..+|. =+-+.
T Consensus 116 s~LagALS~ALCyINR~~~~~~~~~~~~~~RILv~~s~s~d~-----------------------~~QYi-----~~MN~ 167 (276)
T PF03850_consen 116 SLLAGALSMALCYINRISRESPSGGTSLKSRILVIVSGSPDS-----------------------SSQYI-----PLMNC 167 (276)
T ss_pred hhhHHHHHHHHHHHhhhhhcccCCCCCcCccEEEEEecCCCc-----------------------cHHHH-----HHHHH
Confidence 677888888887776221 13457999964332110 01111 12344
Q ss_pred HHHHHHcCcEEEEEEecCCccChhcchhhhhcccceEEEeCC
Q 004238 346 AKQLVSQGHVLDLFASALDQVGVAEMKVAVEKTGGLVVLAES 387 (766)
Q Consensus 346 a~~~~~~~isvdlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~ 387 (766)
...|.+.+|.||++..+. -+-.-|.+.+..|||.-...+.
T Consensus 168 iFaAqk~~v~IDv~~L~~--~~s~fLqQa~d~T~G~y~~~~~ 207 (276)
T PF03850_consen 168 IFAAQKQKVPIDVCKLGG--KDSTFLQQASDITGGIYLKVSK 207 (276)
T ss_pred HHHHhcCCceeEEEEecC--CchHHHHHHHHHhCceeeccCc
Confidence 667788999999999876 4556789999999997776665
No 72
>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=79.91 E-value=1.2 Score=34.59 Aligned_cols=33 Identities=24% Similarity=0.592 Sum_probs=24.7
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRN 88 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N 88 (766)
++-|++|+.--.-+-+-+...-+|+|+.|+..|
T Consensus 22 aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 22 ALICSKCFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred eEECcccchhhcccccccCCceEEEcCCCCCcC
Confidence 456999998754443555556799999999877
No 73
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.56 E-value=1.4 Score=32.89 Aligned_cols=30 Identities=23% Similarity=0.527 Sum_probs=21.1
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRNH 89 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~ 89 (766)
..+|.+|++-+- ++.....++|+.||..-.
T Consensus 3 ~y~C~~CG~~~~----~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVE----LDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEE----ECCCCCceECCCCCCeEE
Confidence 368999999542 333334799999997643
No 74
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=75.40 E-value=6.1 Score=36.49 Aligned_cols=42 Identities=24% Similarity=0.219 Sum_probs=34.0
Q ss_pred EEEEEcccchH--HHHHHHHHHHHHhccCCCCcEEEEEEECCeEEE
Q 004238 138 VFVLDTCMIEE--ELGYARSELKRAIGLLPDNAMVGLVTFGTQAHV 181 (766)
Q Consensus 138 vFvID~s~~~~--~l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~ 181 (766)
+++||+|.+.. +|..+...+...+... +.+|-+|.||..|+-
T Consensus 2 ~vaiDtSGSis~~~l~~fl~ev~~i~~~~--~~~v~vi~~D~~v~~ 45 (126)
T PF09967_consen 2 VVAIDTSGSISDEELRRFLSEVAGILRRF--PAEVHVIQFDAEVQD 45 (126)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHHhC--CCCEEEEEECCEeee
Confidence 68999999974 4888888888887777 456899999998875
No 75
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=68.05 E-value=57 Score=34.53 Aligned_cols=85 Identities=19% Similarity=0.124 Sum_probs=56.1
Q ss_pred CcchhHHHHHHHHHhhcc------CCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCCCcCcCccchhHHHHHHHH
Q 004238 272 SRCTGVALSVATGLLGAC------LPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDLDKDAAPFFKKAVKFYDGL 345 (766)
Q Consensus 272 ~~~~G~AL~~A~~ll~~~------~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~~~~~~~~~~~a~~fY~~l 345 (766)
...+..||..|+-.+.-. .....+||+++..++ +. ..+..=+-+.
T Consensus 118 ~s~lagals~ALcyinr~~~~~~~~~~~~~RIlii~~s~-----------~~------------------~~qYi~~mn~ 168 (279)
T TIGR00627 118 RTVLAGALSDALGYINRSEQSETASEKLKSRILVISITP-----------DM------------------ALQYIPLMNC 168 (279)
T ss_pred cccchhHHHhhhhhhcccccccccCcCCcceEEEEECCC-----------Cc------------------hHHHHHHHHH
Confidence 456777888888877421 113468999998752 00 0011112356
Q ss_pred HHHHHHcCcEEEEEEecCCccChhcchhhhhcccceEEEeC
Q 004238 346 AKQLVSQGHVLDLFASALDQVGVAEMKVAVEKTGGLVVLAE 386 (766)
Q Consensus 346 a~~~~~~~isvdlf~~~~~~~~l~~l~~l~~~TGG~v~~~~ 386 (766)
...|.+.+|.||++..+.+ -+..-++.+++.|||......
T Consensus 169 Ifaaqk~~I~Idv~~L~~e-~~~~~lqQa~~~TgG~Y~~~~ 208 (279)
T TIGR00627 169 IFSAQKQNIPIDVVSIGGD-FTSGFLQQAADITGGSYLHVK 208 (279)
T ss_pred HHHHHHcCceEEEEEeCCc-cccHHHHHHHHHhCCEEeccC
Confidence 7788899999999988643 356789999999999544443
No 76
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=65.81 E-value=4 Score=31.01 Aligned_cols=32 Identities=16% Similarity=0.320 Sum_probs=22.0
Q ss_pred ccCCCCceecCceeEEcCCceEEecCCCCCCCCC
Q 004238 58 RCKTCTAALNAFARVDFTAKIWICPFCYQRNHFP 91 (766)
Q Consensus 58 RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~p 91 (766)
.|..|+..+-+- -..++..|.|+-||..-.+.
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCCeEECC
Confidence 599999977333 12223599999999876553
No 77
>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=63.14 E-value=4.4 Score=27.88 Aligned_cols=24 Identities=25% Similarity=0.764 Sum_probs=16.3
Q ss_pred ccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 58 RCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 58 RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
+|..|+=...+-. .-|.|+.|+..
T Consensus 3 ~C~~CGy~y~~~~------~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGEE------APWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCCc------CCCcCcCCCCc
Confidence 5778875444432 57899999873
No 78
>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=61.09 E-value=11 Score=27.49 Aligned_cols=27 Identities=22% Similarity=0.461 Sum_probs=21.3
Q ss_pred ccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 58 RCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 58 RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
+|.+|++- ...+|.....++|.-||..
T Consensus 2 ~Cp~Cg~~---~~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSK---EIVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSS---EEEEETTTTEEEETTT-BB
T ss_pred CCcCCcCC---ceEEcCCCCeEECCCCCCE
Confidence 69999993 3677888889999999975
No 79
>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=60.81 E-value=4.2 Score=29.65 Aligned_cols=30 Identities=20% Similarity=0.515 Sum_probs=25.1
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
-||..|+....-...+.+ .....|+-||..
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-DDPVPCPECGST 35 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-CCCCcCCCCCCC
Confidence 479999988888877777 678999999983
No 80
>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=58.61 E-value=4.7 Score=30.71 Aligned_cols=30 Identities=20% Similarity=0.646 Sum_probs=20.4
Q ss_pred ccCCCCceecCc-----------eeEEcCCceEEecCCCCC
Q 004238 58 RCKTCTAALNAF-----------ARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 58 RC~~C~ayiNp~-----------~~~~~~~~~W~C~~C~~~ 87 (766)
+|..|+=..+|- ..|++-...|+|+.|+..
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 688888777754 234344457999999864
No 81
>PRK03954 ribonuclease P protein component 4; Validated
Probab=57.23 E-value=6.8 Score=35.78 Aligned_cols=34 Identities=24% Similarity=0.437 Sum_probs=24.5
Q ss_pred ccCCCCceecCc----eeEEcCC---ceEEecCCCCCCCCC
Q 004238 58 RCKTCTAALNAF----ARVDFTA---KIWICPFCYQRNHFP 91 (766)
Q Consensus 58 RC~~C~ayiNp~----~~~~~~~---~~W~C~~C~~~N~~p 91 (766)
-|++|.++|=|- +++..+. -.++|..||+..-+|
T Consensus 66 ~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~P 106 (121)
T PRK03954 66 YCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRYP 106 (121)
T ss_pred HhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEeec
Confidence 499999998663 3344332 234999999998876
No 82
>cd01455 vWA_F11C1-5a_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 not all A
Probab=57.15 E-value=2.1e+02 Score=28.54 Aligned_cols=111 Identities=14% Similarity=-0.028 Sum_probs=66.3
Q ss_pred HHHHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhh-ccCCCCccEEEEEeCCCCCCCCcccccCCCCCCccCCCCC
Q 004238 249 YTLNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLG-ACLPGTGARIVALVGGPCTEGPGTIVSKDLSEPVRSHKDL 327 (766)
Q Consensus 249 ~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~-~~~~~~gGrIi~f~sg~pt~GpG~l~~~~~~~~~rs~~~~ 327 (766)
..+..+|+.++.. ... ..|..||..|+.-++ . .+...--||++++|--|.|- +
T Consensus 75 ~~l~~~l~~~q~g---~ag-----~~TadAi~~av~rl~~~-~~a~~kvvILLTDG~n~~~~--i--------------- 128 (191)
T cd01455 75 ETLKMMHAHSQFC---WSG-----DHTVEATEFAIKELAAK-EDFDEAIVIVLSDANLERYG--I--------------- 128 (191)
T ss_pred HHHHHHHHhcccC---ccC-----ccHHHHHHHHHHHHHhc-CcCCCcEEEEEeCCCcCCCC--C---------------
Confidence 4567777776542 221 233389999998885 2 22223355777777533221 1
Q ss_pred CcCcCccchhHHHHHHHH-HHHHHHcCcEEEEEEecCCccChhcchhhhhcccceEEEeCCCCchhhHHHHHHHHh
Q 004238 328 DKDAAPFFKKAVKFYDGL-AKQLVSQGHVLDLFASALDQVGVAEMKVAVEKTGGLVVLAESFGHSVFKDSFKRIFE 402 (766)
Q Consensus 328 ~~~~~~~~~~a~~fY~~l-a~~~~~~~isvdlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l~ 402 (766)
.| .+. +..+.+.||-|..+.++.. |-.++..+++.|||+.|...+- ..+.+-+..+|+
T Consensus 129 --------~P-----~~aAa~lA~~~gV~iytIgiG~~--d~~~l~~iA~~tgG~~F~A~d~--~~L~~iy~~I~~ 187 (191)
T cd01455 129 --------QP-----KKLADALAREPNVNAFVIFIGSL--SDEADQLQRELPAGKAFVCMDT--SELPHIMQQIFT 187 (191)
T ss_pred --------Ch-----HHHHHHHHHhCCCEEEEEEecCC--CHHHHHHHHhCCCCcEEEeCCH--HHHHHHHHHHHH
Confidence 11 123 3445678888887777653 5677899999999999887542 334444444554
No 83
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=56.56 E-value=7.2 Score=27.59 Aligned_cols=32 Identities=16% Similarity=0.420 Sum_probs=23.6
Q ss_pred CcccCCCCceecCce-eEEcCCceEEecCCCCC
Q 004238 56 PLRCKTCTAALNAFA-RVDFTAKIWICPFCYQR 87 (766)
Q Consensus 56 p~RC~~C~ayiNp~~-~~~~~~~~W~C~~C~~~ 87 (766)
.++|.+|++..+-=- ++..+|++.+|+-|++.
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence 368999998765333 45567889999999875
No 84
>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=56.23 E-value=6.1 Score=31.94 Aligned_cols=30 Identities=27% Similarity=0.422 Sum_probs=20.4
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRNHFP 91 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~p 91 (766)
+.|| .|+.++ --+++.+.-+| .||....+-
T Consensus 3 ifrC-~Cgr~l----ya~e~~kTkkC-~CG~~l~vk 32 (68)
T PF09082_consen 3 IFRC-DCGRYL----YAKEGAKTKKC-VCGKTLKVK 32 (68)
T ss_dssp EEEE-TTS--E----EEETT-SEEEE-TTTEEEE--
T ss_pred EEEe-cCCCEE----EecCCcceeEe-cCCCeeeee
Confidence 6899 799875 34667789999 999987764
No 85
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=56.22 E-value=4.2 Score=28.24 Aligned_cols=30 Identities=20% Similarity=0.356 Sum_probs=15.8
Q ss_pred ccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 58 RCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 58 RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
.|+.|++-+..-.--.++..+|+|+-|+..
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCE
Confidence 488899876544433355679999999864
No 86
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=56.20 E-value=5.5 Score=30.19 Aligned_cols=34 Identities=29% Similarity=0.512 Sum_probs=23.8
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRNHFP 91 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~p 91 (766)
-+||.+|+-.|----.+. .-.-+|+=|++.|.+-
T Consensus 4 eiRC~~CnklLa~~g~~~--~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVI--ELEIKCPRCKTINHVR 37 (51)
T ss_pred ceeccchhHHHhhhcCcc--EEEEECCCCCccceEe
Confidence 379999987765422222 1357999999999873
No 87
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=55.40 E-value=6.6 Score=35.52 Aligned_cols=27 Identities=19% Similarity=0.500 Sum_probs=19.4
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRN 88 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N 88 (766)
-.||..|+.... .....|.||-||..+
T Consensus 70 ~~~C~~Cg~~~~------~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 70 QAWCWDCSQVVE------IHQHDAQCPHCHGER 96 (113)
T ss_pred EEEcccCCCEEe------cCCcCccCcCCCCCC
Confidence 489999995433 223567899999765
No 88
>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=53.38 E-value=7.7 Score=35.23 Aligned_cols=27 Identities=19% Similarity=0.579 Sum_probs=20.0
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRN 88 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N 88 (766)
-.+|.+|+....+- ...|.||-||..+
T Consensus 70 ~~~C~~Cg~~~~~~------~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 70 ECECEDCSEEVSPE------IDLYRCPKCHGIM 96 (115)
T ss_pred EEEcccCCCEEecC------CcCccCcCCcCCC
Confidence 48999999654332 2368999999876
No 89
>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=53.18 E-value=6.9 Score=29.82 Aligned_cols=31 Identities=19% Similarity=0.555 Sum_probs=22.2
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCCCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCYQRN 88 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N 88 (766)
.||.+|+....-+..+.+ .....|+-||..+
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~~ 36 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-DPLATCPECGGEK 36 (52)
T ss_pred EEeCCCCCEeEEEEecCC-CCCCCCCCCCCCc
Confidence 379999986665554444 4568899999853
No 90
>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=51.22 E-value=5.7 Score=29.82 Aligned_cols=30 Identities=20% Similarity=0.610 Sum_probs=16.0
Q ss_pred ccCCCCceecCce-----------eEEcCCceEEecCCCCC
Q 004238 58 RCKTCTAALNAFA-----------RVDFTAKIWICPFCYQR 87 (766)
Q Consensus 58 RC~~C~ayiNp~~-----------~~~~~~~~W~C~~C~~~ 87 (766)
+|..|+-..+|-- .|++-...|+|+.|+..
T Consensus 3 ~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 3 QCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred CCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 5777776555443 23333456999998864
No 91
>PF03731 Ku_N: Ku70/Ku80 N-terminal alpha/beta domain; InterPro: IPR005161 The Ku heterodimer (composed of Ku70 P12956 from SWISSPROT and Ku80 P13010 from SWISSPROT) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the N-terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [].; PDB: 1JEQ_A 1JEY_A.
Probab=50.83 E-value=21 Score=36.18 Aligned_cols=43 Identities=28% Similarity=0.322 Sum_probs=25.7
Q ss_pred EEEEEEEcccchHH--------HHHHHHHHHHHhccC---CCCcEEEEEEECCe
Q 004238 136 VFVFVLDTCMIEEE--------LGYARSELKRAIGLL---PDNAMVGLVTFGTQ 178 (766)
Q Consensus 136 ~~vFvID~s~~~~~--------l~~~~~~l~~~l~~l---p~~~~VglItf~~~ 178 (766)
+.+|+||++.++.+ |+.+.+++...+... .+...||+|.|++.
T Consensus 1 ~~vflID~s~sM~~~~~~~~~~l~~al~~i~~~~~~ki~~~~kD~vgvvl~gt~ 54 (224)
T PF03731_consen 1 ATVFLIDVSPSMFEPSSESESPLEEALKAIEDLMQQKIISSPKDEVGVVLFGTD 54 (224)
T ss_dssp EEEEEEE-SCGGGS-BTTCS-HHHHHHHHHHHHHHHHHHTT---EEEEEEES-S
T ss_pred CEEEEEECCHHHCCCCCCcchhHHHHHHHHHHHHHHHHcCCCCCeEEEEEEcCC
Confidence 36899999999853 555555555555431 23478999999864
No 92
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=49.28 E-value=8.1 Score=24.26 Aligned_cols=21 Identities=33% Similarity=0.793 Sum_probs=12.9
Q ss_pred ccCCCCceecCceeEEcCCceEEecCCCC
Q 004238 58 RCKTCTAALNAFARVDFTAKIWICPFCYQ 86 (766)
Q Consensus 58 RC~~C~ayiNp~~~~~~~~~~W~C~~C~~ 86 (766)
+|.+|++-+.+-.+| |+-||+
T Consensus 1 ~Cp~CG~~~~~~~~f--------C~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKF--------CPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcc--------hhhhCC
Confidence 477777765543332 777775
No 93
>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=49.06 E-value=8.6 Score=27.48 Aligned_cols=29 Identities=21% Similarity=0.616 Sum_probs=21.9
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCYQ 86 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~ 86 (766)
.+|..|+........... +....|+-||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 389999997766655544 56888999997
No 94
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=48.75 E-value=10 Score=34.41 Aligned_cols=28 Identities=25% Similarity=0.598 Sum_probs=18.8
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRN 88 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N 88 (766)
-.||..|+.+...- ....|.||-||..+
T Consensus 70 ~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 70 ECWCETCQQYVTLL-----TQRVRRCPQCHGDM 97 (114)
T ss_pred EEEcccCCCeeecC-----CccCCcCcCcCCCC
Confidence 48899999633221 11248899999875
No 95
>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=48.27 E-value=17 Score=23.38 Aligned_cols=24 Identities=25% Similarity=0.432 Sum_probs=16.1
Q ss_pred cCCCCceecCceeEEcCCceEEecCCCC
Q 004238 59 CKTCTAALNAFARVDFTAKIWICPFCYQ 86 (766)
Q Consensus 59 C~~C~ayiNp~~~~~~~~~~W~C~~C~~ 86 (766)
|.+|+..|. .-.+...++|..|++
T Consensus 1 C~~Cr~~L~----yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLM----YPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEE----cCCCCCCeECCccCc
Confidence 667777553 334667888888875
No 96
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=47.54 E-value=9.9 Score=28.72 Aligned_cols=27 Identities=26% Similarity=0.748 Sum_probs=19.0
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
-+|.+|++-+ ..+.....-.|+-||+.
T Consensus 7 Y~C~~Cg~~~----~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 7 YKCARCGREV----ELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEhhhcCCee----ehhhccCceeCCCCCcE
Confidence 3688888866 44445567788888875
No 97
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=47.35 E-value=13 Score=34.51 Aligned_cols=34 Identities=29% Similarity=0.614 Sum_probs=23.8
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCCCCCCCCc
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCYQRNHFPP 92 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~p~ 92 (766)
++|--|+.. .-...+...+.|.|+-|+..|.+..
T Consensus 1 v~C~fC~~~--s~~~~~~~~~~w~C~~C~q~N~f~e 34 (131)
T PF09779_consen 1 VNCWFCGQN--SKVPYDNRNSNWTCPHCEQYNGFDE 34 (131)
T ss_pred CeeccCCCC--CCCCCCCCCCeeECCCCCCccCccc
Confidence 468888764 2333344455699999999998864
No 98
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=47.09 E-value=13 Score=26.17 Aligned_cols=31 Identities=16% Similarity=0.384 Sum_probs=21.4
Q ss_pred cccCCCCceecCce-eEEcCCceEEecCCCCC
Q 004238 57 LRCKTCTAALNAFA-RVDFTAKIWICPFCYQR 87 (766)
Q Consensus 57 ~RC~~C~ayiNp~~-~~~~~~~~W~C~~C~~~ 87 (766)
++|.+|++-.+-=- ++-..|.+.+|.-|++.
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 67888888654333 24456788899988874
No 99
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=45.61 E-value=12 Score=36.51 Aligned_cols=26 Identities=31% Similarity=0.671 Sum_probs=20.8
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
-.+|++|++-|=+ .+++-+|+-||..
T Consensus 149 ~A~CsrC~~~L~~------~~~~l~Cp~Cg~t 174 (188)
T COG1096 149 YARCSRCRAPLVK------KGNMLKCPNCGNT 174 (188)
T ss_pred EEEccCCCcceEE------cCcEEECCCCCCE
Confidence 3689999996543 4689999999975
No 100
>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=45.35 E-value=14 Score=29.90 Aligned_cols=27 Identities=19% Similarity=0.543 Sum_probs=22.0
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
-.|..|+...-. ...++.|.|+-||..
T Consensus 29 q~C~~CG~~~~~----~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 29 QTCPRCGHRNKK----RRSGRVFTCPNCGFE 55 (69)
T ss_pred cCccCccccccc----ccccceEEcCCCCCE
Confidence 569999987766 456789999999986
No 101
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=44.41 E-value=25 Score=24.28 Aligned_cols=29 Identities=21% Similarity=0.399 Sum_probs=20.1
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRN 88 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N 88 (766)
+.+|..|++-. -+........|.+|+...
T Consensus 3 ~~~C~~C~~~~----i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNG----IVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCe----EEEecCCeEEcccCCcEe
Confidence 57899998854 221334588999999764
No 102
>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=44.24 E-value=11 Score=34.28 Aligned_cols=32 Identities=22% Similarity=0.543 Sum_probs=26.5
Q ss_pred CcccCCCCceecCceeEEc-CCceEEecCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDF-TAKIWICPFCYQR 87 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~-~~~~W~C~~C~~~ 87 (766)
...|..|+-.+..-|.+.. +...|.|++|...
T Consensus 71 ~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k~ 103 (118)
T PF02318_consen 71 GRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQKQ 103 (118)
T ss_dssp CEEETTTTEEEETTSEEETSSSCCEEEHHHHHH
T ss_pred CCcCCcCCccccCccCCcCCCCCCEEChhhHHH
Confidence 4789999999998898874 5679999999764
No 103
>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]
Probab=43.12 E-value=47 Score=38.74 Aligned_cols=49 Identities=22% Similarity=0.381 Sum_probs=34.8
Q ss_pred HhhcccceeeccC----CCCcc-----cccccccccCCeEEEEeCCcEEEEEECCchh
Q 004238 621 VMIQPSLISYSFN----SLPQP-----ALLDVASIAADRILLLDTYFSVVIFHGMTIA 669 (766)
Q Consensus 621 ~~iyP~L~~~~~~----~~p~~-----~~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~ 669 (766)
---+|+||.+... ++|+- ..|-..-+.+.++|+||+...|+||+|+...
T Consensus 730 ~p~qpkLYkV~lGmGyLELPQvel~P~~~l~q~lL~sk~VyiLDc~sDiF~W~GkKs~ 787 (1255)
T KOG0444|consen 730 VPEQPKLYKVNLGMGYLELPQVELLPKGILKQDLLGSKGVYILDCNSDIFLWIGKKSN 787 (1255)
T ss_pred CCCCcceEEEccccceeecchhhhchhhHHHHHhhcCCeEEEEecCCceEEEecccch
Confidence 4568999988631 12332 1233455678999999999999999999754
No 104
>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=41.34 E-value=22 Score=31.47 Aligned_cols=27 Identities=22% Similarity=0.605 Sum_probs=20.0
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
.+.|.+|.+ -|.-- +|..|+|+-|++.
T Consensus 2 lp~CP~C~s---eytY~--dg~~~iCpeC~~E 28 (109)
T TIGR00686 2 LPPCPKCNS---EYTYH--DGTQLICPSCLYE 28 (109)
T ss_pred CCcCCcCCC---cceEe--cCCeeECcccccc
Confidence 467999986 34433 3578999999986
No 105
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.94 E-value=11 Score=34.37 Aligned_cols=28 Identities=25% Similarity=0.596 Sum_probs=18.1
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRN 88 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N 88 (766)
..||..|+.+..+- . ...++||-||..+
T Consensus 71 ~~~C~~Cg~~~~~~----~-~~~~~CP~Cgs~~ 98 (117)
T PRK00564 71 ELECKDCSHVFKPN----A-LDYGVCEKCHSKN 98 (117)
T ss_pred EEEhhhCCCccccC----C-ccCCcCcCCCCCc
Confidence 48999999543221 1 1234599999876
No 106
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=40.86 E-value=14 Score=40.79 Aligned_cols=27 Identities=22% Similarity=0.383 Sum_probs=21.1
Q ss_pred ccCCCCceecCceeEEcCCceEEecCCCCCCCCCc
Q 004238 58 RCKTCTAALNAFARVDFTAKIWICPFCYQRNHFPP 92 (766)
Q Consensus 58 RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~p~ 92 (766)
+|++|+. ......|+|+-|+..|.+..
T Consensus 2 ~c~~cg~--------~~~~~~g~cp~c~~w~~~~e 28 (372)
T cd01121 2 VCSECGY--------VSPKWLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCC--------CCCCccEECcCCCCceeeee
Confidence 6999986 23346799999999998853
No 107
>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=40.14 E-value=18 Score=34.41 Aligned_cols=33 Identities=24% Similarity=0.621 Sum_probs=22.7
Q ss_pred CcccCCCCceecCcee-----------EEcCCceEEecCCCCCC
Q 004238 56 PLRCKTCTAALNAFAR-----------VDFTAKIWICPFCYQRN 88 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~-----------~~~~~~~W~C~~C~~~N 88 (766)
.-||..|.+-+-+-.+ +......|.|+-||+.-
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 4899999995533321 11235699999999864
No 108
>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=39.85 E-value=50 Score=33.64 Aligned_cols=43 Identities=14% Similarity=0.050 Sum_probs=26.6
Q ss_pred CcEEEEEEEcccchHHHHHHHHHHHHHh-ccCCCCcEEEEEEECCeE
Q 004238 134 SPVFVFVLDTCMIEEELGYARSELKRAI-GLLPDNAMVGLVTFGTQA 179 (766)
Q Consensus 134 ~p~~vFvID~s~~~~~l~~~~~~l~~~l-~~lp~~~~VglItf~~~V 179 (766)
|.-+|+++|+|.++.....+.-.+..++ ...+ ++.++.|++.+
T Consensus 57 ~~~lvvl~DvSGSM~~~s~~~l~~~~~l~~~~~---~~~~f~F~~~l 100 (222)
T PF05762_consen 57 PRRLVVLCDVSGSMAGYSEFMLAFLYALQRQFR---RVRVFVFSTRL 100 (222)
T ss_pred CccEEEEEeCCCChHHHHHHHHHHHHHHHHhCC---CEEEEEEeeeh
Confidence 3389999999999987333322233332 3333 77777777654
No 109
>PRK12860 transcriptional activator FlhC; Provisional
Probab=39.56 E-value=14 Score=36.50 Aligned_cols=28 Identities=21% Similarity=0.572 Sum_probs=20.9
Q ss_pred CCcccCCCCceecCce-eEEcCCceEEecCCC
Q 004238 55 APLRCKTCTAALNAFA-RVDFTAKIWICPFCY 85 (766)
Q Consensus 55 ~p~RC~~C~ayiNp~~-~~~~~~~~W~C~~C~ 85 (766)
...+|..|++ .|+ ...+....++|++|.
T Consensus 133 ~l~~C~~Cgg---~fv~~~~e~~~~f~CplC~ 161 (189)
T PRK12860 133 QLARCCRCGG---KFVTHAHDLRHNFVCGLCQ 161 (189)
T ss_pred eeccCCCCCC---CeeccccccCCCCcCCCCC
Confidence 5789999997 443 233446789999999
No 110
>PRK10997 yieM hypothetical protein; Provisional
Probab=39.00 E-value=36 Score=38.93 Aligned_cols=51 Identities=20% Similarity=0.116 Sum_probs=33.7
Q ss_pred cEEEEEEEcccchH-HHHHHHHHHHHHhc--cCCCCcEEEEEEECCeEEEEEcC
Q 004238 135 PVFVFVLDTCMIEE-ELGYARSELKRAIG--LLPDNAMVGLVTFGTQAHVHELG 185 (766)
Q Consensus 135 p~~vFvID~s~~~~-~l~~~~~~l~~~l~--~lp~~~~VglItf~~~V~~~~l~ 185 (766)
--++++||+|.++. .-+....++..+|- .+.++-++++|.|++.+.-|.+.
T Consensus 324 GpiII~VDtSGSM~G~ke~~AkalAaAL~~iAl~q~dr~~li~Fs~~i~~~~l~ 377 (487)
T PRK10997 324 GPFIVCVDTSGSMGGFNEQCAKAFCLALMRIALAENRRCYIMLFSTEVVTYELT 377 (487)
T ss_pred CcEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHhcCCCEEEEEecCCceeeccC
Confidence 34789999999985 21222224344443 34567799999999988776553
No 111
>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=38.75 E-value=16 Score=23.76 Aligned_cols=22 Identities=27% Similarity=0.691 Sum_probs=15.6
Q ss_pred ccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 58 RCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 58 RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
+|..|++-++- ..-.|+.||+.
T Consensus 2 ~CP~C~~~V~~--------~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPE--------SAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchh--------hcCcCCCCCCC
Confidence 58888887743 23578999875
No 112
>PRK12722 transcriptional activator FlhC; Provisional
Probab=38.69 E-value=14 Score=36.36 Aligned_cols=29 Identities=17% Similarity=0.533 Sum_probs=21.4
Q ss_pred CCcccCCCCceecCce-eEEcCCceEEecCCCC
Q 004238 55 APLRCKTCTAALNAFA-RVDFTAKIWICPFCYQ 86 (766)
Q Consensus 55 ~p~RC~~C~ayiNp~~-~~~~~~~~W~C~~C~~ 86 (766)
...+|..|++ .|+ ...+....++|++|+-
T Consensus 133 ~l~~C~~Cgg---~fv~~~~e~~~~f~CplC~~ 162 (187)
T PRK12722 133 QLSSCNCCGG---HFVTHAHDPVGSFVCGLCQP 162 (187)
T ss_pred eeccCCCCCC---CeeccccccCCCCcCCCCCC
Confidence 4788999997 444 2234457899999987
No 113
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=38.62 E-value=22 Score=22.64 Aligned_cols=24 Identities=25% Similarity=0.616 Sum_probs=17.0
Q ss_pred cCCCCceecCceeEEcCCceEEecCCCC
Q 004238 59 CKTCTAALNAFARVDFTAKIWICPFCYQ 86 (766)
Q Consensus 59 C~~C~ayiNp~~~~~~~~~~W~C~~C~~ 86 (766)
|.+|+.-|-|--+ +..|.|+=||.
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 7778777766442 45789998874
No 114
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=38.55 E-value=25 Score=25.96 Aligned_cols=25 Identities=20% Similarity=0.380 Sum_probs=17.5
Q ss_pred ccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 58 RCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 58 RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
+|.+|++-+..- .+..-+|+-||++
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCce
Confidence 688888865532 3457888888875
No 115
>PF12773 DZR: Double zinc ribbon
Probab=38.36 E-value=18 Score=27.12 Aligned_cols=32 Identities=25% Similarity=0.368 Sum_probs=24.2
Q ss_pred CCcccCCCCceecCceeEEcCCceEEecCCCCCCCCC
Q 004238 55 APLRCKTCTAALNAFARVDFTAKIWICPFCYQRNHFP 91 (766)
Q Consensus 55 ~p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~p 91 (766)
+-..|.+|++-+. ......++|+-|++.|+-.
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCcCC
Confidence 4567999999887 3445689999999987643
No 116
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=38.25 E-value=21 Score=27.41 Aligned_cols=32 Identities=16% Similarity=0.288 Sum_probs=27.0
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
+.+|.+|++--.|..+-...|..-.||-|+..
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~ 34 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLY 34 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHH
Confidence 57899999988888877777777999999964
No 117
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.06 E-value=17 Score=33.21 Aligned_cols=31 Identities=16% Similarity=0.631 Sum_probs=21.8
Q ss_pred CCcccCCCCceecCceeEEcCCceEEecCCCCCCC
Q 004238 55 APLRCKTCTAALNAFARVDFTAKIWICPFCYQRNH 89 (766)
Q Consensus 55 ~p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~ 89 (766)
.+-.|.+|++-+.- ..+.-+|.||+|...-.
T Consensus 88 q~r~CARCGGrv~l----rsNKv~wvcnlc~k~q~ 118 (169)
T KOG3799|consen 88 QTRFCARCGGRVSL----RSNKVMWVCNLCRKQQE 118 (169)
T ss_pred hhhHHHhcCCeeee----ccCceEEeccCCcHHHH
Confidence 45668889886543 33446899999987654
No 118
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=35.97 E-value=35 Score=31.83 Aligned_cols=31 Identities=16% Similarity=0.454 Sum_probs=26.2
Q ss_pred cccCCCCceecCceeEEcCCceE--EecCCCCCCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIW--ICPFCYQRNHF 90 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W--~C~~C~~~N~~ 90 (766)
+-|+.|+. |=..+...++.| +|.-||..-++
T Consensus 98 VlC~~C~s---PdT~l~k~~r~~~l~C~ACGa~~~v 130 (133)
T TIGR00311 98 VICRECNR---PDTRIIKEGRVSLLKCEACGAKAPL 130 (133)
T ss_pred EECCCCCC---CCcEEEEeCCeEEEecccCCCCCcc
Confidence 78999997 888887777776 89999998766
No 119
>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=35.20 E-value=44 Score=24.78 Aligned_cols=27 Identities=19% Similarity=0.618 Sum_probs=19.0
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCYQ 86 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~ 86 (766)
+.|.+|++- ..| .+.. .+.|+|.-|++
T Consensus 19 ~~CP~Cg~~-~~~-~~~~-~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-KHY-RLKT-RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-eeE-EeCC-CCeEECCCCCC
Confidence 559999987 222 2322 57999999986
No 120
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=35.13 E-value=14 Score=24.62 Aligned_cols=14 Identities=36% Similarity=0.695 Sum_probs=12.1
Q ss_pred ceEEecCCCCCCCC
Q 004238 77 KIWICPFCYQRNHF 90 (766)
Q Consensus 77 ~~W~C~~C~~~N~~ 90 (766)
+.|.|+.|...|..
T Consensus 3 g~W~C~~C~~~N~~ 16 (30)
T PF00641_consen 3 GDWKCPSCTFMNPA 16 (30)
T ss_dssp SSEEETTTTEEEES
T ss_pred cCccCCCCcCCchH
Confidence 48999999999964
No 121
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=34.92 E-value=22 Score=27.05 Aligned_cols=25 Identities=20% Similarity=0.509 Sum_probs=18.2
Q ss_pred cccCCCCc-eecCceeEEcCCceEEecCCCCC
Q 004238 57 LRCKTCTA-ALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 57 ~RC~~C~a-yiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
..|.+|++ ++-+.- ..|.|.=|+..
T Consensus 21 ~fCP~Cg~~~m~~~~------~r~~C~~Cgyt 46 (50)
T PRK00432 21 KFCPRCGSGFMAEHL------DRWHCGKCGYT 46 (50)
T ss_pred CcCcCCCcchheccC------CcEECCCcCCE
Confidence 46999998 444432 58999999864
No 122
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=34.80 E-value=29 Score=27.24 Aligned_cols=26 Identities=19% Similarity=0.471 Sum_probs=20.3
Q ss_pred CCcccCCCCceecCceeEEcCCceEEecCCCCCCC
Q 004238 55 APLRCKTCTAALNAFARVDFTAKIWICPFCYQRNH 89 (766)
Q Consensus 55 ~p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~ 89 (766)
.+..|.+|+.+.=| .-.|+.||..+.
T Consensus 26 ~l~~C~~CG~~~~~---------H~vC~~CG~Y~g 51 (57)
T PRK12286 26 GLVECPNCGEPKLP---------HRVCPSCGYYKG 51 (57)
T ss_pred cceECCCCCCccCC---------eEECCCCCcCCC
Confidence 46889999998765 458999997653
No 123
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.59 E-value=17 Score=33.40 Aligned_cols=33 Identities=21% Similarity=0.480 Sum_probs=19.7
Q ss_pred CcccCCCCceecCc-eeEEcCCceEEecCCCCCCC
Q 004238 56 PLRCKTCTAALNAF-ARVDFTAKIWICPFCYQRNH 89 (766)
Q Consensus 56 p~RC~~C~ayiNp~-~~~~~~~~~W~C~~C~~~N~ 89 (766)
-.|| .|+.+..+- ...+.-.-.|.||-||..+.
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~ 103 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRA 103 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCCCCCC
Confidence 4899 999765432 11111111378999997663
No 124
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=33.80 E-value=25 Score=24.71 Aligned_cols=31 Identities=13% Similarity=0.414 Sum_probs=16.3
Q ss_pred cccCCCCceecCce-eEEcCCceEEecCCCCC
Q 004238 57 LRCKTCTAALNAFA-RVDFTAKIWICPFCYQR 87 (766)
Q Consensus 57 ~RC~~C~ayiNp~~-~~~~~~~~W~C~~C~~~ 87 (766)
+.|.+|++-..--. .+...+...+|+-|++.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 46777777421111 12223456777777764
No 125
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.69 E-value=21 Score=30.52 Aligned_cols=36 Identities=28% Similarity=0.604 Sum_probs=24.9
Q ss_pred CCcccCCCCceecCceeEEcCCceEEecCCCCCCCCCccc
Q 004238 55 APLRCKTCTAALNAFARVDFTAKIWICPFCYQRNHFPPHY 94 (766)
Q Consensus 55 ~p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~p~~y 94 (766)
.|+||++||--.++ -.+. .--+|+-|+..---++.|
T Consensus 57 ~Pa~CkkCGfef~~-~~ik---~pSRCP~CKSE~Ie~prF 92 (97)
T COG3357 57 RPARCKKCGFEFRD-DKIK---KPSRCPKCKSEWIEEPRF 92 (97)
T ss_pred cChhhcccCccccc-cccC---CcccCCcchhhcccCCce
Confidence 59999999987666 2233 345899999875544433
No 126
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.46 E-value=24 Score=32.99 Aligned_cols=33 Identities=21% Similarity=0.465 Sum_probs=20.0
Q ss_pred CcccCCCCceecCce-------------eEEc--CCceEEecCCCCCC
Q 004238 56 PLRCKTCTAALNAFA-------------RVDF--TAKIWICPFCYQRN 88 (766)
Q Consensus 56 p~RC~~C~ayiNp~~-------------~~~~--~~~~W~C~~C~~~N 88 (766)
..+|..|+....+-- .+.+ ....|.||-||..+
T Consensus 70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 478999996544420 0000 03468899999765
No 127
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=33.44 E-value=23 Score=28.42 Aligned_cols=24 Identities=25% Similarity=0.495 Sum_probs=17.5
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCCCCCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCYQRNHF 90 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~ 90 (766)
.-|++|+...+ + . +|+.||..+..
T Consensus 6 ~AC~~C~~i~~-------~-~--~Cp~Cgs~~~S 29 (64)
T PRK06393 6 RACKKCKRLTP-------E-K--TCPVHGDEKTT 29 (64)
T ss_pred hhHhhCCcccC-------C-C--cCCCCCCCcCC
Confidence 45999998763 1 1 99999997533
No 128
>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=33.09 E-value=41 Score=23.72 Aligned_cols=27 Identities=19% Similarity=0.509 Sum_probs=20.2
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
..+|..|++. +...+ .+.|.|.=||+.
T Consensus 8 ~~~C~~C~~~---~~~~~--dG~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSR---WFYSD--DGFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCe---EeEcc--CCEEEhhhCceE
Confidence 3569999998 44444 359999999975
No 129
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=32.47 E-value=25 Score=34.79 Aligned_cols=38 Identities=21% Similarity=0.473 Sum_probs=24.6
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCCCCCcc
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRNHFPPH 93 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~p~~ 93 (766)
-+-|+.|.-=-+-+.--...-..|+|++|+..|+.|.+
T Consensus 192 alIC~~C~hhngl~~~~ek~~~efiC~~Cn~~n~~~~~ 229 (251)
T COG5415 192 ALICPQCHHHNGLYRLAEKPIIEFICPHCNHKNDEVKE 229 (251)
T ss_pred hhccccccccccccccccccchheecccchhhcCcccc
Confidence 35577776544433333333457999999999987753
No 130
>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=32.27 E-value=16 Score=27.76 Aligned_cols=19 Identities=26% Similarity=0.831 Sum_probs=7.7
Q ss_pred CceeEEcCCceEEecCCCC
Q 004238 68 AFARVDFTAKIWICPFCYQ 86 (766)
Q Consensus 68 p~~~~~~~~~~W~C~~C~~ 86 (766)
-|.......+.|+|++|++
T Consensus 31 ~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 31 SFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp HHHHHHHHS---B-TTT--
T ss_pred HHHHHhhccCCeECcCCcC
Confidence 3333334456799999986
No 131
>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=31.61 E-value=23 Score=21.39 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=6.7
Q ss_pred EEecCCCCCCC
Q 004238 79 WICPFCYQRNH 89 (766)
Q Consensus 79 W~C~~C~~~N~ 89 (766)
|.|++|+....
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 78899987643
No 132
>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=31.46 E-value=12 Score=33.81 Aligned_cols=27 Identities=22% Similarity=0.552 Sum_probs=17.7
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRN 88 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N 88 (766)
-.||..|+.-..+-- ..+.||.||..+
T Consensus 70 ~~~C~~Cg~~~~~~~------~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 70 RARCRDCGHEFEPDE------FDFSCPRCGSPD 96 (113)
T ss_dssp EEEETTTS-EEECHH------CCHH-SSSSSS-
T ss_pred cEECCCCCCEEecCC------CCCCCcCCcCCC
Confidence 488999998655433 336799999986
No 133
>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=31.13 E-value=21 Score=35.03 Aligned_cols=29 Identities=24% Similarity=0.742 Sum_probs=11.5
Q ss_pred CCcccCCCCceecCceeEEcC-CceEEecCCCC
Q 004238 55 APLRCKTCTAALNAFARVDFT-AKIWICPFCYQ 86 (766)
Q Consensus 55 ~p~RC~~C~ayiNp~~~~~~~-~~~W~C~~C~~ 86 (766)
...+|.+|++ .|+.-..+ ...+.|+||+-
T Consensus 133 ~l~~C~~C~~---~fv~~~~~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 133 QLAPCRRCGG---HFVTHAHDPRHSFVCPFCQP 162 (175)
T ss_dssp EEEE-TTT-----EEEEESS--SS----TT---
T ss_pred cccCCCCCCC---CeECcCCCCCcCcCCCCCCC
Confidence 4678999997 44433222 56899999983
No 134
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=30.98 E-value=40 Score=26.49 Aligned_cols=28 Identities=25% Similarity=0.573 Sum_probs=18.9
Q ss_pred CCcccCCCCceecCceeEEcCCceEEecCCCC
Q 004238 55 APLRCKTCTAALNAFARVDFTAKIWICPFCYQ 86 (766)
Q Consensus 55 ~p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~ 86 (766)
.|.+|.+|+..|-|--+ .-+|.|+-||.
T Consensus 8 ~~~~CtSCg~~i~p~e~----~v~F~CPnCGe 35 (61)
T COG2888 8 DPPVCTSCGREIAPGET----AVKFPCPNCGE 35 (61)
T ss_pred CCceeccCCCEeccCCc----eeEeeCCCCCc
Confidence 36788888888765433 34677777774
No 135
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=30.51 E-value=30 Score=27.55 Aligned_cols=23 Identities=26% Similarity=0.693 Sum_probs=16.9
Q ss_pred ccCCCCceecCceeEEcCCceEEecCCCCCCCC
Q 004238 58 RCKTCTAALNAFARVDFTAKIWICPFCYQRNHF 90 (766)
Q Consensus 58 RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~ 90 (766)
-|++|+.... + . +|+.||...-.
T Consensus 5 AC~~C~~i~~-------~-~--~CP~Cgs~~~T 27 (61)
T PRK08351 5 ACRHCHYITT-------E-D--RCPVCGSRDLS 27 (61)
T ss_pred hhhhCCcccC-------C-C--cCCCCcCCccc
Confidence 5999998773 1 1 69999997633
No 136
>PHA00626 hypothetical protein
Probab=30.38 E-value=46 Score=25.80 Aligned_cols=30 Identities=20% Similarity=0.391 Sum_probs=18.3
Q ss_pred ccCCCCc---eecCceeEEcCCceEEecCCCCCCC
Q 004238 58 RCKTCTA---ALNAFARVDFTAKIWICPFCYQRNH 89 (766)
Q Consensus 58 RC~~C~a---yiNp~~~~~~~~~~W~C~~C~~~N~ 89 (766)
.|.+|+. +-|..|+- ..+.++|+-||..-.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~--~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRG--WSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecc--cCcceEcCCCCCeec
Confidence 3667766 22333322 257899999998643
No 137
>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=30.07 E-value=33 Score=30.33 Aligned_cols=27 Identities=19% Similarity=0.589 Sum_probs=21.5
Q ss_pred ccCCCCceecCceeEEcCCceEEecCCCCCCCC
Q 004238 58 RCKTCTAALNAFARVDFTAKIWICPFCYQRNHF 90 (766)
Q Consensus 58 RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~ 90 (766)
.|.+|++.|.|- +..|.|+-|+.....
T Consensus 2 fC~~Cg~~l~~~------~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPK------NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccC------CCeEECcCCCCcccc
Confidence 599999999663 358999999987543
No 138
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=30.02 E-value=1.8e+02 Score=35.29 Aligned_cols=111 Identities=15% Similarity=0.246 Sum_probs=62.6
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCCCCCcccccCCCCCCCccccCCCce--EEEEec-CCCCCCC--CCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRNHFPPHYAAISETNLPCELYPQYTT--VEYTLP-HSMQNPN--NPNPD 130 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~p~~y~~~~~~~~~pEL~p~~~t--vey~~~-~~~~~~~--~~~~~ 130 (766)
+.+|.+|..++ .+-...+.-+|..||+.-++|.. +|.+|+ +-|..+ .+....+ .--|
T Consensus 444 v~~Cp~Cd~~l----t~H~~~~~L~CH~Cg~~~~~p~~-------------Cp~Cgs~~L~~~G~GterieeeL~~~FP- 505 (730)
T COG1198 444 IAECPNCDSPL----TLHKATGQLRCHYCGYQEPIPQS-------------CPECGSEHLRAVGPGTERIEEELKRLFP- 505 (730)
T ss_pred cccCCCCCcce----EEecCCCeeEeCCCCCCCCCCCC-------------CCCCCCCeeEEecccHHHHHHHHHHHCC-
Confidence 44555555542 33445689999999999777632 233333 333322 1100000 0124
Q ss_pred CCCCcEEEEEEEcccchHHHHHHHHHHHHH----------h---ccCCCCcEEEEEEECCeEEEEEcCC
Q 004238 131 PRLSPVFVFVLDTCMIEEELGYARSELKRA----------I---GLLPDNAMVGLVTFGTQAHVHELGF 186 (766)
Q Consensus 131 ~~~~p~~vFvID~s~~~~~l~~~~~~l~~~----------l---~~lp~~~~VglItf~~~V~~~~l~~ 186 (766)
..+++.|--|++.....++.+...+..- | ...|.=+.||++--|..+..-|+..
T Consensus 506 --~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA 572 (730)
T COG1198 506 --GARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRA 572 (730)
T ss_pred --CCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcch
Confidence 6778888888888776665554444321 0 1235458999998888777766654
No 139
>PRK10220 hypothetical protein; Provisional
Probab=29.89 E-value=44 Score=29.71 Aligned_cols=28 Identities=21% Similarity=0.641 Sum_probs=20.0
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRN 88 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N 88 (766)
.+.|..|.+ -|.-- ++..|+|+-|++.-
T Consensus 3 lP~CP~C~s---eytY~--d~~~~vCpeC~hEW 30 (111)
T PRK10220 3 LPHCPKCNS---EYTYE--DNGMYICPECAHEW 30 (111)
T ss_pred CCcCCCCCC---cceEc--CCCeEECCcccCcC
Confidence 467888886 33332 35789999999863
No 140
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=29.83 E-value=46 Score=26.82 Aligned_cols=31 Identities=13% Similarity=0.388 Sum_probs=23.4
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRNH 89 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~ 89 (766)
-++|..|+- --+-|......-+|+.||..=-
T Consensus 19 ~VkCpdC~N---~q~vFshast~V~C~~CG~~l~ 49 (67)
T COG2051 19 RVKCPDCGN---EQVVFSHASTVVTCLICGTTLA 49 (67)
T ss_pred EEECCCCCC---EEEEeccCceEEEecccccEEE
Confidence 478999984 5566666677899999998643
No 141
>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=29.74 E-value=41 Score=23.08 Aligned_cols=29 Identities=17% Similarity=0.484 Sum_probs=17.7
Q ss_pred ccCCCCceecCc-eeEEcCCce-----EEecCCCC
Q 004238 58 RCKTCTAALNAF-ARVDFTAKI-----WICPFCYQ 86 (766)
Q Consensus 58 RC~~C~ayiNp~-~~~~~~~~~-----W~C~~C~~ 86 (766)
||..|+..|-+- ..+...++. |.|..|+.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~ 35 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGK 35 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCC
Confidence 688888887774 333333334 46776665
No 142
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=29.68 E-value=1.7e+02 Score=33.01 Aligned_cols=41 Identities=15% Similarity=0.119 Sum_probs=27.7
Q ss_pred EEEEEEcccchHH-HHHHHHHHHHHhc--cCCCCcEEEEEEECC
Q 004238 137 FVFVLDTCMIEEE-LGYARSELKRAIG--LLPDNAMVGLVTFGT 177 (766)
Q Consensus 137 ~vFvID~s~~~~~-l~~~~~~l~~~l~--~lp~~~~VglItf~~ 177 (766)
++.+||.|+++.- -+....++..+|- .+-+|.++.++.||+
T Consensus 275 villlD~SGSM~G~~e~~AKAvalAl~~~alaenR~~~~~lF~s 318 (437)
T COG2425 275 VILLLDKSGSMSGFKEQWAKAVALALMRIALAENRDCYVILFDS 318 (437)
T ss_pred EEEEEeCCCCcCCcHHHHHHHHHHHHHHHHHHhccceEEEEecc
Confidence 5689999999843 2222234444442 356788999999999
No 143
>PRK00420 hypothetical protein; Validated
Probab=28.49 E-value=41 Score=30.35 Aligned_cols=29 Identities=14% Similarity=0.319 Sum_probs=22.1
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCCCCCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCYQRNHF 90 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~ 90 (766)
-.|..|++ |+.++. ++.-.|+.||..-.+
T Consensus 24 ~~CP~Cg~---pLf~lk--~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCGL---PLFELK--DGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCC---cceecC--CCceECCCCCCeeee
Confidence 56999996 888773 358999999986444
No 144
>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=27.98 E-value=34 Score=23.07 Aligned_cols=27 Identities=19% Similarity=0.554 Sum_probs=13.6
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
.+.|..|++=-+- .+|..++|+-|++.
T Consensus 2 ~p~Cp~C~se~~y-----~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCPLCGSEYTY-----EDGELLVCPECGHE 28 (30)
T ss_dssp S---TTT-----E-----E-SSSEEETTTTEE
T ss_pred CCCCCCCCCccee-----ccCCEEeCCccccc
Confidence 3578888873332 34679999999863
No 145
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=27.73 E-value=68 Score=34.17 Aligned_cols=29 Identities=24% Similarity=0.418 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHhccCCCCcEEEEEEEC
Q 004238 148 EELGYARSELKRAIGLLPDNAMVGLVTFG 176 (766)
Q Consensus 148 ~~l~~~~~~l~~~l~~lp~~~~VglItf~ 176 (766)
.||+.+.++|.++++.|.++.|+++|||-
T Consensus 218 dEL~~L~~~L~~a~~~L~~gGRl~VIsFH 246 (314)
T COG0275 218 DELEELEEALEAALDLLKPGGRLAVISFH 246 (314)
T ss_pred hHHHHHHHHHHHHHHhhCCCcEEEEEEec
Confidence 35999999999999999999999999874
No 146
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=27.11 E-value=44 Score=30.94 Aligned_cols=25 Identities=28% Similarity=0.616 Sum_probs=19.5
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
.-|..|++ |..+ .+ +.-.||.|++.
T Consensus 29 ~hCp~Cg~---PLF~--Kd-G~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGT---PLFR--KD-GEVFCPVCGYR 53 (131)
T ss_pred hhCcccCC---ccee--eC-CeEECCCCCce
Confidence 45999998 7777 33 48999999964
No 147
>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=26.90 E-value=22 Score=24.97 Aligned_cols=28 Identities=18% Similarity=0.328 Sum_probs=19.8
Q ss_pred cCCCCceecCceeEEcCCceEEecCCCC
Q 004238 59 CKTCTAALNAFARVDFTAKIWICPFCYQ 86 (766)
Q Consensus 59 C~~C~ayiNp~~~~~~~~~~W~C~~C~~ 86 (766)
|.+|++-=.|..+-...|....||-|+.
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 8889998899998888888889999974
No 148
>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=26.41 E-value=38 Score=26.36 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=18.7
Q ss_pred CCcccCCCCceecCceeEEcCCceEEecCCCCCC
Q 004238 55 APLRCKTCTAALNAFARVDFTAKIWICPFCYQRN 88 (766)
Q Consensus 55 ~p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N 88 (766)
.++.|..|+.+.=| .-.|+.||..+
T Consensus 25 ~l~~C~~cG~~~~~---------H~vc~~cG~Y~ 49 (55)
T TIGR01031 25 TLVVCPNCGEFKLP---------HRVCPSCGYYK 49 (55)
T ss_pred cceECCCCCCcccC---------eeECCccCeEC
Confidence 46889999996544 45888898654
No 149
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=25.89 E-value=34 Score=36.57 Aligned_cols=35 Identities=20% Similarity=0.452 Sum_probs=24.4
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCCCCCCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCYQRNHFP 91 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~p 91 (766)
+-|+.|+.==+.+-.=+..--.|+|++|+..|+-+
T Consensus 221 LIC~~C~~HNGla~~ee~~yi~F~C~~Cn~LN~~~ 255 (328)
T KOG2846|consen 221 LICSQCHHHNGLARKEEYEYITFRCPHCNALNPAK 255 (328)
T ss_pred hcchhhccccCcCChhhcCceEEECccccccCCCc
Confidence 55999987644444323334689999999999854
No 150
>PF06707 DUF1194: Protein of unknown function (DUF1194); InterPro: IPR010607 This family consists of several hypothetical Rhizobiales specific proteins of around 270 residues in length. The function of this family is unknown.
Probab=25.87 E-value=7e+02 Score=25.16 Aligned_cols=115 Identities=22% Similarity=0.274 Sum_probs=62.3
Q ss_pred HHHHHHhcCCCCCCCCCCCCCCcchhHHHHHHHHHhhccCCCCccEEEEEeCC--CCCCCCcccccCCCCCCccCCCCCC
Q 004238 251 LNSLLDELQPDQWPVAPRTRPSRCTGVALSVATGLLGACLPGTGARIVALVGG--PCTEGPGTIVSKDLSEPVRSHKDLD 328 (766)
Q Consensus 251 i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~gGrIi~f~sg--~pt~GpG~l~~~~~~~~~rs~~~~~ 328 (766)
+..+-+.|...+ .. ....++.|.||..|..++... +..+.|-++=.|| +.|.|+.-+
T Consensus 77 a~a~A~~l~~~~--r~--~~~~Taig~Al~~a~~ll~~~-~~~~~RrVIDvSGDG~~N~G~~p~---------------- 135 (205)
T PF06707_consen 77 AEAFAARLRAAP--RR--FGGRTAIGSALDFAAALLAQN-PFECWRRVIDVSGDGPNNQGPRPV---------------- 135 (205)
T ss_pred HHHHHHHHHhCC--CC--CCCCchHHHHHHHHHHHHHhC-CCCCceEEEEECCCCCCCCCCCcc----------------
Confidence 445555555432 11 223389999999999999842 2335566655554 666664211
Q ss_pred cCcCccchhHHHHHHHHHHHHHHcCcEEEEEEecCCcc----Chhcchh--hhhcccceEEEeCCCCchhhHHHHHHHHh
Q 004238 329 KDAAPFFKKAVKFYDGLAKQLVSQGHVLDLFASALDQV----GVAEMKV--AVEKTGGLVVLAESFGHSVFKDSFKRIFE 402 (766)
Q Consensus 329 ~~~~~~~~~a~~fY~~la~~~~~~~isvdlf~~~~~~~----~l~~l~~--l~~~TGG~v~~~~~f~~~~~~~~l~~~l~ 402 (766)
+..-..+...||.|+=+.+....- ++...-. +..=.|..+.-...| +.|.+.+.|-|.
T Consensus 136 --------------~~ard~~~~~GitINgL~I~~~~~~~~~~L~~yy~~~VIgGpgAFV~~a~~~--~df~~AirrKL~ 199 (205)
T PF06707_consen 136 --------------TSARDAAVAAGITINGLAILDDDPFGGADLDAYYRRCVIGGPGAFVETARGF--EDFAEAIRRKLI 199 (205)
T ss_pred --------------HHHHHHHHHCCeEEeeeEecCCCCCccccHHHHHhhhcccCCCceEEEcCCH--HHHHHHHHHHHH
Confidence 011223456799999998876544 4544332 222223334333334 346666655443
No 151
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=25.85 E-value=29 Score=22.07 Aligned_cols=14 Identities=36% Similarity=0.740 Sum_probs=11.7
Q ss_pred eEEecCCCCCCCCC
Q 004238 78 IWICPFCYQRNHFP 91 (766)
Q Consensus 78 ~W~C~~C~~~N~~p 91 (766)
.|.|+.|+..|...
T Consensus 2 ~W~C~~C~~~N~~~ 15 (26)
T smart00547 2 DWECPACTFLNFAS 15 (26)
T ss_pred cccCCCCCCcChhh
Confidence 69999999998643
No 152
>KOG2353 consensus L-type voltage-dependent Ca2+ channel, alpha2/delta subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=24.22 E-value=1.1e+02 Score=38.83 Aligned_cols=49 Identities=22% Similarity=0.350 Sum_probs=43.7
Q ss_pred CCcEEEEEEEcccchHH--HHHHHHHHHHHhccCCCCcEEEEEEECCeEEE
Q 004238 133 LSPVFVFVLDTCMIEEE--LGYARSELKRAIGLLPDNAMVGLVTFGTQAHV 181 (766)
Q Consensus 133 ~~p~~vFvID~s~~~~~--l~~~~~~l~~~l~~lp~~~~VglItf~~~V~~ 181 (766)
.|--.+|++|+|++... +..++..+..+|+.|.++.-|-++||++.++.
T Consensus 224 ~pKdiviLlD~SgSm~g~~~~lak~tv~~iLdtLs~~Dfvni~tf~~~~~~ 274 (1104)
T KOG2353|consen 224 SPKDIVILLDVSGSMSGLRLDLAKQTVNEILDTLSDNDFVNILTFNSEVNP 274 (1104)
T ss_pred CccceEEEEeccccccchhhHHHHHHHHHHHHhcccCCeEEEEeeccccCc
Confidence 66779999999999754 89999999999999999999999999988765
No 153
>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=23.49 E-value=72 Score=22.69 Aligned_cols=27 Identities=26% Similarity=0.725 Sum_probs=17.6
Q ss_pred ccCCCCceecCceeEEc--CCceEEecCCCC
Q 004238 58 RCKTCTAALNAFARVDF--TAKIWICPFCYQ 86 (766)
Q Consensus 58 RC~~C~ayiNp~~~~~~--~~~~W~C~~C~~ 86 (766)
-|..|++ ---|- +++ +...|.|+-|+.
T Consensus 5 pCP~CGG-~DrFr-~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 5 PCPNCGG-SDRFR-FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CCCCCCC-ccccc-cccCCCCcCEEeCCCCC
Confidence 4777776 22233 444 457899999975
No 154
>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=23.44 E-value=30 Score=23.71 Aligned_cols=10 Identities=40% Similarity=1.172 Sum_probs=4.8
Q ss_pred CCcccCCCCc
Q 004238 55 APLRCKTCTA 64 (766)
Q Consensus 55 ~p~RC~~C~a 64 (766)
+++||..|+.
T Consensus 16 ~~irC~~CG~ 25 (32)
T PF03604_consen 16 DPIRCPECGH 25 (32)
T ss_dssp STSSBSSSS-
T ss_pred CcEECCcCCC
Confidence 4455555553
No 155
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.39 E-value=43 Score=36.12 Aligned_cols=25 Identities=20% Similarity=0.660 Sum_probs=19.9
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRNH 89 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~ 89 (766)
-..|..|+. ..++.|.|+-||...+
T Consensus 309 S~~C~~cg~---------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 309 SKTCPCCGH---------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred cccccccCC---------ccceeEECCCCCCeeh
Confidence 367999999 3368999999998744
No 156
>PF14353 CpXC: CpXC protein
Probab=23.27 E-value=74 Score=29.23 Aligned_cols=35 Identities=14% Similarity=0.536 Sum_probs=22.4
Q ss_pred cccCCCCceec--CceeEEcC-------------CceEEecCCCCCCCCC
Q 004238 57 LRCKTCTAALN--AFARVDFT-------------AKIWICPFCYQRNHFP 91 (766)
Q Consensus 57 ~RC~~C~ayiN--p~~~~~~~-------------~~~W~C~~C~~~N~~p 91 (766)
+.|.+|+.-.. -|..++.. =..++|+-||+...++
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 57889987632 22233321 2489999999987663
No 157
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=22.66 E-value=65 Score=25.28 Aligned_cols=30 Identities=23% Similarity=0.635 Sum_probs=20.4
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCCCC--Ccccc
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRNHF--PPHYA 95 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~--p~~y~ 95 (766)
+-+|.+|+.|- + +=+|+.||....+ |+.|+
T Consensus 5 ~rkC~~cg~YT-----L-----ke~Cp~CG~~t~~~~PprFS 36 (59)
T COG2260 5 IRKCPKCGRYT-----L-----KEKCPVCGGDTKVPHPPRFS 36 (59)
T ss_pred hhcCcCCCcee-----e-----cccCCCCCCccccCCCCCCC
Confidence 45799999872 1 2389999977654 44443
No 158
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=22.19 E-value=47 Score=32.15 Aligned_cols=27 Identities=26% Similarity=0.608 Sum_probs=18.5
Q ss_pred CCceEEecCCCCCCCCCcccccCCCCCCCccccCCCce
Q 004238 75 TAKIWICPFCYQRNHFPPHYAAISETNLPCELYPQYTT 112 (766)
Q Consensus 75 ~~~~W~C~~C~~~N~~p~~y~~~~~~~~~pEL~p~~~t 112 (766)
+|+.|+|+.||..-.- .+||-+|.++.
T Consensus 131 ~~~~~vC~vCGy~~~g-----------e~P~~CPiCga 157 (166)
T COG1592 131 EGKVWVCPVCGYTHEG-----------EAPEVCPICGA 157 (166)
T ss_pred cCCEEEcCCCCCcccC-----------CCCCcCCCCCC
Confidence 3569999999986421 45777776653
No 159
>PRK07218 replication factor A; Provisional
Probab=21.93 E-value=41 Score=37.86 Aligned_cols=24 Identities=17% Similarity=0.225 Sum_probs=19.4
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRNH 89 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~ 89 (766)
+-||+.|+-.+ ..|+|+.||...+
T Consensus 297 i~rCP~C~r~v----------~~~~C~~hG~ve~ 320 (423)
T PRK07218 297 IERCPECGRVI----------QKGQCRSHGAVEG 320 (423)
T ss_pred eecCcCccccc----------cCCcCCCCCCcCC
Confidence 68999999877 2499999997643
No 160
>PRK12366 replication factor A; Reviewed
Probab=21.76 E-value=62 Score=38.67 Aligned_cols=26 Identities=23% Similarity=0.603 Sum_probs=20.2
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
..+|..|+--+ ..+.+.|+|+-|+..
T Consensus 532 y~aCp~CnkKv------~~~~g~~~C~~c~~~ 557 (637)
T PRK12366 532 LYLCPNCRKRV------EEVDGEYICEFCGEV 557 (637)
T ss_pred EecccccCeEe------EcCCCcEECCCCCCC
Confidence 58899996643 345679999999987
No 161
>KOG0445 consensus Actin regulatory protein supervillin (gelsolin/villin family) [Cytoskeleton]
Probab=21.33 E-value=78 Score=36.98 Aligned_cols=30 Identities=17% Similarity=0.383 Sum_probs=26.0
Q ss_pred ccccccccCCeEEEEeCCcEEEEEECCchh
Q 004238 640 LLDVASIAADRILLLDTYFSVVIFHGMTIA 669 (766)
Q Consensus 640 ~Ls~~~l~~~~i~llD~g~~i~i~~G~~v~ 669 (766)
.++-+-|++..+++.|-|..||||.|+.+.
T Consensus 362 ipk~~~l~p~eVLvFDFGSEvYVW~Gk~~~ 391 (919)
T KOG0445|consen 362 IPKCSLLQPKEVLVFDFGSEVYVWHGKEVT 391 (919)
T ss_pred cccccccCcceEEEEecCceEEEEcCccCc
Confidence 355667789999999999999999999973
No 162
>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=21.12 E-value=52 Score=22.80 Aligned_cols=10 Identities=40% Similarity=1.431 Sum_probs=9.1
Q ss_pred eEEecCCCCC
Q 004238 78 IWICPFCYQR 87 (766)
Q Consensus 78 ~W~C~~C~~~ 87 (766)
.|+|..||..
T Consensus 2 ~~~C~~CG~i 11 (34)
T cd00729 2 VWVCPVCGYI 11 (34)
T ss_pred eEECCCCCCE
Confidence 6999999986
No 163
>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=20.98 E-value=94 Score=20.99 Aligned_cols=26 Identities=23% Similarity=0.437 Sum_probs=14.2
Q ss_pred ccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 58 RCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 58 RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
.|.+|++= +....++..-+|+-|+..
T Consensus 5 fC~~CG~~----t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAP----TKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--B----EEE-SSSS-EEESSSS-E
T ss_pred ccCcCCcc----ccCCCCcCEeECCCCcCE
Confidence 58888883 334556788899999864
No 164
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=20.87 E-value=32 Score=38.00 Aligned_cols=30 Identities=23% Similarity=0.471 Sum_probs=21.9
Q ss_pred CCCcccCCCCceecCceeEEcCCceEEecCCCCC
Q 004238 54 YAPLRCKTCTAALNAFARVDFTAKIWICPFCYQR 87 (766)
Q Consensus 54 ~~p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~ 87 (766)
|----|++|+.-++|--... ..|+|+ ||..
T Consensus 238 Yh~~~c~~C~~~~~~~~~~~---~~~~Cp-CG~~ 267 (374)
T TIGR00375 238 YHQTACEACGEPAVSEDAET---ACANCP-CGGR 267 (374)
T ss_pred cchhhhcccCCcCCchhhhh---cCCCCC-CCCc
Confidence 44457999988777654333 359999 9998
No 165
>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=20.84 E-value=1.2e+02 Score=27.57 Aligned_cols=34 Identities=15% Similarity=0.168 Sum_probs=25.4
Q ss_pred hHHHHHHHHHHHHHhccCCC---CcEEEEEEECCeEE
Q 004238 147 EEELGYARSELKRAIGLLPD---NAMVGLVTFGTQAH 180 (766)
Q Consensus 147 ~~~l~~~~~~l~~~l~~lp~---~~~VglItf~~~V~ 180 (766)
..-.+.++++|+.-+..-|. +.+|.+++||+.|-
T Consensus 109 ~~fAe~vkDAi~Dyi~T~P~PT~~~~Vt~~~Fd~~V~ 145 (146)
T PF02905_consen 109 HLFAECVKDAIRDYIMTRPQPTCNTQVTVCSFDDGVM 145 (146)
T ss_dssp HHHHHHHHHHHHHHHCTS-TTGGGEEEEEEEEEEEE-
T ss_pred hHHHHHHHHHHHHHhcCCCCCCcceEEEEEeCCCCCc
Confidence 34457888999888877663 68999999998764
No 166
>PRK08402 replication factor A; Reviewed
Probab=20.78 E-value=71 Score=35.11 Aligned_cols=29 Identities=24% Similarity=0.493 Sum_probs=19.5
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRN 88 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N 88 (766)
..+|..|+-- +..+.+++.|+|.-|+..+
T Consensus 212 y~aCp~CnKk----v~~~~~~~~~~Ce~~~~v~ 240 (355)
T PRK08402 212 YDACPECRRK----VDYDPATDTWICPEHGEVE 240 (355)
T ss_pred EecCCCCCeE----EEEecCCCCEeCCCCCCcC
Confidence 4788887651 1224556799999998643
No 167
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=20.74 E-value=50 Score=35.39 Aligned_cols=28 Identities=25% Similarity=0.699 Sum_probs=21.1
Q ss_pred CCcccCCCCceecCceeEEcCCceEEecCCCCCCCC
Q 004238 55 APLRCKTCTAALNAFARVDFTAKIWICPFCYQRNHF 90 (766)
Q Consensus 55 ~p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~ 90 (766)
..-||.+|+- ....-.|.||-|+..-.+
T Consensus 353 ~~YRC~~CGF--------~a~~l~W~CPsC~~W~Ti 380 (389)
T COG2956 353 PRYRCQNCGF--------TAHTLYWHCPSCRAWETI 380 (389)
T ss_pred CCceecccCC--------cceeeeeeCCCccccccc
Confidence 5689999983 333457999999987665
No 168
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=20.69 E-value=1.3e+02 Score=28.20 Aligned_cols=26 Identities=23% Similarity=0.462 Sum_probs=20.0
Q ss_pred CcccCCCCceecCceeEEcCCceEEecCCCCCCC
Q 004238 56 PLRCKTCTAALNAFARVDFTAKIWICPFCYQRNH 89 (766)
Q Consensus 56 p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~ 89 (766)
=.||.+|+.+.=|= +=.|+-|+....
T Consensus 29 g~kC~~CG~v~~PP--------r~~Cp~C~~~~~ 54 (140)
T COG1545 29 GTKCKKCGRVYFPP--------RAYCPKCGSETE 54 (140)
T ss_pred EEEcCCCCeEEcCC--------cccCCCCCCCCc
Confidence 37899999976553 457999999863
No 169
>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=20.56 E-value=50 Score=40.30 Aligned_cols=26 Identities=23% Similarity=0.500 Sum_probs=20.9
Q ss_pred CCcccCCCCceecCceeEEcCCceEEecCCCCCCCC
Q 004238 55 APLRCKTCTAALNAFARVDFTAKIWICPFCYQRNHF 90 (766)
Q Consensus 55 ~p~RC~~C~ayiNp~~~~~~~~~~W~C~~C~~~N~~ 90 (766)
..-+|.+|+.| +-.++|+.||..+..
T Consensus 624 ~~RKCPkCG~y----------Tlk~rCP~CG~~Te~ 649 (1095)
T TIGR00354 624 AIRKCPQCGKE----------SFWLKCPVCGELTEQ 649 (1095)
T ss_pred EEEECCCCCcc----------cccccCCCCCCcccc
Confidence 45789999997 247899999998754
No 170
>COG1773 Rubredoxin [Energy production and conversion]
Probab=20.43 E-value=48 Score=25.76 Aligned_cols=11 Identities=36% Similarity=1.075 Sum_probs=8.1
Q ss_pred CceEEecCCCC
Q 004238 76 AKIWICPFCYQ 86 (766)
Q Consensus 76 ~~~W~C~~C~~ 86 (766)
--.|.|+.|+.
T Consensus 34 Pd~w~CP~Cg~ 44 (55)
T COG1773 34 PDDWVCPECGV 44 (55)
T ss_pred CCccCCCCCCC
Confidence 34688888885
No 171
>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=20.40 E-value=88 Score=31.96 Aligned_cols=27 Identities=19% Similarity=0.479 Sum_probs=19.5
Q ss_pred CcccCCCCc---eecCceeEEcCCceEEec
Q 004238 56 PLRCKTCTA---ALNAFARVDFTAKIWICP 82 (766)
Q Consensus 56 p~RC~~C~a---yiNp~~~~~~~~~~W~C~ 82 (766)
.-.|..|++ |+.-...=+.+++.|.|+
T Consensus 235 ~~~C~~CGs~~s~LdEvi~dd~G~~~~~CS 264 (277)
T PF06007_consen 235 DGPCALCGSTDSFLDEVIDDDDGGRMFVCS 264 (277)
T ss_pred cCcccccCCCceeceeeEEcCCCCEEEEEC
Confidence 346888875 566665556788999996
No 172
>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=20.26 E-value=58 Score=27.39 Aligned_cols=30 Identities=23% Similarity=0.440 Sum_probs=17.0
Q ss_pred cccCCCCceecCc----eeEE-----cCCceEEecCCCC
Q 004238 57 LRCKTCTAALNAF----ARVD-----FTAKIWICPFCYQ 86 (766)
Q Consensus 57 ~RC~~C~ayiNp~----~~~~-----~~~~~W~C~~C~~ 86 (766)
.-|++|++++=|- .++. .+.-.|+|..||+
T Consensus 47 ~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 47 TICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp TB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred ccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 4599999997665 3455 3445789999984
No 173
>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=20.09 E-value=78 Score=23.29 Aligned_cols=22 Identities=9% Similarity=0.277 Sum_probs=15.1
Q ss_pred cccCCCCceecCceeEEcCCceEEecCCC
Q 004238 57 LRCKTCTAALNAFARVDFTAKIWICPFCY 85 (766)
Q Consensus 57 ~RC~~C~ayiNp~~~~~~~~~~W~C~~C~ 85 (766)
+.|..|+. .|.. |.+|+|..|.
T Consensus 1 I~CDgCg~--~PI~-----G~RykC~~C~ 22 (43)
T cd02342 1 IQCDGCGV--LPIT-----GPRYKSKVKE 22 (43)
T ss_pred CCCCCCCC--Cccc-----ccceEeCCCC
Confidence 45777773 3433 6899999885
Done!