Query 008566
Match_columns 561
No_of_seqs 128 out of 758
Neff 8.0
Searched_HMMs 46136
Date Thu Mar 28 13:46:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008566.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008566hhsearch_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-113 4E-118 964.7 56.4 545 2-555 1-546 (761)
2 KOG1986 Vesicle coat complex C 100.0 1E-106 2E-111 848.2 45.8 525 3-553 2-527 (745)
3 COG5047 SEC23 Vesicle coat com 100.0 7E-100 1E-104 777.3 33.2 534 2-553 1-538 (755)
4 KOG1985 Vesicle coat complex C 100.0 1.8E-95 4E-100 774.4 34.3 464 6-550 166-652 (887)
5 KOG1984 Vesicle coat complex C 100.0 7.6E-90 1.7E-94 732.1 36.6 476 7-553 284-780 (1007)
6 COG5028 Vesicle coat complex C 100.0 7.1E-85 1.5E-89 688.1 35.3 462 6-550 146-628 (861)
7 PTZ00395 Sec24-related protein 100.0 7.7E-81 1.7E-85 690.0 40.0 476 7-546 649-1322(1560)
8 cd01478 Sec23-like Sec23-like: 100.0 3.1E-55 6.8E-60 437.1 28.2 262 128-395 2-267 (267)
9 cd01468 trunk_domain trunk dom 100.0 4.9E-44 1.1E-48 353.8 24.3 226 128-394 2-234 (239)
10 cd01479 Sec24-like Sec24-like: 100.0 1.9E-43 4.2E-48 349.5 22.6 227 128-397 2-240 (244)
11 PF04811 Sec23_trunk: Sec23/Se 100.0 1.3E-42 2.9E-47 344.8 18.9 231 128-396 2-242 (243)
12 PF08033 Sec23_BS: Sec23/Sec24 99.9 7.1E-22 1.5E-26 167.2 11.0 96 407-514 1-96 (96)
13 PF04810 zf-Sec23_Sec24: Sec23 99.6 8.6E-17 1.9E-21 112.2 2.1 40 57-96 1-40 (40)
14 cd01465 vWA_subgroup VWA subgr 98.7 1.5E-06 3.3E-11 80.9 17.8 160 131-385 2-164 (170)
15 cd01463 vWA_VGCC_like VWA Volt 98.7 2E-06 4.4E-11 82.1 18.5 167 128-384 12-189 (190)
16 PRK13685 hypothetical protein; 98.7 2.4E-06 5.2E-11 88.7 20.4 161 129-383 88-275 (326)
17 cd01456 vWA_ywmD_type VWA ywmD 98.6 1.4E-06 3.1E-11 84.3 15.9 168 128-378 19-196 (206)
18 cd01451 vWA_Magnesium_chelatas 98.6 3.5E-06 7.6E-11 79.5 18.3 161 132-388 3-171 (178)
19 cd01466 vWA_C3HC4_type VWA C3H 98.6 1.9E-06 4.1E-11 79.5 15.9 149 132-381 3-154 (155)
20 cd01453 vWA_transcription_fact 98.5 4.4E-06 9.5E-11 79.3 15.9 153 130-383 4-167 (183)
21 cd01467 vWA_BatA_type VWA BatA 98.4 1.3E-05 2.9E-10 75.4 17.4 156 130-383 3-176 (180)
22 TIGR03436 acidobact_VWFA VWFA- 98.4 4.7E-05 1E-09 78.0 21.5 49 128-176 52-102 (296)
23 cd01470 vWA_complement_factors 98.3 2.8E-05 6E-10 74.7 16.8 168 132-385 3-191 (198)
24 cd01472 vWA_collagen von Wille 98.3 5.8E-05 1.3E-09 70.1 17.8 152 132-384 3-164 (164)
25 TIGR00868 hCaCC calcium-activa 98.3 4E-05 8.7E-10 87.5 19.4 155 128-383 303-462 (863)
26 cd01461 vWA_interalpha_trypsin 98.2 9.8E-05 2.1E-09 68.6 17.9 159 129-385 2-163 (171)
27 PF13768 VWA_3: von Willebrand 98.2 3.9E-05 8.4E-10 70.5 14.5 152 132-380 3-155 (155)
28 PF13519 VWA_2: von Willebrand 98.2 2.3E-05 5E-10 72.4 12.8 151 132-382 2-159 (172)
29 cd01480 vWA_collagen_alpha_1-V 98.2 9.4E-05 2E-09 70.3 16.3 157 131-385 4-173 (186)
30 cd01452 VWA_26S_proteasome_sub 98.1 0.0001 2.2E-09 69.8 16.1 145 131-374 5-161 (187)
31 cd01471 vWA_micronemal_protein 98.0 0.00038 8.1E-09 66.0 16.5 148 132-373 3-160 (186)
32 cd01475 vWA_Matrilin VWA_Matri 97.9 0.00052 1.1E-08 67.3 16.9 155 129-385 2-170 (224)
33 cd01474 vWA_ATR ATR (Anthrax T 97.9 0.00045 9.9E-09 65.5 15.7 156 129-385 4-168 (185)
34 cd01482 vWA_collagen_alphaI-XI 97.9 0.0012 2.5E-08 61.4 17.6 44 132-175 3-51 (164)
35 TIGR03788 marine_srt_targ mari 97.9 0.002 4.3E-08 72.6 22.5 187 128-415 270-458 (596)
36 cd01469 vWA_integrins_alpha_su 97.8 0.0016 3.5E-08 61.3 17.8 156 132-385 3-172 (177)
37 cd01450 vWFA_subfamily_ECM Von 97.8 0.0013 2.8E-08 60.1 16.2 144 132-374 3-155 (161)
38 cd01477 vWA_F09G8-8_type VWA F 97.6 0.003 6.4E-08 60.5 16.7 48 129-176 19-77 (193)
39 TIGR02031 BchD-ChlD magnesium 97.6 0.0032 6.9E-08 70.5 18.9 175 129-387 407-586 (589)
40 PRK13406 bchD magnesium chelat 97.6 0.0057 1.2E-07 68.1 19.9 173 128-390 400-576 (584)
41 PF00092 VWA: von Willebrand f 97.6 0.002 4.3E-08 59.9 14.0 156 132-386 2-170 (178)
42 smart00327 VWA von Willebrand 97.5 0.0082 1.8E-07 55.5 17.9 154 130-380 2-164 (177)
43 cd01481 vWA_collagen_alpha3-VI 97.5 0.0058 1.3E-07 56.9 16.5 44 132-175 3-51 (165)
44 PTZ00441 sporozoite surface pr 97.5 0.0068 1.5E-07 66.2 18.7 165 128-386 41-218 (576)
45 cd01476 VWA_integrin_invertebr 97.5 0.0058 1.3E-07 56.4 16.1 41 132-172 3-47 (163)
46 TIGR02442 Cob-chelat-sub cobal 97.4 0.0086 1.9E-07 67.8 18.6 161 128-381 464-632 (633)
47 cd00198 vWFA Von Willebrand fa 97.3 0.016 3.4E-07 52.1 16.5 148 131-374 2-155 (161)
48 COG1240 ChlD Mg-chelatase subu 97.3 0.01 2.3E-07 58.1 15.6 168 129-389 78-252 (261)
49 PF04056 Ssl1: Ssl1-like; Int 97.2 0.0082 1.8E-07 57.0 13.5 90 269-394 80-170 (193)
50 cd01473 vWA_CTRP CTRP for CS 97.2 0.018 3.9E-07 55.1 15.8 149 132-373 3-161 (192)
51 cd01464 vWA_subfamily VWA subf 96.8 0.013 2.9E-07 54.9 11.6 45 132-176 6-58 (176)
52 cd01454 vWA_norD_type norD typ 96.8 0.059 1.3E-06 50.3 15.7 43 131-173 2-48 (174)
53 cd01462 VWA_YIEM_type VWA YIEM 96.6 0.1 2.2E-06 47.4 15.2 43 132-174 3-48 (152)
54 cd01458 vWA_ku Ku70/Ku80 N-ter 96.2 0.22 4.8E-06 48.4 16.1 69 267-360 104-173 (218)
55 KOG2884 26S proteasome regulat 94.7 0.79 1.7E-05 43.7 12.8 99 246-383 71-175 (259)
56 TIGR00578 ku70 ATP-dependent D 94.3 1 2.2E-05 50.7 15.1 73 269-366 117-191 (584)
57 COG4245 TerY Uncharacterized p 91.1 0.42 9.1E-06 44.7 5.3 48 129-177 4-59 (207)
58 cd01457 vWA_ORF176_type VWA OR 89.8 6.3 0.00014 37.5 12.6 45 129-173 2-57 (199)
59 cd01460 vWA_midasin VWA_Midasi 88.0 22 0.00048 35.7 15.4 47 128-175 59-111 (266)
60 KOG2807 RNA polymerase II tran 85.8 23 0.0005 36.1 13.7 86 270-390 144-229 (378)
61 TIGR00627 tfb4 transcription f 84.7 10 0.00023 38.3 11.1 86 268-383 118-209 (279)
62 PF10058 DUF2296: Predicted in 83.6 0.7 1.5E-05 34.4 1.7 33 58-90 22-54 (54)
63 PRK00398 rpoP DNA-directed RNA 82.7 0.95 2.1E-05 32.4 2.0 30 58-91 3-32 (46)
64 PRK10997 yieM hypothetical pro 80.2 58 0.0013 35.7 15.4 52 129-180 323-377 (487)
65 TIGR01053 LSD1 zinc finger dom 79.6 1.6 3.5E-05 28.5 2.0 30 59-92 2-31 (31)
66 PF03850 Tfb4: Transcription f 78.2 18 0.00039 36.6 10.2 87 269-385 116-209 (276)
67 COG5148 RPN10 26S proteasome r 74.1 21 0.00045 33.5 8.4 75 244-358 69-145 (243)
68 smart00661 RPOL9 RNA polymeras 71.2 2.8 6E-05 30.6 1.8 33 60-94 2-34 (52)
69 PF08271 TF_Zn_Ribbon: TFIIB z 69.4 5.9 0.00013 27.8 3.0 27 60-89 2-28 (43)
70 smart00187 INB Integrin beta s 69.1 1.7E+02 0.0037 31.4 23.1 284 129-472 99-391 (423)
71 PF09967 DUF2201: VWA-like dom 68.7 13 0.00027 32.9 5.7 41 133-175 2-44 (126)
72 KOG2353 L-type voltage-depende 67.8 41 0.0009 40.5 11.2 49 128-176 224-274 (1104)
73 PF10122 Mu-like_Com: Mu-like 66.7 2.7 6E-05 30.6 0.9 33 59-93 5-37 (51)
74 PF00362 Integrin_beta: Integr 65.5 2E+02 0.0044 31.0 16.5 282 129-472 102-394 (426)
75 PF09723 Zn-ribbon_8: Zinc rib 64.6 3.5 7.6E-05 28.9 1.1 30 59-89 6-35 (42)
76 PF09082 DUF1922: Domain of un 63.7 3 6.5E-05 32.4 0.6 30 58-93 3-32 (68)
77 cd01455 vWA_F11C1-5a_type Von 60.9 1.4E+02 0.003 28.5 11.4 100 245-384 75-175 (191)
78 PRK12380 hydrogenase nickel in 60.1 5.2 0.00011 34.7 1.5 27 58-90 70-96 (113)
79 PF03731 Ku_N: Ku70/Ku80 N-ter 58.8 17 0.00038 35.1 5.2 64 269-357 105-172 (224)
80 PRK03954 ribonuclease P protei 58.4 6.7 0.00014 34.4 1.9 35 59-93 65-106 (121)
81 cd00350 rubredoxin_like Rubred 58.4 6.7 0.00015 25.9 1.5 23 60-88 3-25 (33)
82 TIGR00100 hypA hydrogenase nic 58.2 5.9 0.00013 34.4 1.6 27 58-90 70-96 (115)
83 TIGR02605 CxxC_CxxC_SSSS putat 57.0 5.9 0.00013 28.9 1.2 31 59-90 6-36 (52)
84 PF11781 RRN7: RNA polymerase 54.1 12 0.00026 25.3 2.2 26 59-89 9-34 (36)
85 PF05762 VWA_CoxE: VWA domain 53.2 25 0.00055 34.2 5.3 43 129-174 56-100 (222)
86 PF13719 zinc_ribbon_5: zinc-r 52.8 8.3 0.00018 26.2 1.3 33 58-90 2-35 (37)
87 PF14803 Nudix_N_2: Nudix N-te 52.3 5.6 0.00012 26.6 0.4 30 60-89 2-31 (34)
88 smart00834 CxxC_CXXC_SSSS Puta 51.1 8.2 0.00018 26.4 1.1 29 59-88 6-34 (41)
89 PF08792 A2L_zn_ribbon: A2L zi 51.0 17 0.00037 24.1 2.5 29 58-90 3-31 (33)
90 PRK03681 hypA hydrogenase nick 50.3 9.5 0.00021 33.1 1.6 28 58-90 70-97 (114)
91 PF12773 DZR: Double zinc ribb 50.0 10 0.00022 27.3 1.5 32 57-93 11-42 (50)
92 PF13240 zinc_ribbon_2: zinc-r 49.5 7.9 0.00017 23.4 0.7 21 60-88 1-21 (23)
93 KOG3799 Rab3 effector RIM1 and 48.7 8.7 0.00019 33.8 1.1 31 57-91 88-118 (169)
94 PF09779 Ima1_N: Ima1 N-termin 48.1 12 0.00025 33.5 1.8 33 59-93 1-33 (131)
95 PF02318 FYVE_2: FYVE-type zin 47.9 8.6 0.00019 33.5 1.0 32 59-90 72-104 (118)
96 cd00730 rubredoxin Rubredoxin; 47.4 9.7 0.00021 27.9 1.0 29 60-88 3-42 (50)
97 PF07282 OrfB_Zn_ribbon: Putat 46.8 13 0.00029 28.8 1.8 28 59-90 29-56 (69)
98 PF06943 zf-LSD1: LSD1 zinc fi 46.1 17 0.00037 22.5 1.8 24 61-88 1-24 (25)
99 PRK12286 rpmF 50S ribosomal pr 44.1 19 0.00041 27.1 2.1 26 57-91 26-51 (57)
100 PRK00564 hypA hydrogenase nick 44.0 9.1 0.0002 33.4 0.5 29 58-91 71-99 (117)
101 PRK00432 30S ribosomal protein 43.8 13 0.00029 27.1 1.3 25 59-89 21-46 (50)
102 PF13717 zinc_ribbon_4: zinc-r 42.6 15 0.00033 24.8 1.3 31 59-89 3-34 (36)
103 PF12760 Zn_Tnp_IS1595: Transp 42.2 25 0.00053 25.0 2.4 27 59-88 19-45 (46)
104 smart00401 ZnF_GATA zinc finge 41.3 16 0.00035 26.8 1.4 32 58-89 3-34 (52)
105 PF10571 UPF0547: Uncharacteri 41.1 14 0.0003 23.1 0.8 23 60-90 2-24 (26)
106 COG0275 Predicted S-adenosylme 39.8 36 0.00078 34.7 4.0 29 143-171 218-246 (314)
107 smart00659 RPOLCX RNA polymera 39.5 24 0.00053 25.0 2.0 25 60-89 4-28 (44)
108 COG1996 RPC10 DNA-directed RNA 39.1 16 0.00036 26.5 1.1 27 59-89 7-33 (49)
109 COG2425 Uncharacterized protei 39.1 2E+02 0.0043 31.1 9.7 43 129-172 273-318 (437)
110 PF00641 zf-RanBP: Zn-finger i 39.1 11 0.00024 24.1 0.2 15 79-93 3-17 (30)
111 COG1096 Predicted RNA-binding 38.1 19 0.00041 33.9 1.7 26 58-89 149-174 (188)
112 PRK03824 hypA hydrogenase nick 38.0 20 0.00042 32.2 1.7 33 58-90 70-117 (135)
113 PF01927 Mut7-C: Mut7-C RNAse 37.5 21 0.00046 32.4 1.9 39 58-96 91-140 (147)
114 PRK12722 transcriptional activ 37.2 17 0.00037 34.4 1.2 29 57-88 133-162 (187)
115 PF08274 PhnA_Zn_Ribbon: PhnA 36.6 20 0.00043 23.3 1.1 25 59-88 3-27 (30)
116 cd01121 Sms Sms (bacterial rad 36.3 19 0.00041 38.1 1.5 27 60-94 2-28 (372)
117 PF00301 Rubredoxin: Rubredoxi 36.3 11 0.00025 27.1 -0.1 10 79-88 33-42 (47)
118 COG1198 PriA Primosomal protei 35.7 1E+02 0.0023 35.6 7.3 106 58-180 444-571 (730)
119 TIGR01384 TFS_arch transcripti 35.5 25 0.00053 29.8 1.8 27 60-92 2-28 (104)
120 COG4867 Uncharacterized protei 35.4 3.6E+02 0.0078 28.9 10.4 100 268-383 532-635 (652)
121 PRK00762 hypA hydrogenase nick 35.0 17 0.00038 32.0 0.9 33 58-91 70-103 (124)
122 smart00778 Prim_Zn_Ribbon Zinc 34.8 43 0.00094 22.8 2.5 27 60-88 5-33 (37)
123 TIGR00311 aIF-2beta translatio 34.3 39 0.00084 30.2 3.0 31 59-92 98-130 (133)
124 TIGR02098 MJ0042_CXXC MJ0042 f 33.6 25 0.00053 23.7 1.2 31 59-89 3-34 (38)
125 COG3357 Predicted transcriptio 33.3 21 0.00046 29.3 1.0 36 57-96 57-92 (97)
126 PF13894 zf-C2H2_4: C2H2-type 32.9 21 0.00046 20.6 0.8 11 81-91 1-11 (24)
127 COG1998 RPS31 Ribosomal protei 32.8 30 0.00064 25.1 1.5 25 59-89 20-46 (51)
128 PHA00626 hypothetical protein 32.7 42 0.00091 25.1 2.3 30 61-92 3-35 (59)
129 PRK06393 rpoE DNA-directed RNA 32.5 25 0.00055 27.1 1.2 25 59-93 6-30 (64)
130 smart00132 LIM Zinc-binding do 32.4 36 0.00078 22.3 2.0 29 60-88 1-35 (39)
131 TIGR00686 phnA alkylphosphonat 32.2 35 0.00076 29.1 2.2 28 58-90 2-29 (109)
132 PF07754 DUF1610: Domain of un 32.0 32 0.0007 21.1 1.4 24 61-88 1-24 (24)
133 COG5415 Predicted integral mem 31.9 39 0.00085 32.3 2.6 38 58-95 192-229 (251)
134 smart00547 ZnF_RBZ Zinc finger 31.8 21 0.00045 21.8 0.6 14 80-93 2-15 (26)
135 COG2051 RPS27A Ribosomal prote 30.4 45 0.00097 25.9 2.2 31 58-91 19-49 (67)
136 PF04032 Rpr2: RNAse P Rpr2/Rp 30.2 29 0.00063 27.9 1.4 30 59-88 47-85 (85)
137 PF08273 Prim_Zn_Ribbon: Zinc- 29.9 38 0.00082 23.5 1.7 27 61-88 6-34 (40)
138 TIGR00006 S-adenosyl-methyltra 29.4 60 0.0013 33.3 3.8 28 144-171 215-242 (305)
139 PF00320 GATA: GATA zinc finge 29.2 17 0.00037 24.5 -0.2 28 61-88 1-28 (36)
140 KOG2846 Predicted membrane pro 28.2 29 0.00062 35.6 1.2 35 59-93 221-255 (328)
141 KOG2487 RNA polymerase II tran 27.7 90 0.0019 31.2 4.4 45 338-385 185-229 (314)
142 PF03660 PHF5: PHF5-like prote 27.5 24 0.00052 29.8 0.4 40 59-98 28-73 (106)
143 PRK08351 DNA-directed RNA poly 27.1 39 0.00085 25.8 1.5 25 60-94 5-29 (61)
144 COG2023 RPR2 RNase P subunit R 27.0 44 0.00096 28.4 1.9 35 59-93 57-95 (105)
145 PF01155 HypA: Hydrogenase exp 26.9 16 0.00034 31.6 -0.8 27 58-90 70-96 (113)
146 COG2956 Predicted N-acetylgluc 26.6 33 0.00072 35.3 1.3 29 57-93 353-381 (389)
147 PF14353 CpXC: CpXC protein 26.4 62 0.0013 28.4 2.9 35 59-93 2-51 (128)
148 PRK08402 replication factor A; 25.9 52 0.0011 34.6 2.6 28 58-89 212-239 (355)
149 PF06827 zf-FPG_IleRS: Zinc fi 25.8 50 0.0011 21.0 1.6 27 60-88 3-29 (30)
150 PF12257 DUF3608: Protein of u 25.8 1.9E+02 0.0041 29.4 6.5 66 270-363 204-274 (281)
151 PRK10220 hypothetical protein; 25.5 61 0.0013 27.7 2.5 29 58-91 3-31 (111)
152 COG0675 Transposase and inacti 25.4 38 0.00082 34.7 1.6 24 59-91 310-333 (364)
153 PF02891 zf-MIZ: MIZ/SP-RING z 25.2 26 0.00056 25.5 0.2 13 76-88 37-49 (50)
154 PF15288 zf-CCHC_6: Zinc knuck 25.1 29 0.00062 24.1 0.4 10 59-68 2-11 (40)
155 PRK00050 16S rRNA m(4)C1402 me 24.8 82 0.0018 32.2 3.8 29 144-172 211-239 (296)
156 PF02905 EBV-NA1: Epstein Barr 24.0 1.8E+02 0.0039 25.5 5.1 34 142-175 109-145 (146)
157 PRK08270 anaerobic ribonucleos 23.9 38 0.00082 38.7 1.3 24 57-89 625-648 (656)
158 cd00729 rubredoxin_SM Rubredox 23.8 43 0.00093 22.3 1.0 12 80-91 2-13 (34)
159 COG1997 RPL43A Ribosomal prote 23.6 84 0.0018 25.8 2.8 33 56-92 33-65 (89)
160 PRK00420 hypothetical protein; 23.5 59 0.0013 28.1 2.1 30 59-93 24-53 (112)
161 PF06707 DUF1194: Protein of u 22.7 7E+02 0.015 24.1 11.1 113 247-396 77-197 (205)
162 PF02150 RNA_POL_M_15KD: RNA p 22.6 1.1E+02 0.0023 20.5 2.8 31 59-92 2-32 (35)
163 PRK08271 anaerobic ribonucleos 22.3 45 0.00098 37.7 1.5 26 57-90 565-590 (623)
164 PF05907 DUF866: Eukaryotic pr 22.1 46 0.001 30.8 1.3 34 59-92 31-76 (161)
165 PF05129 Elf1: Transcription e 21.9 34 0.00073 27.8 0.3 15 79-93 21-35 (81)
166 cd04476 RPA1_DBD_C RPA1_DBD_C: 21.6 64 0.0014 29.6 2.2 29 59-93 35-64 (166)
167 PRK12366 replication factor A; 21.5 61 0.0013 37.0 2.3 26 58-89 532-557 (637)
168 COG1545 Predicted nucleic-acid 21.4 1.6E+02 0.0035 26.4 4.6 62 59-142 30-96 (140)
169 PRK07218 replication factor A; 21.3 44 0.00095 36.0 1.1 23 58-90 297-319 (423)
170 COG2888 Predicted Zn-ribbon RN 21.0 82 0.0018 23.9 2.1 27 58-88 9-35 (61)
171 cd02342 ZZ_UBA_plant Zinc fing 20.7 76 0.0016 22.4 1.8 22 59-87 1-22 (43)
172 COG2093 DNA-directed RNA polym 20.7 47 0.001 25.4 0.8 26 60-93 6-31 (64)
173 PF03604 DNA_RNApol_7kD: DNA d 20.7 40 0.00086 22.2 0.4 10 57-66 16-25 (32)
174 PF09943 DUF2175: Uncharacteri 20.6 46 0.00099 28.1 0.8 12 79-90 1-12 (101)
175 TIGR01031 rpmF_bact ribosomal 20.5 65 0.0014 24.0 1.5 26 57-91 25-50 (55)
176 PRK14810 formamidopyrimidine-D 20.4 82 0.0018 31.8 2.8 27 60-88 246-272 (272)
177 PF12874 zf-met: Zinc-finger o 20.4 59 0.0013 19.3 1.1 11 81-91 1-11 (25)
178 PF05191 ADK_lid: Adenylate ki 20.4 50 0.0011 22.3 0.8 26 61-88 4-29 (36)
179 PRK14892 putative transcriptio 20.3 76 0.0017 26.8 2.1 35 57-92 20-54 (99)
180 TIGR00354 polC DNA polymerase, 20.1 53 0.0011 38.6 1.4 26 57-92 624-649 (1095)
181 cd02340 ZZ_NBR1_like Zinc fing 20.0 75 0.0016 22.3 1.7 21 59-87 1-21 (43)
182 PF13453 zf-TFIIB: Transcripti 20.0 75 0.0016 21.9 1.7 26 61-88 2-27 (41)
No 1
>PLN00162 transport protein sec23; Provisional
Probab=100.00 E-value=1.9e-113 Score=964.65 Aligned_cols=545 Identities=68% Similarity=1.150 Sum_probs=489.8
Q ss_pred CCcccccCCCeeeeeccCCCCCHHHhhhCCCCeEEEEccCCCCCCCCCCCCCCCCCCcccCCCCceecCceEEEcCCcee
Q 008566 2 TEFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRTCRSILNPFSIVDFAAKIW 81 (561)
Q Consensus 2 ~~~~~~~~~~~iR~T~~~~P~~~~~~~~~~lPlg~iv~P~~~~~~~~~~~p~~~~~~~RC~~C~ayiNp~~~~~~~~~~w 81 (561)
|||.+.|+.++||+|||+||+++.++++++|||||+|+||++. +++|+++++|+||++|+|||||||+++.++++|
T Consensus 1 ~~~~~~e~~~gvR~s~n~~P~t~~~~~~~~iPlg~v~tPl~~~----~~vp~v~~~pvRC~~CraylNPf~~~d~~~~~W 76 (761)
T PLN00162 1 MDFAELEAIDGVRMSWNVWPSSKIEASKCVIPLAALYTPLKPL----PELPVLPYDPLRCRTCRAVLNPYCRVDFQAKIW 76 (761)
T ss_pred CchhhhcccCceEeeeecCCCCHHHHhcCCCCeEEEEecCCcC----CCCCcCCCCCCccCCCcCEECCceEEecCCCEE
Confidence 7899999999999999999999999999999999999999987 569999999999999999999999999999999
Q ss_pred EeCCCCCCCCCCccCcCCCCCCCCcccCCCCcceEEeCCCCCCCCCCCcEEEEEEEcccchhhHHHHHHHHHHHhhcCCC
Q 008566 82 ICPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPGPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLPD 161 (561)
Q Consensus 82 ~C~~C~~~N~~p~~y~~~~~~~~~pEl~~~~~tvey~~~~~~~~~~~~p~~vFvID~s~~~~~~~~l~~~l~~~l~~l~~ 161 (561)
+||||+..|.+|++|..+++.++||||.|+++||||.+++....+..||+|+||||+|..+++++.++++|+++|+.||+
T Consensus 77 ~C~~C~~~N~~P~~Y~~~~~~~~p~EL~p~~~TvEY~~p~~~~~~~~pp~fvFvID~s~~~~~l~~lk~sl~~~L~~LP~ 156 (761)
T PLN00162 77 ICPFCFQRNHFPPHYSSISETNLPAELFPQYTTVEYTLPPGSGGAPSPPVFVFVVDTCMIEEELGALKSALLQAIALLPE 156 (761)
T ss_pred EccCCCCCCCCchHhcccCccCCChhhcCCceeEEEECCCCCCCCCCCcEEEEEEecchhHHHHHHHHHHHHHHHHhCCC
Confidence 99999999999999987777889999998999999999821111226999999999999999999999999999999999
Q ss_pred CceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHHhccCCCCCCCCCccccCcCCCCCCccccceeeech
Q 008566 162 NSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAF 241 (561)
Q Consensus 162 ~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 241 (561)
+++|||||||+.||||+++ ... +++++||+|+++++.+++++++++++.+..+.....+.-.++++++..++||+|++
T Consensus 157 ~a~VGlITF~s~V~~~~L~-~~~-~~~~~Vf~g~k~~t~~~l~~~l~l~~~~~~~~~~~~~~~~~~~~~p~~~~fLvpl~ 234 (761)
T PLN00162 157 NALVGLITFGTHVHVHELG-FSE-CSKSYVFRGNKEVSKDQILEQLGLGGKKRRPAGGGIAGARDGLSSSGVNRFLLPAS 234 (761)
T ss_pred CCEEEEEEECCEEEEEEcC-CCC-CcceEEecCCccCCHHHHHHHhccccccccccccccccccccccCCCccceeEEHH
Confidence 9999999999999999998 666 89999999999999999999998765321111000000011234456789999999
Q ss_pred hhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCC
Q 008566 242 DCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHK 321 (561)
Q Consensus 242 ~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~ 321 (561)
||+..|..+|++|++++|++++++|+.||+|+||++|..+|+.+.++.||||++|++||||.|||+|+.+++++++|+|+
T Consensus 235 e~~~~i~~lLe~L~~~~~~~~~~~rp~r~tG~AL~vA~~lL~~~~~~~gGrI~~F~sgppT~GpG~v~~r~~~~~~rsh~ 314 (761)
T PLN00162 235 ECEFTLNSALEELQKDPWPVPPGHRPARCTGAALSVAAGLLGACVPGTGARIMAFVGGPCTEGPGAIVSKDLSEPIRSHK 314 (761)
T ss_pred HHHHHHHHHHHhhhccccccCCCCCCCccHHHHHHHHHHHHhhccCCCceEEEEEeCCCCCCCCceeecccccccccCcc
Confidence 99999999999999999988889999999999999999999987778999999999999999999999999999999999
Q ss_pred CCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccChhcchhhhhccCcEEEEcCCCCccchHHHHHHHHh-cc
Q 008566 322 DLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVFH-SG 400 (561)
Q Consensus 322 ~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~~~~~-~~ 400 (561)
+++++++++++++.+||++||.+|+++||+||||+++.+|+|+++|+.|++.|||.+++|++|+.+.|+++|+++|. +.
T Consensus 315 di~k~~~~~~~~a~~fY~~la~~~~~~gisvDlF~~s~dqvglaem~~l~~~TGG~v~~~~sF~~~~f~~~l~r~~~r~~ 394 (761)
T PLN00162 315 DLDKDAAPYYKKAVKFYEGLAKQLVAQGHVLDVFACSLDQVGVAEMKVAVERTGGLVVLAESFGHSVFKDSLRRVFERDG 394 (761)
T ss_pred ccccchhhhcchHHHHHHHHHHHHHHcCceEEEEEccccccCHHHHhhhHhhcCcEEEEeCCcChHHHHHHHHHHhcccc
Confidence 99998889999999999999999999999999999999999999999999999999999999999999999999995 44
Q ss_pred ccCcCceeeeEEEEEecCCceEEeEEcCccccCCCCCCccCccccCCCCCceEEeCCCCCceEEEEEEEecCCCCccccc
Q 008566 401 DYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPDATLQ 480 (561)
Q Consensus 401 ~~~~~~~~~~~~~vr~S~gl~i~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~~s~~~~f~~~~~~~~~~~l~ 480 (561)
++++.+||+|+||||||+|++|.++|||++...+++++++|+++|.|+|+.|+++++++++||+|+|++++... ...+.
T Consensus 395 ~~~~~~gf~a~~~VrtS~glkv~g~~G~~~s~~~~~~~vsd~~iG~g~T~~w~l~~l~~~~t~av~f~~~~~~~-~~~~~ 473 (761)
T PLN00162 395 EGSLGLSFNGTFEVNCSKDVKVQGAIGPCASLEKKGPSVSDTEIGEGGTTAWKLCGLDKKTSLAVFFEVANSGQ-SNPQP 473 (761)
T ss_pred cccccccceeEEEEEecCCeEEeeeEcCcccccccCCccccccccCCCCceeeecCcCcCCEEEEEEEEccccc-cCCCC
Confidence 44567899999999999999999999999988788888999999999999999999999999999999998621 01122
Q ss_pred CCCCeEEEEEEEEEEeCCCcEEEEEEcCCcccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhccCccceEEee
Q 008566 481 STNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKMEIEVIFITLTLN 555 (561)
Q Consensus 481 ~~~~~~~iQ~a~~Yt~~~G~r~iRV~T~~~~~vs~~~~~~~~~~~~D~~a~~~llak~a~~~~~~~~~~d~~~~~ 555 (561)
....+||||+++||+.+|+|||||+|+++||+. ..++.+++++||+||++++|||+|+.++++++..|++|..
T Consensus 474 -~~~~~~iQ~a~lYt~~~G~rRiRV~T~~~~~~~-~~~~~~v~~~fDqeA~a~llaR~av~k~~~~~~~d~~r~l 546 (761)
T PLN00162 474 -PGQQFFLQFLTRYQHSNGQTRLRVTTVTRRWVE-GSSSEELVAGFDQEAAAVVMARLASHKMETEEEFDATRWL 546 (761)
T ss_pred -CCceEEEEEEEEEEcCCCCEEEEEEccccCccC-CCCHHHHHHhcCHHHHHHHHHHHHHHHHhhCCHHHHHHHH
Confidence 346799999999999999999999999999432 2378899999999999999999999999999988887743
No 2
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.1e-106 Score=848.23 Aligned_cols=525 Identities=55% Similarity=0.965 Sum_probs=490.1
Q ss_pred CcccccCCCeeeeeccCCCCCHHHhhhCCCCeEEEEccCCCCCCCCCCCCCCCCCCcccCCCCceecCceEEEcCCceeE
Q 008566 3 EFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRTCRSILNPFSIVDFAAKIWI 82 (561)
Q Consensus 3 ~~~~~~~~~~iR~T~~~~P~~~~~~~~~~lPlg~iv~P~~~~~~~~~~~p~~~~~~~RC~~C~ayiNp~~~~~~~~~~w~ 82 (561)
.++++|+.++||+|||++|+++.+..++.+|++++|+||... ..+|.+.|+|+||.+|+||+||||.+|.+.+.|.
T Consensus 2 ~~~~~e~~dGvR~twnvwPs~~~~~~~~vvPla~lytPl~e~----~~~~~~~y~P~~C~~C~AvlNPyc~vd~~a~~W~ 77 (745)
T KOG1986|consen 2 FIEDIEEIDGVRFTWNVWPSTRAEASRTVVPLACLYTPLKER----PDLPPIQYDPLRCSKCGAVLNPYCSVDFRAKSWI 77 (745)
T ss_pred cccccccCCCcccccccCCCcccccccccccHHHhccccccC----CCCCccCCCCchhccchhhcCcceeecccCceEe
Confidence 356799999999999999999999999999999999999976 3478899999999999999999999999999999
Q ss_pred eCCCCCCCCCCccCcCCCCCCCCcccCCCCcceEEeCCCCCCCCCCCcEEEEEEEcccchhhHHHHHHHHHHHhhcCCCC
Q 008566 83 CPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPGPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLPDN 162 (561)
Q Consensus 83 C~~C~~~N~~p~~y~~~~~~~~~pEl~~~~~tvey~~~~~~~~~~~~p~~vFvID~s~~~~~~~~l~~~l~~~l~~l~~~ 162 (561)
|+||..+|.+|++|..++..|+|+||.|++++|||.++++.. .||+|+||||++..++++++++++|+.+|+.||++
T Consensus 78 CpfC~qrN~~p~~Y~~is~~n~P~el~Pq~stvEy~l~~~~~---~ppvf~fVvDtc~~eeeL~~LkssL~~~l~lLP~~ 154 (745)
T KOG1986|consen 78 CPFCNQRNPFPPHYSGISENNLPPELLPQYSTVEYTLSPGRV---SPPVFVFVVDTCMDEEELQALKSSLKQSLSLLPEN 154 (745)
T ss_pred ccccccCCCCChhhcccCccCCChhhcCCcceeEEecCCCCC---CCceEEEEEeeccChHHHHHHHHHHHHHHhhCCCc
Confidence 999999999999999999999999999999999999986554 59999999999999999999999999999999999
Q ss_pred ceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechh
Q 008566 163 SLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFD 242 (561)
Q Consensus 163 ~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 242 (561)
++||||||++.|++|+++ ... +.++|||.|+||++.++++++++... .+. .+.+ .. ....+||.|+.+
T Consensus 155 alvGlItfg~~v~v~el~-~~~-~sk~~VF~G~ke~s~~q~~~~L~~~~---~~~----~~~~--~~-~~~~rFL~P~~~ 222 (745)
T KOG1986|consen 155 ALVGLITFGTMVQVHELG-FEE-CSKSYVFSGNKEYSAKQLLDLLGLSG---GAG----KGSE--NQ-SASNRFLLPAQE 222 (745)
T ss_pred ceEEEEEecceEEEEEcC-CCc-ccceeEEeccccccHHHHHHHhcCCc---ccc----cCCc--cc-ccchhhhccHHH
Confidence 999999999999999999 665 89999999999999999999998643 000 0100 11 245699999999
Q ss_pred hHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCC
Q 008566 243 CEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKD 322 (561)
Q Consensus 243 ~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~ 322 (561)
|+..+.++|++|++++|+++.++|+.||||+||.+|..||+.|++++|+||++|++||||.|||.++++++++++|+|++
T Consensus 223 c~~~L~~lle~L~~d~wpV~~g~Rp~RcTG~Al~iA~~Ll~~c~p~~g~rIv~f~gGPcT~GpG~vv~~el~~piRshhd 302 (745)
T KOG1986|consen 223 CEFKLTNLLEELQPDPWPVPPGHRPLRCTGVALSIASGLLEGCFPNTGARIVLFAGGPCTRGPGTVVSRELKEPIRSHHD 302 (745)
T ss_pred HHHHHHHHHHHhcCCCCCCCCCCCcccchhHHHHHHHHHhcccCCCCcceEEEeccCCCCcCCceecchhhcCCCcCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccChhcchhhhhccCcEEEEcCCCCccchHHHHHHHH-hccc
Q 008566 323 LDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF-HSGD 401 (561)
Q Consensus 323 ~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~~~~-~~~~ 401 (561)
++++++++++++.+||++||++++.+|.+||||+++.+++|+++|++|++.|||.+.+.++|+.+.|+++++|+| ++..
T Consensus 303 i~~d~a~y~kKa~KfY~~La~r~~~~ghvlDifa~~lDQvGi~EMk~l~~~TGG~lvl~dsF~~s~Fk~sfqR~f~~d~~ 382 (745)
T KOG1986|consen 303 IEKDNAPYYKKAIKFYEKLAERLANQGHVLDIFAAALDQVGILEMKPLVESTGGVLVLGDSFNTSIFKQSFQRIFTRDGE 382 (745)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHHhCCceEeeeeeeccccchHHHHHHhhcCCcEEEEecccchHHHHHHHHHHhccccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999 5777
Q ss_pred cCcCceeeeEEEEEecCCceEEeEEcCccccCCCCCCccCccccCCCCCceEEeCCCCCceEEEEEEEecCCCCcccccC
Q 008566 402 YDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPDATLQS 481 (561)
Q Consensus 402 ~~~~~~~~~~~~vr~S~gl~i~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~~s~~~~f~~~~~~~~~~~l~~ 481 (561)
+++..||++.|+|+||++++|.+++||+.+.++|++++||+++|.|+|..|+++.+++.+++++.|++..... + +
T Consensus 383 ~~l~~~fn~~leV~tSkdlkI~g~IGp~~Sl~~k~~~vsdt~ig~g~t~~wkm~~ls~~t~~s~~fei~~~~~----~-~ 457 (745)
T KOG1986|consen 383 GDLKMGFNGTLEVKTSKDLKIQGVIGPCVSLNKKGPNVSDTEIGEGNTSAWKMCGLSPSTTLSLFFEISNQHN----I-P 457 (745)
T ss_pred cchhhhcCceEEEEecCCcEEEecccccccccCCCCccccceeccccccceeeeccCCCceEEEEEEeccccC----C-C
Confidence 7788999999999999999999999999999999999999999999999999999999999999999998632 2 2
Q ss_pred CCCeEEEEEEEEEEeCCCcEEEEEEcCCcccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhccCccceEE
Q 008566 482 TNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKMEIEVIFITLT 553 (561)
Q Consensus 482 ~~~~~~iQ~a~~Yt~~~G~r~iRV~T~~~~~vs~~~~~~~~~~~~D~~a~~~llak~a~~~~~~~~~~d~~~ 553 (561)
....+||||++.|.+.+|++|+||+|++++|+.. ...++-.+|||||++++|||+++.++.++++.|++|
T Consensus 458 ~~~~~~iQFiT~Yq~s~g~~riRVtT~~r~~~d~--~~~~i~~~FDqEaaAV~mAR~~~~kae~e~~~d~~r 527 (745)
T KOG1986|consen 458 QSGQGYIQFITQYQHSSGQKRIRVTTLARPWADS--GSPEISQSFDQEAAAVLMARLALLKAETEDGPDVLR 527 (745)
T ss_pred CCCeeEEEEEEEEEcCCCcEEEEEEEeehhhccc--cchHhhhccchHHHHHHHHHHHHHhhhccccchHHH
Confidence 2468999999999999999999999999997765 337899999999999999999999999999999887
No 3
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=100.00 E-value=6.8e-100 Score=777.27 Aligned_cols=534 Identities=44% Similarity=0.809 Sum_probs=492.1
Q ss_pred CCcccccCCCeeeeeccCCCCCHHHhhhCCCCeEEEEccCCCCCCCCCCCCCCCCCCcccCC-CCceecCceEEEcCCce
Q 008566 2 TEFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRT-CRSILNPFSIVDFAAKI 80 (561)
Q Consensus 2 ~~~~~~~~~~~iR~T~~~~P~~~~~~~~~~lPlg~iv~P~~~~~~~~~~~p~~~~~~~RC~~-C~ayiNp~~~~~~~~~~ 80 (561)
|||+.+|+.++||+|||+||.|+.++.++.+|++|+|+||+.. +.+++..++|+.|.. |+||+||||.+|.+.+.
T Consensus 1 m~fe~iee~dgir~twnvfpat~~da~~~~iPia~lY~Pl~e~----~~~~v~~yepv~C~~pC~avlnpyC~id~r~~~ 76 (755)
T COG5047 1 MNFEIIEENDGIRLTWNVFPATRGDATRTVIPIACLYTPLHED----DALTVNYYEPVKCTAPCKAVLNPYCHIDERNQS 76 (755)
T ss_pred CchhhhccccceEEEEecccCCccccccccccHHHhccccccc----cccCcccCCCceecccchhhcCcceeeccCCce
Confidence 7888999999999999999999999999999999999999986 567888899999999 99999999999999999
Q ss_pred eEeCCCCCCCCCCccCcCCCCCCCCcccCCCCcceEEeCCCCCCCCCCCcEEEEEEEcccchhhHHHHHHHHHHHhhcCC
Q 008566 81 WICPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPGPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLP 160 (561)
Q Consensus 81 w~C~~C~~~N~~p~~y~~~~~~~~~pEl~~~~~tvey~~~~~~~~~~~~p~~vFvID~s~~~~~~~~l~~~l~~~l~~l~ 160 (561)
|+|+||+..|.+|++|..+++.++|+||.|++.|+||++++|.. .||+|+||||++...+++.+|+++|+..|..+|
T Consensus 77 W~CpfCnqrn~lp~qy~~iS~~~LplellpqssTiey~lskp~~---~ppvf~fvvD~~~D~e~l~~Lkdslivslsllp 153 (755)
T COG5047 77 WICPFCNQRNTLPPQYRDISNANLPLELLPQSSTIEYTLSKPVI---LPPVFFFVVDACCDEEELTALKDSLIVSLSLLP 153 (755)
T ss_pred EecceecCCCCCChhhcCCCcccCCccccCCCceEEEEccCCcc---CCceEEEEEEeecCHHHHHHHHHHHHHHHhcCC
Confidence 99999999999999999999999999999999999999999876 799999999999999999999999999999999
Q ss_pred CCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHHhccCCCCCCCC--CccccCcCCCCCCccccceee
Q 008566 161 DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPS--TGVIAGVRDGLSSDTIARFLV 238 (561)
Q Consensus 161 ~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~l~ 238 (561)
+++.||||||++.|++|+++ ... .++.|||+|+++|+.++|++++... ...++. ...++++. -....+|+.
T Consensus 154 peaLvglItygt~i~v~el~-ae~-~~r~~VF~g~~eyt~~~L~~ll~~~-~~~~~~~~es~is~~~----~~~~~rFl~ 226 (755)
T COG5047 154 PEALVGLITYGTSIQVHELN-AEN-HRRSYVFSGNKEYTKENLQELLALS-KPTKSGGFESKISGIG----QFASSRFLL 226 (755)
T ss_pred ccceeeEEEecceeEEEecc-ccc-cCcceeecchHHHHHHHHHHHhccc-CCCCcchhhhhccccc----ccchhhhhc
Confidence 99999999999999999998 665 8899999999999999999998765 122221 11123321 013457999
Q ss_pred echhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcc
Q 008566 239 PAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIR 318 (561)
Q Consensus 239 ~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r 318 (561)
|+.+|+.++.++|++|++++|+++.++|+.||||+||.+|..||++++++.|+||++|++||||.|||.|+++++++++|
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 CCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccChhcchhhhhccCcEEEEcCCCCccchHHHHHHHH-
Q 008566 319 SHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF- 397 (561)
Q Consensus 319 ~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~~~~- 397 (561)
+|++++.+.+++.+++.+||+.|+++++++|.++|+|+.+.+++|+.+|.+|...|||.+.+.++|+.++|+++++|+|
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 9999999989999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccccCcCceeeeEEEEEecCCceEEeEEcCccccCCCCCCccCccccCCCCCceEEeCCCCCceEEEEEEEecCCCCcc
Q 008566 398 HSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPDA 477 (561)
Q Consensus 398 ~~~~~~~~~~~~~~~~vr~S~gl~i~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~~s~~~~f~~~~~~~~~~ 477 (561)
++..+++..||+|.|+|.|||++++++++||....+|+..+++|.+||.|.|+.|+++++.|.+++++.|++......+.
T Consensus 387 ~d~~g~l~~gfNa~m~V~TsKnl~~~g~ig~a~~~~k~~~ni~~~eigi~~t~swkm~slsPk~nyal~fei~~~~~~~~ 466 (755)
T COG5047 387 RDSEGYLKMGFNANMEVKTSKNLKIKGLIGHAVSVKKKANNISDSEIGIGATNSWKMASLSPKSNYALYFEIALGAASGS 466 (755)
T ss_pred cCcccchhhhhccceeEeeccCceeeeeecceeeecccccccccccccccccccccccccCCCcceEEEEEeccccCCCc
Confidence 66667888999999999999999999999999998888889999999999999999999999999999999997532211
Q ss_pred cccCCCCeEEEEEEEEEEeCCCcEEEEEEcCCcccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhccCccceEE
Q 008566 478 TLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKMEIEVIFITLT 553 (561)
Q Consensus 478 ~l~~~~~~~~iQ~a~~Yt~~~G~r~iRV~T~~~~~vs~~~~~~~~~~~~D~~a~~~llak~a~~~~~~~~~~d~~~ 553 (561)
- +.....||||.+.|.+++|..||||+|+...|+.. ....+.++|||||+++++||+|+.+++.++..|+.|
T Consensus 467 -~-~~~~~a~iQfiT~yQhss~t~riRVtTvar~f~~~--~~p~i~~SFdqEaaaV~~aR~a~~K~~~ed~~Dv~r 538 (755)
T COG5047 467 -A-QRPAEAYIQFITTYQHSSGTYRIRVTTVARMFTDG--GLPKINRSFDQEAAAVFMARIAAFKAETEDIIDVFR 538 (755)
T ss_pred -c-CCcccchhhhhhhhhccCCcEEEEEeehhhhhccC--CChhhhhcchhhHHHHHHHHHHHhhcccccchhHHH
Confidence 1 12246899999999999999999999999995555 677899999999999999999999999999999887
No 4
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.8e-95 Score=774.40 Aligned_cols=464 Identities=22% Similarity=0.368 Sum_probs=406.9
Q ss_pred cccCCCeeeeeccCCCCCHHHhhhCCCCeEEEEccCCCCCCCCCCCCCCCC-CCcccCCCCceecCceEEEcCCceeEeC
Q 008566 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPY-APLRCRTCRSILNPFSIVDFAAKIWICP 84 (561)
Q Consensus 6 ~~~~~~~iR~T~~~~P~~~~~~~~~~lPlg~iv~P~~~~~~~~~~~p~~~~-~~~RC~~C~ayiNp~~~~~~~~~~w~C~ 84 (561)
-|++|+|+|+|++++|.+.+++++++||||++|+||+++. +..++|++.. .|+||++||+||||||.|++.|++|+||
T Consensus 166 ~nc~p~y~RsTl~~iP~t~sLl~kskLPlglvv~Pf~~~~-d~~~~p~~~~~~IvRCr~CRtYiNPFV~fid~gr~WrCN 244 (887)
T KOG1985|consen 166 SNCSPSYVRSTLSAIPQTQSLLKKSKLPLGLVVHPFAHLD-DIDPLPVITSTLIVRCRRCRTYINPFVEFIDQGRRWRCN 244 (887)
T ss_pred cCCCHHHHHHHHHhCCccHHHHHhcCCCceEEEeeccccc-ccCCCCcccCCceeeehhhhhhcCCeEEecCCCceeeec
Confidence 3899999999999999999999999999999999999876 3356676654 7999999999999999999999999999
Q ss_pred CCCCCCCCCccCcCC--C----CCCCCcccCCCCcceEEeCC-----CCCCCCCCCcEEEEEEEcccchhhHHH---HHH
Q 008566 85 FCFQRNHFPPHYASI--T----DDNLPAELFPQYTTIEYEPP-----GPGEKSSVPPVFMFVVDTCIIEEEMSF---LKS 150 (561)
Q Consensus 85 ~C~~~N~~p~~y~~~--~----~~~~~pEl~~~~~tvey~~~-----~~~~~~~~~p~~vFvID~s~~~~~~~~---l~~ 150 (561)
+|+..|++|.+|... + +...|||+. +.+|||++| |+++ |++|||+||+|.++++.|+ +++
T Consensus 245 lC~~~NdvP~~f~~~~~t~~~~~~~~RpEl~--~s~vE~iAP~eYmlR~P~----Pavy~FliDVS~~a~ksG~L~~~~~ 318 (887)
T KOG1985|consen 245 LCGRVNDVPDDFDWDPLTGAYGDPYSRPELT--SSVVEFIAPSEYMLRPPQ----PAVYVFLIDVSISAIKSGYLETVAR 318 (887)
T ss_pred hhhhhcCCcHHhhcCccccccCCcccCcccc--ceeEEEecCcccccCCCC----CceEEEEEEeehHhhhhhHHHHHHH
Confidence 999999999987632 1 234579995 899999998 4554 9999999999999999765 689
Q ss_pred HHHHHhhcCC--CCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHHhccCCCCCCCCCccccCcCCCC
Q 008566 151 ALSQAIDLLP--DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGL 228 (561)
Q Consensus 151 ~l~~~l~~l~--~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 228 (561)
+|++.||.|| +++||||||||++||+|++. .+.. .|+|+++.+++|+
T Consensus 319 slL~~LD~lpgd~Rt~igfi~fDs~ihfy~~~-~~~~-----------------------------qp~mm~vsdl~d~- 367 (887)
T KOG1985|consen 319 SLLENLDALPGDPRTRIGFITFDSTIHFYSVQ-GDLN-----------------------------QPQMMIVSDLDDP- 367 (887)
T ss_pred HHHHhhhcCCCCCcceEEEEEeeceeeEEecC-CCcC-----------------------------CCceeeecccccc-
Confidence 9999999999 78999999999999999998 3210 2444555666663
Q ss_pred CCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCccc
Q 008566 229 SSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAI 308 (561)
Q Consensus 229 ~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~~~~ggkIi~F~~g~pt~G~G~l 308 (561)
+++..++||+|+++||+.|..+|++|+++ +...+..++|+|+||++|..+|+ ..||||++|.+++||.|.|+|
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 34455899999999999999999999997 56666778999999999999999 899999999999999999999
Q ss_pred ccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccChhcchhhhhccCcEEEEcCCCCcc-
Q 008566 309 VSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHA- 387 (561)
Q Consensus 309 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~- 387 (561)
+.|+..+..+ .++...++.+++.|||+||.+|++.||+||+|+++.+|.|+|+|+.|++.|||.+|||++|+..
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 KPREDPNVRS-----SDEDSQLLSPATDFYKDLALECSKSQICVDLFLFSEQYTDLASLSCLSKYSGGQVYYYPSFDGSN 515 (887)
T ss_pred cccccccccc-----chhhhhccCCCchHHHHHHHHhccCceEEEEEeecccccchhhhhccccccCceeEEccCCCCCC
Confidence 9996443322 2333478999999999999999999999999999999999999999999999999999999987
Q ss_pred -----chHHHHHHHHhccccCcCceeeeEEEEEecCCceEEeEEcCccccCCCCCCccCccccCCCCCceEEeCCCCCce
Q 008566 388 -----VFKDSVRRVFHSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATS 462 (561)
Q Consensus 388 -----~~~~~l~~~~~~~~~~~~~~~~~~~~vr~S~gl~i~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~~s 462 (561)
+|.++|.|++. +++||+|+||||||+|++++.+||||+. ++++++.++++.+|++
T Consensus 516 p~~~~Kf~~el~r~Lt-----r~~~feaVmRiR~S~gl~~~~f~GnFF~---------------RStDLla~~~v~~D~s 575 (887)
T KOG1985|consen 516 PHDVLKFARELARYLT-----RKIGFEAVMRIRCSTGLRMSSFFGNFFV---------------RSTDLLALPNVNPDQS 575 (887)
T ss_pred HHHHHHHHHHHHHHhh-----hhhhhheeEEeeccccccccceeccccc---------------CcHHHhcccCCCCCcc
Confidence 44566666663 4689999999999999999999999996 3578899999999999
Q ss_pred EEEEEEEecCCCCcccccCCCCeEEEEEEEEEEeCCCcEEEEEEcCCcccccCCCCHHHHHhccCHHHHHHHHHHHHHHH
Q 008566 463 LCLVFEIVKKEIPDATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFK 542 (561)
Q Consensus 463 ~~~~f~~~~~~~~~~~l~~~~~~~~iQ~a~~Yt~~~G~r~iRV~T~~~~~vs~~~~~~~~~~~~D~~a~~~llak~a~~~ 542 (561)
++|++++++. + .....+||.|++||...|||||||||+++| +++ ++.++|+++|++|++.+|+++|+.+
T Consensus 576 y~~qisiEes------l--~~~~~~fQvAlLyT~~~GERRIRV~T~~lp-t~~--sl~evY~saD~~AI~~lla~~Av~k 644 (887)
T KOG1985|consen 576 YAFQISIEES------L--TTGFCVFQVALLYTLSKGERRIRVHTLCLP-TVS--SLNEVYASADQEAIASLLAKKAVEK 644 (887)
T ss_pred ceEEEEeehh------c--CCceeEEEeeeeecccCCceeEEEEEeecc-ccc--cHHHHHhhcCHHHHHHHHHHHHHHH
Confidence 9999999997 5 346788999999999999999999999999 888 9999999999999999999999999
Q ss_pred hhccCccc
Q 008566 543 MEIEVIFI 550 (561)
Q Consensus 543 ~~~~~~~d 550 (561)
.++....|
T Consensus 645 sl~ssL~d 652 (887)
T KOG1985|consen 645 SLSSSLSD 652 (887)
T ss_pred HHHhhhhh
Confidence 99855444
No 5
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=7.6e-90 Score=732.13 Aligned_cols=476 Identities=22% Similarity=0.321 Sum_probs=414.7
Q ss_pred ccCCCeeeeeccCCCCCHHHhhhCCCCeEEEEccCCCCCCCCCCCCCCCC---CCcccCCCCceecCceEEEcCCceeEe
Q 008566 7 LEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPY---APLRCRTCRSILNPFSIVDFAAKIWIC 83 (561)
Q Consensus 7 ~~~~~~iR~T~~~~P~~~~~~~~~~lPlg~iv~P~~~~~~~~~~~p~~~~---~~~RC~~C~ayiNp~~~~~~~~~~w~C 83 (561)
|++|+|||+|+|++|.|.+++++++||||++++||+.+.+.|+++|+++. +|+||++|+||+|||++|.++|++|+|
T Consensus 284 N~sPr~mr~T~Y~iP~T~Dl~~as~iPLalvIqPfa~l~p~E~~~~vVd~g~sgPvRC~RCkaYinPFmqF~~~gr~f~C 363 (1007)
T KOG1984|consen 284 NCSPRFMRCTMYTIPCTNDLLKASQIPLALVIQPFATLTPNEAPVPVVDLGESGPVRCNRCKAYINPFMQFIDGGRKFIC 363 (1007)
T ss_pred CCCcchheeecccCCccHhHHHhcCCcceeEecccccCCcccCCCceecCCCCCCcchhhhhhhcCcceEEecCCceEEe
Confidence 99999999999999999999999999999999999999888899999986 699999999999999999999999999
Q ss_pred CCCCCCCCCCccCcCCCC-------CCCCcccCCCCcceEEeCCCC---CCCCCCCcEEEEEEEcccchhhHHH---HHH
Q 008566 84 PFCFQRNHFPPHYASITD-------DNLPAELFPQYTTIEYEPPGP---GEKSSVPPVFMFVVDTCIIEEEMSF---LKS 150 (561)
Q Consensus 84 ~~C~~~N~~p~~y~~~~~-------~~~~pEl~~~~~tvey~~~~~---~~~~~~~p~~vFvID~s~~~~~~~~---l~~ 150 (561)
|||+.+|++|++|++... ...+|||. .++|||++... ..+...+|+|||+||||.++++.|+ +++
T Consensus 364 n~C~~~n~vp~~yf~~L~~~grr~D~~erpEL~--~Gt~dfvatk~Y~~~~k~p~ppafvFmIDVSy~Ai~~G~~~a~ce 441 (1007)
T KOG1984|consen 364 NFCGSKNQVPDDYFNHLGPTGRRVDVEERPELC--LGTVDFVATKDYCRKTKPPKPPAFVFMIDVSYNAISNGAVKAACE 441 (1007)
T ss_pred cCCCccccCChhhcccCCCcccccccccCchhc--ccccceeeehhhhhcCCCCCCceEEEEEEeehhhhhcchHHHHHH
Confidence 999999999999987432 23468995 89999998731 1123369999999999999999775 689
Q ss_pred HHHHHhhcCC---CCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHHhccCCCCCCCCCccccCcCCC
Q 008566 151 ALSQAIDLLP---DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDG 227 (561)
Q Consensus 151 ~l~~~l~~l~---~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 227 (561)
+|+..|+.++ ++++|||||||++|||||++ +++.. |+|++|+|++|
T Consensus 442 ~ik~~l~~lp~~~p~~~Vgivtfd~tvhFfnl~-s~L~q-----------------------------p~mliVsdv~d- 490 (1007)
T KOG1984|consen 442 AIKSVLEDLPREEPNIRVGIVTFDKTVHFFNLS-SNLAQ-----------------------------PQMLIVSDVDD- 490 (1007)
T ss_pred HHHHHHhhcCccCCceEEEEEEecceeEeeccC-ccccC-----------------------------ceEEEeecccc-
Confidence 9999999998 37999999999999999999 76533 33444556655
Q ss_pred CCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCc-
Q 008566 228 LSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPA- 306 (561)
Q Consensus 228 ~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~~~~ggkIi~F~~g~pt~G~G- 306 (561)
+++|..++++|+..|++..|..+|++|+.+ +...+.+..|+|+||++|..+|+. ..|||+++|++..||.|.|
T Consensus 491 vfvPf~~g~~V~~~es~~~i~~lLd~Ip~m---f~~sk~pes~~g~alqaa~lalk~---~~gGKl~vF~s~Lpt~g~g~ 564 (1007)
T KOG1984|consen 491 VFVPFLDGLFVNPNESRKVIELLLDSIPTM---FQDSKIPESVFGSALQAAKLALKA---ADGGKLFVFHSVLPTAGAGG 564 (1007)
T ss_pred cccccccCeeccchHHHHHHHHHHHHhhhh---hccCCCCchhHHHHHHHHHHHHhc---cCCceEEEEecccccccCcc
Confidence 667778899999999999999999999987 577778999999999999999994 2399999999999999998
Q ss_pred ccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccChhcchhhhhccCcEEEEcCCCCc
Q 008566 307 AIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGH 386 (561)
Q Consensus 307 ~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~ 386 (561)
++..++.. .|.++++|| .+|.++.++|++||++|++.|||||||++...|+|+|+++.+++.|||.+|+|.+|..
T Consensus 565 kl~~r~D~----~l~~t~kek-~l~~pq~~~y~~LA~e~v~~g~svDlF~t~~ayvDvAtlg~v~~~TgG~vy~Y~~F~a 639 (1007)
T KOG1984|consen 565 KLSNRDDR----RLIGTDKEK-NLLQPQDKTYTTLAKEFVESGCSVDLFLTPNAYVDVATLGVVPALTGGQVYKYYPFQA 639 (1007)
T ss_pred cccccchh----hhhcccchh-hccCcchhHHHHHHHHHHHhCceEEEEEcccceeeeeeecccccccCceeEEecchhh
Confidence 77776643 445678887 7899999999999999999999999999999999999999999999999999999998
Q ss_pred cchHHHHHHHH-hccccCcCceeeeEEEEEecCCceEEeEEcCccccCCCCCCccCccccCCCCCceEEeCCCCCceEEE
Q 008566 387 AVFKDSVRRVF-HSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCL 465 (561)
Q Consensus 387 ~~~~~~l~~~~-~~~~~~~~~~~~~~~~vr~S~gl~i~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~~s~~~ 465 (561)
.++...|...+ ++. ....||+|.||||||.||++.++||++... ..+..+++.+|.|+++.+
T Consensus 640 ~~D~~rl~nDL~~~v--tk~~gf~a~mrvRtStGirv~~f~Gnf~~~---------------~~tDiela~lD~dkt~~v 702 (1007)
T KOG1984|consen 640 LTDGPRLLNDLVRNV--TKKQGFDAVMRVRTSTGIRVQDFYGNFLMR---------------NPTDIELAALDCDKTLTV 702 (1007)
T ss_pred cccHHHHHHHHHHhc--ccceeeeeEEEEeecCceeeeeeechhhhc---------------CCCCccccccccCceeEE
Confidence 76544333333 221 245799999999999999999999999852 245678999999999999
Q ss_pred EEEEecCCCCcccccCCCCeEEEEEEEEEEeCCCcEEEEEEcCCcccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhc
Q 008566 466 VFEIVKKEIPDATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKMEI 545 (561)
Q Consensus 466 ~f~~~~~~~~~~~l~~~~~~~~iQ~a~~Yt~~~G~r~iRV~T~~~~~vs~~~~~~~~~~~~D~~a~~~llak~a~~~~~~ 545 (561)
+|+|+++ |++ ...++||+|++||+.+|+||+||+|++++ +++ .+.++|+++|.|+++++|+|.|+..+..
T Consensus 703 ~fkhDdk------Lq~-~s~~~fQ~AlLYTti~G~RR~Rv~Nlsl~-~ts--~l~~lyr~~~~d~l~a~maK~a~~~i~~ 772 (1007)
T KOG1984|consen 703 EFKHDDK------LQD-GSDVHFQTALLYTTIDGQRRLRVLNLSLA-VTS--QLSELYRSADTDPLIAIMAKQAAKAILD 772 (1007)
T ss_pred EEecccc------ccC-CcceeEEEEEEEeccCCceeEEEEecchh-hhh--hHHHHHHhcCccHHHHHHHHHHHHhccc
Confidence 9999998 864 45689999999999999999999999999 999 9999999999999999999999999888
Q ss_pred cCccceEE
Q 008566 546 EVIFITLT 553 (561)
Q Consensus 546 ~~~~d~~~ 553 (561)
...-++.+
T Consensus 773 ~~lk~vre 780 (1007)
T KOG1984|consen 773 KPLKEVRE 780 (1007)
T ss_pred ccHHHHHH
Confidence 76554433
No 6
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=100.00 E-value=7.1e-85 Score=688.10 Aligned_cols=462 Identities=22% Similarity=0.390 Sum_probs=393.6
Q ss_pred cccCCCeeeeeccCCCCCHHHhhhCCCCeEEEEccCCCCCCCCCCCCCCCC-CCcccCCCCceecCceEEEcCCceeEeC
Q 008566 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPY-APLRCRTCRSILNPFSIVDFAAKIWICP 84 (561)
Q Consensus 6 ~~~~~~~iR~T~~~~P~~~~~~~~~~lPlg~iv~P~~~~~~~~~~~p~~~~-~~~RC~~C~ayiNp~~~~~~~~~~w~C~ 84 (561)
-|++|+|+|+|++++|.+.+++++++||||++++||.++.+.+.++|+... .|+||++||+|+|||++|.++|++|+||
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 389999999999999999999999999999999999999887777887655 4899999999999999999999999999
Q ss_pred CCCCCCCCCccCcCCCC-------CCCCcccCCCCcceEEeCCCCCC-CCCCCcEEEEEEEcccchhhHHHH---HHHHH
Q 008566 85 FCFQRNHFPPHYASITD-------DNLPAELFPQYTTIEYEPPGPGE-KSSVPPVFMFVVDTCIIEEEMSFL---KSALS 153 (561)
Q Consensus 85 ~C~~~N~~p~~y~~~~~-------~~~~pEl~~~~~tvey~~~~~~~-~~~~~p~~vFvID~s~~~~~~~~l---~~~l~ 153 (561)
+|+.+|++|..+..... ...++||. +++|||.+|..-. +...||+|||+||+|.++.+.|++ .++|+
T Consensus 226 iC~~kN~vp~~~~~~~~~~~~r~d~~~r~El~--~~vvdf~ap~~Y~~~~p~P~~yvFlIDVS~~a~~~g~~~a~~r~Il 303 (861)
T COG5028 226 ICRSKNDVPEGFDNPSGPNDPRSDRYSRPELK--SGVVDFLAPKEYSLRQPPPPVYVFLIDVSFEAIKNGLVKAAIRAIL 303 (861)
T ss_pred eccccccCcccccCcCCCCCccccccccchhh--ceeeEEecccceeeccCCCCEEEEEEEeehHhhhcchHHHHHHHHH
Confidence 99999999988873221 23468996 8999999984211 011399999999999999998765 55666
Q ss_pred HHhhcCC---CCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHHhccCCCCCCCCCccccCcCCCCCC
Q 008566 154 QAIDLLP---DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSS 230 (561)
Q Consensus 154 ~~l~~l~---~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (561)
+.|+.+| +++||+||.||++||+|+++ .+. ++ .++++ .+.++++.+
T Consensus 304 ~~l~~~~~~dpr~kIaii~fD~sl~ffk~s-~d~-----------~~-------~~~~v------------sdld~pFlP 352 (861)
T COG5028 304 ENLDQIPNFDPRTKIAIICFDSSLHFFKLS-PDL-----------DE-------QMLIV------------SDLDEPFLP 352 (861)
T ss_pred hhccCCCCCCCcceEEEEEEcceeeEEecC-CCC-----------cc-------ceeee------------ccccccccc
Confidence 6666665 58999999999999999998 432 00 12221 222232221
Q ss_pred ccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCccccc
Q 008566 231 DTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVS 310 (561)
Q Consensus 231 ~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~~~~ggkIi~F~~g~pt~G~G~l~~ 310 (561)
.+...|++|+++|+..+..||++++.. +...+.++.|+|+||++|..|++ .+||||++|.++.||.|.|+|..
T Consensus 353 f~s~~fv~pl~~~k~~~etLl~~~~~I---f~d~~~pk~~~G~aLk~a~~l~g----~~GGkii~~~stlPn~G~Gkl~~ 425 (861)
T COG5028 353 FPSGLFVLPLKSCKQIIETLLDRVPRI---FQDNKSPKNALGPALKAAKSLIG----GTGGKIIVFLSTLPNMGIGKLQL 425 (861)
T ss_pred CCcchhcccHHHHHHHHHHHHHHhhhh---hcccCCCccccCHHHHHHHHHhh----ccCceEEEEeecCCCcccccccc
Confidence 233689999999998888899999886 46677889999999999999998 89999999999999999999998
Q ss_pred CCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccChhcchhhhhccCcEEEEcCCCCccc--
Q 008566 311 KNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAV-- 388 (561)
Q Consensus 311 ~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~~-- 388 (561)
|+. +|. .++.+...||++++.+|++.||+||+|+++.+|+|+++++.|++.|||.+++|++|+..+
T Consensus 426 r~d-----------~e~-~ll~c~d~fYk~~a~e~~k~gIsvd~Flt~~~yidvaTls~l~~~T~G~~~~Yp~f~~~~~~ 493 (861)
T COG5028 426 RED-----------KES-SLLSCKDSFYKEFAIECSKVGISVDLFLTSEDYIDVATLSHLCRYTGGQTYFYPNFSATRPN 493 (861)
T ss_pred ccc-----------chh-hhccccchHHHHHHHHHHHhcceEEEEeccccccchhhhcchhhccCcceEEcCCcccCCch
Confidence 863 333 478999999999999999999999999999999999999999999999999999999987
Q ss_pred ----hHHHHHHHHhccccCcCceeeeEEEEEecCCceEEeEEcCccccCCCCCCccCccccCCCCCceEEeCCCCCceEE
Q 008566 389 ----FKDSVRRVFHSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLC 464 (561)
Q Consensus 389 ----~~~~l~~~~~~~~~~~~~~~~~~~~vr~S~gl~i~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~~s~~ 464 (561)
|..+|.+.+. ++.||++.||||||+|++++++|||++. | +.+...|+.++.|+|+.
T Consensus 494 d~~kl~~dL~~~ls-----~~~gy~~~~rvR~S~glr~s~fyGnf~~---r------------s~dl~~F~tm~rd~Sl~ 553 (861)
T COG5028 494 DATKLANDLVSHLS-----MEIGYEAVMRVRCSTGLRVSSFYGNFFN---R------------SSDLCAFSTMPRDTSLL 553 (861)
T ss_pred hHHHHHHHHHHhhh-----hhhhhheeeEeeccCceehhhhhccccc---c------------CcccccccccCCCceEE
Confidence 5555555553 5689999999999999999999999996 2 23578899999999999
Q ss_pred EEEEEecCCCCcccccCCCCeEEEEEEEEEEeCCCcEEEEEEcCCcccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhh
Q 008566 465 LVFEIVKKEIPDATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKME 544 (561)
Q Consensus 465 ~~f~~~~~~~~~~~l~~~~~~~~iQ~a~~Yt~~~G~r~iRV~T~~~~~vs~~~~~~~~~~~~D~~a~~~llak~a~~~~~ 544 (561)
|+|+++++ +. ...+|||.|++||..+|+|||||.|++++ +++ ++.++|+++|++|++.+|+|+|+.++.
T Consensus 554 ~~~sid~~------l~--~~~v~fQvAlL~T~~~GeRRiRVvn~s~~-~ss--~~~evyasadq~aIa~~lak~a~~~~~ 622 (861)
T COG5028 554 VEFSIDEK------LM--TSDVYFQVALLYTLNDGERRIRVVNLSLP-TSS--SIREVYASADQLAIACILAKKASTKAL 622 (861)
T ss_pred EEEEeccc------cc--CCceEEEEEEEeeccCCceEEEEEEeccc-cch--hHHHHHHhccHHHHHHHHHHHHHHHhh
Confidence 99999998 64 47899999999999999999999999999 998 999999999999999999999999998
Q ss_pred ccCccc
Q 008566 545 IEVIFI 550 (561)
Q Consensus 545 ~~~~~d 550 (561)
..+--+
T Consensus 623 ~~s~~~ 628 (861)
T COG5028 623 NSSLKE 628 (861)
T ss_pred hhhHHH
Confidence 654333
No 7
>PTZ00395 Sec24-related protein; Provisional
Probab=100.00 E-value=7.7e-81 Score=690.04 Aligned_cols=476 Identities=17% Similarity=0.225 Sum_probs=375.9
Q ss_pred ccCCCeeeeeccCCCCCHHHhhhCCCCeEEEEccCCCCCCCCCCCCCCC-----------CCCcccCCCCceecCceEEE
Q 008566 7 LEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILP-----------YAPLRCRTCRSILNPFSIVD 75 (561)
Q Consensus 7 ~~~~~~iR~T~~~~P~~~~~~~~~~lPlg~iv~P~~~~~~~~~~~p~~~-----------~~~~RC~~C~ayiNp~~~~~ 75 (561)
+++|++||+|||.+|.+.++++.+.||||++++||+.+.++ ++||.++ .+|+||.+|++|+|+++.++
T Consensus 649 n~dP~~~r~tmY~iP~~~~~~~~~~iP~gi~v~Pfa~~~~~-e~~~~~~~~~~~~d~~~~~~~~rc~~c~~y~~~~~~~~ 727 (1560)
T PTZ00395 649 KADPRFLKSTLYQIPLFSETLKLSQIPFGIIVNPFACLNEG-EGIDKIDMKDIINDKEENIEILRCPKCLGYLHATILED 727 (1560)
T ss_pred CCChhhhhhhhhcCcchHHHHHhcCCCceeecchhhhcCCC-CCCcccchhhcccchhhccceeecchhHhhhcchheec
Confidence 89999999999999999999999999999999999998765 4566543 26899999999999999998
Q ss_pred cCCceeEeCCCCCCCCCCcc-------CcC-CC----C-----CCCCcccCCCCcceEEeCC------------------
Q 008566 76 FAAKIWICPFCFQRNHFPPH-------YAS-IT----D-----DNLPAELFPQYTTIEYEPP------------------ 120 (561)
Q Consensus 76 ~~~~~w~C~~C~~~N~~p~~-------y~~-~~----~-----~~~~pEl~~~~~tvey~~~------------------ 120 (561)
-. +++.|+||.+.+.+... |.. +. . ..+.|-| +++||+++|
T Consensus 728 ~~-~~~~c~~c~~~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~ 803 (1560)
T PTZ00395 728 IS-SSVQCVFCDTDFLINENVLFDIFQYNEKIGHKESDHNEHGNSLSPLL---KGSVDIIIPPIYYHNVNKFKLTYTYLN 803 (1560)
T ss_pred cc-ceEEEEecCCcchhhHHHHHHHHHHhhhhccccccccccccccchhh---cCceeEEccchhhccCCccceeeehhh
Confidence 65 79999999999876211 100 00 0 0000000 111111110
Q ss_pred --------------------------------------------------------------------------------
Q 008566 121 -------------------------------------------------------------------------------- 120 (561)
Q Consensus 121 -------------------------------------------------------------------------------- 120 (561)
T Consensus 804 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 883 (1560)
T PTZ00395 804 KNINQTAFMITNKIMSFTKHISNSLVANDSKGGNKATSASAFGDSGDANFLAGGGYTNYGGAGGYNTYDNQSGYNNHDVV 883 (1560)
T ss_pred cchhhhhhhhhhhhhhhhhhhcchheecccccccccchhhhccccccccccccccccccccccccccccccccccccccc
Confidence
Q ss_pred --C----------------------------------------------------------CCCCCCCCcEEEEEEEccc
Q 008566 121 --G----------------------------------------------------------PGEKSSVPPVFMFVVDTCI 140 (561)
Q Consensus 121 --~----------------------------------------------------------~~~~~~~~p~~vFvID~s~ 140 (561)
| |.-+...||+|+||||||.
T Consensus 884 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~PP~YvFLIDVS~ 963 (1560)
T PTZ00395 884 NNRGGSGAGNHLYGKDHDVQNFDNVMDNANFTIHDMKNLICEKNGEPDSAKIRRNSFLAKYPQVKNMLPPYFVFVVECSY 963 (1560)
T ss_pred ccccccCcCcccccCcccccchhhhccCCceeeecchhhhhcccCCchhhhhhccchhhccccccCCCCCEEEEEEECCH
Confidence 0 0001246899999999999
Q ss_pred chhhHHH---HHHHHHHHhhcCC-CCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHHhccCCCCCCC
Q 008566 141 IEEEMSF---LKSALSQAIDLLP-DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKP 216 (561)
Q Consensus 141 ~~~~~~~---l~~~l~~~l~~l~-~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~ 216 (561)
.+++.|+ ++++|+++|+.|+ +++||||||||++||||+++ +....... .++. .+...+|
T Consensus 964 ~AVkSGLl~tacesIK~sLDsL~dpRTRVGIITFDSsLHFYNLk-s~l~~~~~---~~~~-------------~~~l~qP 1026 (1560)
T PTZ00395 964 NAIYNNITYTILEGIRYAVQNVKCPQTKIAIITFNSSIYFYHCK-GGKGVSGE---EGDG-------------GGGSGNH 1026 (1560)
T ss_pred HHHhhChHHHHHHHHHHHHhcCCCCCcEEEEEEecCcEEEEecC-cccccccc---cccc-------------cccCCCc
Confidence 9999875 6889999999997 57999999999999999997 43100000 0000 0001257
Q ss_pred CCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCCcEEEEE
Q 008566 217 STGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAF 296 (561)
Q Consensus 217 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~~~~ggkIi~F 296 (561)
+|+||+|++|+|-+.+.+++||++.|+++.|..+|+.|+++ +........|+|+||++|..+|+. .+.||||++|
T Consensus 1027 QMLVVSDLDDPFLPlP~ddLLVnL~ESRevIe~LLDkLPem---Ft~t~~~esCLGSALqAA~~aLk~--~GGGGKIiVF 1101 (1560)
T PTZ00395 1027 QVIVMSDVDDPFLPLPLEDLFFGCVEEIDKINTLIDTIKSV---STTMQSYGSCGNSALKIAMDMLKE--RNGLGSICMF 1101 (1560)
T ss_pred eEEeecCCccCcCCCCccCeeechHHHHHHHHHHHHHHHHH---hhccCCCcccHHHHHHHHHHHHHh--cCCCceEEEE
Confidence 88999999995533334899999999999999999999886 344555789999999999999982 1235999999
Q ss_pred ecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccC--hhcchhhhhcc
Q 008566 297 VGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVG--VAELKVAVEKT 374 (561)
Q Consensus 297 ~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~--l~~l~~l~~~T 374 (561)
++++|+.|||+|..++. ..+++ .++.++.+||++||.+|++.+|+||||+++..++| +++|+.|++.|
T Consensus 1102 ~SSLPniGpGaLK~Re~---------~~KEk-~Ll~pqd~FYK~LA~ECsk~qISVDLFLfSsqYvDVDVATLg~Lsr~T 1171 (1560)
T PTZ00395 1102 YTTTPNCGIGAIKELKK---------DLQEN-FLEVKQKIFYDSLLLDLYAFNISVDIFIISSNNVRVCVPSLQYVAQNT 1171 (1560)
T ss_pred EcCCCCCCCCccccccc---------ccccc-cccccchHHHHHHHHHHHhcCCceEEEEccCcccccccccccchhccc
Confidence 99999999999986531 12443 56788899999999999999999999999988876 79999999999
Q ss_pred CcEEEEcCCCCccchHHH----HHHHHhccccCcCceeeeEEEEEecCCceEEeEEc--CccccCCCCCCccCccccCCC
Q 008566 375 GGLVVLSDSFGHAVFKDS----VRRVFHSGDYDLGLSSNGIFEINCSKDIKVQGIIG--PCASLEKKGPLCSDAVVGQGN 448 (561)
Q Consensus 375 GG~v~~y~~f~~~~~~~~----l~~~~~~~~~~~~~~~~~~~~vr~S~gl~i~~~~G--~~~~~~~~~~~~sd~~~g~~~ 448 (561)
||.+++|+.|+..+.... |.+.+.+ +.+||+|+||||||+||+|+.+|| +++.. . .+
T Consensus 1172 GGqlyyYPnFna~rD~~KL~~DL~r~LTr----e~iGyEAVMRVRCS~GLrVs~fyG~GnnF~s-~------------rS 1234 (1560)
T PTZ00395 1172 GGKILFVENFLWQKDYKEIYMNIMDTLTS----EDIAYCCELKLRYSHHMSVKKLFCCNNNFNS-I------------IS 1234 (1560)
T ss_pred ceeEEEeCCCcccccHHHHHHHHHHHhhc----cceeeEEEEEEECCCCeEEEEEeccCCcccc-c------------cc
Confidence 999999999998765433 3444421 247999999999999999999994 44421 1 13
Q ss_pred CCceEEeCCCCCceEEEEEEEecCCCCcccccCCCCeEEEEEEEEEEeCCCcEEEEEEcCCcccccCCCCHHHHHhccCH
Q 008566 449 TSAWKMCGLDKATSLCLVFEIVKKEIPDATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQ 528 (561)
Q Consensus 449 ~~~~~~~~~~~~~s~~~~f~~~~~~~~~~~l~~~~~~~~iQ~a~~Yt~~~G~r~iRV~T~~~~~vs~~~~~~~~~~~~D~ 528 (561)
++++.+|.+++|++|+|+|+++++ |. ....+|||+|++||+..|+|||||||+++| |++ ++.++|+++|+
T Consensus 1235 tDLLaLP~Id~DqSfaVeLk~DEk------L~-~~~~AYFQaALLYTSssGERRIRVHTLALP-VTS--sLseVFrsADq 1304 (1560)
T PTZ00395 1235 VDTIKIPKIRHDQTFAFLLNYSDI------SE-SKKQIYFQCACIYTNLWGDRFVRLHTTHMN-LTS--SLSTVFRYTDA 1304 (1560)
T ss_pred cccccccccCCCceEEEEEEeccc------cC-CCCcEEEEEEEeeccCCCcEEEEEEeeeec-ccC--CHHHHHHhhcH
Confidence 467899999999999999999997 64 356799999999999999999999999999 999 99999999999
Q ss_pred HHHHHHHHHHHHHHhhcc
Q 008566 529 EAAAVVMARLVSFKMEIE 546 (561)
Q Consensus 529 ~a~~~llak~a~~~~~~~ 546 (561)
+|++++|+|+|+.++++.
T Consensus 1305 dAIvslLAK~AV~~aLss 1322 (1560)
T PTZ00395 1305 EALMNILIKQLCTNILHN 1322 (1560)
T ss_pred HHHHHHHHHHHHHHhccc
Confidence 999999999999999986
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=3.1e-55 Score=437.09 Aligned_cols=262 Identities=56% Similarity=0.955 Sum_probs=238.9
Q ss_pred CCcEEEEEEEcccchhhHHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHHh
Q 008566 128 VPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQL 207 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~~~~~l~~~l~~~l~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~ 207 (561)
.||+|+||||+|..+++++.++++|+++|+.||++++|||||||++||||+|+ ... +++++||+|+++|+.+++++++
T Consensus 2 ~pp~~vFviDvs~~~~el~~l~~sl~~~L~~lP~~a~VGlITfd~~V~~~~L~-~~~-~~~~~vf~g~~~~~~~~~~~~l 79 (267)
T cd01478 2 SPPVFLFVVDTCMDEEELDALKESLIMSLSLLPPNALVGLITFGTMVQVHELG-FEE-CSKSYVFRGNKDYTAKQIQDML 79 (267)
T ss_pred CCCEEEEEEECccCHHHHHHHHHHHHHHHHhCCCCCEEEEEEECCEEEEEEcC-CCc-CceeeeccCCccCCHHHHHHHh
Confidence 48999999999999999999999999999999999999999999999999998 665 8999999999999999999998
Q ss_pred ccCCCCCCCCCc----cccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHh
Q 008566 208 NFFIKKPKPSTG----VIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG 283 (561)
Q Consensus 208 ~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~ 283 (561)
++.+ +++. +.++.+|++...+.++||+|++||++.|.++|++|+++.|++++++++.||+|+||++|..+|+
T Consensus 80 ~~~~----~~~~~~~~~~~~~~~~~~p~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~r~~r~~G~Al~~A~~ll~ 155 (267)
T cd01478 80 GLGG----PAMRPSASQHPGAGNPLPSAAASRFLLPVSQCEFTLTDLLEQLQPDPWPVPAGHRPLRCTGVALSIAVGLLE 155 (267)
T ss_pred cccc----ccccccccCcCCccccccccccccEEEEHHHHHHHHHHHHHhCcccccccCCCCCCCCchHHHHHHHHHHHH
Confidence 8653 2221 1223344332234579999999999999999999999999888899999999999999999999
Q ss_pred ccCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccC
Q 008566 284 ACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVG 363 (561)
Q Consensus 284 ~~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~ 363 (561)
.+.++.||||++|++||||.|||+|+.+++++++|+|.|++++++++++++.+||++||.+|+++||+||+|+++.+|+|
T Consensus 156 ~~~~~~gGki~~F~sg~pT~GpG~l~~r~~~~~~r~~~d~~~~~~~~~~~a~~fY~~la~~~~~~~vsvDlF~~s~d~vg 235 (267)
T cd01478 156 ACFPNTGARIMLFAGGPCTVGPGAVVSTELKDPIRSHHDIDKDNAKYYKKAVKFYDSLAKRLAANGHAVDIFAGCLDQVG 235 (267)
T ss_pred hhcCCCCcEEEEEECCCCCCCCceeeccccccccccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEEeccccccC
Confidence 77778999999999999999999999999999999999999998889999999999999999999999999999999999
Q ss_pred hhcchhhhhccCcEEEEcCCCCccchHHHHHH
Q 008566 364 VAELKVAVEKTGGLVVLSDSFGHAVFKDSVRR 395 (561)
Q Consensus 364 l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~~ 395 (561)
+++|+.|++.|||.+++|++|+.+.|+++++|
T Consensus 236 laem~~l~~~TGG~v~~~~~f~~~~f~~s~~~ 267 (267)
T cd01478 236 LLEMKVLVNSTGGHVVLSDSFTTSIFKQSFQR 267 (267)
T ss_pred HHHHHHHHHhcCcEEEEeCCcchHHHHHHhcC
Confidence 99999999999999999999999999988764
No 9
>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=4.9e-44 Score=353.85 Aligned_cols=226 Identities=41% Similarity=0.645 Sum_probs=192.8
Q ss_pred CCcEEEEEEEcccchh---hHHHHHHHHHHHhhcCC--CCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHH
Q 008566 128 VPPVFMFVVDTCIIEE---EMSFLKSALSQAIDLLP--DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQ 202 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~---~~~~l~~~l~~~l~~l~--~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~ 202 (561)
.||+|+||||+|.+++ +++.++++|+++|+.|| ++++|||||||+.||||+++ +....++++|++
T Consensus 2 ~pp~~vFvID~s~~ai~~~~l~~~~~sl~~~l~~lp~~~~~~igiITf~~~V~~~~~~-~~~~~~~~~v~~--------- 71 (239)
T cd01468 2 QPPVFVFVIDVSYEAIKEGLLQALKESLLASLDLLPGDPRARVGLITYDSTVHFYNLS-SDLAQPKMYVVS--------- 71 (239)
T ss_pred CCCEEEEEEEcchHhccccHHHHHHHHHHHHHHhCCCCCCcEEEEEEeCCeEEEEECC-CCCCCCeEEEeC---------
Confidence 4999999999999954 46778999999999999 99999999999999999998 543124455543
Q ss_pred HHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHH
Q 008566 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (561)
Q Consensus 203 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll 282 (561)
|++| .++|...++++++.|+++.|.++|++|++..+.. ...++.||+|+||++|..+|
T Consensus 72 --------------------dl~d-~f~p~~~~~l~~~~e~~~~i~~~l~~l~~~~~~~-~~~~~~~~~G~Al~~A~~ll 129 (239)
T cd01468 72 --------------------DLKD-VFLPLPDRFLVPLSECKKVIHDLLEQLPPMFWPV-PTHRPERCLGPALQAAFLLL 129 (239)
T ss_pred --------------------CCcc-CcCCCcCceeeeHHHHHHHHHHHHHhhhhhcccc-CCCCCcccHHHHHHHHHHHH
Confidence 3333 2234456899999999999999999999874432 36778899999999999999
Q ss_pred hccCCCC--CcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCC
Q 008566 283 GACVPGS--GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (561)
Q Consensus 283 ~~~~~~~--ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~ 360 (561)
+ .. ||||++|++|+||.|||+|..++.++++|+|. + +++++++.+||++||.+|+++||+||+|+++.+
T Consensus 130 ~----~~~~gGkI~~f~sg~pt~GpG~l~~~~~~~~~~~~~----e-~~~~~~a~~fY~~la~~~~~~~isvdlF~~~~~ 200 (239)
T cd01468 130 K----GTFAGGRIIVFQGGLPTVGPGKLKSREDKEPIRSHD----E-AQLLKPATKFYKSLAKECVKSGICVDLFAFSLD 200 (239)
T ss_pred h----hcCCCceEEEEECCCCCCCCCccccCcccccCCCcc----c-hhcccccHHHHHHHHHHHHHcCeEEEEEecccc
Confidence 9 45 99999999999999999999999888888762 2 478899999999999999999999999999999
Q ss_pred ccChhcchhhhhccCcEEEEcCCCCccchHHHHH
Q 008566 361 QVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVR 394 (561)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~ 394 (561)
++|+++|++|++.|||.+++|++|+..+..+.|.
T Consensus 201 ~~dl~~l~~l~~~TGG~v~~y~~f~~~~~~~~~~ 234 (239)
T cd01468 201 YVDVATLKQLAKSTGGQVYLYDSFQAPNDGSKFK 234 (239)
T ss_pred ccCHHHhhhhhhcCCceEEEeCCCCCcccHHHHH
Confidence 9999999999999999999999996654444333
No 10
>cd01479 Sec24-like Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24
Probab=100.00 E-value=1.9e-43 Score=349.53 Aligned_cols=227 Identities=23% Similarity=0.338 Sum_probs=189.6
Q ss_pred CCcEEEEEEEcccchhh---HHHHHHHHHHHhhcCCCC---ceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHH
Q 008566 128 VPPVFMFVVDTCIIEEE---MSFLKSALSQAIDLLPDN---SLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~~---~~~l~~~l~~~l~~l~~~---~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~ 201 (561)
.||+|+||||+|..+++ ++.++++|+++|+.||++ ++|||||||+.||||+++ +....++
T Consensus 2 ~pp~~~FvIDvs~~a~~~g~~~~~~~si~~~L~~lp~~~~~~~VgiITfd~~v~~y~l~-~~~~~~q------------- 67 (244)
T cd01479 2 QPAVYVFLIDVSYNAIKSGLLATACEALLSNLDNLPGDDPRTRVGFITFDSTLHFFNLK-SSLEQPQ------------- 67 (244)
T ss_pred CCCEEEEEEEccHHHHhhChHHHHHHHHHHHHHhcCCCCCCeEEEEEEECCeEEEEECC-CCCCCCe-------------
Confidence 48999999999999987 456899999999999976 999999999999999998 5431222
Q ss_pred HHHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHH
Q 008566 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (561)
Q Consensus 202 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~l 281 (561)
+++++|++| .++|..++||+|++|+++.|.++|++|+.. +.+..++.+|+|+||++|..+
T Consensus 68 ----------------~~vv~dl~d-~f~P~~~~~lv~l~e~~~~i~~lL~~L~~~---~~~~~~~~~c~G~Al~~A~~l 127 (244)
T cd01479 68 ----------------MMVVSDLDD-PFLPLPDGLLVNLKESRQVIEDLLDQIPEM---FQDTKETESALGPALQAAFLL 127 (244)
T ss_pred ----------------EEEeeCccc-ccCCCCcceeecHHHHHHHHHHHHHHHHHH---HhcCCCCcccHHHHHHHHHHH
Confidence 223344444 233455789999999999999999999653 566778899999999999999
Q ss_pred HhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCc
Q 008566 282 LGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (561)
Q Consensus 282 l~~~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~ 361 (561)
|+ +.||||++|++|+||.|||+|+.++.++ ++.| ++|+ ++++++++||++||.+|+++||+||+|+++.++
T Consensus 128 L~----~~GGkIi~f~s~~pt~GpG~l~~~~~~~-~~~~---~~e~-~~~~p~~~fY~~la~~~~~~~isvDlF~~~~~~ 198 (244)
T cd01479 128 LK----ETGGKIIVFQSSLPTLGAGKLKSREDPK-LLST---DKEK-QLLQPQTDFYKKLALECVKSQISVDLFLFSNQY 198 (244)
T ss_pred HH----hcCCEEEEEeCCCCCcCCcccccCcccc-ccCc---hhhh-hhcCcchHHHHHHHHHHHHcCeEEEEEEccCcc
Confidence 99 8999999999999999999999987544 4443 2443 688999999999999999999999999999999
Q ss_pred cChhcchhhhhccCcEEEEcC--CCCccc----hHHHHHHHH
Q 008566 362 VGVAELKVAVEKTGGLVVLSD--SFGHAV----FKDSVRRVF 397 (561)
Q Consensus 362 ~~l~~l~~l~~~TGG~v~~y~--~f~~~~----~~~~l~~~~ 397 (561)
+|+++|+.|++.|||.+++|+ +|+..+ +..+|.+.+
T Consensus 199 ~dla~l~~l~~~TGG~v~~y~~~~~~~~~d~~kl~~dl~~~l 240 (244)
T cd01479 199 VDVATLGCLSRLTGGQVYYYPSFNFSAPNDVEKLVNELARYL 240 (244)
T ss_pred cChhhhhhhhhhcCceEEEECCccCCchhhHHHHHHHHHHHh
Confidence 999999999999999999999 666543 334444444
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=1.3e-42 Score=344.80 Aligned_cols=231 Identities=32% Similarity=0.519 Sum_probs=173.8
Q ss_pred CCcEEEEEEEcccchhh---HHHHHHHHHHHhhcCC--CCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHH
Q 008566 128 VPPVFMFVVDTCIIEEE---MSFLKSALSQAIDLLP--DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQ 202 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~~---~~~l~~~l~~~l~~l~--~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~ 202 (561)
.||+|+||||+|..+++ ++.++++|+++|+.|| +++||||||||+.||+|+++ .....++..+.
T Consensus 2 ~pp~y~FvID~s~~av~~g~~~~~~~sl~~~l~~l~~~~~~~vgiitfd~~V~~y~l~-~~~~~~~~~v~---------- 70 (243)
T PF04811_consen 2 QPPVYVFVIDVSYEAVQSGLLQSLIESLKSALDSLPGDERTRVGIITFDSSVHFYNLS-SSLSQPQMIVV---------- 70 (243)
T ss_dssp S--EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTSSTSTT-EEEEEEESSSEEEEETT-TTSSSTEEEEE----------
T ss_pred CCCEEEEEEECchhhhhccHHHHHHHHHHHHHHhccCCCCcEEEEEEeCCEEEEEECC-CCcCCCcccch----------
Confidence 49999999999999666 4568999999999999 89999999999999999998 53322333332
Q ss_pred HHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHH
Q 008566 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (561)
Q Consensus 203 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll 282 (561)
++++| .++|..++||++++++++.|.++|++|++. ++.....++.||+|+||++|..+|
T Consensus 71 -------------------~dl~~-~~~p~~~~llv~~~e~~~~i~~ll~~L~~~-~~~~~~~~~~~c~G~Al~~A~~ll 129 (243)
T PF04811_consen 71 -------------------SDLDD-PFIPLPDGLLVPLSECRDAIEELLESLPSI-FPETAGKRPERCLGSALSAALSLL 129 (243)
T ss_dssp -------------------HHTTS-HHSSTSSSSSEETTTCHHHHHHHHHHHHHH-STT-TTB-----HHHHHHHHHHHH
T ss_pred -------------------HHHhh-cccCCcccEEEEhHHhHHHHHHHHHHhhhh-cccccccCccccHHHHHHHHHHHH
Confidence 22333 122334799999999999999999999883 333334778899999999999999
Q ss_pred hccCCCCCcEEEEEecCCCCCCC-cccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCc
Q 008566 283 GACVPGSGARILAFVGGPSTEGP-AAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (561)
Q Consensus 283 ~~~~~~~ggkIi~F~~g~pt~G~-G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~ 361 (561)
+. ...||||++|++|+||.|| |++..++.. ++.++++++..+++++.+||++||.+|+++||+||+|+++.++
T Consensus 130 ~~--~~~gGkI~~F~s~~pt~G~Gg~l~~~~~~----~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~ 203 (243)
T PF04811_consen 130 SS--RNTGGKILVFTSGPPTYGPGGSLKKREDS----SHYDTEKEKALLLPPANEFYKKLAEECSKQGISVDLFVFSSDY 203 (243)
T ss_dssp HH--HTS-EEEEEEESS---SSSTTSS-SBTTS----CCCCHCTTHHCHSHSSSHHHHHHHHHHHHCTEEEEEEEECSS-
T ss_pred hc--cccCCEEEEEeccCCCCCCCceecccccc----cccccccchhhhccccchHHHHHHHHHHhcCCEEEEEeecCCC
Confidence 83 1489999999999999999 666665432 5667777766788899999999999999999999999999999
Q ss_pred cChhcchhhhhccCcEEEEcCCCCcc----chHHHHHHH
Q 008566 362 VGVAELKVAVEKTGGLVVLSDSFGHA----VFKDSVRRV 396 (561)
Q Consensus 362 ~~l~~l~~l~~~TGG~v~~y~~f~~~----~~~~~l~~~ 396 (561)
+|+++|+.|++.|||.+++|++|+.+ ++.++|+|+
T Consensus 204 ~~l~tl~~l~~~TGG~l~~y~~f~~~~~~~~l~~dl~r~ 242 (243)
T PF04811_consen 204 VDLATLGPLARYTGGSLYYYPNFNAERDGEKLRQDLKRL 242 (243)
T ss_dssp -SHHHHTHHHHCTT-EEEEETTTTCHHHHHHHHHHHHHH
T ss_pred CCcHhHHHHHHhCceeEEEeCCCCCchhHHHHHHHHHHh
Confidence 99999999999999999999999955 445555544
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=99.87 E-value=7.1e-22 Score=167.21 Aligned_cols=96 Identities=42% Similarity=0.727 Sum_probs=85.0
Q ss_pred eeeeEEEEEecCCceEEeEEcCccccCCCCCCccCccccCCCCCceEEeCCCCCceEEEEEEEecCCCCcccccCCCCeE
Q 008566 407 SSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPDATLQSTNNQF 486 (561)
Q Consensus 407 ~~~~~~~vr~S~gl~i~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~~s~~~~f~~~~~~~~~~~l~~~~~~~ 486 (561)
||+|+||||||+|++|++++||+... +++|+.++|.++++.|.+++++++++|+|+|+++++ ++ ..+.+
T Consensus 1 g~~~~l~vr~S~gl~v~~~~G~~~~~----~~~s~~~~g~~~~~~~~~~~l~~~~s~~~~~~~~~~------~~-~~~~~ 69 (96)
T PF08033_consen 1 GFNAVLRVRCSKGLKVSGVIGPCFNR----SSVSDNEIGEGDTTRWKLPSLDPDTSFAFEFEIDED------LP-NGSQA 69 (96)
T ss_dssp EEEEEEEEEE-TTEEEEEEESSSEES----STBESSECSBSSCSEEEEEEEETT--EEEEEEESSB------TB-TTSEE
T ss_pred CceEEEEEEECCCeEEEEEEcCcccc----ccccceeeccCCccEEEecccCCCCEEEEEEEECCC------CC-CCCeE
Confidence 79999999999999999999999975 357888999999999999999999999999999876 53 35789
Q ss_pred EEEEEEEEEeCCCcEEEEEEcCCccccc
Q 008566 487 YFQFLTYYQHNCGQMRLRVTTLSRRWVA 514 (561)
Q Consensus 487 ~iQ~a~~Yt~~~G~r~iRV~T~~~~~vs 514 (561)
|||++++||+.+|+|++||+|+++| ++
T Consensus 70 ~iQ~~~~Yt~~~G~r~iRV~T~~l~-vt 96 (96)
T PF08033_consen 70 YIQFALLYTDSNGERRIRVTTLSLP-VT 96 (96)
T ss_dssp EEEEEEEEEETTSEEEEEEEEEEEE-EE
T ss_pred EEEEEEEEECCCCCEEEEEEeeccc-cC
Confidence 9999999999999999999999999 64
No 13
>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=99.63 E-value=8.6e-17 Score=112.17 Aligned_cols=40 Identities=55% Similarity=1.250 Sum_probs=29.0
Q ss_pred CCcccCCCCceecCceEEEcCCceeEeCCCCCCCCCCccC
Q 008566 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHY 96 (561)
Q Consensus 57 ~~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p~~y 96 (561)
+|+||++|+||||||++++.++++|+|+||++.|.+|++|
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 4899999999999999999999999999999999999887
No 14
>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=98.67 E-value=1.5e-06 Score=80.86 Aligned_cols=160 Identities=16% Similarity=0.205 Sum_probs=109.5
Q ss_pred EEEEEEEcccchhh--HHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHHhc
Q 008566 131 VFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLN 208 (561)
Q Consensus 131 ~~vFvID~s~~~~~--~~~l~~~l~~~l~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~ 208 (561)
.++|++|+|.+... +..+++++...++.++++.+|++++|++..+..--. ..
T Consensus 2 ~~~~vlD~S~SM~~~~~~~~k~a~~~~~~~l~~~~~v~li~f~~~~~~~~~~--~~------------------------ 55 (170)
T cd01465 2 NLVFVIDRSGSMDGPKLPLVKSALKLLVDQLRPDDRLAIVTYDGAAETVLPA--TP------------------------ 55 (170)
T ss_pred cEEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEecCCccEEecC--cc------------------------
Confidence 37899999998754 566788999999999999999999999764432100 00
Q ss_pred cCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccCC-
Q 008566 209 FFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVP- 287 (561)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~~- 287 (561)
....+.+...|+.+... ..+-++.||..|...+.....
T Consensus 56 --------------------------------~~~~~~l~~~l~~~~~~---------g~T~~~~al~~a~~~~~~~~~~ 94 (170)
T cd01465 56 --------------------------------VRDKAAILAAIDRLTAG---------GSTAGGAGIQLGYQEAQKHFVP 94 (170)
T ss_pred --------------------------------cchHHHHHHHHHcCCCC---------CCCCHHHHHHHHHHHHHhhcCC
Confidence 00112344555554321 234588999999888763211
Q ss_pred CCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccChhcc
Q 008566 288 GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAEL 367 (561)
Q Consensus 288 ~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l~~l 367 (561)
..-.+|++|++|.++.|+... +-+.+....+...++.|+.+.++ +..+...|
T Consensus 95 ~~~~~ivl~TDG~~~~~~~~~---------------------------~~~~~~~~~~~~~~v~i~~i~~g-~~~~~~~l 146 (170)
T cd01465 95 GGVNRILLATDGDFNVGETDP---------------------------DELARLVAQKRESGITLSTLGFG-DNYNEDLM 146 (170)
T ss_pred CCeeEEEEEeCCCCCCCCCCH---------------------------HHHHHHHHHhhcCCeEEEEEEeC-CCcCHHHH
Confidence 112679999999987764110 11234455567789999999997 67789999
Q ss_pred hhhhhccCcEEEEcCCCC
Q 008566 368 KVAVEKTGGLVVLSDSFG 385 (561)
Q Consensus 368 ~~l~~~TGG~v~~y~~f~ 385 (561)
..++..++|..++.++..
T Consensus 147 ~~ia~~~~g~~~~~~~~~ 164 (170)
T cd01465 147 EAIADAGNGNTAYIDNLA 164 (170)
T ss_pred HHHHhcCCceEEEeCCHH
Confidence 999999999988775533
No 15
>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=98.66 E-value=2e-06 Score=82.07 Aligned_cols=167 Identities=17% Similarity=0.168 Sum_probs=106.8
Q ss_pred CCcEEEEEEEcccchh--hHHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHH
Q 008566 128 VPPVFMFVVDTCIIEE--EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~--~~~~l~~~l~~~l~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (561)
.|-.++||||+|.++. .++.+++++...++.|+++.+||||+|++.++..--- ...
T Consensus 12 ~p~~vv~llD~SgSM~~~~l~~ak~~~~~ll~~l~~~d~v~lv~F~~~~~~~~~~-~~~--------------------- 69 (190)
T cd01463 12 SPKDIVILLDVSGSMTGQRLHLAKQTVSSILDTLSDNDFFNIITFSNEVNPVVPC-FND--------------------- 69 (190)
T ss_pred CCceEEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCCCEEEEEEeCCCeeEEeee-ccc---------------------
Confidence 3778999999999874 3566899999999999999999999999987754211 000
Q ss_pred HhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhcc
Q 008566 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (561)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~ 285 (561)
.++....+.++.+...|+.|+.. ..+.++.||..|...+...
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 00011112333555556655432 2356899999999888731
Q ss_pred --------CCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHH-HHHhcCcEEEEEe
Q 008566 286 --------VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSK-QLVHQGHVLDLFA 356 (561)
Q Consensus 286 --------~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~-~~~~~~isvdlf~ 356 (561)
.+.....|+++++|.++.+.- ..+.+.. .....++.|..|.
T Consensus 112 ~~~~~~~~~~~~~~~iillTDG~~~~~~~------------------------------~~~~~~~~~~~~~~v~i~tig 161 (190)
T cd01463 112 LQSNHSGSRSQCNQAIMLITDGVPENYKE------------------------------IFDKYNWDKNSEIPVRVFTYL 161 (190)
T ss_pred hhcccccccCCceeEEEEEeCCCCCcHhH------------------------------HHHHhcccccCCCcEEEEEEe
Confidence 012234799999997653210 0111100 0011245555555
Q ss_pred ecCCccChhcchhhhhccCcEEEEcCCC
Q 008566 357 CALDQVGVAELKVAVEKTGGLVVLSDSF 384 (561)
Q Consensus 357 ~s~~~~~l~~l~~l~~~TGG~v~~y~~f 384 (561)
++.+..|...|..|+..+||..++.++.
T Consensus 162 iG~~~~d~~~L~~lA~~~~G~~~~i~~~ 189 (190)
T cd01463 162 IGREVTDRREIQWMACENKGYYSHIQSL 189 (190)
T ss_pred cCCccccchHHHHHHhhcCCeEEEcccC
Confidence 6555458889999999999999988753
No 16
>PRK13685 hypothetical protein; Provisional
Probab=98.65 E-value=2.4e-06 Score=88.66 Aligned_cols=161 Identities=20% Similarity=0.191 Sum_probs=112.8
Q ss_pred CcEEEEEEEcccchh-------hHHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHH
Q 008566 129 PPVFMFVVDTCIIEE-------EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (561)
Q Consensus 129 ~p~~vFvID~s~~~~-------~~~~l~~~l~~~l~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~ 201 (561)
+..+|||||+|.++. .++..+++++..++.++++.+||+|+|++..++. .
T Consensus 88 ~~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l~~~d~vglv~Fa~~a~~~--~--------------------- 144 (326)
T PRK13685 88 RAVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELTPGINLGLIAFAGTATVL--V--------------------- 144 (326)
T ss_pred CceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhCCCCCeEEEEEEcCceeec--C---------------------
Confidence 456899999999975 3677899999999999889999999999764421 1
Q ss_pred HHHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHH
Q 008566 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (561)
Q Consensus 202 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~l 281 (561)
| ....++.+...|+.|... ...+.|.|+..|...
T Consensus 145 --------------------p-----------------~t~d~~~l~~~l~~l~~~---------~~T~~g~al~~A~~~ 178 (326)
T PRK13685 145 --------------------S-----------------PTTNREATKNAIDKLQLA---------DRTATGEAIFTALQA 178 (326)
T ss_pred --------------------C-----------------CCCCHHHHHHHHHhCCCC---------CCcchHHHHHHHHHH
Confidence 0 011234677777777542 235678999988887
Q ss_pred Hhcc-------CCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEE
Q 008566 282 LGAC-------VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDL 354 (561)
Q Consensus 282 l~~~-------~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdl 354 (561)
+... .....+.|+++++|-.+.|...... ... .+.++.+.+.||.|..
T Consensus 179 l~~~~~~~~~~~~~~~~~IILlTDG~~~~~~~~~~~---------------------~~~----~~aa~~a~~~gi~i~~ 233 (326)
T PRK13685 179 IATVGAVIGGGDTPPPARIVLMSDGKETVPTNPDNP---------------------RGA----YTAARTAKDQGVPIST 233 (326)
T ss_pred HHhhhcccccccCCCCCEEEEEcCCCCCCCCCCCCc---------------------ccH----HHHHHHHHHcCCeEEE
Confidence 7521 1123478999999987765311000 000 1345667788999999
Q ss_pred EeecCCc-------------cChhcchhhhhccCcEEEEcCC
Q 008566 355 FACALDQ-------------VGVAELKVAVEKTGGLVVLSDS 383 (561)
Q Consensus 355 f~~s~~~-------------~~l~~l~~l~~~TGG~v~~y~~ 383 (561)
+.++.+. .|-..|..+++.|||+.++.++
T Consensus 234 Ig~G~~~g~~~~~g~~~~~~~d~~~L~~iA~~tgG~~~~~~~ 275 (326)
T PRK13685 234 ISFGTPYGSVEINGQRQPVPVDDESLKKIAQLSGGEFYTAAS 275 (326)
T ss_pred EEECCCCCCcCcCCceeeecCCHHHHHHHHHhcCCEEEEcCC
Confidence 9887642 5778899999999998888755
No 17
>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=98.60 E-value=1.4e-06 Score=84.28 Aligned_cols=168 Identities=24% Similarity=0.296 Sum_probs=107.5
Q ss_pred CCcEEEEEEEcccchh--------hHHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCC
Q 008566 128 VPPVFMFVVDTCIIEE--------EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVS 199 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~--------~~~~l~~~l~~~l~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~ 199 (561)
.+..++||||+|.++. .++.+++++...++.++++.+|||++|++.+.- . ..- + .+
T Consensus 19 ~~~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~l~~~~~v~lv~F~~~~~~---~-~~~---~-~~-------- 82 (206)
T cd01456 19 LPPNVAIVLDNSGSMREVDGGGETRLDNAKAALDETANALPDGTRLGLWTFSGDGDN---P-LDV---R-VL-------- 82 (206)
T ss_pred CCCcEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHhCCCCceEEEEEecCCCCC---C-ccc---c-cc--------
Confidence 5788999999999976 356789999999999999999999999985421 0 000 0 00
Q ss_pred HHHHHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHcc-CCCCCCCCCCCCCcchhHHHHHH
Q 008566 200 KDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQ-KDPWPVPPDQRSTRCTGTALSIA 278 (561)
Q Consensus 200 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~-~~~~~~~~~~~~~~c~G~Al~~A 278 (561)
+|-.+ +. .....+. ...+..+.+.|+.|. .. ..+.++.||..|
T Consensus 83 ---------------------~p~~~--~~-~~~~~~~---~~~~~~l~~~i~~i~~~~---------G~T~l~~aL~~a 126 (206)
T cd01456 83 ---------------------VPKGC--LT-APVNGFP---SAQRSALDAALNSLQTPT---------GWTPLAAALAEA 126 (206)
T ss_pred ---------------------ccccc--cc-cccCCCC---cccHHHHHHHHHhhcCCC---------CcChHHHHHHHH
Confidence 00000 00 0000000 023456777777775 21 346789999999
Q ss_pred HHHHhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHH-HhcCcEEEEEee
Q 008566 279 ASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQL-VHQGHVLDLFAC 357 (561)
Q Consensus 279 ~~ll~~~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~-~~~~isvdlf~~ 357 (561)
..++. ......|+++++|.++.|.... +..+++.... ...+|.|+.+.+
T Consensus 127 ~~~l~---~~~~~~iillTDG~~~~~~~~~---------------------------~~~~~~~~~~~~~~~i~i~~igi 176 (206)
T cd01456 127 AAYVD---PGRVNVVVLITDGEDTCGPDPC---------------------------EVARELAKRRTPAPPIKVNVIDF 176 (206)
T ss_pred HHHhC---CCCcceEEEEcCCCccCCCCHH---------------------------HHHHHHHHhcCCCCCceEEEEEe
Confidence 98885 1333789999999876653000 0111222110 225899999988
Q ss_pred cCCccChhcchhhhhccCcEE
Q 008566 358 ALDQVGVAELKVAVEKTGGLV 378 (561)
Q Consensus 358 s~~~~~l~~l~~l~~~TGG~v 378 (561)
+.+ .+...|..++..|||..
T Consensus 177 G~~-~~~~~l~~iA~~tgG~~ 196 (206)
T cd01456 177 GGD-ADRAELEAIAEATGGTY 196 (206)
T ss_pred cCc-ccHHHHHHHHHhcCCeE
Confidence 754 67889999999999988
No 18
>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=98.60 E-value=3.5e-06 Score=79.54 Aligned_cols=161 Identities=19% Similarity=0.108 Sum_probs=107.7
Q ss_pred EEEEEEcccchh---hHHHHHHHHHHHhhc-CCCCceEEEEEECCe-EEEEEcCCCCCCCCeeEeecCCccCCHHHHHHH
Q 008566 132 FMFVVDTCIIEE---EMSFLKSALSQAIDL-LPDNSLVGLITFGTL-VQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQ 206 (561)
Q Consensus 132 ~vFvID~s~~~~---~~~~l~~~l~~~l~~-l~~~~~VglItf~~~-V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~ 206 (561)
++|+||+|.++. .+..++.++...+.. ++++.+||+|+|++. .++. +. .
T Consensus 3 v~lvlD~SgSM~~~~rl~~ak~a~~~~~~~~~~~~d~v~lv~F~~~~~~~~-~~-~------------------------ 56 (178)
T cd01451 3 VIFVVDASGSMAARHRMAAAKGAVLSLLRDAYQRRDKVALIAFRGTEAEVL-LP-P------------------------ 56 (178)
T ss_pred EEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCceEE-eC-C------------------------
Confidence 689999999975 456678888877754 567889999999864 2211 11 0
Q ss_pred hccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccC
Q 008566 207 LNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACV 286 (561)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~ 286 (561)
......+...|+.++. ...+.++.||..|...++...
T Consensus 57 ----------------------------------t~~~~~~~~~l~~l~~---------~G~T~l~~aL~~a~~~l~~~~ 93 (178)
T cd01451 57 ----------------------------------TRSVELAKRRLARLPT---------GGGTPLAAGLLAAYELAAEQA 93 (178)
T ss_pred ----------------------------------CCCHHHHHHHHHhCCC---------CCCCcHHHHHHHHHHHHHHHh
Confidence 0011123445555432 134678999999998882111
Q ss_pred CCC--CcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHH-HHHHHHHHhcCcEEEEEeecCCccC
Q 008566 287 PGS--GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFY-DALSKQLVHQGHVLDLFACALDQVG 363 (561)
Q Consensus 287 ~~~--ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY-~~la~~~~~~~isvdlf~~s~~~~~ 363 (561)
... -..|+++++|.++.|.... ..- ..++.++...||.+..+.......+
T Consensus 94 ~~~~~~~~ivliTDG~~~~g~~~~---------------------------~~~~~~~~~~l~~~gi~v~~I~~~~~~~~ 146 (178)
T cd01451 94 RDPGQRPLIVVITDGRANVGPDPT---------------------------ADRALAAARKLRARGISALVIDTEGRPVR 146 (178)
T ss_pred cCCCCceEEEEECCCCCCCCCCch---------------------------hHHHHHHHHHHHhcCCcEEEEeCCCCccC
Confidence 122 2689999999888764100 011 4567778888988876666555567
Q ss_pred hhcchhhhhccCcEEEEcCCCCccc
Q 008566 364 VAELKVAVEKTGGLVVLSDSFGHAV 388 (561)
Q Consensus 364 l~~l~~l~~~TGG~v~~y~~f~~~~ 388 (561)
-..|..|++.|||+.++.++.+...
T Consensus 147 ~~~l~~iA~~tgG~~~~~~d~~~~~ 171 (178)
T cd01451 147 RGLAKDLARALGGQYVRLPDLSADA 171 (178)
T ss_pred ccHHHHHHHHcCCeEEEcCcCCHHH
Confidence 7789999999999999998887643
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=98.60 E-value=1.9e-06 Score=79.45 Aligned_cols=149 Identities=19% Similarity=0.197 Sum_probs=103.3
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHHhcc
Q 008566 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNF 209 (561)
Q Consensus 132 ~vFvID~s~~~~~--~~~l~~~l~~~l~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~ 209 (561)
++|+||.|.++.. ++.+++++...++.|+++.+||||+|++..+.+ . .. .
T Consensus 3 v~~vlD~S~SM~~~rl~~ak~a~~~l~~~l~~~~~~~li~F~~~~~~~--~--~~-----------~------------- 54 (155)
T cd01466 3 LVAVLDVSGSMAGDKLQLVKHALRFVISSLGDADRLSIVTFSTSAKRL--S--PL-----------R------------- 54 (155)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcceEEEEEecCCcccc--C--CC-----------c-------------
Confidence 5799999999764 567899999999999999999999999864432 1 00 0
Q ss_pred CCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhcc-CCC
Q 008566 210 FIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC-VPG 288 (561)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~-~~~ 288 (561)
+ . -.+.++.+.++++.+... ..++++.||..|..++... ..+
T Consensus 55 ------------~-----~-----------~~~~~~~~~~~i~~~~~~---------g~T~~~~al~~a~~~~~~~~~~~ 97 (155)
T cd01466 55 ------------R-----M-----------TAKGKRSAKRVVDGLQAG---------GGTNVVGGLKKALKVLGDRRQKN 97 (155)
T ss_pred ------------c-----c-----------CHHHHHHHHHHHHhccCC---------CCccHHHHHHHHHHHHhhcccCC
Confidence 0 0 011233566666665432 3578999999999998632 113
Q ss_pred CCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccChhcch
Q 008566 289 SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELK 368 (561)
Q Consensus 289 ~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l~~l~ 368 (561)
....|+++++|.++.|... .++.+.++.|..+.++. ..+..+|.
T Consensus 98 ~~~~iillTDG~~~~~~~~-----------------------------------~~~~~~~v~v~~igig~-~~~~~~l~ 141 (155)
T cd01466 98 PVASIMLLSDGQDNHGAVV-----------------------------------LRADNAPIPIHTFGLGA-SHDPALLA 141 (155)
T ss_pred CceEEEEEcCCCCCcchhh-----------------------------------hcccCCCceEEEEecCC-CCCHHHHH
Confidence 3468999999987765100 00123577788877753 46888999
Q ss_pred hhhhccCcEEEEc
Q 008566 369 VAVEKTGGLVVLS 381 (561)
Q Consensus 369 ~l~~~TGG~v~~y 381 (561)
.|+..|||+.++.
T Consensus 142 ~iA~~t~G~~~~~ 154 (155)
T cd01466 142 FIAEITGGTFSYV 154 (155)
T ss_pred HHHhccCceEEEe
Confidence 9999999998874
No 20
>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=98.50 E-value=4.4e-06 Score=79.31 Aligned_cols=153 Identities=13% Similarity=0.070 Sum_probs=99.3
Q ss_pred cEEEEEEEcccchh-------hHHHHHHHHHHHhhcC---CCCceEEEEEE-CCeEEEEEcCCCCCCCCeeEeecCCccC
Q 008566 130 PVFMFVVDTCIIEE-------EMSFLKSALSQAIDLL---PDNSLVGLITF-GTLVQVHELGGFGQIIPKTYVFKGSKDV 198 (561)
Q Consensus 130 p~~vFvID~s~~~~-------~~~~l~~~l~~~l~~l---~~~~~VglItf-~~~V~~y~l~~~~~~~~~~~v~~g~~~~ 198 (561)
...+++||+|.++. +++..+..+...++.+ .+..+||||+| +..-++- .
T Consensus 4 r~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~a~~~--~------------------ 63 (183)
T cd01453 4 RHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKL--T------------------ 63 (183)
T ss_pred eEEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCccEEE--E------------------
Confidence 35799999999975 4667888888777754 45689999999 4322221 1
Q ss_pred CHHHHHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHH
Q 008566 199 SKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIA 278 (561)
Q Consensus 199 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A 278 (561)
|+....+.+...|+.+.. + .....++.||..|
T Consensus 64 ----------------------------------------PlT~D~~~~~~~L~~~~~-----~---~G~t~l~~aL~~A 95 (183)
T cd01453 64 ----------------------------------------DLTGNPRKHIQALKTARE-----C---SGEPSLQNGLEMA 95 (183)
T ss_pred ----------------------------------------CCCCCHHHHHHHhhcccC-----C---CCchhHHHHHHHH
Confidence 111111133444443311 1 1236799999999
Q ss_pred HHHHhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeec
Q 008566 279 ASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACA 358 (561)
Q Consensus 279 ~~ll~~~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s 358 (561)
...++.......++|++++++.-+.+| .-+.++++.+.+.||.|++..++
T Consensus 96 ~~~l~~~~~~~~~~iiil~sd~~~~~~------------------------------~~~~~~~~~l~~~~I~v~~IgiG 145 (183)
T cd01453 96 LESLKHMPSHGSREVLIIFSSLSTCDP------------------------------GNIYETIDKLKKENIRVSVIGLS 145 (183)
T ss_pred HHHHhcCCccCceEEEEEEcCCCcCCh------------------------------hhHHHHHHHHHHcCcEEEEEEec
Confidence 999973111234678888775321111 01145788888999999999986
Q ss_pred CCccChhcchhhhhccCcEEEEcCC
Q 008566 359 LDQVGVAELKVAVEKTGGLVVLSDS 383 (561)
Q Consensus 359 ~~~~~l~~l~~l~~~TGG~v~~y~~ 383 (561)
. +...|..+|+.|||+.+...+
T Consensus 146 ~---~~~~L~~ia~~tgG~~~~~~~ 167 (183)
T cd01453 146 A---EMHICKEICKATNGTYKVILD 167 (183)
T ss_pred h---HHHHHHHHHHHhCCeeEeeCC
Confidence 4 467899999999999987755
No 21
>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=98.44 E-value=1.3e-05 Score=75.39 Aligned_cols=156 Identities=18% Similarity=0.193 Sum_probs=101.6
Q ss_pred cEEEEEEEcccchh--------hHHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHH
Q 008566 130 PVFMFVVDTCIIEE--------EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (561)
Q Consensus 130 p~~vFvID~s~~~~--------~~~~l~~~l~~~l~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~ 201 (561)
.-++|+||+|.+.. .++.++..+...+... ++.+||+++|++.++.. . . .
T Consensus 3 ~~vv~vlD~S~SM~~~~~~~~~r~~~a~~~~~~~~~~~-~~~~v~lv~f~~~~~~~--~-~-~----------------- 60 (180)
T cd01467 3 RDIMIALDVSGSMLAQDFVKPSRLEAAKEVLSDFIDRR-ENDRIGLVVFAGAAFTQ--A-P-L----------------- 60 (180)
T ss_pred ceEEEEEECCcccccccCCCCCHHHHHHHHHHHHHHhC-CCCeEEEEEEcCCeeec--c-C-C-----------------
Confidence 45799999999863 2455677776666554 57899999998765432 1 0 0
Q ss_pred HHHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHH
Q 008566 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (561)
Q Consensus 202 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~l 281 (561)
...+..+.++++.|... . ....+.++.||..|..+
T Consensus 61 ---------------------------------------~~~~~~~~~~l~~l~~~----~--~~g~T~l~~al~~a~~~ 95 (180)
T cd01467 61 ---------------------------------------TLDRESLKELLEDIKIG----L--AGQGTAIGDAIGLAIKR 95 (180)
T ss_pred ---------------------------------------CccHHHHHHHHHHhhhc----c--cCCCCcHHHHHHHHHHH
Confidence 00112344555555421 0 11345688999999988
Q ss_pred HhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCC-
Q 008566 282 LGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD- 360 (561)
Q Consensus 282 l~~~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~- 360 (561)
+... ......|+++++|.++.|+ . .+ .+.+..+.+.||.|+.+.++..
T Consensus 96 l~~~-~~~~~~iiliTDG~~~~g~--~-----------------------~~-----~~~~~~~~~~gi~i~~i~ig~~~ 144 (180)
T cd01467 96 LKNS-EAKERVIVLLTDGENNAGE--I-----------------------DP-----ATAAELAKNKGVRIYTIGVGKSG 144 (180)
T ss_pred HHhc-CCCCCEEEEEeCCCCCCCC--C-----------------------CH-----HHHHHHHHHCCCEEEEEEecCCC
Confidence 8631 2334679999999876543 0 00 1223445578999999888762
Q ss_pred ---------ccChhcchhhhhccCcEEEEcCC
Q 008566 361 ---------QVGVAELKVAVEKTGGLVVLSDS 383 (561)
Q Consensus 361 ---------~~~l~~l~~l~~~TGG~v~~y~~ 383 (561)
..+...|..|++.|||..++..+
T Consensus 145 ~~~~~~~~~~~~~~~l~~la~~tgG~~~~~~~ 176 (180)
T cd01467 145 SGPKPDGSTILDEDSLVEIADKTGGRIFRALD 176 (180)
T ss_pred CCcCCCCcccCCHHHHHHHHHhcCCEEEEecC
Confidence 46778899999999999998764
No 22
>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=98.39 E-value=4.7e-05 Score=77.96 Aligned_cols=49 Identities=22% Similarity=0.265 Sum_probs=40.6
Q ss_pred CCcEEEEEEEcccchhh-HHHHHHHHHHHhhc-CCCCceEEEEEECCeEEE
Q 008566 128 VPPVFMFVVDTCIIEEE-MSFLKSALSQAIDL-LPDNSLVGLITFGTLVQV 176 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~~-~~~l~~~l~~~l~~-l~~~~~VglItf~~~V~~ 176 (561)
.|...+|+||+|.++.. +..+++++...++. ++++.+||||+|++.+++
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 37899999999998754 45578888888876 788999999999987665
No 23
>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=98.32 E-value=2.8e-05 Score=74.68 Aligned_cols=168 Identities=14% Similarity=0.102 Sum_probs=99.7
Q ss_pred EEEEEEcccchh--hHHHHHHHHHHHhhcCC---CCceEEEEEECCeEEEE-EcCCCCCCCCeeEeecCCccCCHHHHHH
Q 008566 132 FMFVVDTCIIEE--EMSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (561)
Q Consensus 132 ~vFvID~s~~~~--~~~~l~~~l~~~l~~l~---~~~~VglItf~~~V~~y-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (561)
++||||+|.+.. .++.+++++...++.|+ .+.+||||+|++..+.. .+. ...
T Consensus 3 i~~vlD~SgSM~~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~~~~~~~~-~~~--------------------- 60 (198)
T cd01470 3 IYIALDASDSIGEEDFDEAKNAIKTLIEKISSYEVSPRYEIISYASDPKEIVSIR-DFN--------------------- 60 (198)
T ss_pred EEEEEECCCCccHHHHHHHHHHHHHHHHHccccCCCceEEEEEecCCceEEEecc-cCC---------------------
Confidence 689999999875 35668899999888886 36899999999876542 222 100
Q ss_pred HhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhcc
Q 008566 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (561)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~ 285 (561)
...+..+...|+.+.... ......+.++.||..|...+...
T Consensus 61 -----------------------------------~~~~~~~~~~l~~~~~~~----~~~~ggT~~~~Al~~~~~~l~~~ 101 (198)
T cd01470 61 -----------------------------------SNDADDVIKRLEDFNYDD----HGDKTGTNTAAALKKVYERMALE 101 (198)
T ss_pred -----------------------------------CCCHHHHHHHHHhCCccc----ccCccchhHHHHHHHHHHHHHHH
Confidence 001123444555554321 01123456888888887665310
Q ss_pred C-C------CCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHH------HHHhcCcEE
Q 008566 286 V-P------GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSK------QLVHQGHVL 352 (561)
Q Consensus 286 ~-~------~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~------~~~~~~isv 352 (561)
. . ..--.|+++++|.+|.|... ....+.++++.. .+...++.|
T Consensus 102 ~~~~~~~~~~~~~~iillTDG~~~~g~~~------------------------~~~~~~~~~~~~~~~~~~~~~~~~v~i 157 (198)
T cd01470 102 KVRNKEAFNETRHVIILFTDGKSNMGGSP------------------------LPTVDKIKNLVYKNNKSDNPREDYLDV 157 (198)
T ss_pred HhcCccchhhcceEEEEEcCCCcCCCCCh------------------------hHHHHHHHHHHhcccccccchhcceeE
Confidence 0 0 01134789999998876310 011122222211 123446655
Q ss_pred EEEeecCCccChhcchhhhhccCc--EEEEcCCCC
Q 008566 353 DLFACALDQVGVAELKVAVEKTGG--LVVLSDSFG 385 (561)
Q Consensus 353 dlf~~s~~~~~l~~l~~l~~~TGG--~v~~y~~f~ 385 (561)
..+..+ +.+|-.+|..|+..||| +++...+|.
T Consensus 158 ~~iGvG-~~~~~~~L~~iA~~~~g~~~~f~~~~~~ 191 (198)
T cd01470 158 YVFGVG-DDVNKEELNDLASKKDNERHFFKLKDYE 191 (198)
T ss_pred EEEecC-cccCHHHHHHHhcCCCCCceEEEeCCHH
Confidence 555553 35789999999999999 577776654
No 24
>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=5.8e-05 Score=70.06 Aligned_cols=152 Identities=16% Similarity=0.188 Sum_probs=95.4
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcCC---CCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHH
Q 008566 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQ 206 (561)
Q Consensus 132 ~vFvID~s~~~~~--~~~l~~~l~~~l~~l~---~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~ 206 (561)
.+|+||.|.+... ++.++++++..++.|. ++.++|||+|++..+.. .. ..
T Consensus 3 vv~vlD~SgSm~~~~~~~~k~~~~~~~~~l~~~~~~~~~giv~Fs~~~~~~-~~-~~----------------------- 57 (164)
T cd01472 3 IVFLVDGSESIGLSNFNLVKDFVKRVVERLDIGPDGVRVGVVQYSDDPRTE-FY-LN----------------------- 57 (164)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHhhcccCCCCeEEEEEEEcCceeEE-Ee-cC-----------------------
Confidence 5899999998654 4557888888877774 46799999999876542 11 00
Q ss_pred hccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhcc-
Q 008566 207 LNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC- 285 (561)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~- 285 (561)
. ...++.+.+.|+.++.. ...+.+|.||..|...+...
T Consensus 58 ----------------------------~-----~~~~~~~~~~l~~l~~~--------~g~T~~~~al~~a~~~l~~~~ 96 (164)
T cd01472 58 ----------------------------T-----YRSKDDVLEAVKNLRYI--------GGGTNTGKALKYVRENLFTEA 96 (164)
T ss_pred ----------------------------C-----CCCHHHHHHHHHhCcCC--------CCCchHHHHHHHHHHHhCCcc
Confidence 0 01122455556666431 13467999999999988631
Q ss_pred ---CCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCcc
Q 008566 286 ---VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (561)
Q Consensus 286 ---~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~ 362 (561)
.+.....|+++++|.++.+. ...+..+.+.||.+..+.. ...
T Consensus 97 ~~~~~~~~~~iiliTDG~~~~~~---------------------------------~~~~~~l~~~gv~i~~ig~--g~~ 141 (164)
T cd01472 97 SGSREGVPKVLVVITDGKSQDDV---------------------------------EEPAVELKQAGIEVFAVGV--KNA 141 (164)
T ss_pred cCCCCCCCEEEEEEcCCCCCchH---------------------------------HHHHHHHHHCCCEEEEEEC--CcC
Confidence 22344567888887432110 0122344557775554444 334
Q ss_pred ChhcchhhhhccCc-EEEEcCCC
Q 008566 363 GVAELKVAVEKTGG-LVVLSDSF 384 (561)
Q Consensus 363 ~l~~l~~l~~~TGG-~v~~y~~f 384 (561)
|...|..++..++| .++.+.+|
T Consensus 142 ~~~~L~~ia~~~~~~~~~~~~~~ 164 (164)
T cd01472 142 DEEELKQIASDPKELYVFNVADF 164 (164)
T ss_pred CHHHHHHHHCCCchheEEeccCC
Confidence 99999999999987 56655543
No 25
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=98.28 E-value=4e-05 Score=87.46 Aligned_cols=155 Identities=15% Similarity=0.210 Sum_probs=103.2
Q ss_pred CCcEEEEEEEcccchh---hHHHHHHHHHHHh-hcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHH
Q 008566 128 VPPVFMFVVDTCIIEE---EMSFLKSALSQAI-DLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQL 203 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~---~~~~l~~~l~~~l-~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l 203 (561)
.++.+++|||+|.++. .+..++++++..+ +.++++.+||||+|++..++. . .. .
T Consensus 303 ~~r~VVLVLDvSGSM~g~dRL~~lkqAA~~fL~~~l~~~DrVGLVtFsssA~vl--~--pL-t----------------- 360 (863)
T TIGR00868 303 RQRIVCLVLDKSGSMTVEDRLKRMNQAAKLFLLQTVEKGSWVGMVTFDSAAYIK--N--EL-I----------------- 360 (863)
T ss_pred CCceEEEEEECCccccccCHHHHHHHHHHHHHHHhCCCCCEEEEEEECCceeEe--e--cc-c-----------------
Confidence 3566999999999975 3667788887765 457888999999999976543 1 10 0
Q ss_pred HHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHh
Q 008566 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG 283 (561)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~ 283 (561)
.+ . . ...++.|...+. .. ....++++.||..|..+|.
T Consensus 361 -~I---------------t------------s-----~~dr~aL~~~L~---~~-------A~GGT~I~~GL~~Alq~L~ 397 (863)
T TIGR00868 361 -QI---------------T------------S-----SAERDALTANLP---TA-------ASGGTSICSGLKAAFQVIK 397 (863)
T ss_pred -cC---------------C------------c-----HHHHHHHHHhhc---cc-------cCCCCcHHHHHHHHHHHHH
Confidence 00 0 0 011222333222 11 1245789999999999988
Q ss_pred ccC-CCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCcc
Q 008566 284 ACV-PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (561)
Q Consensus 284 ~~~-~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~ 362 (561)
... +..+..|+++++|-.+.+ ..+...+.+.|+.|..+.++.+.
T Consensus 398 ~~~~~~~~~~IILLTDGedn~~----------------------------------~~~l~~lk~~gVtI~TIg~G~da- 442 (863)
T TIGR00868 398 KSYQSTDGSEIVLLTDGEDNTI----------------------------------SSCFEEVKQSGAIIHTIALGPSA- 442 (863)
T ss_pred hcccccCCCEEEEEeCCCCCCH----------------------------------HHHHHHHHHcCCEEEEEEeCCCh-
Confidence 432 235678999988864311 12334456689999999987653
Q ss_pred ChhcchhhhhccCcEEEEcCC
Q 008566 363 GVAELKVAVEKTGGLVVLSDS 383 (561)
Q Consensus 363 ~l~~l~~l~~~TGG~v~~y~~ 383 (561)
-..|..||+.|||..++.++
T Consensus 443 -d~~L~~IA~~TGG~~f~asd 462 (863)
T TIGR00868 443 -AKELEELSDMTGGLRFYASD 462 (863)
T ss_pred -HHHHHHHHHhcCCEEEEeCC
Confidence 24589999999999999875
No 26
>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=98.23 E-value=9.8e-05 Score=68.63 Aligned_cols=159 Identities=21% Similarity=0.206 Sum_probs=102.4
Q ss_pred CcEEEEEEEcccchhh--HHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHH
Q 008566 129 PPVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQ 206 (561)
Q Consensus 129 ~p~~vFvID~s~~~~~--~~~l~~~l~~~l~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~ 206 (561)
|.-++|++|+|.++.. +..+++++...+..+++..+|++++|++.++.+ . ... +
T Consensus 2 ~~~v~~vlD~S~SM~~~~~~~~~~al~~~l~~l~~~~~~~l~~Fs~~~~~~--~-~~~------~--------------- 57 (171)
T cd01461 2 PKEVVFVIDTSGSMSGTKIEQTKEALLTALKDLPPGDYFNIIGFSDTVEEF--S-PSS------V--------------- 57 (171)
T ss_pred CceEEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEeCCCceee--c-Ccc------e---------------
Confidence 5568999999999853 466788999999999988899999999875543 1 100 0
Q ss_pred hccCCCCCCCCCccccCcCCCCCCccccceeeec-hhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhcc
Q 008566 207 LNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPA-FDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (561)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~ 285 (561)
+. .+....+.+.++.+.. .....+..||..|...+..
T Consensus 58 --------------------------------~~~~~~~~~~~~~l~~~~~---------~g~T~l~~al~~a~~~l~~- 95 (171)
T cd01461 58 --------------------------------SATAENVAAAIEYVNRLQA---------LGGTNMNDALEAALELLNS- 95 (171)
T ss_pred --------------------------------eCCHHHHHHHHHHHHhcCC---------CCCcCHHHHHHHHHHhhcc-
Confidence 00 0111123344444432 1235688899998888752
Q ss_pred CCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccChh
Q 008566 286 VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVA 365 (561)
Q Consensus 286 ~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l~ 365 (561)
.......|++|++|.++. ..+.+ +..+++.+.++.|..+.++. ..+-.
T Consensus 96 ~~~~~~~iillTDG~~~~------------------------------~~~~~-~~~~~~~~~~i~i~~i~~g~-~~~~~ 143 (171)
T cd01461 96 SPGSVPQIILLTDGEVTN------------------------------ESQIL-KNVREALSGRIRLFTFGIGS-DVNTY 143 (171)
T ss_pred CCCCccEEEEEeCCCCCC------------------------------HHHHH-HHHHHhcCCCceEEEEEeCC-ccCHH
Confidence 123456788888875211 01233 33344444577777776653 45778
Q ss_pred cchhhhhccCcEEEEcCCCC
Q 008566 366 ELKVAVEKTGGLVVLSDSFG 385 (561)
Q Consensus 366 ~l~~l~~~TGG~v~~y~~f~ 385 (561)
.|..++..|||..++..+-.
T Consensus 144 ~l~~ia~~~gG~~~~~~~~~ 163 (171)
T cd01461 144 LLERLAREGRGIARRIYETD 163 (171)
T ss_pred HHHHHHHcCCCeEEEecChH
Confidence 89999999999999987644
No 27
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=98.21 E-value=3.9e-05 Score=70.51 Aligned_cols=152 Identities=20% Similarity=0.208 Sum_probs=100.4
Q ss_pred EEEEEEcccchhhH-HHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHHHhccC
Q 008566 132 FMFVVDTCIIEEEM-SFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFF 210 (561)
Q Consensus 132 ~vFvID~s~~~~~~-~~l~~~l~~~l~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~ 210 (561)
+|||||+|.++... +.++++|+.+++.|+++.++.||+|++.+..|.-. .. . .+
T Consensus 3 vvilvD~S~Sm~g~~~~~k~al~~~l~~L~~~d~fnii~f~~~~~~~~~~-~~---------------------~-~~-- 57 (155)
T PF13768_consen 3 VVILVDTSGSMSGEKELVKDALRAILRSLPPGDRFNIIAFGSSVRPLFPG-LV---------------------P-AT-- 57 (155)
T ss_pred EEEEEeCCCCCCCcHHHHHHHHHHHHHhCCCCCEEEEEEeCCEeeEcchh-HH---------------------H-Hh--
Confidence 69999999987543 77899999999999999999999999976654311 00 0 00
Q ss_pred CCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCC
Q 008566 211 IKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSG 290 (561)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~~~~g 290 (561)
.+..+...+.|+.++.. ...+.+..||+.|...+. .+..-
T Consensus 58 ------------------------------~~~~~~a~~~I~~~~~~--------~G~t~l~~aL~~a~~~~~--~~~~~ 97 (155)
T PF13768_consen 58 ------------------------------EENRQEALQWIKSLEAN--------SGGTDLLAALRAALALLQ--RPGCV 97 (155)
T ss_pred ------------------------------HHHHHHHHHHHHHhccc--------CCCccHHHHHHHHHHhcc--cCCCc
Confidence 12222344445554431 234678999999988762 23566
Q ss_pred cEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccChhcchhh
Q 008566 291 ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVA 370 (561)
Q Consensus 291 gkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l~~l~~l 370 (561)
-.|+++++|.++.++ ....+.+. .+. ..+.++.|.++. ..+-..|..|
T Consensus 98 ~~IilltDG~~~~~~-----------------------------~~i~~~v~-~~~-~~~~i~~~~~g~-~~~~~~L~~L 145 (155)
T PF13768_consen 98 RAIILLTDGQPVSGE-----------------------------EEILDLVR-RAR-GHIRIFTFGIGS-DADADFLREL 145 (155)
T ss_pred cEEEEEEeccCCCCH-----------------------------HHHHHHHH-hcC-CCceEEEEEECC-hhHHHHHHHH
Confidence 789999988763322 11222222 111 456677777754 4667889999
Q ss_pred hhccCcEEEE
Q 008566 371 VEKTGGLVVL 380 (561)
Q Consensus 371 ~~~TGG~v~~ 380 (561)
++.|||..++
T Consensus 146 A~~~~G~~~f 155 (155)
T PF13768_consen 146 ARATGGSFHF 155 (155)
T ss_pred HHcCCCEEEC
Confidence 9999998753
No 28
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=98.19 E-value=2.3e-05 Score=72.44 Aligned_cols=151 Identities=23% Similarity=0.240 Sum_probs=96.5
Q ss_pred EEEEEEcccchhh-------HHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHH
Q 008566 132 FMFVVDTCIIEEE-------MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (561)
Q Consensus 132 ~vFvID~s~~~~~-------~~~l~~~l~~~l~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (561)
+|||||.|.++.. ...++.++...++.+| +.+|||++|++...+. .
T Consensus 2 vv~v~D~SgSM~~~~~~~~~~~~~~~~~~~~~~~~~-~~~v~l~~f~~~~~~~--~------------------------ 54 (172)
T PF13519_consen 2 VVFVLDNSGSMNGYDGNRTRIDQAKDALNELLANLP-GDRVGLVSFSDSSRTL--S------------------------ 54 (172)
T ss_dssp EEEEEE-SGGGGTTTSSS-HHHHHHHHHHHHHHHHT-TSEEEEEEESTSCEEE--E------------------------
T ss_pred EEEEEECCcccCCCCCCCcHHHHHHHHHHHHHHHCC-CCEEEEEEeccccccc--c------------------------
Confidence 6899999999764 4567888888888887 4499999999753211 0
Q ss_pred HHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhc
Q 008566 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (561)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~ 284 (561)
|+...++.+.+.++++.... ......+++.|+..|..++..
T Consensus 55 ----------------------------------~~t~~~~~~~~~l~~~~~~~-----~~~~~t~~~~al~~a~~~~~~ 95 (172)
T PF13519_consen 55 ----------------------------------PLTSDKDELKNALNKLSPQG-----MPGGGTNLYDALQEAAKMLAS 95 (172)
T ss_dssp ----------------------------------EEESSHHHHHHHHHTHHHHG-------SSS--HHHHHHHHHHHHHC
T ss_pred ----------------------------------cccccHHHHHHHhhcccccc-----cCccCCcHHHHHHHHHHHHHh
Confidence 00111234455555544310 111346789999999999983
Q ss_pred cCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccCh
Q 008566 285 CVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGV 364 (561)
Q Consensus 285 ~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l 364 (561)
. +.....|++|++|.++ . .. .+.+..+.+.+|.|..+.++.+...-
T Consensus 96 ~-~~~~~~iv~iTDG~~~-------~------------------~~--------~~~~~~~~~~~i~i~~v~~~~~~~~~ 141 (172)
T PF13519_consen 96 S-DNRRRAIVLITDGEDN-------S------------------SD--------IEAAKALKQQGITIYTVGIGSDSDAN 141 (172)
T ss_dssp --SSEEEEEEEEES-TTH-------C------------------HH--------HHHHHHHHCTTEEEEEEEES-TT-EH
T ss_pred C-CCCceEEEEecCCCCC-------c------------------ch--------hHHHHHHHHcCCeEEEEEECCCccHH
Confidence 1 1234567777776433 0 00 02666788999999999988776655
Q ss_pred hcchhhhhccCcEEEEcC
Q 008566 365 AELKVAVEKTGGLVVLSD 382 (561)
Q Consensus 365 ~~l~~l~~~TGG~v~~y~ 382 (561)
..|..+++.|||..+...
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 29
>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=98.16 E-value=9.4e-05 Score=70.34 Aligned_cols=157 Identities=15% Similarity=0.139 Sum_probs=99.2
Q ss_pred EEEEEEEcccchh--hHHHHHHHHHHHhhcC---------CCCceEEEEEECCeEEEE-EcCCCCCCCCeeEeecCCccC
Q 008566 131 VFMFVVDTCIIEE--EMSFLKSALSQAIDLL---------PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDV 198 (561)
Q Consensus 131 ~~vFvID~s~~~~--~~~~l~~~l~~~l~~l---------~~~~~VglItf~~~V~~y-~l~~~~~~~~~~~v~~g~~~~ 198 (561)
-.+|+||.|.+.. .++..++.++..++.| +++.+||+|+|++..++. .+. .
T Consensus 4 dvv~vlD~S~Sm~~~~~~~~k~~~~~~~~~l~~~~~~~i~~~~~rvglv~fs~~~~~~~~l~-~---------------- 66 (186)
T cd01480 4 DITFVLDSSESVGLQNFDITKNFVKRVAERFLKDYYRKDPAGSWRVGVVQYSDQQEVEAGFL-R---------------- 66 (186)
T ss_pred eEEEEEeCCCccchhhHHHHHHHHHHHHHHHhhhhccCCCCCceEEEEEEecCCceeeEecc-c----------------
Confidence 4799999999875 3455677777777766 346899999999764432 111 0
Q ss_pred CHHHHHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHH
Q 008566 199 SKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIA 278 (561)
Q Consensus 199 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A 278 (561)
. ...+..+.+.|+.++.. ...+.+|.||..|
T Consensus 67 -------------------------------------~----~~~~~~l~~~i~~l~~~--------gg~T~~~~AL~~a 97 (186)
T cd01480 67 -------------------------------------D----IRNYTSLKEAVDNLEYI--------GGGTFTDCALKYA 97 (186)
T ss_pred -------------------------------------c----cCCHHHHHHHHHhCccC--------CCCccHHHHHHHH
Confidence 0 01133566777776431 1346799999999
Q ss_pred HHHHhc-cCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEee
Q 008566 279 ASLLGA-CVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFAC 357 (561)
Q Consensus 279 ~~ll~~-~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~ 357 (561)
...+.. ........|+++++|.++.++ + .-..+.+.++.+.||.|-.+..
T Consensus 98 ~~~l~~~~~~~~~~~iillTDG~~~~~~--------------------~---------~~~~~~~~~~~~~gi~i~~vgi 148 (186)
T cd01480 98 TEQLLEGSHQKENKFLLVITDGHSDGSP--------------------D---------GGIEKAVNEADHLGIKIFFVAV 148 (186)
T ss_pred HHHHhccCCCCCceEEEEEeCCCcCCCc--------------------c---------hhHHHHHHHHHHCCCEEEEEec
Confidence 988864 122344677888888653211 0 0112445667788887655555
Q ss_pred cCCccChhcchhhhhccCcEEEEcCCCC
Q 008566 358 ALDQVGVAELKVAVEKTGGLVVLSDSFG 385 (561)
Q Consensus 358 s~~~~~l~~l~~l~~~TGG~v~~y~~f~ 385 (561)
+. .+...|..++...+|. ++.++|.
T Consensus 149 g~--~~~~~L~~IA~~~~~~-~~~~~~~ 173 (186)
T cd01480 149 GS--QNEEPLSRIACDGKSA-LYRENFA 173 (186)
T ss_pred Cc--cchHHHHHHHcCCcch-hhhcchh
Confidence 43 7888899999887775 5555544
No 30
>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=98.15 E-value=0.0001 Score=69.79 Aligned_cols=145 Identities=21% Similarity=0.202 Sum_probs=94.3
Q ss_pred EEEEEEEcccchhh-------HHHHHHHHHHHh----hcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCC
Q 008566 131 VFMFVVDTCIIEEE-------MSFLKSALSQAI----DLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVS 199 (561)
Q Consensus 131 ~~vFvID~s~~~~~-------~~~l~~~l~~~l----~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~ 199 (561)
+.+++||+|..+.+ ++..++++...+ +..| ..+||||+|..... |-+
T Consensus 5 a~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np-~~~vGlv~fag~~a-~v~-------------------- 62 (187)
T cd01452 5 ATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNP-ENNVGLMTMAGNSP-EVL-------------------- 62 (187)
T ss_pred EEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCC-CccEEEEEecCCce-EEE--------------------
Confidence 56899999998643 556677766553 5445 55999999986211 111
Q ss_pred HHHHHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHH
Q 008566 200 KDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAA 279 (561)
Q Consensus 200 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~ 279 (561)
+|+......+...|+.+... ....+|.||+.|.
T Consensus 63 --------------------------------------~plT~D~~~~~~~L~~i~~~---------g~~~l~~AL~~A~ 95 (187)
T cd01452 63 --------------------------------------VTLTNDQGKILSKLHDVQPK---------GKANFITGIQIAQ 95 (187)
T ss_pred --------------------------------------ECCCCCHHHHHHHHHhCCCC---------CcchHHHHHHHHH
Confidence 11111233566667765431 2345999999999
Q ss_pred HHHhccCCC-CCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeec
Q 008566 280 SLLGACVPG-SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACA 358 (561)
Q Consensus 280 ~ll~~~~~~-~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s 358 (561)
..|+..-.. ...||++|++++-+.=+ .+. .++++++.++||.||++.++
T Consensus 96 ~~L~~~~~~~~~~rivi~v~S~~~~d~-----------------------------~~i-~~~~~~lkk~~I~v~vI~~G 145 (187)
T cd01452 96 LALKHRQNKNQKQRIVAFVGSPIEEDE-----------------------------KDL-VKLAKRLKKNNVSVDIINFG 145 (187)
T ss_pred HHHhcCCCcCCcceEEEEEecCCcCCH-----------------------------HHH-HHHHHHHHHcCCeEEEEEeC
Confidence 999742212 33599999987632111 122 36889999999999999998
Q ss_pred CCccChhcchhhhhcc
Q 008566 359 LDQVGVAELKVAVEKT 374 (561)
Q Consensus 359 ~~~~~l~~l~~l~~~T 374 (561)
...-+..-|..+.+..
T Consensus 146 ~~~~~~~~l~~~~~~~ 161 (187)
T cd01452 146 EIDDNTEKLTAFIDAV 161 (187)
T ss_pred CCCCCHHHHHHHHHHh
Confidence 7766666666666655
No 31
>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=97.97 E-value=0.00038 Score=66.02 Aligned_cols=148 Identities=14% Similarity=0.077 Sum_probs=90.4
Q ss_pred EEEEEEcccchhh---HHHHHHHHHHHhhcCC---CCceEEEEEECCeEEE-EEcCCCCCCCCeeEeecCCccCCHHHHH
Q 008566 132 FMFVVDTCIIEEE---MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQV-HELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (561)
Q Consensus 132 ~vFvID~s~~~~~---~~~l~~~l~~~l~~l~---~~~~VglItf~~~V~~-y~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (561)
++|+||.|.+... +..+++.+...++.++ ++.+||+|+|++..+. +.+. ...
T Consensus 3 v~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~~~~~l~-~~~-------------------- 61 (186)
T cd01471 3 LYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAKELIRLS-SPN-------------------- 61 (186)
T ss_pred EEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCceEEEECC-Ccc--------------------
Confidence 6899999998754 4557888888888764 6789999999987653 3333 100
Q ss_pred HHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhc
Q 008566 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (561)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~ 284 (561)
...++.+..+++.|.... . ....+.++.||..|...+..
T Consensus 62 ------------------------------------~~~~~~~~~~i~~l~~~~--~---~~G~T~l~~aL~~a~~~l~~ 100 (186)
T cd01471 62 ------------------------------------STNKDLALNAIRALLSLY--Y---PNGSTNTTSALLVVEKHLFD 100 (186)
T ss_pred ------------------------------------ccchHHHHHHHHHHHhCc--C---CCCCccHHHHHHHHHHHhhc
Confidence 001122333444443321 1 12346799999999988863
Q ss_pred c---CCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCc
Q 008566 285 C---VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (561)
Q Consensus 285 ~---~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~ 361 (561)
. .+.....|+++++|.++.++. . .+.++++.+.|+.|-++.++ ..
T Consensus 101 ~~~~r~~~~~~villTDG~~~~~~~----------------------~---------~~~a~~l~~~gv~v~~igiG-~~ 148 (186)
T cd01471 101 TRGNRENAPQLVIIMTDGIPDSKFR----------------------T---------LKEARKLRERGVIIAVLGVG-QG 148 (186)
T ss_pred cCCCcccCceEEEEEccCCCCCCcc----------------------h---------hHHHHHHHHCCCEEEEEEee-hh
Confidence 1 122334688888887643210 0 12455666778766666654 34
Q ss_pred cChhcchhhhhc
Q 008566 362 VGVAELKVAVEK 373 (561)
Q Consensus 362 ~~l~~l~~l~~~ 373 (561)
.|...|..|+..
T Consensus 149 ~d~~~l~~ia~~ 160 (186)
T cd01471 149 VNHEENRSLVGC 160 (186)
T ss_pred hCHHHHHHhcCC
Confidence 677777776654
No 32
>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=97.92 E-value=0.00052 Score=67.29 Aligned_cols=155 Identities=22% Similarity=0.350 Sum_probs=96.6
Q ss_pred CcEEEEEEEcccchh--hHHHHHHHHHHHhhcC---CCCceEEEEEECCeEEEE-EcCCCCCCCCeeEeecCCccCCHHH
Q 008566 129 PPVFMFVVDTCIIEE--EMSFLKSALSQAIDLL---PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQ 202 (561)
Q Consensus 129 ~p~~vFvID~s~~~~--~~~~l~~~l~~~l~~l---~~~~~VglItf~~~V~~y-~l~~~~~~~~~~~v~~g~~~~~~~~ 202 (561)
|.-++|+||.|.+.. +++.+++.++..++.| ++.+|||+|+|++.+++. .+. .
T Consensus 2 ~~DlvfllD~S~Sm~~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~~~~~~l~-~-------------------- 60 (224)
T cd01475 2 PTDLVFLIDSSRSVRPENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTVKQEFPLG-R-------------------- 60 (224)
T ss_pred CccEEEEEeCCCCCCHHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCceeEEeccc-c--------------------
Confidence 445899999999864 4566888888877776 357899999999876542 111 0
Q ss_pred HHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHH
Q 008566 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (561)
Q Consensus 203 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll 282 (561)
...++.+.+.|+.++.. . ..+.+|.||..|...+
T Consensus 61 --------------------------------------~~~~~~l~~~i~~i~~~----~----~~t~tg~AL~~a~~~~ 94 (224)
T cd01475 61 --------------------------------------FKSKADLKRAVRRMEYL----E----TGTMTGLAIQYAMNNA 94 (224)
T ss_pred --------------------------------------cCCHHHHHHHHHhCcCC----C----CCChHHHHHHHHHHHh
Confidence 00122455566665432 1 2356899999887643
Q ss_pred -hcc---CCCC---CcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEE
Q 008566 283 -GAC---VPGS---GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLF 355 (561)
Q Consensus 283 -~~~---~~~~---ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf 355 (561)
... .+.. -..|+++++|.++.. .++.+.++...||. +|
T Consensus 95 ~~~~~g~r~~~~~~~kvvillTDG~s~~~---------------------------------~~~~a~~lk~~gv~--i~ 139 (224)
T cd01475 95 FSEAEGARPGSERVPRVGIVVTDGRPQDD---------------------------------VSEVAAKARALGIE--MF 139 (224)
T ss_pred CChhcCCCCCCCCCCeEEEEEcCCCCccc---------------------------------HHHHHHHHHHCCcE--EE
Confidence 210 1111 234678888753110 13456777778875 45
Q ss_pred eecCCccChhcchhhhhccC-cEEEEcCCCC
Q 008566 356 ACALDQVGVAELKVAVEKTG-GLVVLSDSFG 385 (561)
Q Consensus 356 ~~s~~~~~l~~l~~l~~~TG-G~v~~y~~f~ 385 (561)
+.+-...+..+|..++..++ +.++..++|+
T Consensus 140 ~VgvG~~~~~~L~~ias~~~~~~~f~~~~~~ 170 (224)
T cd01475 140 AVGVGRADEEELREIASEPLADHVFYVEDFS 170 (224)
T ss_pred EEeCCcCCHHHHHHHhCCCcHhcEEEeCCHH
Confidence 55544568889999997765 4677776666
No 33
>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=97.90 E-value=0.00045 Score=65.51 Aligned_cols=156 Identities=17% Similarity=0.101 Sum_probs=88.5
Q ss_pred CcEEEEEEEcccchhhH-HHHHHHHHHHhhcC-CCCceEEEEEECCeEEEE-EcCCCCCCCCeeEeecCCccCCHHHHHH
Q 008566 129 PPVFMFVVDTCIIEEEM-SFLKSALSQAIDLL-PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (561)
Q Consensus 129 ~p~~vFvID~s~~~~~~-~~l~~~l~~~l~~l-~~~~~VglItf~~~V~~y-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (561)
+.-++|+||.|.+.... ....+.++..++.+ .++.|||+|+|++..++. .+. .
T Consensus 4 ~~Dvv~llD~SgSm~~~~~~~~~~~~~l~~~~~~~~~rvglv~Fs~~~~~~~~l~-~----------------------- 59 (185)
T cd01474 4 HFDLYFVLDKSGSVAANWIEIYDFVEQLVDRFNSPGLRFSFITFSTRATKILPLT-D----------------------- 59 (185)
T ss_pred ceeEEEEEeCcCchhhhHHHHHHHHHHHHHHcCCCCcEEEEEEecCCceEEEecc-c-----------------------
Confidence 45689999999987542 12234444444443 356999999999865432 111 0
Q ss_pred HhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhcc
Q 008566 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (561)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~ 285 (561)
....+.+.++.|... .+ ...+.+|.||..|...+...
T Consensus 60 -------------------------------------~~~~~~~~l~~l~~~---~~---~g~T~~~~aL~~a~~~l~~~ 96 (185)
T cd01474 60 -------------------------------------DSSAIIKGLEVLKKV---TP---SGQTYIHEGLENANEQIFNR 96 (185)
T ss_pred -------------------------------------cHHHHHHHHHHHhcc---CC---CCCCcHHHHHHHHHHHHHhh
Confidence 001233334444332 11 14578999999998776310
Q ss_pred CCCCC-----cEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCC
Q 008566 286 VPGSG-----ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (561)
Q Consensus 286 ~~~~g-----gkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~ 360 (561)
..| ..|+++++|.++...+. .+ ...++.+.+.|+.|-.+.. .
T Consensus 97 --~~~~r~~~~~villTDG~~~~~~~~------------------------~~-----~~~a~~l~~~gv~i~~vgv--~ 143 (185)
T cd01474 97 --NGGGRETVSVIIALTDGQLLLNGHK------------------------YP-----EHEAKLSRKLGAIVYCVGV--T 143 (185)
T ss_pred --ccCCCCCCeEEEEEcCCCcCCCCCc------------------------ch-----HHHHHHHHHcCCEEEEEee--c
Confidence 122 34888888875311000 00 1224456677886555544 5
Q ss_pred ccChhcchhhhhccCcEEE-EcCCCC
Q 008566 361 QVGVAELKVAVEKTGGLVV-LSDSFG 385 (561)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~-~y~~f~ 385 (561)
..+..+|..++..++ .+| ...+|+
T Consensus 144 ~~~~~~L~~iA~~~~-~~f~~~~~~~ 168 (185)
T cd01474 144 DFLKSQLINIADSKE-YVFPVTSGFQ 168 (185)
T ss_pred hhhHHHHHHHhCCCC-eeEecCccHH
Confidence 678889999998775 454 334554
No 34
>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=0.0012 Score=61.39 Aligned_cols=44 Identities=25% Similarity=0.472 Sum_probs=34.0
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcC---CCCceEEEEEECCeEE
Q 008566 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLL---PDNSLVGLITFGTLVQ 175 (561)
Q Consensus 132 ~vFvID~s~~~~~--~~~l~~~l~~~l~~l---~~~~~VglItf~~~V~ 175 (561)
++|++|.|.+... +..+++.++..+..+ +++.+||||+|++..+
T Consensus 3 v~~vlD~S~Sm~~~~~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~~ 51 (164)
T cd01482 3 IVFLVDGSWSIGRSNFNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDPR 51 (164)
T ss_pred EEEEEeCCCCcChhhHHHHHHHHHHHHhheeeCCCceEEEEEEECCCee
Confidence 6899999998754 455777777766655 4689999999998654
No 35
>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=97.86 E-value=0.002 Score=72.56 Aligned_cols=187 Identities=16% Similarity=0.108 Sum_probs=114.5
Q ss_pred CCcEEEEEEEcccchh--hHHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHH
Q 008566 128 VPPVFMFVVDTCIIEE--EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~--~~~~l~~~l~~~l~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (561)
.+..++||||+|.++. ..+.+++++..+|..|+++.+|+||.|++.+..+.-. .. ..+
T Consensus 270 ~p~~vvfvlD~SgSM~g~~i~~ak~al~~~l~~L~~~d~~~ii~F~~~~~~~~~~-~~-------------~~~------ 329 (596)
T TIGR03788 270 LPRELVFVIDTSGSMAGESIEQAKSALLLALDQLRPGDRFNIIQFDSDVTLLFPV-PV-------------PAT------ 329 (596)
T ss_pred CCceEEEEEECCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEECCcceEeccc-cc-------------cCC------
Confidence 4667999999999975 3566899999999999999999999999987755211 00 000
Q ss_pred HhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhcc
Q 008566 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (561)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~ 285 (561)
.+....+...|+.|... ..+.+..||..|.......
T Consensus 330 -----------------------------------~~~~~~a~~~i~~l~a~---------GgT~l~~aL~~a~~~~~~~ 365 (596)
T TIGR03788 330 -----------------------------------AHNLARARQFVAGLQAD---------GGTEMAGALSAALRDDGPE 365 (596)
T ss_pred -----------------------------------HHHHHHHHHHHhhCCCC---------CCccHHHHHHHHHHhhccc
Confidence 11122344455555432 3456889999888764321
Q ss_pred CCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccChh
Q 008566 286 VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVA 365 (561)
Q Consensus 286 ~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l~ 365 (561)
....-..|+++++|..+. + .+..+.+.. ...++.+..|.++. ..+-.
T Consensus 366 ~~~~~~~iillTDG~~~~----------------------~--------~~~~~~~~~--~~~~~ri~tvGiG~-~~n~~ 412 (596)
T TIGR03788 366 SSGALRQVVFLTDGAVGN----------------------E--------DALFQLIRT--KLGDSRLFTVGIGS-APNSY 412 (596)
T ss_pred CCCceeEEEEEeCCCCCC----------------------H--------HHHHHHHHH--hcCCceEEEEEeCC-CcCHH
Confidence 112234799999985210 0 012222211 22456666666654 46778
Q ss_pred cchhhhhccCcEEEEcCCCCccchHHHHHHHHhccccCcCceeeeEEEEE
Q 008566 366 ELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVFHSGDYDLGLSSNGIFEIN 415 (561)
Q Consensus 366 ~l~~l~~~TGG~v~~y~~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~vr 415 (561)
.|..|++.+||..++..+ .+...+.+.+++.... .+...+..+++.
T Consensus 413 lL~~lA~~g~G~~~~i~~--~~~~~~~~~~~l~~~~--~p~l~~v~v~~~ 458 (596)
T TIGR03788 413 FMRKAAQFGRGSFTFIGS--TDEVQRKMSQLFAKLE--QPALTDIALTFD 458 (596)
T ss_pred HHHHHHHcCCCEEEECCC--HHHHHHHHHHHHHhhc--CeEEEEEEEEEc
Confidence 899999999998777654 2334455566664431 234555555553
No 36
>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=97.82 E-value=0.0016 Score=61.34 Aligned_cols=156 Identities=16% Similarity=0.157 Sum_probs=97.5
Q ss_pred EEEEEEcccchh--hHHHHHHHHHHHhhcCC---CCceEEEEEECCeEEEE-EcCCCCCCCCeeEeecCCccCCHHHHHH
Q 008566 132 FMFVVDTCIIEE--EMSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (561)
Q Consensus 132 ~vFvID~s~~~~--~~~~l~~~l~~~l~~l~---~~~~VglItf~~~V~~y-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (561)
++|+||.|.+.. +.+.+++.++..++.+. +++|||+|+|++..++. ++. .
T Consensus 3 i~fvlD~S~S~~~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~~~~~~l~-~----------------------- 58 (177)
T cd01469 3 IVFVLDGSGSIYPDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESFRTEFTLN-E----------------------- 58 (177)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCceeEEEecC-c-----------------------
Confidence 689999999864 35667777877777664 47899999999876542 221 0
Q ss_pred HhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHh-c
Q 008566 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG-A 284 (561)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~-~ 284 (561)
+ .....+.++++.++.. . ..+.+|.||..|...+- .
T Consensus 59 ------------------------------~-----~~~~~~~~~i~~~~~~----~----g~T~~~~AL~~a~~~l~~~ 95 (177)
T cd01469 59 ------------------------------Y-----RTKEEPLSLVKHISQL----L----GLTNTATAIQYVVTELFSE 95 (177)
T ss_pred ------------------------------c-----CCHHHHHHHHHhCccC----C----CCccHHHHHHHHHHHhcCc
Confidence 0 0011244555555432 1 23679999999987752 1
Q ss_pred ---cCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCc
Q 008566 285 ---CVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (561)
Q Consensus 285 ---~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~ 361 (561)
..+.....+++++.|..+.++ .. +..++.+...|+.|-.+..+...
T Consensus 96 ~~g~R~~~~kv~illTDG~~~~~~-----------------------~~--------~~~~~~~k~~gv~v~~Vgvg~~~ 144 (177)
T cd01469 96 SNGARKDATKVLVVITDGESHDDP-----------------------LL--------KDVIPQAEREGIIRYAIGVGGHF 144 (177)
T ss_pred ccCCCCCCCeEEEEEeCCCCCCcc-----------------------cc--------HHHHHHHHHCCcEEEEEEecccc
Confidence 112233458888888754432 00 23455566788866666665432
Q ss_pred ---cChhcchhhhhccC-cEEEEcCCCC
Q 008566 362 ---VGVAELKVAVEKTG-GLVVLSDSFG 385 (561)
Q Consensus 362 ---~~l~~l~~l~~~TG-G~v~~y~~f~ 385 (561)
.+..+|..++..++ .+++..++|+
T Consensus 145 ~~~~~~~~L~~ias~p~~~h~f~~~~~~ 172 (177)
T cd01469 145 QRENSREELKTIASKPPEEHFFNVTDFA 172 (177)
T ss_pred cccccHHHHHHHhcCCcHHhEEEecCHH
Confidence 34688888888876 4677777765
No 37
>cd01450 vWFA_subfamily_ECM Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A
Probab=97.79 E-value=0.0013 Score=60.09 Aligned_cols=144 Identities=19% Similarity=0.183 Sum_probs=95.9
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcCC---CCceEEEEEECCeEEEE-EcCCCCCCCCeeEeecCCccCCHHHHHH
Q 008566 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (561)
Q Consensus 132 ~vFvID~s~~~~~--~~~l~~~l~~~l~~l~---~~~~VglItf~~~V~~y-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (561)
++|++|+|.+... ++.+++.+...++.+. ++.+++|++|++..... ++. .
T Consensus 3 i~~llD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~~~~~~~-~----------------------- 58 (161)
T cd01450 3 IVFLLDGSESVGPENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVRVEFSLN-D----------------------- 58 (161)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCceEEEECC-C-----------------------
Confidence 5799999998764 5667888888777665 48899999999854322 111 0
Q ss_pred HhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhcc
Q 008566 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (561)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~ 285 (561)
. . .++.+.+.++.+.... + ..+.++.||..|...+...
T Consensus 59 -----------------------------~-----~-~~~~~~~~i~~~~~~~-----~--~~t~~~~al~~a~~~~~~~ 96 (161)
T cd01450 59 -----------------------------Y-----K-SKDDLLKAVKNLKYLG-----G--GGTNTGKALQYALEQLFSE 96 (161)
T ss_pred -----------------------------C-----C-CHHHHHHHHHhcccCC-----C--CCccHHHHHHHHHHHhccc
Confidence 0 0 1224555565554321 1 3567899999999888742
Q ss_pred C---CCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCcc
Q 008566 286 V---PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (561)
Q Consensus 286 ~---~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~ 362 (561)
. ...-..|++|++|.++.++ -..++.+++.+.++.|..+.++. .
T Consensus 97 ~~~~~~~~~~iiliTDG~~~~~~-------------------------------~~~~~~~~~~~~~v~v~~i~~g~--~ 143 (161)
T cd01450 97 SNARENVPKVIIVLTDGRSDDGG-------------------------------DPKEAAAKLKDEGIKVFVVGVGP--A 143 (161)
T ss_pred ccccCCCCeEEEEECCCCCCCCc-------------------------------chHHHHHHHHHCCCEEEEEeccc--c
Confidence 1 2445679999999876542 01245566667788888877765 6
Q ss_pred Chhcchhhhhcc
Q 008566 363 GVAELKVAVEKT 374 (561)
Q Consensus 363 ~l~~l~~l~~~T 374 (561)
+...|..|+..+
T Consensus 144 ~~~~l~~la~~~ 155 (161)
T cd01450 144 DEEELREIASCP 155 (161)
T ss_pred CHHHHHHHhCCC
Confidence 888899999888
No 38
>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=97.64 E-value=0.003 Score=60.47 Aligned_cols=48 Identities=23% Similarity=0.283 Sum_probs=35.5
Q ss_pred CcEEEEEEEcccchh--hHHHHHHHHHHHhhcC---------CCCceEEEEEECCeEEE
Q 008566 129 PPVFMFVVDTCIIEE--EMSFLKSALSQAIDLL---------PDNSLVGLITFGTLVQV 176 (561)
Q Consensus 129 ~p~~vFvID~s~~~~--~~~~l~~~l~~~l~~l---------~~~~~VglItf~~~V~~ 176 (561)
.-=+||+||.|.+.. +++.+++.++..+..+ |+.+|||+|+|++..++
T Consensus 19 ~~DivfvlD~S~Sm~~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a~~ 77 (193)
T cd01477 19 WLDIVFVVDNSKGMTQGGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNATV 77 (193)
T ss_pred eeeEEEEEeCCCCcchhhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCceEE
Confidence 455899999999854 4566777777666543 34589999999987654
No 39
>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=97.61 E-value=0.0032 Score=70.54 Aligned_cols=175 Identities=17% Similarity=0.079 Sum_probs=113.1
Q ss_pred CcEEEEEEEcccchhh--HHHHHHHHHHHhhcC-CCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHH
Q 008566 129 PPVFMFVVDTCIIEEE--MSFLKSALSQAIDLL-PDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (561)
Q Consensus 129 ~p~~vFvID~s~~~~~--~~~l~~~l~~~l~~l-~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (561)
...++||||.|.++.. +..++.++...+..+ .++.+||||+|+....-+-+. ..
T Consensus 407 ~~~v~fvvD~SGSM~~~rl~~aK~av~~Ll~~~~~~~D~v~Li~F~~~~a~~~lp-~t---------------------- 463 (589)
T TIGR02031 407 GRLLIFVVDASGSAAVARMSEAKGAVELLLGEAYVHRDQVSLIAFRGTAAEVLLP-PS---------------------- 463 (589)
T ss_pred CceEEEEEECCCCCChHHHHHHHHHHHHHHHhhccCCCEEEEEEECCCCceEECC-CC----------------------
Confidence 5678999999998753 566788888877754 456799999998543111111 00
Q ss_pred HhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhcc
Q 008566 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (561)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~ 285 (561)
.....+...|+.|+.. ..+-++.||..|..++...
T Consensus 464 ------------------------------------~~~~~~~~~L~~l~~g---------GgTpL~~gL~~A~~~~~~~ 498 (589)
T TIGR02031 464 ------------------------------------RSVEQAKRRLDVLPGG---------GGTPLAAGLAAAFQTALQA 498 (589)
T ss_pred ------------------------------------CCHHHHHHHHhcCCCC---------CCCcHHHHHHHHHHHHHHh
Confidence 0111234445555331 2456899999999888642
Q ss_pred CCCCC--cEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccC
Q 008566 286 VPGSG--ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVG 363 (561)
Q Consensus 286 ~~~~g--gkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~ 363 (561)
... + -.|+++++|-+|.|.+...... + .-..+..+-...++..+...||.+=++-+...+.+
T Consensus 499 ~~~-~~~~~ivllTDG~~nv~~~~~~~~~------------~---~~~~~~~~~~~~~a~~~~~~gi~~~vid~~~~~~~ 562 (589)
T TIGR02031 499 RSS-GGTPTIVLITDGRGNIPLDGDPESI------------K---ADREQAAEEALALARKIREAGMPALVIDTAMRFVS 562 (589)
T ss_pred ccc-CCceEEEEECCCCCCCCCCcccccc------------c---ccchhHHHHHHHHHHHHHhcCCeEEEEeCCCCCcc
Confidence 222 3 3699999999988753110000 0 00122334446778889999987666666556566
Q ss_pred hhcchhhhhccCcEEEEcCCCCcc
Q 008566 364 VAELKVAVEKTGGLVVLSDSFGHA 387 (561)
Q Consensus 364 l~~l~~l~~~TGG~v~~y~~f~~~ 387 (561)
..-+..|++..||..++.++-+..
T Consensus 563 ~~~~~~lA~~~~g~y~~l~~~~a~ 586 (589)
T TIGR02031 563 TGFAQKLARKMGAHYIYLPNATAA 586 (589)
T ss_pred chHHHHHHHhcCCcEEeCCCCChh
Confidence 666889999999999999887654
No 40
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=97.56 E-value=0.0057 Score=68.10 Aligned_cols=173 Identities=14% Similarity=0.065 Sum_probs=109.9
Q ss_pred CCcEEEEEEEcccchh--hHHHHHHHHHHHhhc-CCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHH
Q 008566 128 VPPVFMFVVDTCIIEE--EMSFLKSALSQAIDL-LPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~--~~~~l~~~l~~~l~~-l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (561)
.+-.++||||+|.++. .+..+|.++...|+. +.++.+|+||+|+....-+-+. .
T Consensus 400 ~~~~vvfvvD~SGSM~~~rl~~aK~a~~~ll~~ay~~rD~v~lI~F~g~~a~~~lp-p---------------------- 456 (584)
T PRK13406 400 SETTTIFVVDASGSAALHRLAEAKGAVELLLAEAYVRRDQVALVAFRGRGAELLLP-P---------------------- 456 (584)
T ss_pred CCccEEEEEECCCCCcHhHHHHHHHHHHHHHHhhcCCCCEEEEEEECCCceeEEcC-C----------------------
Confidence 4688999999999974 456678888887754 4678899999997531111111 0
Q ss_pred HHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhc
Q 008566 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (561)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~ 284 (561)
..+...+...|+.|+.. ..+.++.||..|..++..
T Consensus 457 ------------------------------------T~~~~~~~~~L~~l~~g---------GgTpL~~gL~~A~~~l~~ 491 (584)
T PRK13406 457 ------------------------------------TRSLVRAKRSLAGLPGG---------GGTPLAAGLDAAAALALQ 491 (584)
T ss_pred ------------------------------------CcCHHHHHHHHhcCCCC---------CCChHHHHHHHHHHHHHH
Confidence 00112334445554331 346789999999988763
Q ss_pred cC-CCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccC
Q 008566 285 CV-PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVG 363 (561)
Q Consensus 285 ~~-~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~ 363 (561)
.. ++.--.|+++|+|-+|.|.+.-..+. .-...+ ..++..+...||.+=++-+... .
T Consensus 492 ~~~~~~~~~iVLlTDG~~n~~~~~~~~~~----------------~~~~~~----~~~a~~~~~~gi~~~vId~g~~--~ 549 (584)
T PRK13406 492 VRRKGMTPTVVLLTDGRANIARDGTAGRA----------------QAEEDA----LAAARALRAAGLPALVIDTSPR--P 549 (584)
T ss_pred hccCCCceEEEEEeCCCCCCCcccccccc----------------chhhHH----HHHHHHHHhcCCeEEEEecCCC--C
Confidence 22 12236899999999888653211110 000111 3457777888876555555433 3
Q ss_pred hhcchhhhhccCcEEEEcCCCCccchH
Q 008566 364 VAELKVAVEKTGGLVVLSDSFGHAVFK 390 (561)
Q Consensus 364 l~~l~~l~~~TGG~v~~y~~f~~~~~~ 390 (561)
...+..|++.+||..+..+.-+...+.
T Consensus 550 ~~~~~~LA~~~gg~y~~l~~~~a~~~~ 576 (584)
T PRK13406 550 QPQARALAEAMGARYLPLPRADAGRLS 576 (584)
T ss_pred cHHHHHHHHhcCCeEEECCCCCHHHHH
Confidence 445889999999999999998876443
No 41
>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=97.55 E-value=0.002 Score=59.93 Aligned_cols=156 Identities=21% Similarity=0.251 Sum_probs=94.6
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcC---CCCceEEEEEECCeEEEE-EcCCCCCCCCeeEeecCCccCCHHHHHH
Q 008566 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLL---PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (561)
Q Consensus 132 ~vFvID~s~~~~~--~~~l~~~l~~~l~~l---~~~~~VglItf~~~V~~y-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (561)
++|+||.|.+... ...+++.+...++.+ +++.|||+|+|++..+.+ .+. ..
T Consensus 2 ivflvD~S~sm~~~~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~~~~~~~-~~---------------------- 58 (178)
T PF00092_consen 2 IVFLVDTSGSMSGDNFEKAKQFVKSIISRLSISNNGTRVGIVTFSDSARVLFSLT-DY---------------------- 58 (178)
T ss_dssp EEEEEE-STTSCHHHHHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEEEEEETT-SH----------------------
T ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHHhhhccccccccceeeeecccccccccc-cc----------------------
Confidence 5899999998765 556788888888754 568999999999987633 222 10
Q ss_pred HhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHH-HHccCCCCCCCCCCCCCcchhHHHHHHHHHHhc
Q 008566 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVL-EELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (561)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll-~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~ 284 (561)
.....+.+.+ +.+.. ....+.+|.||..|...+..
T Consensus 59 ------------------------------------~~~~~~~~~i~~~~~~--------~~g~t~~~~aL~~a~~~l~~ 94 (178)
T PF00092_consen 59 ------------------------------------QSKNDLLNAINDSIPS--------SGGGTNLGAALKFAREQLFS 94 (178)
T ss_dssp ------------------------------------SSHHHHHHHHHTTGGC--------CBSSB-HHHHHHHHHHHTTS
T ss_pred ------------------------------------cccccccccccccccc--------cchhhhHHHHHhhhhhcccc
Confidence 0011222222 33222 12345699999999998763
Q ss_pred c----CCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCC
Q 008566 285 C----VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (561)
Q Consensus 285 ~----~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~ 360 (561)
. .+..-.-|+++++|.++.++- .. ..+..+.+. ..|.+|+++.+
T Consensus 95 ~~~~~r~~~~~~iiliTDG~~~~~~~--------------------------~~-----~~~~~~~~~-~~i~~~~ig~~ 142 (178)
T PF00092_consen 95 SNNGGRPNSPKVIILITDGNSNDSDS--------------------------PS-----EEAANLKKS-NGIKVIAIGID 142 (178)
T ss_dssp GGGTTGTTSEEEEEEEESSSSSSHSG--------------------------HH-----HHHHHHHHH-CTEEEEEEEES
T ss_pred cccccccccccceEEEEeecccCCcc--------------------------hH-----HHHHHHHHh-cCcEEEEEecC
Confidence 2 223345588888887654320 00 111111111 44577777666
Q ss_pred ccChhcchhhhhcc--CcEEEEcCCCCc
Q 008566 361 QVGVAELKVAVEKT--GGLVVLSDSFGH 386 (561)
Q Consensus 361 ~~~l~~l~~l~~~T--GG~v~~y~~f~~ 386 (561)
..+...|..|+..+ +|++++..++..
T Consensus 143 ~~~~~~l~~la~~~~~~~~~~~~~~~~~ 170 (178)
T PF00092_consen 143 NADNEELRELASCPTSEGHVFYLADFSD 170 (178)
T ss_dssp CCHHHHHHHHSHSSTCHHHEEEESSHHH
T ss_pred cCCHHHHHHHhCCCCCCCcEEEcCCHHH
Confidence 77888899998663 478888877664
No 42
>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=97.53 E-value=0.0082 Score=55.46 Aligned_cols=154 Identities=21% Similarity=0.154 Sum_probs=99.3
Q ss_pred cEEEEEEEcccchhh--HHHHHHHHHHHhhcCCC---CceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHH
Q 008566 130 PVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPD---NSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (561)
Q Consensus 130 p~~vFvID~s~~~~~--~~~l~~~l~~~l~~l~~---~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (561)
.-++|+||+|.++.. +..+++.+...+..+.. +.+||+++|++..+.+.-- .
T Consensus 2 ~~v~l~vD~S~SM~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ii~f~~~~~~~~~~-~---------------------- 58 (177)
T smart00327 2 LDVVFLLDGSGSMGPNRFEKAKEFVLKLVEQLDIGPDGDRVGLVTFSDDATVLFPL-N---------------------- 58 (177)
T ss_pred ccEEEEEeCCCccchHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeCCCceEEEcc-c----------------------
Confidence 347899999998832 45677777777777765 8999999999843332100 0
Q ss_pred HHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhc
Q 008566 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (561)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~ 284 (561)
.....+.+...++.+... .....-++.|+..|...+..
T Consensus 59 -----------------------------------~~~~~~~~~~~i~~~~~~-------~~~~~~~~~al~~~~~~~~~ 96 (177)
T smart00327 59 -----------------------------------DSRSKDALLEALASLSYK-------LGGGTNLGAALQYALENLFS 96 (177)
T ss_pred -----------------------------------ccCCHHHHHHHHHhcCCC-------CCCCchHHHHHHHHHHHhcC
Confidence 001122455556655431 11234588899988888752
Q ss_pred cCCC----CCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCC
Q 008566 285 CVPG----SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (561)
Q Consensus 285 ~~~~----~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~ 360 (561)
.... ..-.|++|++|.++.+ +.+.+...++.+.++.+..+.++..
T Consensus 97 ~~~~~~~~~~~~iviitDg~~~~~-------------------------------~~~~~~~~~~~~~~i~i~~i~~~~~ 145 (177)
T smart00327 97 KSAGSRRGAPKVLILITDGESNDG-------------------------------GDLLKAAKELKRSGVKVFVVGVGND 145 (177)
T ss_pred cCCCCCCCCCeEEEEEcCCCCCCC-------------------------------ccHHHHHHHHHHCCCEEEEEEccCc
Confidence 1111 1346888888765433 1234566777788888888887654
Q ss_pred ccChhcchhhhhccCcEEEE
Q 008566 361 QVGVAELKVAVEKTGGLVVL 380 (561)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~~ 380 (561)
. +-..+..++..++|...+
T Consensus 146 ~-~~~~l~~~~~~~~~~~~~ 164 (177)
T smart00327 146 V-DEEELKKLASAPGGVYVF 164 (177)
T ss_pred c-CHHHHHHHhCCCcceEEe
Confidence 3 778899999999987755
No 43
>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=97.52 E-value=0.0058 Score=56.92 Aligned_cols=44 Identities=14% Similarity=0.291 Sum_probs=34.4
Q ss_pred EEEEEEcccchh--hHHHHHHHHHHHhhcCC---CCceEEEEEECCeEE
Q 008566 132 FMFVVDTCIIEE--EMSFLKSALSQAIDLLP---DNSLVGLITFGTLVQ 175 (561)
Q Consensus 132 ~vFvID~s~~~~--~~~~l~~~l~~~l~~l~---~~~~VglItf~~~V~ 175 (561)
++|+||.|.+-- +++.+++-++..++.++ +.+|||+|+|++..+
T Consensus 3 ivfllD~S~Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~ 51 (165)
T cd01481 3 IVFLIDGSDNVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPR 51 (165)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCee
Confidence 589999999854 45667777777777664 579999999998654
No 44
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=97.49 E-value=0.0068 Score=66.20 Aligned_cols=165 Identities=12% Similarity=0.024 Sum_probs=96.1
Q ss_pred CCcEEEEEEEcccchhhH---HHHHHHHHHHhhcCC---CCceEEEEEECCeEEE-EEcCCCCCCCCeeEeecCCccCCH
Q 008566 128 VPPVFMFVVDTCIIEEEM---SFLKSALSQAIDLLP---DNSLVGLITFGTLVQV-HELGGFGQIIPKTYVFKGSKDVSK 200 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~~~---~~l~~~l~~~l~~l~---~~~~VglItf~~~V~~-y~l~~~~~~~~~~~v~~g~~~~~~ 200 (561)
..--++||||.|.+.... +.++..+...+..+. +..+||+++|++..+. +.+. +.. .+
T Consensus 41 ~~lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~r~vfpL~-s~~------------s~-- 105 (576)
T PTZ00441 41 EEVDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNTTELIRLG-SGA------------SK-- 105 (576)
T ss_pred CCceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCceEEEecC-CCc------------cc--
Confidence 356789999999987532 446666677666663 5689999999986543 3332 110 00
Q ss_pred HHHHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHH
Q 008566 201 DQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAAS 280 (561)
Q Consensus 201 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ 280 (561)
.++.+...|..|.... .+ ...+.+|.||..|..
T Consensus 106 ------------------------------------------Dk~~aL~~I~sL~~~~--~p---gGgTnig~AL~~Aae 138 (576)
T PTZ00441 106 ------------------------------------------DKEQALIIVKSLRKTY--LP---YGKTNMTDALLEVRK 138 (576)
T ss_pred ------------------------------------------cHHHHHHHHHHHHhhc--cC---CCCccHHHHHHHHHH
Confidence 0112333333333210 01 124668999998887
Q ss_pred HHhcc--CCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeec
Q 008566 281 LLGAC--VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACA 358 (561)
Q Consensus 281 ll~~~--~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s 358 (561)
.+... .....+.||+++.|.++.+. . . .+.++++...||.|-+|.++
T Consensus 139 ~L~sr~~R~nvpKVVILLTDG~sns~~-----------------------d-------v-leaAq~LR~~GVeI~vIGVG 187 (576)
T PTZ00441 139 HLNDRVNRENAIQLVILMTDGIPNSKY-----------------------R-------A-LEESRKLKDRNVKLAVIGIG 187 (576)
T ss_pred HHhhcccccCCceEEEEEecCCCCCcc-----------------------c-------H-HHHHHHHHHCCCEEEEEEeC
Confidence 77521 12234678899888743210 0 0 12356677788866666664
Q ss_pred CCccChhcchhhh----hccCcEEEEcCCCCc
Q 008566 359 LDQVGVAELKVAV----EKTGGLVVLSDSFGH 386 (561)
Q Consensus 359 ~~~~~l~~l~~l~----~~TGG~v~~y~~f~~ 386 (561)
. ..+...+..|+ ...+|.+|.+.+|..
T Consensus 188 ~-g~n~e~LrlIAgC~p~~g~c~~Y~vadf~e 218 (576)
T PTZ00441 188 Q-GINHQFNRLLAGCRPREGKCKFYSDADWEE 218 (576)
T ss_pred C-CcCHHHHHHHhccCCCCCCCceEEeCCHHH
Confidence 3 45665566566 335567888878853
No 45
>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=97.49 E-value=0.0058 Score=56.36 Aligned_cols=41 Identities=22% Similarity=0.332 Sum_probs=31.2
Q ss_pred EEEEEEcccchhh-HHHHHHHHHHHhhcCC---CCceEEEEEECC
Q 008566 132 FMFVVDTCIIEEE-MSFLKSALSQAIDLLP---DNSLVGLITFGT 172 (561)
Q Consensus 132 ~vFvID~s~~~~~-~~~l~~~l~~~l~~l~---~~~~VglItf~~ 172 (561)
++|++|+|.+... +...++.++..++.|. +..+||+|+|++
T Consensus 3 v~~llD~S~Sm~~~~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~~ 47 (163)
T cd01476 3 LLFVLDSSGSVRGKFEKYKKYIERIVEGLEIGPTATRVALITYSG 47 (163)
T ss_pred EEEEEeCCcchhhhHHHHHHHHHHHHHhcCCCCCCcEEEEEEEcC
Confidence 6899999998754 3345666777776664 479999999998
No 46
>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=97.37 E-value=0.0086 Score=67.78 Aligned_cols=161 Identities=18% Similarity=0.139 Sum_probs=102.9
Q ss_pred CCcEEEEEEEcccchh---hHHHHHHHHHHHhhc-CCCCceEEEEEECCe-EEEEEcCCCCCCCCeeEeecCCccCCHHH
Q 008566 128 VPPVFMFVVDTCIIEE---EMSFLKSALSQAIDL-LPDNSLVGLITFGTL-VQVHELGGFGQIIPKTYVFKGSKDVSKDQ 202 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~---~~~~l~~~l~~~l~~-l~~~~~VglItf~~~-V~~y~l~~~~~~~~~~~v~~g~~~~~~~~ 202 (561)
....++|+||+|.++. .+..++.++...+.. +..+.+||||+|+.. ..+. +.
T Consensus 464 ~~~~vv~vvD~SgSM~~~~rl~~ak~a~~~ll~~a~~~~D~v~lI~F~g~~a~~~-~p---------------------- 520 (633)
T TIGR02442 464 AGNLVIFVVDASGSMAARGRMAAAKGAVLSLLRDAYQKRDKVALITFRGEEAEVL-LP---------------------- 520 (633)
T ss_pred CCceEEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCceEE-cC----------------------
Confidence 3567899999999974 345567777666653 456789999999743 2111 11
Q ss_pred HHHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHH
Q 008566 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (561)
Q Consensus 203 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll 282 (561)
.......+...|+.|+.. ..+.++.||..|..++
T Consensus 521 -------------------------------------~t~~~~~~~~~L~~l~~g---------G~Tpl~~aL~~A~~~l 554 (633)
T TIGR02442 521 -------------------------------------PTSSVELAARRLEELPTG---------GRTPLAAGLLKAAEVL 554 (633)
T ss_pred -------------------------------------CCCCHHHHHHHHHhCCCC---------CCCCHHHHHHHHHHHH
Confidence 011122344455555431 3456899999999888
Q ss_pred hcc---CCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecC
Q 008566 283 GAC---VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACAL 359 (561)
Q Consensus 283 ~~~---~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~ 359 (561)
... .+...+.|+++++|.+|.|.+. . . +..+ -..++.++.+.||.+.++-+..
T Consensus 555 ~~~~~~~~~~~~~vvliTDG~~n~~~~~--~-~--------------------~~~~-~~~~a~~l~~~~i~~~vIdt~~ 610 (633)
T TIGR02442 555 SNELLRDDDGRPLLVVITDGRANVADGG--E-P--------------------PTDD-ARTIAAKLAARGILFVVIDTES 610 (633)
T ss_pred HHhhccCCCCceEEEEECCCCCCCCCCC--C-C--------------------hHHH-HHHHHHHHHhcCCeEEEEeCCC
Confidence 721 2234577999999998875210 0 0 0001 1456777777788766665555
Q ss_pred CccChhcchhhhhccCcEEEEc
Q 008566 360 DQVGVAELKVAVEKTGGLVVLS 381 (561)
Q Consensus 360 ~~~~l~~l~~l~~~TGG~v~~y 381 (561)
..++..-+..||+.+||..+..
T Consensus 611 ~~~~~~~~~~lA~~~gg~y~~l 632 (633)
T TIGR02442 611 GFVRLGLAEDLARALGGEYVRL 632 (633)
T ss_pred CCcchhHHHHHHHhhCCeEEec
Confidence 6667778999999999998764
No 47
>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=97.31 E-value=0.016 Score=52.12 Aligned_cols=148 Identities=24% Similarity=0.299 Sum_probs=94.0
Q ss_pred EEEEEEEcccch--hhHHHHHHHHHHHhhcCCC---CceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHHH
Q 008566 131 VFMFVVDTCIIE--EEMSFLKSALSQAIDLLPD---NSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (561)
Q Consensus 131 ~~vFvID~s~~~--~~~~~l~~~l~~~l~~l~~---~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (561)
.++|+||.|.++ .....+++.+...+..++. ..+|+++.|+...+.+--- .
T Consensus 2 ~v~~viD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~f~~~~~~~~~~--~---------------------- 57 (161)
T cd00198 2 DIVFLLDVSGSMGGEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARVVLPL--T---------------------- 57 (161)
T ss_pred cEEEEEeCCCCcCcchHHHHHHHHHHHHHhcccCCCCcEEEEEEecCccceeecc--c----------------------
Confidence 378999999986 3456678888888888875 7899999999733222100 0
Q ss_pred HhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhcc
Q 008566 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (561)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~ 285 (561)
.. ...+.+...++.+.. .......+..|+..|...+...
T Consensus 58 -----------------------------~~-----~~~~~~~~~~~~~~~-------~~~~~t~~~~al~~~~~~~~~~ 96 (161)
T cd00198 58 -----------------------------TD-----TDKADLLEAIDALKK-------GLGGGTNIGAALRLALELLKSA 96 (161)
T ss_pred -----------------------------cc-----CCHHHHHHHHHhccc-------CCCCCccHHHHHHHHHHHhccc
Confidence 00 012234455555432 1123355788899998888632
Q ss_pred -CCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccCh
Q 008566 286 -VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGV 364 (561)
Q Consensus 286 -~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l 364 (561)
.......|++|++|.++.++ . -..+....+.+.++.+.++.++. ..+-
T Consensus 97 ~~~~~~~~lvvitDg~~~~~~-----~-------------------------~~~~~~~~~~~~~v~v~~v~~g~-~~~~ 145 (161)
T cd00198 97 KRPNARRVIILLTDGEPNDGP-----E-------------------------LLAEAARELRKLGITVYTIGIGD-DANE 145 (161)
T ss_pred CCCCCceEEEEEeCCCCCCCc-----c-------------------------hhHHHHHHHHHcCCEEEEEEcCC-CCCH
Confidence 12456778888888754443 0 01234555667799998888875 3456
Q ss_pred hcchhhhhcc
Q 008566 365 AELKVAVEKT 374 (561)
Q Consensus 365 ~~l~~l~~~T 374 (561)
..+..|+..+
T Consensus 146 ~~l~~l~~~~ 155 (161)
T cd00198 146 DELKEIADKT 155 (161)
T ss_pred HHHHHHhccc
Confidence 6788888877
No 48
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=97.30 E-value=0.01 Score=58.06 Aligned_cols=168 Identities=17% Similarity=0.121 Sum_probs=110.6
Q ss_pred CcEEEEEEEcccchhh---HHHHHHHHHHHhhcCC-CCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHH
Q 008566 129 PPVFMFVVDTCIIEEE---MSFLKSALSQAIDLLP-DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (561)
Q Consensus 129 ~p~~vFvID~s~~~~~---~~~l~~~l~~~l~~l~-~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (561)
..-+|||||.|.++.. ...+|-++...|..-. .+-+|++|+|.. ...
T Consensus 78 g~lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~dAYq~RdkvavI~F~G---------~~A-------------------- 128 (261)
T COG1240 78 GNLIVFVVDASGSMAARRRMAAAKGAALSLLRDAYQRRDKVAVIAFRG---------EKA-------------------- 128 (261)
T ss_pred CCcEEEEEeCcccchhHHHHHHHHHHHHHHHHHHHHccceEEEEEecC---------Ccc--------------------
Confidence 5668999999999754 4456666666665433 467999998873 110
Q ss_pred HHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhc
Q 008566 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (561)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~ 284 (561)
.+++|...+-+.+.+.|+.|+.. + ++=+..||..|..++..
T Consensus 129 ------------------------------~lll~pT~sv~~~~~~L~~l~~G------G---~TPL~~aL~~a~ev~~r 169 (261)
T COG1240 129 ------------------------------ELLLPPTSSVELAERALERLPTG------G---KTPLADALRQAYEVLAR 169 (261)
T ss_pred ------------------------------eEEeCCcccHHHHHHHHHhCCCC------C---CCchHHHHHHHHHHHHH
Confidence 12222233334566667766542 2 23388999999999885
Q ss_pred cC---CCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCc
Q 008566 285 CV---PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (561)
Q Consensus 285 ~~---~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~ 361 (561)
.. +..--.+++.++|.||.+.+.=+. ... ...+.++...|+-+=+.-+-..+
T Consensus 170 ~~r~~p~~~~~~vviTDGr~n~~~~~~~~---------------------~e~----~~~a~~~~~~g~~~lvid~e~~~ 224 (261)
T COG1240 170 EKRRGPDRRPVMVVITDGRANVPIPLGPK---------------------AET----LEAASKLRLRGIQLLVIDTEGSE 224 (261)
T ss_pred hhccCCCcceEEEEEeCCccCCCCCCchH---------------------HHH----HHHHHHHhhcCCcEEEEecCCcc
Confidence 43 234568899999998876521100 111 23455666677755555555667
Q ss_pred cChhcchhhhhccCcEEEEcCCCCccch
Q 008566 362 VGVAELKVAVEKTGGLVVLSDSFGHAVF 389 (561)
Q Consensus 362 ~~l~~l~~l~~~TGG~v~~y~~f~~~~~ 389 (561)
+.+.-...||...||..++.++.++..+
T Consensus 225 ~~~g~~~~iA~~~Gg~~~~L~~l~~~~i 252 (261)
T COG1240 225 VRLGLAEEIARASGGEYYHLDDLSDDSI 252 (261)
T ss_pred ccccHHHHHHHHhCCeEEecccccchHH
Confidence 7777788999999999999999887543
No 49
>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=97.21 E-value=0.0082 Score=57.02 Aligned_cols=90 Identities=23% Similarity=0.274 Sum_probs=61.5
Q ss_pred cchhHHHHHHHHHHhccCCCCCc-EEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHh
Q 008566 269 RCTGTALSIAASLLGACVPGSGA-RILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVH 347 (561)
Q Consensus 269 ~c~G~Al~~A~~ll~~~~~~~gg-kIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~ 347 (561)
-.+-.||+.|...|+.. +..+. .|+++.++.-|.-||.+ + +..+.+.+
T Consensus 80 ~SLqN~Le~A~~~L~~~-p~~~srEIlvi~gSl~t~Dp~di-----------------------------~-~ti~~l~~ 128 (193)
T PF04056_consen 80 PSLQNGLEMARSSLKHM-PSHGSREILVIFGSLTTCDPGDI-----------------------------H-ETIESLKK 128 (193)
T ss_pred hhHHHHHHHHHHHHhhC-ccccceEEEEEEeecccCCchhH-----------------------------H-HHHHHHHH
Confidence 45889999999998842 23344 45555665555544332 2 56778899
Q ss_pred cCcEEEEEeecCCccChhcchhhhhccCcEEEEcCCCCccchHHHHH
Q 008566 348 QGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVR 394 (561)
Q Consensus 348 ~~isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~ 394 (561)
.+|-|+++.++. .+...+.||+.|||..... .++.+|++-|.
T Consensus 129 ~~IrvsvI~laa---Ev~I~k~i~~~T~G~y~V~--lde~H~~~lL~ 170 (193)
T PF04056_consen 129 ENIRVSVISLAA---EVYICKKICKETGGTYGVI--LDEDHFKELLM 170 (193)
T ss_pred cCCEEEEEEEhH---HHHHHHHHHHhhCCEEEEe--cCHHHHHHHHH
Confidence 999999999976 5678899999999954443 44455554333
No 50
>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=97.18 E-value=0.018 Score=55.06 Aligned_cols=149 Identities=13% Similarity=0.057 Sum_probs=87.9
Q ss_pred EEEEEEcccchhhH--H-HHHHHHHHHhhcCC---CCceEEEEEECCeEEEE-EcCCCCCCCCeeEeecCCccCCHHHHH
Q 008566 132 FMFVVDTCIIEEEM--S-FLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (561)
Q Consensus 132 ~vFvID~s~~~~~~--~-~l~~~l~~~l~~l~---~~~~VglItf~~~V~~y-~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (561)
++|+||.|.+..+. . .+++.++..++.+. +++|||+|+|++..++. .+. ...
T Consensus 3 i~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~~~~~~~-~~~-------------------- 61 (192)
T cd01473 3 LTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNRDVVPFS-DEE-------------------- 61 (192)
T ss_pred EEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCceeEEecC-ccc--------------------
Confidence 58999999987543 3 35666777776654 57999999999866542 222 100
Q ss_pred HHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhc
Q 008566 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (561)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~ 284 (561)
...++.+...++.|... +. ....+.+|.||..|...+..
T Consensus 62 ------------------------------------~~~~~~l~~~i~~l~~~---~~--~~g~T~~~~AL~~a~~~~~~ 100 (192)
T cd01473 62 ------------------------------------RYDKNELLKKINDLKNS---YR--SGGETYIVEALKYGLKNYTK 100 (192)
T ss_pred ------------------------------------ccCHHHHHHHHHHHHhc---cC--CCCcCcHHHHHHHHHHHhcc
Confidence 01123455666666532 11 11346799999999877652
Q ss_pred cC--CC-CCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCc
Q 008566 285 CV--PG-SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (561)
Q Consensus 285 ~~--~~-~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~ 361 (561)
.. +. ..--++++|.|..+.+- + .--.+.++.+.+.||.+-.+..+.
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 10 00 11237777777532210 0 001256777888999777776654
Q ss_pred cChhcchhhhhc
Q 008566 362 VGVAELKVAVEK 373 (561)
Q Consensus 362 ~~l~~l~~l~~~ 373 (561)
.+-.+|..++..
T Consensus 150 ~~~~el~~ia~~ 161 (192)
T cd01473 150 ASENKLKLLAGC 161 (192)
T ss_pred ccHHHHHHhcCC
Confidence 456777777764
No 51
>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=96.85 E-value=0.013 Score=54.87 Aligned_cols=45 Identities=20% Similarity=0.264 Sum_probs=35.1
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcCC------CCceEEEEEECCeEEE
Q 008566 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP------DNSLVGLITFGTLVQV 176 (561)
Q Consensus 132 ~vFvID~s~~~~~--~~~l~~~l~~~l~~l~------~~~~VglItf~~~V~~ 176 (561)
++|+||+|.+... +..+++++...++.+. ++.+||||+|++..+.
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 5799999998753 4567888888887775 3579999999986543
No 52
>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=96.82 E-value=0.059 Score=50.35 Aligned_cols=43 Identities=14% Similarity=0.095 Sum_probs=34.7
Q ss_pred EEEEEEEcccchhh---HHHHHHHHHHHhhcCCC-CceEEEEEECCe
Q 008566 131 VFMFVVDTCIIEEE---MSFLKSALSQAIDLLPD-NSLVGLITFGTL 173 (561)
Q Consensus 131 ~~vFvID~s~~~~~---~~~l~~~l~~~l~~l~~-~~~VglItf~~~ 173 (561)
+++|+||+|.++.. ++.+++++...++.+.+ +.++|+++|++.
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 57899999999744 56678887777777764 889999999975
No 53
>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=96.58 E-value=0.1 Score=47.39 Aligned_cols=43 Identities=16% Similarity=0.098 Sum_probs=31.6
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcCC-CCceEEEEEECCeE
Q 008566 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP-DNSLVGLITFGTLV 174 (561)
Q Consensus 132 ~vFvID~s~~~~~--~~~l~~~l~~~l~~l~-~~~~VglItf~~~V 174 (561)
++|+||+|.++.. ....+..+...++.+. ++.+|++|+|++..
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 6899999999764 3445555555555554 47799999999873
No 54
>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=96.24 E-value=0.22 Score=48.44 Aligned_cols=69 Identities=19% Similarity=0.190 Sum_probs=46.4
Q ss_pred CCcchhHHHHHHHHHHhccCC-CCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHH
Q 008566 267 STRCTGTALSIAASLLGACVP-GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQL 345 (561)
Q Consensus 267 ~~~c~G~Al~~A~~ll~~~~~-~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~ 345 (561)
....++.||.+|..++..... ...-+|++||+|--..|.. ....+-...++.++
T Consensus 104 ~~~~l~~aL~~a~~~~~~~~~~~~~k~IvL~TDg~~p~~~~-------------------------~~~~~~~~~~a~~l 158 (218)
T cd01458 104 GQVSLSDALWVCLDLFSKGKKKKSHKRIFLFTNNDDPHGGD-------------------------SIKDSQAAVKAEDL 158 (218)
T ss_pred CCccHHHHHHHHHHHHHhccccccccEEEEECCCCCCCCCC-------------------------HHHHHHHHHHHHHH
Confidence 456799999999999985222 2345799999975333210 00112345788889
Q ss_pred HhcCcEEEEEeecCC
Q 008566 346 VHQGHVLDLFACALD 360 (561)
Q Consensus 346 ~~~~isvdlf~~s~~ 360 (561)
.+.||.+.+|.+..+
T Consensus 159 ~~~gI~i~~i~i~~~ 173 (218)
T cd01458 159 KDKGIELELFPLSSP 173 (218)
T ss_pred HhCCcEEEEEecCCC
Confidence 889999999887554
No 55
>KOG2884 consensus 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=94.66 E-value=0.79 Score=43.72 Aligned_cols=99 Identities=22% Similarity=0.223 Sum_probs=64.4
Q ss_pred HHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhc-cCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCC
Q 008566 246 TLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA-CVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLD 324 (561)
Q Consensus 246 ~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~-~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~ 324 (561)
+|...+..++.. .+--++.+|++|...|+. ..++.--||++|.++|-..
T Consensus 71 kils~lh~i~~~---------g~~~~~~~i~iA~lalkhRqnk~~~~riVvFvGSpi~e--------------------- 120 (259)
T KOG2884|consen 71 KILSKLHGIQPH---------GKANFMTGIQIAQLALKHRQNKNQKQRIVVFVGSPIEE--------------------- 120 (259)
T ss_pred HHHHHhcCCCcC---------CcccHHHHHHHHHHHHHhhcCCCcceEEEEEecCcchh---------------------
Confidence 455566665542 223488999999988883 1223337999999987311
Q ss_pred CCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCccChhcchhhhhccCcE-----EEEcCC
Q 008566 325 KDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGL-----VVLSDS 383 (561)
Q Consensus 325 ~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~~l~~l~~l~~~TGG~-----v~~y~~ 383 (561)
..+-.-++|+++.+++++|||+.++-...+-.-+......++|+ +...++
T Consensus 121 ---------~ekeLv~~akrlkk~~Vaidii~FGE~~~~~e~l~~fida~N~~~~gshlv~Vpp 175 (259)
T KOG2884|consen 121 ---------SEKELVKLAKRLKKNKVAIDIINFGEAENNTEKLFEFIDALNGKGDGSHLVSVPP 175 (259)
T ss_pred ---------hHHHHHHHHHHHHhcCeeEEEEEeccccccHHHHHHHHHHhcCCCCCceEEEeCC
Confidence 11234578999999999999999986655534444455544443 666655
No 56
>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=94.27 E-value=1 Score=50.66 Aligned_cols=73 Identities=19% Similarity=0.248 Sum_probs=44.9
Q ss_pred cchhHHHHHHHHHHhccCCCCCc-EEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHh
Q 008566 269 RCTGTALSIAASLLGACVPGSGA-RILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVH 347 (561)
Q Consensus 269 ~c~G~Al~~A~~ll~~~~~~~gg-kIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~ 347 (561)
..+..||.+|..++..+.++.+. ||++||+--.-.+ + ++ .....+ ...+..+..
T Consensus 117 ~~l~daL~~~~~~f~~~~~k~~~kRI~lfTd~D~P~~-----------------~-~~---~~~~~a----~~~a~dl~~ 171 (584)
T TIGR00578 117 YSLSEVLWVCANLFSDVQFRMSHKRIMLFTNEDNPHG-----------------N-DS---AKASRA----RTKAGDLRD 171 (584)
T ss_pred CcHHHHHHHHHHHHHhcchhhcCcEEEEECCCCCCCC-----------------C-ch---hHHHHH----HHHHHHHHh
Confidence 46899999999999854445554 5999997421111 0 00 000111 235788889
Q ss_pred cCcEEEEEeecC-CccChhc
Q 008566 348 QGHVLDLFACAL-DQVGVAE 366 (561)
Q Consensus 348 ~~isvdlf~~s~-~~~~l~~ 366 (561)
.||.+++|.++. +.+|...
T Consensus 172 ~gi~ielf~l~~~~~Fd~s~ 191 (584)
T TIGR00578 172 TGIFLDLMHLKKPGGFDISL 191 (584)
T ss_pred cCeEEEEEecCCCCCCChhh
Confidence 999999997653 3355543
No 57
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=91.08 E-value=0.42 Score=44.68 Aligned_cols=48 Identities=25% Similarity=0.344 Sum_probs=37.6
Q ss_pred CcEEEEEEEcccchh--hHHHHHHHHHHHhhcCC------CCceEEEEEECCeEEEE
Q 008566 129 PPVFMFVVDTCIIEE--EMSFLKSALSQAIDLLP------DNSLVGLITFGTLVQVH 177 (561)
Q Consensus 129 ~p~~vFvID~s~~~~--~~~~l~~~l~~~l~~l~------~~~~VglItf~~~V~~y 177 (561)
-|+ +|++|+|.+.. ..+.+..+|...++.|. +.+.++||||+..++++
T Consensus 4 lP~-~lllDtSgSM~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~~a~~~ 59 (207)
T COG4245 4 LPC-YLLLDTSGSMIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGPARVI 59 (207)
T ss_pred CCE-EEEEecCcccccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecCcceEE
Confidence 455 47999999875 46778888888888775 35799999999876666
No 58
>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=89.75 E-value=6.3 Score=37.55 Aligned_cols=45 Identities=9% Similarity=0.014 Sum_probs=32.1
Q ss_pred CcEEEEEEEcccchhh---------HHHHHHHHHHHhhcCC--CCceEEEEEECCe
Q 008566 129 PPVFMFVVDTCIIEEE---------MSFLKSALSQAIDLLP--DNSLVGLITFGTL 173 (561)
Q Consensus 129 ~p~~vFvID~s~~~~~---------~~~l~~~l~~~l~~l~--~~~~VglItf~~~ 173 (561)
+.-++|+||.|.++.. .+.+++++...+..+. +..++++++|++.
T Consensus 2 ~~dvv~~ID~SgSM~~~~~~~~~~k~~~ak~~~~~l~~~~~~~D~d~i~l~~f~~~ 57 (199)
T cd01457 2 NRDYTLLIDKSGSMAEADEAKERSRWEEAQESTRALARKCEEYDSDGITVYLFSGD 57 (199)
T ss_pred CcCEEEEEECCCcCCCCCCCCCchHHHHHHHHHHHHHHHHHhcCCCCeEEEEecCC
Confidence 3458999999999753 4667888777776554 3456888887653
No 59
>cd01460 vWA_midasin VWA_Midasin: Midasin is a member of the AAA ATPase family. The proteins of this family are unified by their common archetectural organization that is based upon a conserved ATPase domain. The AAA domain of midasin contains six tandem AAA protomers. The AAA domains in midasin is followed by a D/E rich domain that is following by a VWA domain. The members of this subgroup have a conserved MIDAS motif. The function of this domain is not exactly known although it has been speculated to play a crucial role in midasin function.
Probab=87.99 E-value=22 Score=35.71 Aligned_cols=47 Identities=23% Similarity=0.250 Sum_probs=34.3
Q ss_pred CCcEEEEEEEcccchhhHHH------HHHHHHHHhhcCCCCceEEEEEECCeEE
Q 008566 128 VPPVFMFVVDTCIIEEEMSF------LKSALSQAIDLLPDNSLVGLITFGTLVQ 175 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~~~~~------l~~~l~~~l~~l~~~~~VglItf~~~V~ 175 (561)
....++++||.|.++.+.+. .+..|..+++.++ ..+||++.|+..+.
T Consensus 59 r~~qIvlaID~S~SM~~~~~~~~aleak~lIs~al~~Le-~g~vgVv~Fg~~~~ 111 (266)
T cd01460 59 RDYQILIAIDDSKSMSENNSKKLALESLCLVSKALTLLE-VGQLGVCSFGEDVQ 111 (266)
T ss_pred cCceEEEEEecchhcccccccccHHHHHHHHHHHHHhCc-CCcEEEEEeCCCce
Confidence 58899999999999865321 3445555566555 57999999998653
No 60
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=85.79 E-value=23 Score=36.08 Aligned_cols=86 Identities=21% Similarity=0.203 Sum_probs=54.4
Q ss_pred chhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHHHHhcC
Q 008566 270 CTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQG 349 (561)
Q Consensus 270 c~G~Al~~A~~ll~~~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~ 349 (561)
.+-.||+.|...|+..-....=.|++..++..|.-||.+ |+ .-+.+.+..
T Consensus 144 SLqNaLe~a~~~Lk~~p~H~sREVLii~sslsT~DPgdi-----------------------------~~-tI~~lk~~k 193 (378)
T KOG2807|consen 144 SLQNALELAREVLKHMPGHVSREVLIIFSSLSTCDPGDI-----------------------------YE-TIDKLKAYK 193 (378)
T ss_pred HHHHHHHHHHHHhcCCCcccceEEEEEEeeecccCcccH-----------------------------HH-HHHHHHhhC
Confidence 466888888888872111122345666676777666544 33 334577788
Q ss_pred cEEEEEeecCCccChhcchhhhhccCcEEEEcCCCCccchH
Q 008566 350 HVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFK 390 (561)
Q Consensus 350 isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~ 390 (561)
|-|.++..+. .+..-..||+.||| .|+=..++..++
T Consensus 194 IRvsvIgLsa---Ev~icK~l~kaT~G--~Y~V~lDe~Hlk 229 (378)
T KOG2807|consen 194 IRVSVIGLSA---EVFICKELCKATGG--RYSVALDEGHLK 229 (378)
T ss_pred eEEEEEeech---hHHHHHHHHHhhCC--eEEEEeCHHHHH
Confidence 9999998765 45667899999999 333234444443
No 61
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.69 E-value=10 Score=38.28 Aligned_cols=86 Identities=19% Similarity=0.091 Sum_probs=58.0
Q ss_pred CcchhHHHHHHHHHHhcc------CCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHH
Q 008566 268 TRCTGTALSIAASLLGAC------VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDAL 341 (561)
Q Consensus 268 ~~c~G~Al~~A~~ll~~~------~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~l 341 (561)
...+..||..|+..+.-. .....+||+++..++ +. ..+.-=+-+.
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 345678888888777532 123468999998753 10 1111223477
Q ss_pred HHHHHhcCcEEEEEeecCCccChhcchhhhhccCcEEEEcCC
Q 008566 342 SKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDS 383 (561)
Q Consensus 342 a~~~~~~~isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~ 383 (561)
...|.+.+|.||++..+.+ -+..-++.+++.|||.-....+
T Consensus 169 Ifaaqk~~I~Idv~~L~~e-~~~~~lqQa~~~TgG~Y~~~~~ 209 (279)
T TIGR00627 169 IFSAQKQNIPIDVVSIGGD-FTSGFLQQAADITGGSYLHVKK 209 (279)
T ss_pred HHHHHHcCceEEEEEeCCc-cccHHHHHHHHHhCCEEeccCC
Confidence 7889999999999998653 3577899999999995444443
No 62
>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=83.64 E-value=0.7 Score=34.41 Aligned_cols=33 Identities=27% Similarity=0.507 Sum_probs=24.8
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N 90 (561)
+.-|++|+.----+-+.+...-+|+|..|+..|
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 456999998755443555556789999999887
No 63
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.71 E-value=0.95 Score=32.39 Aligned_cols=30 Identities=23% Similarity=0.484 Sum_probs=21.3
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~ 91 (561)
..+|.+|++-+- +++....+.|+.||..-.
T Consensus 3 ~y~C~~CG~~~~----~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVE----LDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEE----ECCCCCceECCCCCCeEE
Confidence 368999999654 333333799999996654
No 64
>PRK10997 yieM hypothetical protein; Provisional
Probab=80.15 E-value=58 Score=35.68 Aligned_cols=52 Identities=25% Similarity=0.188 Sum_probs=34.5
Q ss_pred CcEEEEEEEcccchhhH-HHHHHHHHHHhh--cCCCCceEEEEEECCeEEEEEcC
Q 008566 129 PPVFMFVVDTCIIEEEM-SFLKSALSQAID--LLPDNSLVGLITFGTLVQVHELG 180 (561)
Q Consensus 129 ~p~~vFvID~s~~~~~~-~~l~~~l~~~l~--~l~~~~~VglItf~~~V~~y~l~ 180 (561)
.--+++|||+|+++... +....++..+|- .+.++-++++|.|++.+.-|.+.
T Consensus 323 kGpiII~VDtSGSM~G~ke~~AkalAaAL~~iAl~q~dr~~li~Fs~~i~~~~l~ 377 (487)
T PRK10997 323 RGPFIVCVDTSGSMGGFNEQCAKAFCLALMRIALAENRRCYIMLFSTEVVTYELT 377 (487)
T ss_pred CCcEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHhcCCCEEEEEecCCceeeccC
Confidence 34478899999998622 222234444443 35678899999999987766554
No 65
>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=79.58 E-value=1.6 Score=28.51 Aligned_cols=30 Identities=27% Similarity=0.505 Sum_probs=23.0
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~ 92 (561)
+.|..|+.-+- .-.+...+.|..|...|.+
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 57999998775 2256688999999988753
No 66
>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=78.24 E-value=18 Score=36.58 Aligned_cols=87 Identities=18% Similarity=0.102 Sum_probs=59.6
Q ss_pred cchhHHHHHHHHHHhccC-------CCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHH
Q 008566 269 RCTGTALSIAASLLGACV-------PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDAL 341 (561)
Q Consensus 269 ~c~G~Al~~A~~ll~~~~-------~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~l 341 (561)
..+..||..|+-.+.-.. ....+||+++.++-+.. ..+.-=+.+.
T Consensus 116 s~LagALS~ALCyINR~~~~~~~~~~~~~~RILv~~s~s~d~----------------------------~~QYi~~MN~ 167 (276)
T PF03850_consen 116 SLLAGALSMALCYINRISRESPSGGTSLKSRILVIVSGSPDS----------------------------SSQYIPLMNC 167 (276)
T ss_pred hhhHHHHHHHHHHHhhhhhcccCCCCCcCccEEEEEecCCCc----------------------------cHHHHHHHHH
Confidence 567888888887776331 24567999964432110 1111223456
Q ss_pred HHHHHhcCcEEEEEeecCCccChhcchhhhhccCcEEEEcCCCC
Q 008566 342 SKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFG 385 (561)
Q Consensus 342 a~~~~~~~isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~ 385 (561)
.-.|.+.+|.||++..+. -+-.-|+..+..|||.-...+...
T Consensus 168 iFaAqk~~v~IDv~~L~~--~~s~fLqQa~d~T~G~y~~~~~~~ 209 (276)
T PF03850_consen 168 IFAAQKQKVPIDVCKLGG--KDSTFLQQASDITGGIYLKVSKPE 209 (276)
T ss_pred HHHHhcCCceeEEEEecC--CchHHHHHHHHHhCceeeccCccc
Confidence 677889999999999976 366679999999999888877643
No 67
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=74.08 E-value=21 Score=33.54 Aligned_cols=75 Identities=25% Similarity=0.301 Sum_probs=51.7
Q ss_pred HHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCC--cEEEEEecCCCCCCCcccccCCCCCCccCCC
Q 008566 244 EFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSG--ARILAFVGGPSTEGPAAIVSKNLSEPIRSHK 321 (561)
Q Consensus 244 ~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~~~~g--gkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~ 321 (561)
+.+|...|..++-. .+--.+.+|+.|..+++. ..+.| -||++|.++|...
T Consensus 69 ~gkilt~lhd~~~~---------g~a~~~~~lqiaql~lkh-R~nk~q~qriVaFvgSpi~e------------------ 120 (243)
T COG5148 69 RGKILTFLHDIRLH---------GGADIMRCLQIAQLILKH-RDNKGQRQRIVAFVGSPIQE------------------ 120 (243)
T ss_pred hhHHHHHhcccccc---------CcchHHHHHHHHHHHHhc-ccCCccceEEEEEecCcccc------------------
Confidence 34677777766542 122378899999988883 22444 7999999987311
Q ss_pred CCCCCCCccchhhHHHHHHHHHHHHhcCcEEEEEeec
Q 008566 322 DLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACA 358 (561)
Q Consensus 322 ~~~~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s 358 (561)
+ .+-.-.+++++.++|++||++-++
T Consensus 121 ---s---------edeLirlak~lkknnVAidii~fG 145 (243)
T COG5148 121 ---S---------EDELIRLAKQLKKNNVAIDIIFFG 145 (243)
T ss_pred ---c---------HHHHHHHHHHHHhcCeeEEEEehh
Confidence 1 122346899999999999999775
No 68
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=71.16 E-value=2.8 Score=30.55 Aligned_cols=33 Identities=18% Similarity=0.413 Sum_probs=22.6
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCCCCCCCc
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p~ 94 (561)
.|..|+..+-+- -..++..|.|+-|+..-.+.+
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCCeEECCC
Confidence 599999976332 122234899999998776653
No 69
>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=69.42 E-value=5.9 Score=27.80 Aligned_cols=27 Identities=26% Similarity=0.502 Sum_probs=20.7
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCCC
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
+|+.|++-- ..+|...+.++|.-||..
T Consensus 2 ~Cp~Cg~~~---~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE---IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE---EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc---eEEcCCCCeEECCCCCCE
Confidence 699999933 567777778999999965
No 70
>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=69.06 E-value=1.7e+02 Score=31.44 Aligned_cols=284 Identities=13% Similarity=0.079 Sum_probs=138.7
Q ss_pred CcEEEEEEEcccchhh----HHHHHHHHHHHhhcCCCCceEEEEEECCeEE-EEEcCCCCCCCCeeEeecCCccCCHHHH
Q 008566 129 PPVFMFVVDTCIIEEE----MSFLKSALSQAIDLLPDNSLVGLITFGTLVQ-VHELGGFGQIIPKTYVFKGSKDVSKDQL 203 (561)
Q Consensus 129 ~p~~vFvID~s~~~~~----~~~l~~~l~~~l~~l~~~~~VglItf~~~V~-~y~l~~~~~~~~~~~v~~g~~~~~~~~l 203 (561)
|-=..|+.|+|.++.+ +..+...|...|..+..+.|+||=+|=+..- =|-.. ..+.+
T Consensus 99 PvDLYyLMDlS~SM~ddl~~lk~lg~~L~~~m~~it~n~rlGfGsFVDK~v~P~~~t------------------~p~~l 160 (423)
T smart00187 99 PVDLYYLMDLSYSMKDDLDNLKSLGDDLAREMKGLTSNFRLGFGSFVDKTVSPFVST------------------RPEKL 160 (423)
T ss_pred ccceEEEEeCCccHHHHHHHHHHHHHHHHHHHHhcccCceeeEEEeecCccCCcccC------------------CHHHh
Confidence 5557789999999864 3345567777888888899999987765321 11110 01122
Q ss_pred HHHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHh
Q 008566 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG 283 (561)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~ 283 (561)
.....- .-+.+. ++.--.-.+++.+......+.+....-. .+...|...+-+-+++|+--=+
T Consensus 161 ~~PC~~----------~~~~c~----p~f~f~~~L~LT~~~~~F~~~V~~~~iS----gN~D~PEgG~DAimQaaVC~~~ 222 (423)
T smart00187 161 ENPCPN----------YNLTCE----PPYGFKHVLSLTDDTDEFNEEVKKQRIS----GNLDAPEGGFDAIMQAAVCTEQ 222 (423)
T ss_pred cCCCcC----------CCCCcC----CCcceeeeccCCCCHHHHHHHHhhceee----cCCcCCcccHHHHHHHHhhccc
Confidence 111100 000111 0111134467777666677777664332 2223345456566666632111
Q ss_pred ccCCCCCcEEEEEecCCCC--CCCcccccCCCCCCccCCCCCCCCCCcc-chhhHHHHHHHHHHHHhcCcEEEEEeecCC
Q 008566 284 ACVPGSGARILAFVGGPST--EGPAAIVSKNLSEPIRSHKDLDKDSAPH-YHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (561)
Q Consensus 284 ~~~~~~ggkIi~F~~g~pt--~G~G~l~~~~~~~~~r~~~~~~~~~~~~-~~~~~~fY~~la~~~~~~~isvdlf~~s~~ 360 (561)
..-+...-||++|++-.+- -|-|+|..--..+..+-|-+-. ..... ......--..|++++.+++|- =||+.+..
T Consensus 223 IGWR~~a~rllv~~TDa~fH~AGDGkLaGIv~PNDg~CHL~~~-g~Yt~s~~~DYPSi~ql~~kL~e~nI~-~IFAVT~~ 300 (423)
T smart00187 223 IGWREDARRLLVFSTDAGFHFAGDGKLAGIVQPNDGQCHLDNN-GEYTMSTTQDYPSIGQLNQKLAENNIN-PIFAVTKK 300 (423)
T ss_pred cccCCCceEEEEEEcCCCccccCCcceeeEecCCCCcceeCCC-CCcCccCcCCCCCHHHHHHHHHhcCce-EEEEEccc
Confidence 1122345688888876553 5777765543333333442211 00000 000011134688888888884 58888777
Q ss_pred ccChhcchhhhhccCcEEEEcCCCCccchHHHHHHHHhccccCcCceeeeEEEEEe-cCCceEEeEEcCccccCCCCCCc
Q 008566 361 QVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVFHSGDYDLGLSSNGIFEINC-SKDIKVQGIIGPCASLEKKGPLC 439 (561)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~vr~-S~gl~i~~~~G~~~~~~~~~~~~ 439 (561)
..++. ..|+.+-.|...--=+-+ ..++..++++. |....-.++|+... +.+++++- ...|......
T Consensus 301 ~~~~Y--~~Ls~lipgs~vg~Ls~D----SsNIv~LI~~a--Y~~i~S~V~l~~~~~p~~v~~~y-~s~C~~g~~~---- 367 (423)
T smart00187 301 QVSLY--KELSALIPGSSVGVLSED----SSNVVELIKDA--YNKISSRVELEDNSLPEGVSVTY-TSSCPGGVVG---- 367 (423)
T ss_pred chhHH--HHHHHhcCcceeeecccC----cchHHHHHHHH--HHhhceEEEEecCCCCCcEEEEE-EeeCCCCCcc----
Confidence 66653 444544444333111111 12333344321 12234456666553 55676653 2233321100
Q ss_pred cCccccCCCCCceEEeCCCCCceEEEEEEEecC
Q 008566 440 SDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKK 472 (561)
Q Consensus 440 sd~~~g~~~~~~~~~~~~~~~~s~~~~f~~~~~ 472 (561)
.+ .-...++.-.+++.|..+++-.
T Consensus 368 ----~~-----~~~C~~v~iG~~V~F~v~vta~ 391 (423)
T smart00187 368 ----PG-----TRKCEGVKIGDTVSFEVTVTAT 391 (423)
T ss_pred ----cC-----CcccCCcccCCEEEEEEEEEeC
Confidence 00 0134456666777777777743
No 71
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=68.70 E-value=13 Score=32.91 Aligned_cols=41 Identities=22% Similarity=0.230 Sum_probs=28.8
Q ss_pred EEEEEcccchh--hHHHHHHHHHHHhhcCCCCceEEEEEECCeEE
Q 008566 133 MFVVDTCIIEE--EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQ 175 (561)
Q Consensus 133 vFvID~s~~~~--~~~~l~~~l~~~l~~l~~~~~VglItf~~~V~ 175 (561)
+++||+|++.. ++..+..-+...++.. +.+|-+|.||..|+
T Consensus 2 ~vaiDtSGSis~~~l~~fl~ev~~i~~~~--~~~v~vi~~D~~v~ 44 (126)
T PF09967_consen 2 VVAIDTSGSISDEELRRFLSEVAGILRRF--PAEVHVIQFDAEVQ 44 (126)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHHhC--CCCEEEEEECCEee
Confidence 68999999864 3444455555555555 55689999998765
No 72
>KOG2353 consensus L-type voltage-dependent Ca2+ channel, alpha2/delta subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=67.79 E-value=41 Score=40.48 Aligned_cols=49 Identities=22% Similarity=0.408 Sum_probs=42.5
Q ss_pred CCcEEEEEEEcccchhh--HHHHHHHHHHHhhcCCCCceEEEEEECCeEEE
Q 008566 128 VPPVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQV 176 (561)
Q Consensus 128 ~~p~~vFvID~s~~~~~--~~~l~~~l~~~l~~l~~~~~VglItf~~~V~~ 176 (561)
.+--.+|++|+|++... +...+..+.++|+.|.++..|-++||++.++.
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 57789999999998654 56789999999999999999999999986554
No 73
>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=66.69 E-value=2.7 Score=30.58 Aligned_cols=33 Identities=30% Similarity=0.531 Sum_probs=23.4
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p 93 (561)
+||.+|+-.+----.+. .-.-+|+=|++.|.+-
T Consensus 5 iRC~~CnklLa~~g~~~--~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVI--ELEIKCPRCKTINHVR 37 (51)
T ss_pred eeccchhHHHhhhcCcc--EEEEECCCCCccceEe
Confidence 79999987765421111 1248999999999874
No 74
>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=65.48 E-value=2e+02 Score=31.03 Aligned_cols=282 Identities=11% Similarity=0.091 Sum_probs=129.0
Q ss_pred CcEEEEEEEcccchhh-HHH---HHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCeeEeecCCccCCHHHHH
Q 008566 129 PPVFMFVVDTCIIEEE-MSF---LKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (561)
Q Consensus 129 ~p~~vFvID~s~~~~~-~~~---l~~~l~~~l~~l~~~~~VglItf~~~V~~y~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (561)
|-=..|++|+|.++.. ++. +...|...|..+-.+.|+||=+|=+..- ..+. + .+.+.+.
T Consensus 102 PvDLYyLmDlS~Sm~ddl~~l~~lg~~l~~~~~~it~~~~~GfGsfvdK~~-~P~~-~---------------~~p~~l~ 164 (426)
T PF00362_consen 102 PVDLYYLMDLSYSMKDDLENLKSLGQDLAEEMRNITSNFRLGFGSFVDKPV-MPFV-S---------------TTPEKLK 164 (426)
T ss_dssp -EEEEEEEE-SGGGHHHHHHHCCCCHHHHHHHHTT-SSEEEEEEEESSSSS-TTTS-T----------------SSHCHH
T ss_pred ceeEEEEeechhhhhhhHHHHHHHHHHHHHHHHhcCccceEechhhccccc-CCcc-c---------------CChhhhc
Confidence 5557889999998754 333 4567888888899999999988865321 0010 0 0112222
Q ss_pred HHhccCCCCCCCCCccccCcCCCCCCccccceeeechhhHHHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhc
Q 008566 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (561)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~ 284 (561)
....-. -+.+. .+..-.-.+++.+........+++..- + .+...|...+=+-+++|+--=..
T Consensus 165 ~pc~~~----------~~~c~----~~~~f~~~l~Lt~~~~~F~~~v~~~~i-s---~n~D~PEgg~dal~Qa~vC~~~i 226 (426)
T PF00362_consen 165 NPCPSK----------NPNCQ----PPFSFRHVLSLTDDITEFNEEVNKQKI-S---GNLDAPEGGLDALMQAAVCQEEI 226 (426)
T ss_dssp STSCCT----------TS--B-------SEEEEEEEES-HHHHHHHHHTS---B-----SSSSBSHHHHHHHHHH-HHHH
T ss_pred Cccccc----------CCCCC----CCeeeEEeecccchHHHHHHhhhhccc-c---CCCCCCccccchheeeeeccccc
Confidence 211000 00111 011124456777766677777765332 1 22233555555666666432111
Q ss_pred cCCCCCcEEEEEecCCC--CCCCcccccCCCCCCccCCCCCCCCCCccc---hhhHHHHHHHHHHHHhcCcEEEEEeecC
Q 008566 285 CVPGSGARILAFVGGPS--TEGPAAIVSKNLSEPIRSHKDLDKDSAPHY---HKAVKFYDALSKQLVHQGHVLDLFACAL 359 (561)
Q Consensus 285 ~~~~~ggkIi~F~~g~p--t~G~G~l~~~~~~~~~r~~~~~~~~~~~~~---~~~~~fY~~la~~~~~~~isvdlf~~s~ 359 (561)
.-+...-||++|++-.+ .-|-|++..--..+..+-|-+- +. .|. .....-...|.+.+.+++| +=||+.+.
T Consensus 227 gWr~~a~~llv~~TD~~fH~agDg~l~gi~~pnd~~Chl~~--~~-~y~~~~~~DYPSv~ql~~~l~e~~i-~~IFAVt~ 302 (426)
T PF00362_consen 227 GWRNEARRLLVFSTDAGFHFAGDGKLAGIVKPNDGKCHLDD--NG-MYTASTEQDYPSVGQLVRKLSENNI-NPIFAVTK 302 (426)
T ss_dssp T--STSEEEEEEEESS-B--TTGGGGGT--S---SS--BST--TS-BBGGGGCS----HHHHHHHHHHTTE-EEEEEEEG
T ss_pred CcccCceEEEEEEcCCccccccccccceeeecCCCceEECC--CC-cccccccccCCCHHHHHHHHHHcCC-EEEEEEch
Confidence 12355678888877644 4788888765544444455332 11 111 1223445678888888888 55888777
Q ss_pred CccChhcchhhhhccCc-EEEEcCCCCccchHHHHHHHHhccccCcCceeeeEEEEEe-cCCceEEeEEcCccccCCCCC
Q 008566 360 DQVGVAELKVAVEKTGG-LVVLSDSFGHAVFKDSVRRVFHSGDYDLGLSSNGIFEINC-SKDIKVQGIIGPCASLEKKGP 437 (561)
Q Consensus 360 ~~~~l~~l~~l~~~TGG-~v~~y~~f~~~~~~~~l~~~~~~~~~~~~~~~~~~~~vr~-S~gl~i~~~~G~~~~~~~~~~ 437 (561)
...++. ..|+..-+| .+-.... +.+...+-++..+. ...-.+.++... ++++++ .+..+|......
T Consensus 303 ~~~~~Y--~~L~~~i~~s~vg~L~~-dSsNIv~LI~~aY~------~i~s~V~L~~~~~p~~v~v-~y~s~C~~~~~~-- 370 (426)
T PF00362_consen 303 DVYSIY--EELSNLIPGSSVGELSS-DSSNIVQLIKEAYN------KISSKVELKHDNAPDGVKV-SYTSNCPNGSTV-- 370 (426)
T ss_dssp GGHHHH--HHHHHHSTTEEEEEEST-TSHTHHHHHHHHHH------HHCTEEEEEECS--TTEEE-EEEEEESSSEEE--
T ss_pred hhhhHH--HHHhhcCCCceeccccc-CchhHHHHHHHHHH------HHhheEEEEecCCCCcEEE-EEEEEccCCccc--
Confidence 655533 344443333 3434433 22222222222222 123445555333 335666 444444431100
Q ss_pred CccCccccCCCCCceEEeCCCCCceEEEEEEEecC
Q 008566 438 LCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKK 472 (561)
Q Consensus 438 ~~sd~~~g~~~~~~~~~~~~~~~~s~~~~f~~~~~ 472 (561)
...-...++...+++.|.+.++-.
T Consensus 371 -----------~~~~~C~~V~iG~~V~F~VtVta~ 394 (426)
T PF00362_consen 371 -----------PGTNECSNVKIGDTVTFNVTVTAK 394 (426)
T ss_dssp -----------ECCEEECSE-TT-EEEEEEEEEES
T ss_pred -----------CcCccccCEecCCEEEEEEEEEEe
Confidence 011234556666777777766654
No 75
>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=64.64 E-value=3.5 Score=28.87 Aligned_cols=30 Identities=20% Similarity=0.437 Sum_probs=25.0
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
.||..|+....-+..+.+ .....|+-||..
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 589999988888877766 668999999973
No 76
>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=63.68 E-value=3 Score=32.39 Aligned_cols=30 Identities=27% Similarity=0.453 Sum_probs=20.4
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p 93 (561)
+.|| .|+.|+= .+++.+.-+| .||....+.
T Consensus 3 ifrC-~Cgr~ly----a~e~~kTkkC-~CG~~l~vk 32 (68)
T PF09082_consen 3 IFRC-DCGRYLY----AKEGAKTKKC-VCGKTLKVK 32 (68)
T ss_dssp EEEE-TTS--EE----EETT-SEEEE-TTTEEEE--
T ss_pred EEEe-cCCCEEE----ecCCcceeEe-cCCCeeeee
Confidence 6899 7999863 4567789999 999888774
No 77
>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=60.92 E-value=1.4e+02 Score=28.51 Aligned_cols=100 Identities=13% Similarity=-0.077 Sum_probs=61.5
Q ss_pred HHHHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCC
Q 008566 245 FTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLD 324 (561)
Q Consensus 245 ~~i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~ 324 (561)
+.+..+|+.++-. .. + + .|..||..|..-+....+...--||+++.|--|.|- +
T Consensus 75 ~~l~~~l~~~q~g---~a-g--~--~TadAi~~av~rl~~~~~a~~kvvILLTDG~n~~~~--i---------------- 128 (191)
T cd01455 75 ETLKMMHAHSQFC---WS-G--D--HTVEATEFAIKELAAKEDFDEAIVIVLSDANLERYG--I---------------- 128 (191)
T ss_pred HHHHHHHHhcccC---cc-C--c--cHHHHHHHHHHHHHhcCcCCCcEEEEEeCCCcCCCC--C----------------
Confidence 4677777766442 11 1 1 233888888888751122234466777777544331 1
Q ss_pred CCCCccchhhHHHHHHH-HHHHHhcCcEEEEEeecCCccChhcchhhhhccCcEEEEcCCC
Q 008566 325 KDSAPHYHKAVKFYDAL-SKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSF 384 (561)
Q Consensus 325 ~~~~~~~~~~~~fY~~l-a~~~~~~~isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~f 384 (561)
.| .+. +..+.+.||-|..+.++.. |-.++..+++.|||+-|...+-
T Consensus 129 -------~P-----~~aAa~lA~~~gV~iytIgiG~~--d~~~l~~iA~~tgG~~F~A~d~ 175 (191)
T cd01455 129 -------QP-----KKLADALAREPNVNAFVIFIGSL--SDEADQLQRELPAGKAFVCMDT 175 (191)
T ss_pred -------Ch-----HHHHHHHHHhCCCEEEEEEecCC--CHHHHHHHHhCCCCcEEEeCCH
Confidence 11 133 3445678887777766543 6677899999999999998653
No 78
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=60.06 E-value=5.2 Score=34.70 Aligned_cols=27 Identities=19% Similarity=0.564 Sum_probs=19.5
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N 90 (561)
..||..|+.... .....|.|+-||..+
T Consensus 70 ~~~C~~Cg~~~~------~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 70 QAWCWDCSQVVE------IHQHDAQCPHCHGER 96 (113)
T ss_pred EEEcccCCCEEe------cCCcCccCcCCCCCC
Confidence 489999995433 223468899999765
No 79
>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=58.77 E-value=17 Score=35.10 Aligned_cols=64 Identities=27% Similarity=0.467 Sum_probs=36.8
Q ss_pred cchhHHHHHHHHHHhc--cCCCC-CcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHH-HHHH
Q 008566 269 RCTGTALSIAASLLGA--CVPGS-GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDA-LSKQ 344 (561)
Q Consensus 269 ~c~G~Al~~A~~ll~~--~~~~~-ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~-la~~ 344 (561)
..+..||.+|..++.. +.... .-||++||..- +| |. +.+ .+.. -.++ .+..
T Consensus 105 ~~l~~al~v~~~~~~~~~~~~k~~~krI~l~Td~d---~p--------------~~--~~~---~~~~---~~~~l~~~D 159 (224)
T PF03731_consen 105 GDLSDALWVASDMFRERTCKKKKNKKRIFLFTDND---GP--------------HE--DDD---ELER---IIQKLKAKD 159 (224)
T ss_dssp --HHHHHHHHHHHHHCHCTTS-ECEEEEEEEES-S---ST--------------TT---CC---CHHH---HHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHHHhhcccCCCcEEEEEeCCC---CC--------------CC--CHH---HHHH---HHHhhcccc
Confidence 4688999999999984 33333 45777777642 11 00 011 0111 1112 2677
Q ss_pred HHhcCcEEEEEee
Q 008566 345 LVHQGHVLDLFAC 357 (561)
Q Consensus 345 ~~~~~isvdlf~~ 357 (561)
+...+|.+++|.+
T Consensus 160 l~~~~i~~~~~~l 172 (224)
T PF03731_consen 160 LQDNGIEIELFFL 172 (224)
T ss_dssp HHHHTEEEEEEEC
T ss_pred chhcCcceeEeec
Confidence 8899999999987
No 80
>PRK03954 ribonuclease P protein component 4; Validated
Probab=58.44 E-value=6.7 Score=34.39 Aligned_cols=35 Identities=23% Similarity=0.425 Sum_probs=24.8
Q ss_pred cccCCCCceecCc----eEEEcCC---ceeEeCCCCCCCCCC
Q 008566 59 LRCRTCRSILNPF----SIVDFAA---KIWICPFCFQRNHFP 93 (561)
Q Consensus 59 ~RC~~C~ayiNp~----~~~~~~~---~~w~C~~C~~~N~~p 93 (561)
.-|++|.+|+=|- +.+..+. -.++|..||+....|
T Consensus 65 ~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~P 106 (121)
T PRK03954 65 RYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRYP 106 (121)
T ss_pred HHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEeec
Confidence 4599999998663 3343322 235999999988876
No 81
>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=58.37 E-value=6.7 Score=25.87 Aligned_cols=23 Identities=30% Similarity=0.833 Sum_probs=14.6
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
+|..|+=...+- ...|.|+.|+.
T Consensus 3 ~C~~CGy~y~~~------~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGE------EAPWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCC------cCCCcCcCCCC
Confidence 577777443432 24688888886
No 82
>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=58.18 E-value=5.9 Score=34.43 Aligned_cols=27 Identities=22% Similarity=0.682 Sum_probs=20.0
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N 90 (561)
-.||.+|+....+ ....|.|+-||..+
T Consensus 70 ~~~C~~Cg~~~~~------~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 70 ECECEDCSEEVSP------EIDLYRCPKCHGIM 96 (115)
T ss_pred EEEcccCCCEEec------CCcCccCcCCcCCC
Confidence 4899999955443 22358999999876
No 83
>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=56.97 E-value=5.9 Score=28.90 Aligned_cols=31 Identities=19% Similarity=0.460 Sum_probs=22.3
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N 90 (561)
.||.+|+....-+..+.+ .....|+-||..+
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~~ 36 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-DPLATCPECGGEK 36 (52)
T ss_pred EEeCCCCCEeEEEEecCC-CCCCCCCCCCCCc
Confidence 489999986665555443 4568899999754
No 84
>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=54.13 E-value=12 Score=25.30 Aligned_cols=26 Identities=23% Similarity=0.521 Sum_probs=19.4
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
.+|..|++. +...+ .+.|.|.-||+.
T Consensus 9 ~~C~~C~~~---~~~~~--dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSR---WFYSD--DGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCe---EeEcc--CCEEEhhhCceE
Confidence 569999999 33333 347999999975
No 85
>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=53.25 E-value=25 Score=34.19 Aligned_cols=43 Identities=16% Similarity=0.182 Sum_probs=27.6
Q ss_pred Cc-EEEEEEEcccchhhH-HHHHHHHHHHhhcCCCCceEEEEEECCeE
Q 008566 129 PP-VFMFVVDTCIIEEEM-SFLKSALSQAIDLLPDNSLVGLITFGTLV 174 (561)
Q Consensus 129 ~p-~~vFvID~s~~~~~~-~~l~~~l~~~l~~l~~~~~VglItf~~~V 174 (561)
.| -+|+++|+|+++... ..+...+..+....+ ++.++.|++.+
T Consensus 56 ~~~~lvvl~DvSGSM~~~s~~~l~~~~~l~~~~~---~~~~f~F~~~l 100 (222)
T PF05762_consen 56 KPRRLVVLCDVSGSMAGYSEFMLAFLYALQRQFR---RVRVFVFSTRL 100 (222)
T ss_pred CCccEEEEEeCCCChHHHHHHHHHHHHHHHHhCC---CEEEEEEeeeh
Confidence 44 899999999998773 334433333333333 77777788643
No 86
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=52.83 E-value=8.3 Score=26.17 Aligned_cols=33 Identities=15% Similarity=0.324 Sum_probs=23.0
Q ss_pred CcccCCCCceecCc-eEEEcCCceeEeCCCCCCC
Q 008566 58 PLRCRTCRSILNPF-SIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 58 ~~RC~~C~ayiNp~-~~~~~~~~~w~C~~C~~~N 90 (561)
.++|.+|++-.+-= .++...+++.+|.-|++.-
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 36788888876633 2344567788999998753
No 87
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=52.33 E-value=5.6 Score=26.59 Aligned_cols=30 Identities=20% Similarity=0.270 Sum_probs=15.3
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCCC
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
.|..|++=+..-.--.++..+|+|.-|+..
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 488898876543332245578999999864
No 88
>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=51.12 E-value=8.2 Score=26.40 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=21.7
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
.||..|+........... +....|+-||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 489999997776655543 55788999997
No 89
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=50.96 E-value=17 Score=24.07 Aligned_cols=29 Identities=24% Similarity=0.428 Sum_probs=19.7
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N 90 (561)
+.+|..|++-. -+........|.+|+...
T Consensus 3 ~~~C~~C~~~~----i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNG----IVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCe----EEEecCCeEEcccCCcEe
Confidence 46899998865 221233479999999754
No 90
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=50.33 E-value=9.5 Score=33.11 Aligned_cols=28 Identities=21% Similarity=0.618 Sum_probs=19.0
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N 90 (561)
..||..|+.+...- ....|.|+-||..+
T Consensus 70 ~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 70 ECWCETCQQYVTLL-----TQRVRRCPQCHGDM 97 (114)
T ss_pred EEEcccCCCeeecC-----CccCCcCcCcCCCC
Confidence 48999999643311 12238899999776
No 91
>PF12773 DZR: Double zinc ribbon
Probab=49.99 E-value=10 Score=27.30 Aligned_cols=32 Identities=25% Similarity=0.330 Sum_probs=24.6
Q ss_pred CCcccCCCCceecCceEEEcCCceeEeCCCCCCCCCC
Q 008566 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (561)
Q Consensus 57 ~~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p 93 (561)
+-..|.+|++-+. ......++|.-|++.|...
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCcCC
Confidence 4577999999888 3345679999999987654
No 92
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=49.50 E-value=7.9 Score=23.37 Aligned_cols=21 Identities=24% Similarity=0.619 Sum_probs=11.9
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
+|.+|++-+..=.+ .|+-||+
T Consensus 1 ~Cp~CG~~~~~~~~--------fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAK--------FCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCc--------chhhhCC
Confidence 47777766653222 2666665
No 93
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=48.67 E-value=8.7 Score=33.80 Aligned_cols=31 Identities=16% Similarity=0.544 Sum_probs=22.2
Q ss_pred CCcccCCCCceecCceEEEcCCceeEeCCCCCCCC
Q 008566 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (561)
Q Consensus 57 ~~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~ 91 (561)
.+-.|.+|++-+..- .+.-+|.||+|...-.
T Consensus 88 q~r~CARCGGrv~lr----sNKv~wvcnlc~k~q~ 118 (169)
T KOG3799|consen 88 QTRFCARCGGRVSLR----SNKVMWVCNLCRKQQE 118 (169)
T ss_pred hhhHHHhcCCeeeec----cCceEEeccCCcHHHH
Confidence 355678999877643 3345899999997654
No 94
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=48.08 E-value=12 Score=33.46 Aligned_cols=33 Identities=30% Similarity=0.560 Sum_probs=23.3
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p 93 (561)
++|.-|+..- -+..+.....|.|.-|+..|.+.
T Consensus 1 v~C~fC~~~s--~~~~~~~~~~w~C~~C~q~N~f~ 33 (131)
T PF09779_consen 1 VNCWFCGQNS--KVPYDNRNSNWTCPHCEQYNGFD 33 (131)
T ss_pred CeeccCCCCC--CCCCCCCCCeeECCCCCCccCcc
Confidence 4688888763 23333444569999999999985
No 95
>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=47.87 E-value=8.6 Score=33.53 Aligned_cols=32 Identities=22% Similarity=0.517 Sum_probs=25.4
Q ss_pred cccCCCCceecCceEEEc-CCceeEeCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDF-AAKIWICPFCFQRN 90 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~-~~~~w~C~~C~~~N 90 (561)
..|..|+-.+..-|.+.. ....|.|.+|...-
T Consensus 72 ~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k~r 104 (118)
T PF02318_consen 72 RVCVDCKHRVCKKCGVYSKKEPIWLCKVCQKQR 104 (118)
T ss_dssp EEETTTTEEEETTSEEETSSSCCEEEHHHHHHH
T ss_pred CcCCcCCccccCccCCcCCCCCCEEChhhHHHH
Confidence 678888888888888874 46789999997543
No 96
>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=47.39 E-value=9.7 Score=27.86 Aligned_cols=29 Identities=31% Similarity=0.809 Sum_probs=16.7
Q ss_pred ccCCCCceecCce-----------EEEcCCceeEeCCCCC
Q 008566 60 RCRTCRSILNPFS-----------IVDFAAKIWICPFCFQ 88 (561)
Q Consensus 60 RC~~C~ayiNp~~-----------~~~~~~~~w~C~~C~~ 88 (561)
+|..|+=..+|-- .|++--..|+|+.|+.
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCC
Confidence 5777775556431 2222234588888874
No 97
>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=46.76 E-value=13 Score=28.76 Aligned_cols=28 Identities=18% Similarity=0.459 Sum_probs=21.9
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N 90 (561)
-.|..|+...-. ...++.|.|+-||..-
T Consensus 29 q~C~~CG~~~~~----~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 29 QTCPRCGHRNKK----RRSGRVFTCPNCGFEM 56 (69)
T ss_pred cCccCccccccc----ccccceEEcCCCCCEE
Confidence 459999988776 4557899999999763
No 98
>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=46.13 E-value=17 Score=22.50 Aligned_cols=24 Identities=29% Similarity=0.620 Sum_probs=14.3
Q ss_pred cCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 61 C~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
|.+|+..+. .-.+...+.|..|.+
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 566666553 224456677777764
No 99
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=44.14 E-value=19 Score=27.14 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=20.5
Q ss_pred CCcccCCCCceecCceEEEcCCceeEeCCCCCCCC
Q 008566 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (561)
Q Consensus 57 ~~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~ 91 (561)
.+..|.+|+.+.=| .-.|..||..+.
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 35789999998765 578999997664
No 100
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=43.99 E-value=9.1 Score=33.38 Aligned_cols=29 Identities=24% Similarity=0.676 Sum_probs=18.4
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~ 91 (561)
..||..|+.+..+- . ...+.|+-||..+.
T Consensus 71 ~~~C~~Cg~~~~~~----~-~~~~~CP~Cgs~~~ 99 (117)
T PRK00564 71 ELECKDCSHVFKPN----A-LDYGVCEKCHSKNV 99 (117)
T ss_pred EEEhhhCCCccccC----C-ccCCcCcCCCCCce
Confidence 48999999443321 1 12245999998763
No 101
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=43.82 E-value=13 Score=27.12 Aligned_cols=25 Identities=24% Similarity=0.549 Sum_probs=17.9
Q ss_pred cccCCCCc-eecCceEEEcCCceeEeCCCCCC
Q 008566 59 LRCRTCRS-ILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 59 ~RC~~C~a-yiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
..|.+|++ ++-+ . ...|.|.-|+..
T Consensus 21 ~fCP~Cg~~~m~~----~--~~r~~C~~Cgyt 46 (50)
T PRK00432 21 KFCPRCGSGFMAE----H--LDRWHCGKCGYT 46 (50)
T ss_pred CcCcCCCcchhec----c--CCcEECCCcCCE
Confidence 47999998 4443 2 257999999853
No 102
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=42.59 E-value=15 Score=24.76 Aligned_cols=31 Identities=13% Similarity=0.284 Sum_probs=19.7
Q ss_pred cccCCCCceecCce-EEEcCCceeEeCCCCCC
Q 008566 59 LRCRTCRSILNPFS-IVDFAAKIWICPFCFQR 89 (561)
Q Consensus 59 ~RC~~C~ayiNp~~-~~~~~~~~w~C~~C~~~ 89 (561)
++|.+|++-.+-=- ++-..|.+.+|.-|++.
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 56888877654332 23355677888888764
No 103
>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=42.18 E-value=25 Score=25.03 Aligned_cols=27 Identities=19% Similarity=0.432 Sum_probs=19.2
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
+.|.+|++- . +..+.. .+.|.|.-|++
T Consensus 19 ~~CP~Cg~~-~-~~~~~~-~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-K-HYRLKT-RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-e-eEEeCC-CCeEECCCCCC
Confidence 569999987 3 333322 46899999985
No 104
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=41.33 E-value=16 Score=26.85 Aligned_cols=32 Identities=16% Similarity=0.271 Sum_probs=26.4
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
+.+|.+|+.--.|..+-...|..-.||-|+-.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~ 34 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLY 34 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHH
Confidence 46899999988888877777777999999954
No 105
>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=41.10 E-value=14 Score=23.10 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=16.1
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCCCC
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N 90 (561)
+|..|++-|+- ..-.|+.||+..
T Consensus 2 ~CP~C~~~V~~--------~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPE--------SAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchh--------hcCcCCCCCCCC
Confidence 58888888742 246788898753
No 106
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=39.80 E-value=36 Score=34.71 Aligned_cols=29 Identities=34% Similarity=0.548 Sum_probs=25.8
Q ss_pred hhHHHHHHHHHHHhhcCCCCceEEEEEEC
Q 008566 143 EEMSFLKSALSQAIDLLPDNSLVGLITFG 171 (561)
Q Consensus 143 ~~~~~l~~~l~~~l~~l~~~~~VglItf~ 171 (561)
.|++.++++|.++++.|.++.|+++|||-
T Consensus 218 dEL~~L~~~L~~a~~~L~~gGRl~VIsFH 246 (314)
T COG0275 218 DELEELEEALEAALDLLKPGGRLAVISFH 246 (314)
T ss_pred hHHHHHHHHHHHHHHhhCCCcEEEEEEec
Confidence 46788999999999999999999999664
No 107
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=39.48 E-value=24 Score=25.01 Aligned_cols=25 Identities=20% Similarity=0.307 Sum_probs=15.2
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCCC
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
+|.+|++-+..- .+..-.|+-||+.
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCce
Confidence 577777755432 2345777777754
No 108
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=39.10 E-value=16 Score=26.52 Aligned_cols=27 Identities=26% Similarity=0.667 Sum_probs=14.6
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
-+|.+|++-+ ..+....--.|+-||+.
T Consensus 7 Y~C~~Cg~~~----~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 7 YKCARCGREV----ELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEhhhcCCee----ehhhccCceeCCCCCcE
Confidence 3566666665 22333444666666654
No 109
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=39.09 E-value=2e+02 Score=31.11 Aligned_cols=43 Identities=19% Similarity=0.214 Sum_probs=28.5
Q ss_pred CcEEEEEEEcccchhhHHH-HHHHHHHHhh--cCCCCceEEEEEECC
Q 008566 129 PPVFMFVVDTCIIEEEMSF-LKSALSQAID--LLPDNSLVGLITFGT 172 (561)
Q Consensus 129 ~p~~vFvID~s~~~~~~~~-l~~~l~~~l~--~l~~~~~VglItf~~ 172 (561)
+| ++.+||.|+++.-... ...|+..+|- .+.+|-++.++.|++
T Consensus 273 Gp-villlD~SGSM~G~~e~~AKAvalAl~~~alaenR~~~~~lF~s 318 (437)
T COG2425 273 GP-VILLLDKSGSMSGFKEQWAKAVALALMRIALAENRDCYVILFDS 318 (437)
T ss_pred CC-EEEEEeCCCCcCCcHHHHHHHHHHHHHHHHHHhccceEEEEecc
Confidence 44 5569999999754321 2223333332 456899999999999
No 110
>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=39.07 E-value=11 Score=24.12 Aligned_cols=15 Identities=33% Similarity=0.651 Sum_probs=12.4
Q ss_pred ceeEeCCCCCCCCCC
Q 008566 79 KIWICPFCFQRNHFP 93 (561)
Q Consensus 79 ~~w~C~~C~~~N~~p 93 (561)
+.|.|..|...|...
T Consensus 3 g~W~C~~C~~~N~~~ 17 (30)
T PF00641_consen 3 GDWKCPSCTFMNPAS 17 (30)
T ss_dssp SSEEETTTTEEEESS
T ss_pred cCccCCCCcCCchHH
Confidence 379999999999753
No 111
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=38.14 E-value=19 Score=33.88 Aligned_cols=26 Identities=31% Similarity=0.651 Sum_probs=21.3
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
-.||.+|++-|=+ .+++.+|+-||..
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 3899999998753 4678999999964
No 112
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.96 E-value=20 Score=32.17 Aligned_cols=33 Identities=24% Similarity=0.426 Sum_probs=19.9
Q ss_pred CcccCCCCceecCce---E----------EEc--CCceeEeCCCCCCC
Q 008566 58 PLRCRTCRSILNPFS---I----------VDF--AAKIWICPFCFQRN 90 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~---~----------~~~--~~~~w~C~~C~~~N 90 (561)
..+|..|+.....-- + +.+ ....|.|+-||..+
T Consensus 70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 488999996554320 0 000 03458899999765
No 113
>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=37.49 E-value=21 Score=32.36 Aligned_cols=39 Identities=28% Similarity=0.542 Sum_probs=24.9
Q ss_pred CcccCCCCceecCceEE-----------EcCCceeEeCCCCCCCCCCccC
Q 008566 58 PLRCRTCRSILNPFSIV-----------DFAAKIWICPFCFQRNHFPPHY 96 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~-----------~~~~~~w~C~~C~~~N~~p~~y 96 (561)
..||..|.+-+-+-.+- .....-|.|+-||+.-=-..+|
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHW 140 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccH
Confidence 48999999955433221 1134589999999876333343
No 114
>PRK12722 transcriptional activator FlhC; Provisional
Probab=37.17 E-value=17 Score=34.40 Aligned_cols=29 Identities=14% Similarity=0.438 Sum_probs=20.5
Q ss_pred CCcccCCCCc-eecCceEEEcCCceeEeCCCCC
Q 008566 57 APLRCRTCRS-ILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 57 ~~~RC~~C~a-yiNp~~~~~~~~~~w~C~~C~~ 88 (561)
...+|..|++ ||-.. .+....++|++|.-
T Consensus 133 ~l~~C~~Cgg~fv~~~---~e~~~~f~CplC~~ 162 (187)
T PRK12722 133 QLSSCNCCGGHFVTHA---HDPVGSFVCGLCQP 162 (187)
T ss_pred eeccCCCCCCCeeccc---cccCCCCcCCCCCC
Confidence 4789999986 44222 23356799999996
No 115
>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=36.60 E-value=20 Score=23.26 Aligned_cols=25 Identities=24% Similarity=0.567 Sum_probs=12.9
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
+.|..|++=-+- .++..++|+-|++
T Consensus 3 p~Cp~C~se~~y-----~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 3 PKCPLCGSEYTY-----EDGELLVCPECGH 27 (30)
T ss_dssp ---TTT-----E-----E-SSSEEETTTTE
T ss_pred CCCCCCCCccee-----ccCCEEeCCcccc
Confidence 678888875442 3467899999985
No 116
>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=36.30 E-value=19 Score=38.12 Aligned_cols=27 Identities=22% Similarity=0.445 Sum_probs=20.6
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCCCCCCCc
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p~ 94 (561)
+|.+|+.- ...-.|+|+-|+..|.+..
T Consensus 2 ~c~~cg~~--------~~~~~g~cp~c~~w~~~~e 28 (372)
T cd01121 2 VCSECGYV--------SPKWLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCC--------CCCccEECcCCCCceeeee
Confidence 69999853 2233599999999999863
No 117
>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=36.29 E-value=11 Score=27.12 Aligned_cols=10 Identities=40% Similarity=1.308 Sum_probs=5.1
Q ss_pred ceeEeCCCCC
Q 008566 79 KIWICPFCFQ 88 (561)
Q Consensus 79 ~~w~C~~C~~ 88 (561)
..|+|+.|+.
T Consensus 33 ~~w~CP~C~a 42 (47)
T PF00301_consen 33 DDWVCPVCGA 42 (47)
T ss_dssp TT-B-TTTSS
T ss_pred CCCcCcCCCC
Confidence 3477777774
No 118
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=35.68 E-value=1e+02 Score=35.56 Aligned_cols=106 Identities=18% Similarity=0.259 Sum_probs=61.0
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCCCCCccCcCCCCCCCCcccCCCCc--ceEEeCCCC-----C--CCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHYASITDDNLPAELFPQYT--TIEYEPPGP-----G--EKSSV 128 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p~~y~~~~~~~~~pEl~~~~~--tvey~~~~~-----~--~~~~~ 128 (561)
+.+|.+|-+++. +-...+.-.|-.||+.-.+|. -+|+++ .+.|.-+.. . ..-+.
T Consensus 444 v~~Cp~Cd~~lt----~H~~~~~L~CH~Cg~~~~~p~-------------~Cp~Cgs~~L~~~G~GterieeeL~~~FP~ 506 (730)
T COG1198 444 IAECPNCDSPLT----LHKATGQLRCHYCGYQEPIPQ-------------SCPECGSEHLRAVGPGTERIEEELKRLFPG 506 (730)
T ss_pred cccCCCCCcceE----EecCCCeeEeCCCCCCCCCCC-------------CCCCCCCCeeEEecccHHHHHHHHHHHCCC
Confidence 567777776643 445567899999999977762 223332 233332200 0 00124
Q ss_pred CcEEEEEEEcccchhhHHHHHHHHHH-------------HhhcCCCCceEEEEEECCeEEEEEcC
Q 008566 129 PPVFMFVVDTCIIEEEMSFLKSALSQ-------------AIDLLPDNSLVGLITFGTLVQVHELG 180 (561)
Q Consensus 129 ~p~~vFvID~s~~~~~~~~l~~~l~~-------------~l~~l~~~~~VglItf~~~V~~y~l~ 180 (561)
.+++.|--|++.....++.+...+.. -=...|.-+.||++--|..+..-|+.
T Consensus 507 ~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfR 571 (730)
T COG1198 507 ARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFR 571 (730)
T ss_pred CcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcc
Confidence 77888777777765554432221111 11234556899999888877776666
No 119
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=35.46 E-value=25 Score=29.75 Aligned_cols=27 Identities=26% Similarity=0.725 Sum_probs=21.5
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCCCCCC
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~ 92 (561)
.|.+|++.|.|- +..|.|.-|+.....
T Consensus 2 fC~~Cg~~l~~~------~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPK------NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccC------CCeEECcCCCCcccc
Confidence 599999999652 347999999987654
No 120
>COG4867 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=35.38 E-value=3.6e+02 Score=28.89 Aligned_cols=100 Identities=19% Similarity=0.204 Sum_probs=64.2
Q ss_pred CcchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCC----CCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHH
Q 008566 268 TRCTGTALSIAASLLGACVPGSGARILAFVGGPSTE----GPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSK 343 (561)
Q Consensus 268 ~~c~G~Al~~A~~ll~~~~~~~ggkIi~F~~g~pt~----G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~ 343 (561)
.+.+--||..|..+++-. ...--.|++.|.|-||- |-|.....+.. +|-. .+... ... -.
T Consensus 532 gTNlhhaL~LA~r~l~Rh-~~~~~~il~vTDGePtAhle~~DG~~~~f~yp--------~DP~--t~~~T----vr~-~d 595 (652)
T COG4867 532 GTNLHHALALAGRHLRRH-AGAQPVVLVVTDGEPTAHLEDGDGTSVFFDYP--------PDPR--TIAHT----VRG-FD 595 (652)
T ss_pred ccchHHHHHHHHHHHHhC-cccCceEEEEeCCCccccccCCCCceEecCCC--------CChh--HHHHH----HHH-HH
Confidence 355778899999888731 13346799999998873 44444332211 1100 01111 112 24
Q ss_pred HHHhcCcEEEEEeecCCccChhcchhhhhccCcEEEEcCC
Q 008566 344 QLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDS 383 (561)
Q Consensus 344 ~~~~~~isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~ 383 (561)
.|.+.|+-+++|....+.-=..-+..+++.++|+++.-+.
T Consensus 596 ~~~r~G~q~t~FrLg~DpgL~~Fv~qva~rv~G~vv~pdl 635 (652)
T COG4867 596 DMARLGAQVTIFRLGSDPGLARFIDQVARRVQGRVVVPDL 635 (652)
T ss_pred HHHhccceeeEEeecCCHhHHHHHHHHHHHhCCeEEecCc
Confidence 5788999999999988774444578999999999987654
No 121
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.98 E-value=17 Score=31.98 Aligned_cols=33 Identities=21% Similarity=0.399 Sum_probs=19.6
Q ss_pred CcccCCCCceecCc-eEEEcCCceeEeCCCCCCCC
Q 008566 58 PLRCRTCRSILNPF-SIVDFAAKIWICPFCFQRNH 91 (561)
Q Consensus 58 ~~RC~~C~ayiNp~-~~~~~~~~~w~C~~C~~~N~ 91 (561)
..|| .|+.+..+- ...+.-.-.|.|+-||..+.
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~ 103 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRA 103 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCCCCCC
Confidence 4899 999775432 11111011378999997663
No 122
>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=34.78 E-value=43 Score=22.84 Aligned_cols=27 Identities=26% Similarity=0.727 Sum_probs=17.7
Q ss_pred ccCCCCceecCceEEEc--CCceeEeCCCCC
Q 008566 60 RCRTCRSILNPFSIVDF--AAKIWICPFCFQ 88 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~--~~~~w~C~~C~~ 88 (561)
-|..|++ ---|- +++ +...|+|+-|+.
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 3788877 23333 443 346799999985
No 123
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=34.32 E-value=39 Score=30.21 Aligned_cols=31 Identities=19% Similarity=0.477 Sum_probs=24.1
Q ss_pred cccCCCCceecCceEEEcCCcee--EeCCCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIW--ICPFCFQRNHF 92 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w--~C~~C~~~N~~ 92 (561)
+-|+.|+. |=..+...++.| +|.-||..-++
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 88999997 656665556666 89999998776
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=33.58 E-value=25 Score=23.72 Aligned_cols=31 Identities=16% Similarity=0.366 Sum_probs=14.5
Q ss_pred cccCCCCceecCc-eEEEcCCceeEeCCCCCC
Q 008566 59 LRCRTCRSILNPF-SIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 59 ~RC~~C~ayiNp~-~~~~~~~~~w~C~~C~~~ 89 (561)
+.|.+|++-..-= -.+...+....|+-|++.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 4566666642211 111123445667766653
No 125
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.34 E-value=21 Score=29.30 Aligned_cols=36 Identities=25% Similarity=0.511 Sum_probs=24.4
Q ss_pred CCcccCCCCceecCceEEEcCCceeEeCCCCCCCCCCccC
Q 008566 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHY 96 (561)
Q Consensus 57 ~~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p~~y 96 (561)
.|+||++||--.++ -++ ..--.|+-|+..-.-++.|
T Consensus 57 ~Pa~CkkCGfef~~-~~i---k~pSRCP~CKSE~Ie~prF 92 (97)
T COG3357 57 RPARCKKCGFEFRD-DKI---KKPSRCPKCKSEWIEEPRF 92 (97)
T ss_pred cChhhcccCccccc-ccc---CCcccCCcchhhcccCCce
Confidence 58999999976665 222 2346799999776555444
No 126
>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=32.89 E-value=21 Score=20.56 Aligned_cols=11 Identities=27% Similarity=0.815 Sum_probs=6.7
Q ss_pred eEeCCCCCCCC
Q 008566 81 WICPFCFQRNH 91 (561)
Q Consensus 81 w~C~~C~~~N~ 91 (561)
|.|++|+....
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 78899987654
No 127
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=32.81 E-value=30 Score=25.14 Aligned_cols=25 Identities=20% Similarity=0.465 Sum_probs=18.1
Q ss_pred cccCCCC--ceecCceEEEcCCceeEeCCCCCC
Q 008566 59 LRCRTCR--SILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 59 ~RC~~C~--ayiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
..|.+|+ .++- +.+.+|-|.-||..
T Consensus 20 ~~CPrCG~gvfmA------~H~dR~~CGkCgyT 46 (51)
T COG1998 20 RFCPRCGPGVFMA------DHKDRWACGKCGYT 46 (51)
T ss_pred ccCCCCCCcchhh------hcCceeEeccccce
Confidence 6799999 5554 23458999999953
No 128
>PHA00626 hypothetical protein
Probab=32.65 E-value=42 Score=25.05 Aligned_cols=30 Identities=17% Similarity=0.228 Sum_probs=18.6
Q ss_pred cCCCCc---eecCceEEEcCCceeEeCCCCCCCCC
Q 008566 61 CRTCRS---ILNPFSIVDFAAKIWICPFCFQRNHF 92 (561)
Q Consensus 61 C~~C~a---yiNp~~~~~~~~~~w~C~~C~~~N~~ 92 (561)
|.+|++ +-+..|+- ..+.++|.-||....-
T Consensus 3 CP~CGS~~Ivrcg~cr~--~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 3 CPKCGSGNIAKEKTMRG--WSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCceeeeeceecc--cCcceEcCCCCCeech
Confidence 777776 22333322 2567999999977653
No 129
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=32.47 E-value=25 Score=27.09 Aligned_cols=25 Identities=20% Similarity=0.549 Sum_probs=18.0
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p 93 (561)
.-|++|+...+ .. +|+.||..+..+
T Consensus 6 ~AC~~C~~i~~--------~~--~Cp~Cgs~~~S~ 30 (64)
T PRK06393 6 RACKKCKRLTP--------EK--TCPVHGDEKTTT 30 (64)
T ss_pred hhHhhCCcccC--------CC--cCCCCCCCcCCc
Confidence 35999998773 21 899999875444
No 130
>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=32.36 E-value=36 Score=22.29 Aligned_cols=29 Identities=17% Similarity=0.466 Sum_probs=16.7
Q ss_pred ccCCCCceecCc-eEEEcCCce-----eEeCCCCC
Q 008566 60 RCRTCRSILNPF-SIVDFAAKI-----WICPFCFQ 88 (561)
Q Consensus 60 RC~~C~ayiNp~-~~~~~~~~~-----w~C~~C~~ 88 (561)
||..|+..|-+- ..+...++. |.|.-|+.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~ 35 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGK 35 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCC
Confidence 688888887764 223333333 46666654
No 131
>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=32.24 E-value=35 Score=29.10 Aligned_cols=28 Identities=25% Similarity=0.578 Sum_probs=19.4
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N 90 (561)
.+.|.+|.+- |. . ++|..|+|+-|++.-
T Consensus 2 lp~CP~C~se---yt-Y-~dg~~~iCpeC~~EW 29 (109)
T TIGR00686 2 LPPCPKCNSE---YT-Y-HDGTQLICPSCLYEW 29 (109)
T ss_pred CCcCCcCCCc---ce-E-ecCCeeECccccccc
Confidence 4679888753 22 2 346689999999754
No 132
>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=31.97 E-value=32 Score=21.08 Aligned_cols=24 Identities=29% Similarity=0.618 Sum_probs=14.7
Q ss_pred cCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 61 C~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
|.+|+.-|-|--+ +..|.|+-||.
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 5667666655432 34688888873
No 133
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=31.87 E-value=39 Score=32.25 Aligned_cols=38 Identities=21% Similarity=0.495 Sum_probs=26.1
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCCCCCcc
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPH 95 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p~~ 95 (561)
-.-|++|.-=-+.+.--+..-..|+|.+|++.|..+.+
T Consensus 192 alIC~~C~hhngl~~~~ek~~~efiC~~Cn~~n~~~~~ 229 (251)
T COG5415 192 ALICPQCHHHNGLYRLAEKPIIEFICPHCNHKNDEVKE 229 (251)
T ss_pred hhccccccccccccccccccchheecccchhhcCcccc
Confidence 36688887655555433333447999999999987643
No 134
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=31.83 E-value=21 Score=21.81 Aligned_cols=14 Identities=36% Similarity=0.733 Sum_probs=11.8
Q ss_pred eeEeCCCCCCCCCC
Q 008566 80 IWICPFCFQRNHFP 93 (561)
Q Consensus 80 ~w~C~~C~~~N~~p 93 (561)
.|.|..|...|...
T Consensus 2 ~W~C~~C~~~N~~~ 15 (26)
T smart00547 2 DWECPACTFLNFAS 15 (26)
T ss_pred cccCCCCCCcChhh
Confidence 59999999999653
No 135
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=30.40 E-value=45 Score=25.85 Aligned_cols=31 Identities=16% Similarity=0.443 Sum_probs=22.2
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~ 91 (561)
-++|..|+- --+-|.-.....+|..||..=-
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 488999984 4444555567899999997543
No 136
>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=30.25 E-value=29 Score=27.93 Aligned_cols=30 Identities=23% Similarity=0.460 Sum_probs=17.0
Q ss_pred cccCCCCceecCc----eEEE-----cCCceeEeCCCCC
Q 008566 59 LRCRTCRSILNPF----SIVD-----FAAKIWICPFCFQ 88 (561)
Q Consensus 59 ~RC~~C~ayiNp~----~~~~-----~~~~~w~C~~C~~ 88 (561)
.-|++|++++=|- +++. .+.-.|+|..|++
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 5699999987665 3444 2346799999984
No 137
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=29.89 E-value=38 Score=23.54 Aligned_cols=27 Identities=33% Similarity=0.752 Sum_probs=14.7
Q ss_pred cCCCCceecCceEEEc--CCceeEeCCCCC
Q 008566 61 CRTCRSILNPFSIVDF--AAKIWICPFCFQ 88 (561)
Q Consensus 61 C~~C~ayiNp~~~~~~--~~~~w~C~~C~~ 88 (561)
|..|++ -.-|..+++ +...|+|+-|+.
T Consensus 6 CP~CGG-~DrFri~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 6 CPICGG-KDRFRIFDDKDGRGTWICRQCGG 34 (40)
T ss_dssp -TTTT--TTTEEEETT----S-EEETTTTB
T ss_pred CCCCcC-ccccccCcCcccCCCEECCCCCC
Confidence 777877 444544543 346899999943
No 138
>TIGR00006 S-adenosyl-methyltransferase MraW. Genetics paper in 1972 links mra cluster to peptidoglycan biosynthesis in E. coli. Seems to be common in proteobacteria.wn.
Probab=29.38 E-value=60 Score=33.33 Aligned_cols=28 Identities=32% Similarity=0.434 Sum_probs=24.6
Q ss_pred hHHHHHHHHHHHhhcCCCCceEEEEEEC
Q 008566 144 EMSFLKSALSQAIDLLPDNSLVGLITFG 171 (561)
Q Consensus 144 ~~~~l~~~l~~~l~~l~~~~~VglItf~ 171 (561)
|++.|..+|..+.+.|.++.|+++|||-
T Consensus 215 EL~~L~~~L~~~~~~L~~gGrl~VISfH 242 (305)
T TIGR00006 215 ELEELEEALQFAPNLLAPGGRLSIISFH 242 (305)
T ss_pred hHHHHHHHHHHHHHHhcCCCEEEEEecC
Confidence 4677899999999999999999999764
No 139
>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=29.16 E-value=17 Score=24.48 Aligned_cols=28 Identities=18% Similarity=0.304 Sum_probs=18.9
Q ss_pred cCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 61 C~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
|.+|++==.|..+-.+.|....||-|+.
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 7888888888888888787779998874
No 140
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=28.18 E-value=29 Score=35.59 Aligned_cols=35 Identities=20% Similarity=0.383 Sum_probs=25.7
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p 93 (561)
.-|++|+.==+-+-.-+..--.|.|.+|++.|+-.
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 67999988755554433444679999999999854
No 141
>KOG2487 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription; Replication, recombination and repair]
Probab=27.65 E-value=90 Score=31.22 Aligned_cols=45 Identities=20% Similarity=0.118 Sum_probs=35.9
Q ss_pred HHHHHHHHHhcCcEEEEEeecCCccChhcchhhhhccCcEEEEcCCCC
Q 008566 338 YDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFG 385 (561)
Q Consensus 338 Y~~la~~~~~~~isvdlf~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~ 385 (561)
|-+.--.+.+++|.||++.+..+ -..|.+.|..|||...+.+.-.
T Consensus 185 ~MNciFaAqKq~I~Idv~~l~~~---s~~LqQa~D~TGG~YL~v~~~~ 229 (314)
T KOG2487|consen 185 YMNCIFAAQKQNIPIDVVSLGGD---SGFLQQACDITGGDYLHVEKPD 229 (314)
T ss_pred HHHHHHHHHhcCceeEEEEecCC---chHHHHHHhhcCCeeEecCCcc
Confidence 44556677889999999999776 3468899999999988887644
No 142
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=27.54 E-value=24 Score=29.77 Aligned_cols=40 Identities=23% Similarity=0.404 Sum_probs=18.9
Q ss_pred cccCCCCceecCceEEE------cCCceeEeCCCCCCCCCCccCcC
Q 008566 59 LRCRTCRSILNPFSIVD------FAAKIWICPFCFQRNHFPPHYAS 98 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~------~~~~~w~C~~C~~~N~~p~~y~~ 98 (561)
-||.-|-+|+.|-..+- .+...-.|-+||....+.+.|++
T Consensus 28 GkCpiCDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~~g~sdAYYC 73 (106)
T PF03660_consen 28 GKCPICDSYVRPCTKVRICDECSFGSLQGRCIICGSGPGVSDAYYC 73 (106)
T ss_dssp T--TTT-------EE-EEEHHHHTSSTTSB-TTTSSSB--EE-EE-
T ss_pred CcccccCCccCCcceEEECCcCCCCCcCceEEEecCCCCcccceeh
Confidence 68999999999976553 35566789999977777778875
No 143
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=27.10 E-value=39 Score=25.83 Aligned_cols=25 Identities=32% Similarity=0.713 Sum_probs=17.6
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCCCCCCCc
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p~ 94 (561)
-|.+|+.... .. +|+.||...-..+
T Consensus 5 AC~~C~~i~~--------~~--~CP~Cgs~~~T~~ 29 (61)
T PRK08351 5 ACRHCHYITT--------ED--RCPVCGSRDLSDE 29 (61)
T ss_pred hhhhCCcccC--------CC--cCCCCcCCccccc
Confidence 4999998773 11 5999998764443
No 144
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=26.96 E-value=44 Score=28.41 Aligned_cols=35 Identities=20% Similarity=0.373 Sum_probs=26.2
Q ss_pred cccCCCCceecCc----eEEEcCCceeEeCCCCCCCCCC
Q 008566 59 LRCRTCRSILNPF----SIVDFAAKIWICPFCFQRNHFP 93 (561)
Q Consensus 59 ~RC~~C~ayiNp~----~~~~~~~~~w~C~~C~~~N~~p 93 (561)
--|++|.+++=|. +.+..+.-.|+|.-||..--.|
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p 95 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYP 95 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEec
Confidence 4599999986666 3444444789999999877665
No 145
>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=26.90 E-value=16 Score=31.65 Aligned_cols=27 Identities=30% Similarity=0.627 Sum_probs=17.6
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N 90 (561)
-.||..|+.-..+- ...+.|+.||..+
T Consensus 70 ~~~C~~Cg~~~~~~------~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 70 RARCRDCGHEFEPD------EFDFSCPRCGSPD 96 (113)
T ss_dssp EEEETTTS-EEECH------HCCHH-SSSSSS-
T ss_pred cEECCCCCCEEecC------CCCCCCcCCcCCC
Confidence 48999999876532 2347799999886
No 146
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=26.65 E-value=33 Score=35.28 Aligned_cols=29 Identities=24% Similarity=0.642 Sum_probs=21.5
Q ss_pred CCcccCCCCceecCceEEEcCCceeEeCCCCCCCCCC
Q 008566 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (561)
Q Consensus 57 ~~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p 93 (561)
..-||.+|+- ....-.|-|+-|+..-.+-
T Consensus 353 ~~YRC~~CGF--------~a~~l~W~CPsC~~W~Tik 381 (389)
T COG2956 353 PRYRCQNCGF--------TAHTLYWHCPSCRAWETIK 381 (389)
T ss_pred CCceecccCC--------cceeeeeeCCCcccccccC
Confidence 4689999983 2334579999999887653
No 147
>PF14353 CpXC: CpXC protein
Probab=26.45 E-value=62 Score=28.39 Aligned_cols=35 Identities=14% Similarity=0.475 Sum_probs=22.7
Q ss_pred cccCCCCceec--CceEEEcC-------------CceeEeCCCCCCCCCC
Q 008566 59 LRCRTCRSILN--PFSIVDFA-------------AKIWICPFCFQRNHFP 93 (561)
Q Consensus 59 ~RC~~C~ayiN--p~~~~~~~-------------~~~w~C~~C~~~N~~p 93 (561)
+.|.+|+.-.. -|..++.. =..++|+-||+...++
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 57889987633 22333321 1479999999988764
No 148
>PRK08402 replication factor A; Reviewed
Probab=25.86 E-value=52 Score=34.58 Aligned_cols=28 Identities=32% Similarity=0.477 Sum_probs=19.0
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
.++|..|+- -+..+.+++.|.|.-|+..
T Consensus 212 y~aCp~CnK----kv~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 212 YDACPECRR----KVDYDPATDTWICPEHGEV 239 (355)
T ss_pred EecCCCCCe----EEEEecCCCCEeCCCCCCc
Confidence 478988754 2222455678999999863
No 149
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=25.79 E-value=50 Score=20.99 Aligned_cols=27 Identities=22% Similarity=0.754 Sum_probs=15.1
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
.|.+|+.++-.... .+...+.|+-|..
T Consensus 3 ~C~rC~~~~~~~~~--~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGI--NGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEE--TTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEe--cCCCCeECcCCcC
Confidence 49999999654332 3445799999974
No 150
>PF12257 DUF3608: Protein of unknown function (DUF3608); InterPro: IPR022046 This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with PF00610 from PFAM.
Probab=25.76 E-value=1.9e+02 Score=29.35 Aligned_cols=66 Identities=14% Similarity=0.219 Sum_probs=44.5
Q ss_pred chhHHHHHHHHHHhcc-----CCCCCcEEEEEecCCCCCCCcccccCCCCCCccCCCCCCCCCCccchhhHHHHHHHHHH
Q 008566 270 CTGTALSIAASLLGAC-----VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQ 344 (561)
Q Consensus 270 c~G~Al~~A~~ll~~~-----~~~~ggkIi~F~~g~pt~G~G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~ 344 (561)
.+--|+..|+..+... ...+|-.|++-+.|. |-... ..+..+...++
T Consensus 204 NiLEaINlaln~~~~~~idRdl~rTG~~iivITpG~-----Gvf~V-----------------------d~~ll~~T~~r 255 (281)
T PF12257_consen 204 NILEAINLALNQFDKHYIDRDLRRTGQSIIVITPGT-----GVFEV-----------------------DYDLLRLTTQR 255 (281)
T ss_pred cHHHHHHHHhhhcccccccCcccccCceEEEEcCCC-----ceEEE-----------------------CHHHHHHHHHH
Confidence 3456677776666532 234788888877754 33322 23566778899
Q ss_pred HHhcCcEEEEEeecCCccC
Q 008566 345 LVHQGHVLDLFACALDQVG 363 (561)
Q Consensus 345 ~~~~~isvdlf~~s~~~~~ 363 (561)
+..+|+++|+.+.+.....
T Consensus 256 l~~~gi~~DlIcL~~~PLH 274 (281)
T PF12257_consen 256 LLDNGIGIDLICLSKPPLH 274 (281)
T ss_pred HHhcCccEEEEEcCCCCcc
Confidence 9999999999999866543
No 151
>PRK10220 hypothetical protein; Provisional
Probab=25.54 E-value=61 Score=27.71 Aligned_cols=29 Identities=24% Similarity=0.599 Sum_probs=19.6
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~ 91 (561)
.+.|.+|.+- |. . .++..|+|+-|++.-.
T Consensus 3 lP~CP~C~se---yt-Y-~d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 3 LPHCPKCNSE---YT-Y-EDNGMYICPECAHEWN 31 (111)
T ss_pred CCcCCCCCCc---ce-E-cCCCeEECCcccCcCC
Confidence 3668888753 11 2 3466899999997643
No 152
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.37 E-value=38 Score=34.66 Aligned_cols=24 Identities=21% Similarity=0.665 Sum_probs=19.2
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~ 91 (561)
..|..|+. ..++.|.|+-||...+
T Consensus 310 ~~C~~cg~---------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 310 KTCPCCGH---------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred ccccccCC---------ccceeEECCCCCCeeh
Confidence 56999998 3367899999998754
No 153
>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=25.17 E-value=26 Score=25.53 Aligned_cols=13 Identities=31% Similarity=0.943 Sum_probs=5.3
Q ss_pred cCCceeEeCCCCC
Q 008566 76 FAAKIWICPFCFQ 88 (561)
Q Consensus 76 ~~~~~w~C~~C~~ 88 (561)
...+.|.|++|++
T Consensus 37 ~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 37 QRTPKWKCPICNK 49 (50)
T ss_dssp HHS---B-TTT--
T ss_pred hccCCeECcCCcC
Confidence 3456799999986
No 154
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=25.09 E-value=29 Score=24.12 Aligned_cols=10 Identities=20% Similarity=0.913 Sum_probs=7.6
Q ss_pred cccCCCCcee
Q 008566 59 LRCRTCRSIL 68 (561)
Q Consensus 59 ~RC~~C~ayi 68 (561)
+||.+|++|=
T Consensus 2 ~kC~~CG~~G 11 (40)
T PF15288_consen 2 VKCKNCGAFG 11 (40)
T ss_pred cccccccccc
Confidence 5788888873
No 155
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=24.78 E-value=82 Score=32.23 Aligned_cols=29 Identities=34% Similarity=0.529 Sum_probs=24.9
Q ss_pred hHHHHHHHHHHHhhcCCCCceEEEEEECC
Q 008566 144 EMSFLKSALSQAIDLLPDNSLVGLITFGT 172 (561)
Q Consensus 144 ~~~~l~~~l~~~l~~l~~~~~VglItf~~ 172 (561)
|++.|...|.++.+.|.++.++++|||-+
T Consensus 211 El~~L~~~L~~~~~~L~~gGrl~visfHS 239 (296)
T PRK00050 211 ELEELERALEAALDLLKPGGRLAVISFHS 239 (296)
T ss_pred hHHHHHHHHHHHHHHhcCCCEEEEEecCc
Confidence 46678899999999999999999997753
No 156
>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=23.97 E-value=1.8e+02 Score=25.50 Aligned_cols=34 Identities=24% Similarity=0.207 Sum_probs=24.3
Q ss_pred hhhHHHHHHHHHHHhhcCCC---CceEEEEEECCeEE
Q 008566 142 EEEMSFLKSALSQAIDLLPD---NSLVGLITFGTLVQ 175 (561)
Q Consensus 142 ~~~~~~l~~~l~~~l~~l~~---~~~VglItf~~~V~ 175 (561)
.+--+.++++|+.-+..-|. +++|.+++|++.|-
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 34445688888887765553 68999999998764
No 157
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=23.91 E-value=38 Score=38.71 Aligned_cols=24 Identities=21% Similarity=0.356 Sum_probs=18.5
Q ss_pred CCcccCCCCceecCceEEEcCCceeEeCCCCCC
Q 008566 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 57 ~~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
..-+|..|+ |+ .|..|.|+-||..
T Consensus 625 ~~~~C~~CG-~~--------~g~~~~CP~CG~~ 648 (656)
T PRK08270 625 TFSICPKHG-YL--------SGEHEFCPKCGEE 648 (656)
T ss_pred CCcccCCCC-Cc--------CCCCCCCcCCcCc
Confidence 468899999 44 3567999999944
No 158
>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=23.78 E-value=43 Score=22.25 Aligned_cols=12 Identities=33% Similarity=1.204 Sum_probs=9.8
Q ss_pred eeEeCCCCCCCC
Q 008566 80 IWICPFCFQRNH 91 (561)
Q Consensus 80 ~w~C~~C~~~N~ 91 (561)
.|+|..||..-.
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 699999997743
No 159
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=23.57 E-value=84 Score=25.78 Aligned_cols=33 Identities=21% Similarity=0.238 Sum_probs=23.6
Q ss_pred CCCcccCCCCceecCceEEEcCCceeEeCCCCCCCCC
Q 008566 56 YAPLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (561)
Q Consensus 56 ~~~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~ 92 (561)
.+...|..|+.= -++... .+.|+|.-|+..-.-
T Consensus 33 ~~~~~Cp~C~~~---~VkR~a-~GIW~C~kCg~~fAG 65 (89)
T COG1997 33 RAKHVCPFCGRT---TVKRIA-TGIWKCRKCGAKFAG 65 (89)
T ss_pred hcCCcCCCCCCc---ceeeec-cCeEEcCCCCCeecc
Confidence 367889999864 344433 459999999987654
No 160
>PRK00420 hypothetical protein; Validated
Probab=23.46 E-value=59 Score=28.10 Aligned_cols=30 Identities=17% Similarity=0.307 Sum_probs=22.0
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p 93 (561)
-.|..|+ .|+.++. ++.-.|+.||..-.+.
T Consensus 24 ~~CP~Cg---~pLf~lk--~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPVCG---LPLFELK--DGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCCCC---CcceecC--CCceECCCCCCeeeec
Confidence 4699999 5777663 3479999999866553
No 161
>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=22.74 E-value=7e+02 Score=24.06 Aligned_cols=113 Identities=23% Similarity=0.336 Sum_probs=61.8
Q ss_pred HHHHHHHccCCCCCCCCCCCCCcchhHHHHHHHHHHhccCCCCCcEEEEEecC--CCCCCCcccccCCCCCCccCCCCCC
Q 008566 247 LNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGG--PSTEGPAAIVSKNLSEPIRSHKDLD 324 (561)
Q Consensus 247 i~~ll~~L~~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~~~~ggkIi~F~~g--~pt~G~G~l~~~~~~~~~r~~~~~~ 324 (561)
+..+-+.|...+ -.....++.|.||..|..++.. .+..+.|-++=.+| +.|.|+.-+
T Consensus 77 a~a~A~~l~~~~----r~~~~~Taig~Al~~a~~ll~~-~~~~~~RrVIDvSGDG~~N~G~~p~---------------- 135 (205)
T PF06707_consen 77 AEAFAARLRAAP----RRFGGRTAIGSALDFAAALLAQ-NPFECWRRVIDVSGDGPNNQGPRPV---------------- 135 (205)
T ss_pred HHHHHHHHHhCC----CCCCCCchHHHHHHHHHHHHHh-CCCCCceEEEEECCCCCCCCCCCcc----------------
Confidence 444555554431 1222338999999999999984 22336666666655 555554111
Q ss_pred CCCCccchhhHHHHHHHHHHHHhcCcEEEEEeecCCcc----Chhcch--hhhhccCcEEEEcCCCCccchHHHHHHH
Q 008566 325 KDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV----GVAELK--VAVEKTGGLVVLSDSFGHAVFKDSVRRV 396 (561)
Q Consensus 325 ~~~~~~~~~~~~fY~~la~~~~~~~isvdlf~~s~~~~----~l~~l~--~l~~~TGG~v~~y~~f~~~~~~~~l~~~ 396 (561)
...-..+...||.||=+.+....- +|...- .+..-.|.-+....+|. .|.+.+.+-
T Consensus 136 --------------~~ard~~~~~GitINgL~I~~~~~~~~~~L~~yy~~~VIgGpgAFV~~a~~~~--df~~AirrK 197 (205)
T PF06707_consen 136 --------------TSARDAAVAAGITINGLAILDDDPFGGADLDAYYRRCVIGGPGAFVETARGFE--DFAEAIRRK 197 (205)
T ss_pred --------------HHHHHHHHHCCeEEeeeEecCCCCCccccHHHHHhhhcccCCCceEEEcCCHH--HHHHHHHHH
Confidence 012234566899999998876554 454432 23333333344443443 355555543
No 162
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=22.63 E-value=1.1e+02 Score=20.52 Aligned_cols=31 Identities=23% Similarity=0.492 Sum_probs=20.1
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~ 92 (561)
..|..|+..+=| +-+..+.. .|.-|+..-++
T Consensus 2 ~FCp~C~nlL~p--~~~~~~~~-~C~~C~Y~~~~ 32 (35)
T PF02150_consen 2 RFCPECGNLLYP--KEDKEKRV-ACRTCGYEEPI 32 (35)
T ss_dssp -BETTTTSBEEE--EEETTTTE-EESSSS-EEE-
T ss_pred eeCCCCCccceE--cCCCccCc-CCCCCCCccCC
Confidence 369999998854 44555555 89999976544
No 163
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.31 E-value=45 Score=37.75 Aligned_cols=26 Identities=23% Similarity=0.447 Sum_probs=19.8
Q ss_pred CCcccCCCCceecCceEEEcCCceeEeCCCCCCC
Q 008566 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 57 ~~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N 90 (561)
.+-+|..|+. + ..+..|.|+-||..+
T Consensus 565 ~~~iC~~CG~-~-------~~g~~~~CP~CGs~~ 590 (623)
T PRK08271 565 KITICNDCHH-I-------DKRTGKRCPICGSEN 590 (623)
T ss_pred CCccCCCCCC-c-------CCCCCcCCcCCCCcc
Confidence 5689999994 3 235579999999765
No 164
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=22.09 E-value=46 Score=30.76 Aligned_cols=34 Identities=21% Similarity=0.649 Sum_probs=20.5
Q ss_pred cccCCCCc------eecCceEEEcC------CceeEeCCCCCCCCC
Q 008566 59 LRCRTCRS------ILNPFSIVDFA------AKIWICPFCFQRNHF 92 (561)
Q Consensus 59 ~RC~~C~a------yiNp~~~~~~~------~~~w~C~~C~~~N~~ 92 (561)
+.|.+|+- |||++-+.+.. +-.|+|-+|++.+.+
T Consensus 31 vkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~si 76 (161)
T PF05907_consen 31 VKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRESSI 76 (161)
T ss_dssp EEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEE
T ss_pred EEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCccEE
Confidence 78999995 68888777643 357999999998875
No 165
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=21.85 E-value=34 Score=27.75 Aligned_cols=15 Identities=33% Similarity=0.961 Sum_probs=6.6
Q ss_pred ceeEeCCCCCCCCCC
Q 008566 79 KIWICPFCFQRNHFP 93 (561)
Q Consensus 79 ~~w~C~~C~~~N~~p 93 (561)
+.|.|+||++.+.+.
T Consensus 21 ~~F~CPfC~~~~sV~ 35 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVS 35 (81)
T ss_dssp S----TTT--SS-EE
T ss_pred ceEcCCcCCCCCeEE
Confidence 579999999999874
No 166
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=21.60 E-value=64 Score=29.65 Aligned_cols=29 Identities=17% Similarity=0.352 Sum_probs=19.5
Q ss_pred cccCCCCceecCceEEEcCC-ceeEeCCCCCCCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAA-KIWICPFCFQRNHFP 93 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~-~~w~C~~C~~~N~~p 93 (561)
..|..|+.=+ ...+ +.|.|.-|+....-|
T Consensus 35 ~aC~~C~kkv------~~~~~~~~~C~~C~~~~~~~ 64 (166)
T cd04476 35 PACPGCNKKV------VEEGNGTYRCEKCNKSVPNP 64 (166)
T ss_pred ccccccCccc------EeCCCCcEECCCCCCcCCCc
Confidence 5688886533 2333 689999999886443
No 167
>PRK12366 replication factor A; Reviewed
Probab=21.48 E-value=61 Score=36.98 Aligned_cols=26 Identities=27% Similarity=0.631 Sum_probs=19.5
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~ 89 (561)
..+|..|+--+ ..+.+.|.|.-|+..
T Consensus 532 y~aCp~CnkKv------~~~~g~~~C~~c~~~ 557 (637)
T PRK12366 532 LYLCPNCRKRV------EEVDGEYICEFCGEV 557 (637)
T ss_pred EecccccCeEe------EcCCCcEECCCCCCC
Confidence 58999995543 234568999999977
No 168
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=21.37 E-value=1.6e+02 Score=26.42 Aligned_cols=62 Identities=23% Similarity=0.345 Sum_probs=36.5
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCCCCCCCCccCcCCCCCCCCcccCCCCc-----ceEEeCCCCCCCCCCCcEEE
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHYASITDDNLPAELFPQYT-----TIEYEPPGPGEKSSVPPVFM 133 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p~~y~~~~~~~~~pEl~~~~~-----tvey~~~~~~~~~~~~p~~v 133 (561)
.||++|+.+.=|= +-.|+-|+....+. + -|+. ..+ |+.|..+.. ....+|.++
T Consensus 30 ~kC~~CG~v~~PP--------r~~Cp~C~~~~~~E--~---------vels-~~G~V~t~Tv~~~~~~~--~~~~~P~vi 87 (140)
T COG1545 30 TKCKKCGRVYFPP--------RAYCPKCGSETELE--W---------VELS-GEGKVETYTVVYVKPPG--FSLEEPYVI 87 (140)
T ss_pred EEcCCCCeEEcCC--------cccCCCCCCCCceE--E---------EEeC-CCeEEEEEEEEeeCCCC--cccCCCEEE
Confidence 8999999886553 35789999886332 1 1332 233 334443321 112378888
Q ss_pred EEEEcccch
Q 008566 134 FVVDTCIIE 142 (561)
Q Consensus 134 FvID~s~~~ 142 (561)
.+|++-...
T Consensus 88 aiV~l~~~~ 96 (140)
T COG1545 88 AIVELEEGG 96 (140)
T ss_pred EEEEeCCCC
Confidence 888876533
No 169
>PRK07218 replication factor A; Provisional
Probab=21.33 E-value=44 Score=35.97 Aligned_cols=23 Identities=17% Similarity=0.273 Sum_probs=18.7
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N 90 (561)
+-||+.|+--+. +|+|+.||...
T Consensus 297 i~rCP~C~r~v~----------~~~C~~hG~ve 319 (423)
T PRK07218 297 IERCPECGRVIQ----------KGQCRSHGAVE 319 (423)
T ss_pred eecCcCcccccc----------CCcCCCCCCcC
Confidence 689999988772 39999999663
No 170
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=20.98 E-value=82 Score=23.89 Aligned_cols=27 Identities=30% Similarity=0.655 Sum_probs=17.7
Q ss_pred CcccCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 58 ~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
+.+|..|+.-|-|-- ..-.|.|+-||.
T Consensus 9 ~~~CtSCg~~i~p~e----~~v~F~CPnCGe 35 (61)
T COG2888 9 PPVCTSCGREIAPGE----TAVKFPCPNCGE 35 (61)
T ss_pred CceeccCCCEeccCC----ceeEeeCCCCCc
Confidence 677888888776543 234577777773
No 171
>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=20.75 E-value=76 Score=22.44 Aligned_cols=22 Identities=14% Similarity=0.356 Sum_probs=14.5
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCF 87 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~ 87 (561)
+.|..|+. .|.. |.+|+|.-|.
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 35777773 3333 6689999885
No 172
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=20.74 E-value=47 Score=25.42 Aligned_cols=26 Identities=23% Similarity=0.653 Sum_probs=18.4
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCCCCCCC
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~p 93 (561)
-|++|+..++. ..=+|+.||...-..
T Consensus 6 AC~~Ck~l~~~--------d~e~CP~Cgs~~~te 31 (64)
T COG2093 6 ACKNCKRLTPE--------DTEICPVCGSTDLTE 31 (64)
T ss_pred HHhhccccCCC--------CCccCCCCCCcccch
Confidence 48899887762 346899999765443
No 173
>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=20.74 E-value=40 Score=22.20 Aligned_cols=10 Identities=40% Similarity=1.185 Sum_probs=5.5
Q ss_pred CCcccCCCCc
Q 008566 57 APLRCRTCRS 66 (561)
Q Consensus 57 ~~~RC~~C~a 66 (561)
+++||..|+.
T Consensus 16 ~~irC~~CG~ 25 (32)
T PF03604_consen 16 DPIRCPECGH 25 (32)
T ss_dssp STSSBSSSS-
T ss_pred CcEECCcCCC
Confidence 4566666654
No 174
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=20.61 E-value=46 Score=28.15 Aligned_cols=12 Identities=33% Similarity=0.741 Sum_probs=9.2
Q ss_pred ceeEeCCCCCCC
Q 008566 79 KIWICPFCFQRN 90 (561)
Q Consensus 79 ~~w~C~~C~~~N 90 (561)
++|+|-+||..=
T Consensus 1 ~kWkC~iCg~~I 12 (101)
T PF09943_consen 1 KKWKCYICGKPI 12 (101)
T ss_pred CceEEEecCCee
Confidence 369999999543
No 175
>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=20.47 E-value=65 Score=24.04 Aligned_cols=26 Identities=23% Similarity=0.529 Sum_probs=19.1
Q ss_pred CCcccCCCCceecCceEEEcCCceeEeCCCCCCCC
Q 008566 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (561)
Q Consensus 57 ~~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~ 91 (561)
.+..|..|+.+.=| ...|..||+.+.
T Consensus 25 ~l~~C~~cG~~~~~---------H~vc~~cG~Y~g 50 (55)
T TIGR01031 25 TLVVCPNCGEFKLP---------HRVCPSCGYYKG 50 (55)
T ss_pred cceECCCCCCcccC---------eeECCccCeECC
Confidence 45889999997543 467888886653
No 176
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.44 E-value=82 Score=31.77 Aligned_cols=27 Identities=22% Similarity=0.637 Sum_probs=18.8
Q ss_pred ccCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 60 RC~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
-|.+|++-|=- ....+...|.|+-|+.
T Consensus 246 pCprCG~~I~~--~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 246 PCLNCKTPIRR--VVVAGRSSHYCPHCQK 272 (272)
T ss_pred cCCCCCCeeEE--EEECCCccEECcCCcC
Confidence 49999987621 2224457899999974
No 177
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=20.40 E-value=59 Score=19.28 Aligned_cols=11 Identities=18% Similarity=0.640 Sum_probs=7.8
Q ss_pred eEeCCCCCCCC
Q 008566 81 WICPFCFQRNH 91 (561)
Q Consensus 81 w~C~~C~~~N~ 91 (561)
|.|.+|+..-.
T Consensus 1 ~~C~~C~~~f~ 11 (25)
T PF12874_consen 1 FYCDICNKSFS 11 (25)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCCcC
Confidence 78888876543
No 178
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=20.37 E-value=50 Score=22.31 Aligned_cols=26 Identities=19% Similarity=0.231 Sum_probs=11.1
Q ss_pred cCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 61 C~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
|..|++.-|.+.. +.....+|..||.
T Consensus 4 C~~Cg~~Yh~~~~--pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 4 CPKCGRIYHIEFN--PPKVEGVCDNCGG 29 (36)
T ss_dssp ETTTTEEEETTTB----SSTTBCTTTTE
T ss_pred cCCCCCccccccC--CCCCCCccCCCCC
Confidence 5555555554332 1223345555553
No 179
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.28 E-value=76 Score=26.81 Aligned_cols=35 Identities=17% Similarity=0.324 Sum_probs=25.8
Q ss_pred CCcccCCCCceecCceEEEcCCceeEeCCCCCCCCC
Q 008566 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (561)
Q Consensus 57 ~~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~ 92 (561)
..+.|.+|++. ..-+.++.+..+-.|.-||..+.-
T Consensus 20 t~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKV-SISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCe-EeeeecCCCcceEECCCCCCccCE
Confidence 35889999963 444556666678999999988753
No 180
>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=20.10 E-value=53 Score=38.55 Aligned_cols=26 Identities=23% Similarity=0.413 Sum_probs=20.8
Q ss_pred CCcccCCCCceecCceEEEcCCceeEeCCCCCCCCC
Q 008566 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (561)
Q Consensus 57 ~~~RC~~C~ayiNp~~~~~~~~~~w~C~~C~~~N~~ 92 (561)
..-+|.+|+.|- -.++|+.||..+..
T Consensus 624 ~~RKCPkCG~yT----------lk~rCP~CG~~Te~ 649 (1095)
T TIGR00354 624 AIRKCPQCGKES----------FWLKCPVCGELTEQ 649 (1095)
T ss_pred EEEECCCCCccc----------ccccCCCCCCcccc
Confidence 457999999882 35999999998754
No 181
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=20.02 E-value=75 Score=22.32 Aligned_cols=21 Identities=19% Similarity=0.613 Sum_probs=15.2
Q ss_pred cccCCCCceecCceEEEcCCceeEeCCCC
Q 008566 59 LRCRTCRSILNPFSIVDFAAKIWICPFCF 87 (561)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~~~~w~C~~C~ 87 (561)
+.|..|+..| .|.+|+|..|.
T Consensus 1 v~Cd~C~~~i--------~G~ry~C~~C~ 21 (43)
T cd02340 1 VICDGCQGPI--------VGVRYKCLVCP 21 (43)
T ss_pred CCCCCCCCcC--------cCCeEECCCCC
Confidence 4688888722 25689999997
No 182
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.01 E-value=75 Score=21.87 Aligned_cols=26 Identities=31% Similarity=0.695 Sum_probs=16.1
Q ss_pred cCCCCceecCceEEEcCCceeEeCCCCC
Q 008566 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (561)
Q Consensus 61 C~~C~ayiNp~~~~~~~~~~w~C~~C~~ 88 (561)
|.+|+.-+.+.-. .+-..+.|.-|+-
T Consensus 2 CP~C~~~l~~~~~--~~~~id~C~~C~G 27 (41)
T PF13453_consen 2 CPRCGTELEPVRL--GDVEIDVCPSCGG 27 (41)
T ss_pred cCCCCcccceEEE--CCEEEEECCCCCe
Confidence 7777776665543 2235677777764
Done!