Query 007267
Match_columns 610
No_of_seqs 197 out of 843
Neff 8.1
Searched_HMMs 46136
Date Thu Mar 28 21:15:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007267.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007267hhsearch_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 6E-113 1E-117 970.7 51.2 583 2-607 11-760 (761)
2 KOG1984 Vesicle coat complex C 100.0 2E-111 5E-116 903.6 44.1 568 2-610 289-1007(1007)
3 KOG1985 Vesicle coat complex C 100.0 4E-109 8E-114 885.6 41.9 560 1-607 171-887 (887)
4 KOG1986 Vesicle coat complex C 100.0 1E-106 2E-111 854.4 40.8 574 2-606 11-742 (745)
5 PTZ00395 Sec24-related protein 100.0 1.5E-97 3E-102 829.5 46.9 565 2-609 654-1557(1560)
6 COG5047 SEC23 Vesicle coat com 100.0 1.1E-98 2E-103 773.6 29.5 576 2-606 11-752 (755)
7 COG5028 Vesicle coat complex C 100.0 1.1E-96 2E-101 783.4 41.0 552 2-607 152-861 (861)
8 cd01478 Sec23-like Sec23-like: 100.0 4.3E-48 9.2E-53 389.5 22.5 241 119-372 1-267 (267)
9 cd01479 Sec24-like Sec24-like: 100.0 6.2E-46 1.4E-50 370.9 21.9 229 119-377 1-243 (244)
10 cd01468 trunk_domain trunk dom 100.0 5E-45 1.1E-49 364.7 22.0 228 119-372 1-239 (239)
11 PF04811 Sec23_trunk: Sec23/Se 100.0 4.7E-43 1E-47 351.8 17.8 230 119-374 1-243 (243)
12 PF08033 Sec23_BS: Sec23/Sec24 99.6 1.4E-15 3E-20 129.9 8.7 78 379-460 1-87 (96)
13 PF04810 zf-Sec23_Sec24: Sec23 99.5 4.3E-15 9.3E-20 104.2 2.0 38 49-86 1-40 (40)
14 PRK13685 hypothetical protein; 98.9 5.5E-08 1.2E-12 102.0 18.1 180 122-381 89-293 (326)
15 cd01453 vWA_transcription_fact 98.9 3.6E-08 7.7E-13 94.6 14.4 162 123-372 5-177 (183)
16 cd01451 vWA_Magnesium_chelatas 98.8 1.1E-07 2.3E-12 90.9 16.2 166 124-367 3-173 (178)
17 cd01456 vWA_ywmD_type VWA ywmD 98.8 8.9E-08 1.9E-12 93.7 15.5 169 119-355 18-196 (206)
18 cd01466 vWA_C3HC4_type VWA C3H 98.8 1.4E-07 3E-12 88.0 15.8 149 124-358 3-154 (155)
19 cd01465 vWA_subgroup VWA subgr 98.8 3.2E-07 7E-12 86.5 18.4 159 124-361 3-163 (170)
20 cd01463 vWA_VGCC_like VWA Volt 98.8 6.3E-07 1.4E-11 86.5 18.5 168 121-361 13-189 (190)
21 cd01467 vWA_BatA_type VWA BatA 98.6 1.6E-06 3.5E-11 82.6 17.7 155 123-360 4-176 (180)
22 cd01452 VWA_26S_proteasome_sub 98.6 1.3E-06 2.7E-11 83.5 15.9 145 123-351 5-161 (187)
23 cd01472 vWA_collagen von Wille 98.6 1.9E-06 4.1E-11 81.0 16.8 152 124-359 3-162 (164)
24 TIGR00868 hCaCC calcium-activa 98.6 3.2E-06 6.9E-11 97.2 20.2 155 121-360 304-462 (863)
25 PF13768 VWA_3: von Willebrand 98.5 2.4E-06 5.3E-11 79.4 14.0 150 124-356 3-154 (155)
26 cd01480 vWA_collagen_alpha_1-V 98.5 3.2E-06 7E-11 81.3 15.2 159 123-362 4-173 (186)
27 TIGR03436 acidobact_VWFA VWFA- 98.4 6.8E-06 1.5E-10 85.1 16.9 171 120-358 52-238 (296)
28 cd01470 vWA_complement_factors 98.4 1.3E-05 2.8E-10 77.9 17.5 169 124-361 3-190 (198)
29 cd01461 vWA_interalpha_trypsin 98.4 1.3E-05 2.8E-10 75.5 16.6 158 122-361 3-162 (171)
30 PF13519 VWA_2: von Willebrand 98.4 1.7E-06 3.7E-11 81.1 10.0 150 124-358 2-158 (172)
31 cd01474 vWA_ATR ATR (Anthrax T 98.3 3.6E-05 7.8E-10 73.9 16.4 158 123-362 6-168 (185)
32 cd01471 vWA_micronemal_protein 98.3 3E-05 6.5E-10 74.4 15.8 150 124-350 3-160 (186)
33 cd01469 vWA_integrins_alpha_su 98.2 8.7E-05 1.9E-09 70.7 17.2 159 124-362 3-172 (177)
34 cd01482 vWA_collagen_alphaI-XI 98.2 0.00011 2.5E-09 69.0 17.2 151 124-358 3-161 (164)
35 cd01475 vWA_Matrilin VWA_Matri 98.1 9.6E-05 2.1E-09 73.3 16.3 156 123-362 4-170 (224)
36 cd01450 vWFA_subfamily_ECM Von 98.1 0.00012 2.5E-09 67.9 14.7 149 124-353 3-157 (161)
37 TIGR03788 marine_srt_targ mari 98.0 0.00026 5.6E-09 80.5 19.7 183 121-387 271-458 (596)
38 cd01477 vWA_F09G8-8_type VWA F 98.0 0.00019 4.1E-09 69.4 15.9 154 123-354 21-188 (193)
39 PRK13406 bchD magnesium chelat 98.0 0.00025 5.5E-09 79.5 18.5 175 121-370 401-579 (584)
40 TIGR02031 BchD-ChlD magnesium 97.9 0.0004 8.7E-09 78.5 18.1 177 121-364 407-586 (589)
41 smart00327 VWA von Willebrand 97.9 0.00086 1.9E-08 62.9 17.2 155 123-357 3-164 (177)
42 TIGR02442 Cob-chelat-sub cobal 97.9 0.00028 6.1E-09 80.6 15.7 160 121-358 465-632 (633)
43 cd01481 vWA_collagen_alpha3-VI 97.9 0.0013 2.7E-08 62.0 17.6 154 124-361 3-165 (165)
44 PTZ00441 sporozoite surface pr 97.8 0.00076 1.6E-08 74.1 17.7 164 122-362 43-217 (576)
45 cd01476 VWA_integrin_invertebr 97.8 0.00091 2E-08 62.5 16.0 108 124-282 3-117 (163)
46 PF00092 VWA: von Willebrand f 97.8 0.00033 7.2E-09 66.1 13.1 158 124-362 2-169 (178)
47 COG1240 ChlD Mg-chelatase subu 97.8 0.00061 1.3E-08 67.1 14.8 169 122-367 79-253 (261)
48 cd00198 vWFA Von Willebrand fa 97.7 0.0013 2.7E-08 60.2 15.5 149 123-351 2-155 (161)
49 cd01464 vWA_subfamily VWA subf 97.7 0.00031 6.8E-09 66.8 10.5 45 124-168 6-58 (176)
50 PF00626 Gelsolin: Gelsolin re 97.7 6.5E-05 1.4E-09 60.8 4.8 60 506-572 14-75 (76)
51 cd01454 vWA_norD_type norD typ 97.4 0.0062 1.4E-07 57.6 16.1 146 123-338 2-154 (174)
52 PF04056 Ssl1: Ssl1-like; Int 97.4 0.002 4.4E-08 61.6 11.5 164 127-375 1-174 (193)
53 cd01473 vWA_CTRP CTRP for CS 97.3 0.013 2.7E-07 56.7 16.2 151 124-350 3-161 (192)
54 cd01458 vWA_ku Ku70/Ku80 N-ter 97.2 0.0068 1.5E-07 59.8 14.1 158 123-337 3-173 (218)
55 COG4245 TerY Uncharacterized p 97.2 0.0029 6.2E-08 59.1 10.4 49 121-170 4-60 (207)
56 cd01462 VWA_YIEM_type VWA YIEM 97.1 0.014 2.9E-07 53.9 13.7 130 124-337 3-135 (152)
57 smart00262 GEL Gelsolin homolo 96.5 0.011 2.4E-07 49.4 7.8 62 506-573 22-84 (90)
58 KOG2884 26S proteasome regulat 96.0 0.23 5E-06 47.6 14.2 155 123-360 5-175 (259)
59 cd01460 vWA_midasin VWA_Midasi 95.4 0.64 1.4E-05 47.1 15.8 46 120-167 59-111 (266)
60 cd01455 vWA_F11C1-5a_type Von 94.9 1 2.2E-05 43.2 14.6 98 213-360 75-174 (191)
61 cd01457 vWA_ORF176_type VWA OR 94.4 0.83 1.8E-05 44.2 13.1 43 123-165 4-57 (199)
62 smart00187 INB Integrin beta s 93.1 15 0.00032 39.6 22.5 272 124-430 102-390 (423)
63 COG5148 RPN10 26S proteasome r 91.9 5.6 0.00012 37.5 13.4 131 123-335 5-145 (243)
64 KOG0443 Actin regulatory prote 89.1 0.8 1.7E-05 52.0 6.4 64 507-576 645-712 (827)
65 PF03850 Tfb4: Transcription f 88.9 30 0.00064 35.4 18.2 98 246-373 116-218 (276)
66 TIGR00578 ku70 ATP-dependent D 88.5 11 0.00024 42.9 15.2 73 246-342 117-190 (584)
67 KOG2353 L-type voltage-depende 87.8 11 0.00025 45.4 15.2 203 100-381 203-419 (1104)
68 COG2425 Uncharacterized protei 86.0 13 0.00029 40.2 13.2 149 121-359 273-424 (437)
69 PF00362 Integrin_beta: Integr 83.2 37 0.00079 37.0 15.3 265 124-431 105-394 (426)
70 KOG2807 RNA polymerase II tran 82.6 19 0.00041 37.0 11.7 98 244-377 141-238 (378)
71 KOG0443 Actin regulatory prote 82.2 3 6.6E-05 47.5 6.6 72 507-583 282-358 (827)
72 TIGR00627 tfb4 transcription f 80.8 14 0.00031 37.7 10.4 100 245-374 118-221 (279)
73 PF10058 DUF2296: Predicted in 77.2 1.3 2.7E-05 33.3 1.2 32 49-80 21-54 (54)
74 PF06707 DUF1194: Protein of u 77.2 74 0.0016 30.9 18.4 104 244-378 93-202 (205)
75 PRK00398 rpoP DNA-directed RNA 77.2 1.4 3.1E-05 31.7 1.4 27 51-81 4-32 (46)
76 PRK10997 yieM hypothetical pro 77.1 21 0.00045 39.5 10.9 49 123-171 325-376 (487)
77 PF09967 DUF2201: VWA-like dom 76.9 6.4 0.00014 35.1 5.9 42 125-168 2-45 (126)
78 TIGR01053 LSD1 zinc finger dom 68.5 3.6 7.7E-05 27.1 1.6 30 51-82 2-31 (31)
79 PF09082 DUF1922: Domain of un 67.1 1.3 2.9E-05 34.5 -0.8 31 50-84 3-33 (68)
80 PF10122 Mu-like_Com: Mu-like 66.1 1.5 3.3E-05 32.1 -0.5 35 50-84 4-38 (51)
81 cd00730 rubredoxin Rubredoxin; 60.7 3.9 8.5E-05 30.1 0.8 28 52-79 3-43 (50)
82 cd00350 rubredoxin_like Rubred 60.1 5.7 0.00012 26.4 1.4 23 52-78 3-25 (33)
83 PF00301 Rubredoxin: Rubredoxi 59.7 3.8 8.3E-05 29.8 0.5 28 52-79 3-43 (47)
84 PF11781 RRN7: RNA polymerase 57.9 7.1 0.00015 26.6 1.6 27 50-79 8-34 (36)
85 smart00661 RPOL9 RNA polymeras 56.9 6.2 0.00013 28.9 1.3 31 52-83 2-33 (52)
86 PF03731 Ku_N: Ku70/Ku80 N-ter 55.4 22 0.00048 34.8 5.4 67 245-334 104-172 (224)
87 KOG0444 Cytoskeletal regulator 54.3 24 0.00053 39.8 5.7 68 508-581 647-716 (1255)
88 TIGR00100 hypA hydrogenase nic 52.5 6.5 0.00014 34.5 0.9 26 51-80 71-96 (115)
89 TIGR00686 phnA alkylphosphonat 52.3 11 0.00025 32.2 2.3 28 50-80 2-29 (109)
90 PF12760 Zn_Tnp_IS1595: Transp 52.1 12 0.00027 26.8 2.2 27 50-78 18-45 (46)
91 PRK12380 hydrogenase nickel in 51.7 6.7 0.00014 34.3 0.9 27 51-81 71-97 (113)
92 PF05762 VWA_CoxE: VWA domain 50.5 35 0.00076 33.6 5.9 33 244-279 128-160 (222)
93 PF13240 zinc_ribbon_2: zinc-r 50.3 7.1 0.00015 23.7 0.5 21 52-78 1-21 (23)
94 COG1198 PriA Primosomal protei 49.8 39 0.00085 39.3 6.8 114 51-174 436-573 (730)
95 PF02318 FYVE_2: FYVE-type zin 48.9 9.5 0.00021 33.6 1.4 31 50-80 71-104 (118)
96 COG0275 Predicted S-adenosylme 47.3 26 0.00056 36.1 4.3 31 134-164 217-247 (314)
97 PF02905 EBV-NA1: Epstein Barr 44.9 25 0.00055 30.8 3.3 33 135-167 110-145 (146)
98 PRK03681 hypA hydrogenase nick 43.6 9.3 0.0002 33.5 0.5 26 51-80 71-97 (114)
99 COG1096 Predicted RNA-binding 43.6 14 0.00029 35.1 1.6 25 51-79 150-174 (188)
100 PRK00564 hypA hydrogenase nick 43.6 9.1 0.0002 33.7 0.4 28 50-81 71-99 (117)
101 cd01121 Sms Sms (bacterial rad 43.4 11 0.00024 40.3 1.2 28 52-85 2-29 (372)
102 PF08792 A2L_zn_ribbon: A2L zi 43.4 20 0.00043 23.9 1.9 30 49-80 2-31 (33)
103 PF09723 Zn-ribbon_8: Zinc rib 43.0 12 0.00026 26.3 0.9 29 51-79 6-35 (42)
104 TIGR02605 CxxC_CxxC_SSSS putat 42.6 13 0.00028 27.3 1.0 30 51-80 6-36 (52)
105 PF08274 PhnA_Zn_Ribbon: PhnA 42.4 17 0.00037 23.7 1.4 26 50-78 2-27 (30)
106 PRK00432 30S ribosomal protein 42.1 15 0.00033 27.0 1.4 26 51-79 21-46 (50)
107 PF11265 Med25_VWA: Mediator c 41.6 3.6E+02 0.0079 26.7 15.1 88 247-357 111-204 (226)
108 PRK03954 ribonuclease P protei 41.4 14 0.00029 32.8 1.2 33 52-84 66-107 (121)
109 PRK10220 hypothetical protein; 40.9 21 0.00046 30.6 2.2 29 50-81 3-31 (111)
110 COG2956 Predicted N-acetylgluc 40.4 14 0.0003 38.3 1.2 28 49-84 353-382 (389)
111 PRK00762 hypA hydrogenase nick 40.2 12 0.00025 33.4 0.6 31 50-81 70-103 (124)
112 PF07282 OrfB_Zn_ribbon: Putat 39.8 19 0.0004 28.2 1.7 29 50-80 28-56 (69)
113 PHA00626 hypothetical protein 37.8 25 0.00055 26.3 1.9 31 52-82 2-35 (59)
114 smart00834 CxxC_CXXC_SSSS Puta 37.3 17 0.00037 25.0 1.0 28 51-78 6-34 (41)
115 smart00659 RPOLCX RNA polymera 37.0 25 0.00055 25.1 1.8 26 52-80 4-29 (44)
116 PRK00420 hypothetical protein; 37.0 21 0.00045 31.1 1.6 30 51-83 24-53 (112)
117 PF00641 zf-RanBP: Zn-finger i 36.5 14 0.0003 23.8 0.3 15 69-83 3-17 (30)
118 PF08271 TF_Zn_Ribbon: TFIIB z 36.4 18 0.00039 25.5 1.0 25 52-79 2-28 (43)
119 TIGR00006 S-adenosyl-methyltra 36.0 44 0.00096 34.6 4.1 30 135-164 214-243 (305)
120 PF14803 Nudix_N_2: Nudix N-te 35.4 25 0.00054 23.7 1.4 28 52-79 2-31 (34)
121 COG4867 Uncharacterized protei 35.3 1.8E+02 0.0038 31.3 8.3 97 245-359 532-634 (652)
122 COG0266 Nei Formamidopyrimidin 34.7 22 0.00047 36.1 1.6 30 49-78 244-273 (273)
123 PF05191 ADK_lid: Adenylate ki 34.7 20 0.00043 24.4 0.9 26 53-78 4-29 (36)
124 PF10138 vWA-TerF-like: vWA fo 34.1 4.5E+02 0.0097 25.5 11.0 42 123-164 3-50 (200)
125 PF09779 Ima1_N: Ima1 N-termin 33.8 23 0.00049 31.9 1.4 33 51-85 1-35 (131)
126 PF06827 zf-FPG_IleRS: Zinc fi 33.8 17 0.00037 23.4 0.5 27 52-78 3-29 (30)
127 KOG3799 Rab3 effector RIM1 and 33.6 23 0.0005 31.5 1.3 27 52-82 91-119 (169)
128 PRK03824 hypA hydrogenase nick 32.5 21 0.00045 32.3 0.9 31 50-80 70-117 (135)
129 KOG0444 Cytoskeletal regulator 32.4 85 0.0018 35.7 5.7 60 508-578 765-830 (1255)
130 PF01927 Mut7-C: Mut7-C RNAse 32.4 25 0.00055 32.2 1.5 31 50-80 91-134 (147)
131 PRK00050 16S rRNA m(4)C1402 me 31.9 56 0.0012 33.7 4.1 30 135-164 210-239 (296)
132 COG4416 Com Mu-like prophage p 30.4 7.3 0.00016 28.8 -1.9 33 50-82 4-36 (60)
133 PRK06393 rpoE DNA-directed RNA 30.3 25 0.00053 27.3 0.9 26 51-84 6-31 (64)
134 TIGR01384 TFS_arch transcripti 30.0 28 0.00062 29.7 1.3 27 52-82 2-28 (104)
135 PRK12286 rpmF 50S ribosomal pr 29.8 38 0.00083 25.7 1.8 25 49-80 26-50 (57)
136 PF13719 zinc_ribbon_5: zinc-r 29.7 32 0.00069 23.5 1.3 29 51-79 3-34 (37)
137 KOG3768 DEAD box RNA helicase 29.6 90 0.0019 34.9 5.2 47 339-388 192-238 (888)
138 PF13894 zf-C2H2_4: C2H2-type 29.5 28 0.0006 20.2 0.9 13 71-83 1-13 (24)
139 PF10571 UPF0547: Uncharacteri 28.7 25 0.00054 22.1 0.6 22 52-79 2-23 (26)
140 COG1996 RPC10 DNA-directed RNA 28.4 28 0.0006 25.5 0.8 26 51-80 7-34 (49)
141 COG1773 Rubredoxin [Energy pro 27.9 26 0.00056 26.4 0.6 14 65-78 29-44 (55)
142 smart00547 ZnF_RBZ Zinc finger 27.3 27 0.00058 21.5 0.5 14 70-83 2-15 (26)
143 KOG2846 Predicted membrane pro 26.1 30 0.00064 35.8 0.9 36 50-85 220-257 (328)
144 PF07754 DUF1610: Domain of un 25.4 54 0.0012 20.3 1.6 23 53-77 1-23 (24)
145 PF02891 zf-MIZ: MIZ/SP-RING z 25.1 24 0.00053 25.9 0.0 10 69-78 40-49 (50)
146 PRK12860 transcriptional activ 24.8 34 0.00074 32.7 1.0 27 49-77 133-161 (189)
147 PF03604 DNA_RNApol_7kD: DNA d 24.5 47 0.001 22.0 1.3 14 47-60 14-27 (32)
148 PF01155 HypA: Hydrogenase exp 24.4 21 0.00046 31.1 -0.4 26 51-80 71-96 (113)
149 COG5415 Predicted integral mem 24.3 38 0.00083 32.5 1.2 35 51-85 193-229 (251)
150 TIGR00595 priA primosomal prot 24.2 37 0.00081 37.9 1.3 35 51-85 214-255 (505)
151 COG1998 RPS31 Ribosomal protei 24.1 45 0.00097 24.4 1.2 27 51-79 20-46 (51)
152 PF15288 zf-CCHC_6: Zinc knuck 24.0 31 0.00067 24.1 0.4 9 51-59 2-10 (40)
153 COG0777 AccD Acetyl-CoA carbox 23.8 28 0.00061 35.1 0.2 34 50-85 28-62 (294)
154 PF05129 Elf1: Transcription e 23.7 30 0.00065 28.3 0.3 16 69-84 21-36 (81)
155 PF01795 Methyltransf_5: MraW 23.1 57 0.0012 33.9 2.3 30 135-164 215-244 (310)
156 PRK14810 formamidopyrimidine-D 23.1 44 0.00096 34.1 1.5 26 50-78 244-272 (272)
157 PF12773 DZR: Double zinc ribb 22.7 42 0.0009 24.3 0.9 32 49-83 11-42 (50)
158 COG0675 Transposase and inacti 22.5 47 0.001 34.4 1.7 25 50-81 309-333 (364)
159 COG2023 RPR2 RNase P subunit R 22.4 58 0.0013 27.9 1.8 32 52-83 58-95 (105)
160 TIGR01031 rpmF_bact ribosomal 22.1 53 0.0012 24.7 1.4 25 49-80 25-49 (55)
161 COG1645 Uncharacterized Zn-fin 22.1 57 0.0012 29.2 1.8 25 51-79 29-53 (131)
162 KOG2487 RNA polymerase II tran 21.9 1.3E+02 0.0027 30.5 4.2 44 315-361 185-228 (314)
163 COG3357 Predicted transcriptio 21.4 36 0.00078 28.2 0.3 35 49-85 57-91 (97)
164 COG2888 Predicted Zn-ribbon RN 21.4 82 0.0018 24.0 2.2 14 49-62 8-21 (61)
165 COG1545 Predicted nucleic-acid 21.4 1.4E+02 0.0031 27.0 4.3 66 50-132 29-94 (140)
166 PF13717 zinc_ribbon_4: zinc-r 21.3 51 0.0011 22.3 1.1 28 51-78 3-33 (36)
167 PF12172 DUF35_N: Rubredoxin-l 21.3 67 0.0014 21.7 1.6 24 50-79 11-34 (37)
168 PF09788 Tmemb_55A: Transmembr 21.0 1E+02 0.0022 30.8 3.4 35 49-83 64-98 (256)
169 TIGR00354 polC DNA polymerase, 21.0 46 0.001 39.3 1.2 25 51-83 626-650 (1095)
170 PRK08351 DNA-directed RNA poly 20.9 50 0.0011 25.4 1.0 26 52-85 5-30 (61)
171 PRK01103 formamidopyrimidine/5 20.8 55 0.0012 33.4 1.7 27 51-78 246-273 (274)
172 PF13248 zf-ribbon_3: zinc-rib 20.8 43 0.00092 20.8 0.5 8 51-58 3-10 (26)
173 PRK12722 transcriptional activ 20.7 47 0.001 31.7 1.0 26 50-78 134-162 (187)
174 PF08273 Prim_Zn_Ribbon: Zinc- 20.5 58 0.0013 22.8 1.2 25 53-78 6-34 (40)
175 smart00778 Prim_Zn_Ribbon Zinc 20.3 81 0.0018 21.7 1.8 25 52-78 5-33 (37)
No 1
>PLN00162 transport protein sec23; Provisional
Probab=100.00 E-value=5.7e-113 Score=970.71 Aligned_cols=583 Identities=24% Similarity=0.347 Sum_probs=497.0
Q ss_pred eeecccCccCCCHHHHHhcCCceeeEEccCCCCCCCCCCCcccCCCCCCCcCcCcCeeEecCceEeC--ceeEEcCCCCC
Q 007267 2 AVRATVSRFPSDPDAQEASGLPWGVTVTPFATKDENGAAPVYGSDGHMLPRCENCYAYFNTYCELEQ--WAWTCSLCGSL 79 (610)
Q Consensus 2 ~vR~t~~~~P~~~~~~~~~~lPlg~~v~Pf~~~~~~~~~~~~~~~~~~~~RC~~C~ayiNp~~~~~~--~~w~C~~C~~~ 79 (610)
|||+|||+||.++.++++++|||||+||||++.++ +| .+ ...|+||++|+|||||||+|+. ++|+||||+..
T Consensus 11 gvR~s~n~~P~t~~~~~~~~iPlg~v~tPl~~~~~--vp-~v---~~~pvRC~~CraylNPf~~~d~~~~~W~C~~C~~~ 84 (761)
T PLN00162 11 GVRMSWNVWPSSKIEASKCVIPLAALYTPLKPLPE--LP-VL---PYDPLRCRTCRAVLNPYCRVDFQAKIWICPFCFQR 84 (761)
T ss_pred ceEeeeecCCCCHHHHhcCCCCeEEEEecCCcCCC--CC-cC---CCCCCccCCCcCEECCceEEecCCCEEEccCCCCC
Confidence 79999999999999999999999999999998753 33 33 2479999999999999999993 79999999999
Q ss_pred CCCChhhhcccCCCcCcccc--ccccEEEEecCCCCccccCCCCcEEEEEEeCCCChhHHHHHHHHHHHHHHhCCCCcEE
Q 007267 80 NGLSSQAIARYTHPQSCAEM--ISSFIDLDLPLEGSEEETMQARPVYVAAVDLSSSEEFLELTRSALQAALEAVPSGALF 157 (610)
Q Consensus 80 N~~p~~~~~~~~~~~~~pEL--~~~tvey~~p~~y~~~~~~~~~p~~vFvID~s~~~~~l~~l~~~l~~~l~~lp~~~~V 157 (610)
|++|++|.. ..+...+||| .++||||.+|+ |.. .++.||+|+||||+|..+++++.+|++|+++|+.||++++|
T Consensus 85 N~~P~~Y~~-~~~~~~p~EL~p~~~TvEY~~p~-~~~--~~~~pp~fvFvID~s~~~~~l~~lk~sl~~~L~~LP~~a~V 160 (761)
T PLN00162 85 NHFPPHYSS-ISETNLPAELFPQYTTVEYTLPP-GSG--GAPSPPVFVFVVDTCMIEEELGALKSALLQAIALLPENALV 160 (761)
T ss_pred CCCchHhcc-cCccCCChhhcCCceeEEEECCC-CCC--CCCCCcEEEEEEecchhHHHHHHHHHHHHHHHHhCCCCCEE
Confidence 999999642 2223446799 78999999997 653 35678999999999999999999999999999999999999
Q ss_pred EEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccccc-----------------------Ccc-CcCccchHhHHH
Q 007267 158 GLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV-----------------------MPL-SQFLAPVETFKE 213 (610)
Q Consensus 158 glITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~-----------------------~p~-~~~l~~~~e~~~ 213 (610)
||||||+.||||+|+...+.+.+||. +.+++...++++. +|. ++||+|++||+.
T Consensus 161 GlITF~s~V~~~~L~~~~~~~~~Vf~--g~k~~t~~~l~~~l~l~~~~~~~~~~~~~~~~~~~~~p~~~~fLvpl~e~~~ 238 (761)
T PLN00162 161 GLITFGTHVHVHELGFSECSKSYVFR--GNKEVSKDQILEQLGLGGKKRRPAGGGIAGARDGLSSSGVNRFLLPASECEF 238 (761)
T ss_pred EEEEECCEEEEEEcCCCCCcceEEec--CCccCCHHHHHHHhccccccccccccccccccccccCCCccceeEEHHHHHH
Confidence 99999999999999887766667775 4444433333322 232 689999999999
Q ss_pred HHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecCCCCCCCcccccccCc
Q 007267 214 NITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPPDHGAGQLDTRRYG 293 (610)
Q Consensus 214 ~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~pt~GpG~l~~~~~~ 293 (610)
.|+++||+|+++ .|+..++. ++.||+|+||++|..+|+...++ .||||++|++||||.|||+|+.++.+
T Consensus 239 ~i~~lLe~L~~~-~~~~~~~~--------rp~r~tG~AL~vA~~lL~~~~~~--~gGrI~~F~sgppT~GpG~v~~r~~~ 307 (761)
T PLN00162 239 TLNSALEELQKD-PWPVPPGH--------RPARCTGAALSVAAGLLGACVPG--TGARIMAFVGGPCTEGPGAIVSKDLS 307 (761)
T ss_pred HHHHHHHhhhcc-ccccCCCC--------CCCccHHHHHHHHHHHHhhccCC--CceEEEEEeCCCCCCCCceeeccccc
Confidence 999999999998 57655432 48899999999999999976543 37999999999999999999999999
Q ss_pred CcccCCCc--chhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeCCCCCCchhHHHH
Q 007267 294 EQYASKGE--DADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYSSTDDSTLPQDIY 371 (610)
Q Consensus 294 ~~~~~~~~--~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~~~~~~l~~dl~ 371 (610)
+.+|++.. ++++++++++.+||++||.+|+++||+||+|+++.+|+|++||+.|++.|||.+++|++|+.++|+++|+
T Consensus 308 ~~~rsh~di~k~~~~~~~~a~~fY~~la~~~~~~gisvDlF~~s~dqvglaem~~l~~~TGG~v~~~~sF~~~~f~~~l~ 387 (761)
T PLN00162 308 EPIRSHKDLDKDAAPYYKKAVKFYEGLAKQLVAQGHVLDVFACSLDQVGVAEMKVAVERTGGLVVLAESFGHSVFKDSLR 387 (761)
T ss_pred ccccCccccccchhhhcchHHHHHHHHHHHHHHcCceEEEEEccccccCHHHHhhhHhhcCcEEEEeCCcChHHHHHHHH
Confidence 99987553 3456899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhccC------cceeeEEEEEccCCeeeeeeeeccccCCCC-------------CcceeeeecCCCccEEEEEEEecCC
Q 007267 372 RMLSRP------YAFNCIMRLRTSSEFKPGHSYGHFFPDPQY-------------ENVQHIICCDSYATYAYDFDFANAA 432 (610)
Q Consensus 372 ~~l~~~------~~~~a~lrvr~S~gl~v~~~~G~~~~~~~~-------------~~~~~i~~~~~~~t~a~~fe~~~~~ 432 (610)
|.|+|+ +||+|+||||||+||+|++++|||++..++ .+.|.++++|+++|++|+||+++..
T Consensus 388 r~~~r~~~~~~~~gf~a~~~VrtS~glkv~g~~G~~~s~~~~~~~vsd~~iG~g~T~~w~l~~l~~~~t~av~f~~~~~~ 467 (761)
T PLN00162 388 RVFERDGEGSLGLSFNGTFEVNCSKDVKVQGAIGPCASLEKKGPSVSDTEIGEGGTTAWKLCGLDKKTSLAVFFEVANSG 467 (761)
T ss_pred HHhcccccccccccceeEEEEEecCCeEEeeeEcCcccccccCCccccccccCCCCceeeecCcCcCCEEEEEEEEcccc
Confidence 999974 799999999999999999999999864332 2359999999999999999998753
Q ss_pred C-cCCCCCCccEEEEEEEeeecCCccccc--cccc---c--c--------------------------------------
Q 007267 433 G-FARHTSEQPMLQIAFQYTVVVPPEELS--SEGL---G--S-------------------------------------- 466 (610)
Q Consensus 433 ~-l~~~~~~~~~iQ~a~~Yt~~~g~~~~~--n~~~---~--s-------------------------------------- 466 (610)
+ .+....+.+|||||++||+.+|+||+| |... . +
T Consensus 468 ~~~~~~~~~~~~iQ~a~lYt~~~G~rRiRV~T~~~~~~~~~~~~~v~~~fDqeA~a~llaR~av~k~~~~~~~d~~r~ld 547 (761)
T PLN00162 468 QSNPQPPGQQFFLQFLTRYQHSNGQTRLRVTTVTRRWVEGSSSEELVAGFDQEAAAVVMARLASHKMETEEEFDATRWLD 547 (761)
T ss_pred ccCCCCCCceEEEEEEEEEEcCCCCEEEEEEccccCccCCCCHHHHHHhcCHHHHHHHHHHHHHHHHhhCCHHHHHHHHH
Confidence 1 111235679999999999999999887 2110 0 0
Q ss_pred -----------ccccCChhhhHh----hhccccc-----------ccCCCCCCCcccccccchhhhcCC-----------
Q 007267 467 -----------VSSALEPSSLQR----AVYPLLT-----------SYSTPDKQAFPRHSLSRAALITSG----------- 509 (610)
Q Consensus 467 -----------~~~~~~~~~~~~----~~yP~l~-----------~~~spde~~~~~~~l~r~~~~~s~----------- 509 (610)
.|++.++.++++ .+||+|| +|.||||++|+|+.++|+++.++.
T Consensus 548 ~~li~~~~~f~~Yrk~~~~s~~Lp~~~~~lP~f~~~LrRS~~l~~~n~spDera~~r~~l~~~~~~~sl~mI~P~L~sy~ 627 (761)
T PLN00162 548 RALIRLCSKFGDYRKDDPSSFRLSPNFSLYPQFMFNLRRSQFVQVFNNSPDETAYFRMMLNRENVTNSLVMIQPTLISYS 627 (761)
T ss_pred HHHHHHHHHHhhhcccCCccccCCHHHHHHHHHHHHHhhhhhccCCCCCchHHHHHHHHHhcCCHHHHHHhhCCeEEEec
Confidence 078888888776 7899999 488999999999999998663322
Q ss_pred -----------------CcEEEEecCcEEEEEecCCCCC--CCCCC-CChhHHHHHHH-------HHHHhcCCCCceEEE
Q 007267 510 -----------------SPIFLLDAFTTIIVFYSSTADP--TLPFP-PPQDCLLRTTI-------NKMKQERSITPKLIF 562 (610)
Q Consensus 510 -----------------~~iyllD~g~~~~i~~G~~v~~--~~~~~-~~~~~~~~~~i-------~~i~~~r~~~p~l~~ 562 (610)
++|||||+||+++||+|++|++ +++|| +|+++++++++ ++|.++|+|+||+++
T Consensus 628 ~~~~P~pv~Ld~~si~~d~ilLLD~~f~vvi~~G~~ia~w~~~~~~~~~~~~~~~~~l~~p~~~a~~~~~~Rfp~Pr~i~ 707 (761)
T PLN00162 628 FNGPPEPVLLDVASIAADRILLLDSYFSVVIFHGSTIAQWRKAGYHNQPEHEAFAQLLEAPQADAQAIIKERFPVPRLVV 707 (761)
T ss_pred CCCCCcceecchhhccCCceEEEeCCCEEEEEecCcccchhhcCCCCCcchhhHHHHHHhHHHHHHHHHhcCCCCCeEEE
Confidence 6999999999999999999999 88898 89999998888 688899999999999
Q ss_pred EeCCCCcHHHHHhhccCCCCCC------CCCC--cccccHHHHHHHHHHHHHH
Q 007267 563 IRGGQDDATIFENYLIEEQDVD------GSGL--TSVMGFVSFLEEISQSVVE 607 (610)
Q Consensus 563 ~~~~~~~~~~f~~~LveD~~~~------~~~~--~~~~sy~dfl~~lh~~i~~ 607 (610)
|+||+||+||+++||++..+.+ |+.+ +++.|+..|+.||+|.+++
T Consensus 708 ~~~~~SqaRfl~~klnPs~~~~~~~~~~~~~~~~tdd~sl~~f~~~l~~~~v~ 760 (761)
T PLN00162 708 CDQHGSQARFLLAKLNPSATYNSANAMGGSDIIFTDDVSLQVFMEHLQRLAVQ 760 (761)
T ss_pred eCCCCcHHHHHHHhcCCcccccCCCCCCCCCeeecCCcCHHHHHHHHHHHhcC
Confidence 9999999999999999986532 2222 5789999999999998764
No 2
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.2e-111 Score=903.55 Aligned_cols=568 Identities=22% Similarity=0.377 Sum_probs=506.4
Q ss_pred eeecccCccCCCHHHHHhcCCceeeEEccCCCCCCCCCCCcccCCC-CCCCcCcCcCeeEecCceEeC--ceeEEcCCCC
Q 007267 2 AVRATVSRFPSDPDAQEASGLPWGVTVTPFATKDENGAAPVYGSDG-HMLPRCENCYAYFNTYCELEQ--WAWTCSLCGS 78 (610)
Q Consensus 2 ~vR~t~~~~P~~~~~~~~~~lPlg~~v~Pf~~~~~~~~~~~~~~~~-~~~~RC~~C~ayiNp~~~~~~--~~w~C~~C~~ 78 (610)
+||+|+|++|+|.++++.++||||++|+||+...+.|.++.+++.+ ..|+||+||+||||||++|++ ++|+||||+.
T Consensus 289 ~mr~T~Y~iP~T~Dl~~as~iPLalvIqPfa~l~p~E~~~~vVd~g~sgPvRC~RCkaYinPFmqF~~~gr~f~Cn~C~~ 368 (1007)
T KOG1984|consen 289 FMRCTMYTIPCTNDLLKASQIPLALVIQPFATLTPNEAPVPVVDLGESGPVRCNRCKAYINPFMQFIDGGRKFICNFCGS 368 (1007)
T ss_pred hheeecccCCccHhHHHhcCCcceeEecccccCCcccCCCceecCCCCCCcchhhhhhhcCcceEEecCCceEEecCCCc
Confidence 5899999999999999999999999999999988777766666554 458899999999999999984 6899999999
Q ss_pred CCCCChhhhcccCC------CcCccccccccEEEEecCCCCccccCCCCcEEEEEEeCCCCh---hHHHHHHHHHHHHHH
Q 007267 79 LNGLSSQAIARYTH------PQSCAEMISSFIDLDLPLEGSEEETMQARPVYVAAVDLSSSE---EFLELTRSALQAALE 149 (610)
Q Consensus 79 ~N~~p~~~~~~~~~------~~~~pEL~~~tvey~~p~~y~~~~~~~~~p~~vFvID~s~~~---~~l~~l~~~l~~~l~ 149 (610)
+|++|++|++++.+ .++||||+.|+|||+++++|+.++..+.+|+|||+||||+++ +...+++++|++.|+
T Consensus 369 ~n~vp~~yf~~L~~~grr~D~~erpEL~~Gt~dfvatk~Y~~~~k~p~ppafvFmIDVSy~Ai~~G~~~a~ce~ik~~l~ 448 (1007)
T KOG1984|consen 369 KNQVPDDYFNHLGPTGRRVDVEERPELCLGTVDFVATKDYCRKTKPPKPPAFVFMIDVSYNAISNGAVKAACEAIKSVLE 448 (1007)
T ss_pred cccCChhhcccCCCcccccccccCchhcccccceeeehhhhhcCCCCCCceEEEEEEeehhhhhcchHHHHHHHHHHHHh
Confidence 99999999876543 677999999999999999999877778999999999999986 788999999999999
Q ss_pred hCC---CCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccc-cCcc-CcCccchHhHHHHHHHHHHhcCC
Q 007267 150 AVP---SGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELED-VMPL-SQFLAPVETFKENITSALETLRP 224 (610)
Q Consensus 150 ~lp---~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~-~~p~-~~~l~~~~e~~~~i~~~L~~L~~ 224 (610)
.+| ++++|||||||++|||||+++.+.+++|. ++.|++| ++|+ +++|+...|++..|+.+|++|+.
T Consensus 449 ~lp~~~p~~~Vgivtfd~tvhFfnl~s~L~qp~ml---------iVsdv~dvfvPf~~g~~V~~~es~~~i~~lLd~Ip~ 519 (1007)
T KOG1984|consen 449 DLPREEPNIRVGIVTFDKTVHFFNLSSNLAQPQML---------IVSDVDDVFVPFLDGLFVNPNESRKVIELLLDSIPT 519 (1007)
T ss_pred hcCccCCceEEEEEEecceeEeeccCccccCceEE---------EeecccccccccccCeeccchHHHHHHHHHHHHhhh
Confidence 987 48999999999999999999988887774 5688988 4897 68999999999999999999999
Q ss_pred CCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecCCCCCCCc-ccccccCcCcccCCCcch
Q 007267 225 TTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPPDHGAG-QLDTRRYGEQYASKGEDA 303 (610)
Q Consensus 225 ~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~pt~GpG-~l~~~~~~~~~~~~~~~~ 303 (610)
++++.+. +..|+|+||++|..+|++.. +||+++|++.+||.|.| +++.+++...+ ++++
T Consensus 520 mf~~sk~------------pes~~g~alqaa~lalk~~~-----gGKl~vF~s~Lpt~g~g~kl~~r~D~~l~---~t~k 579 (1007)
T KOG1984|consen 520 MFQDSKI------------PESVFGSALQAAKLALKAAD-----GGKLFVFHSVLPTAGAGGKLSNRDDRRLI---GTDK 579 (1007)
T ss_pred hhccCCC------------CchhHHHHHHHHHHHHhccC-----CceEEEEecccccccCcccccccchhhhh---cccc
Confidence 9876543 67899999999999999874 39999999999999986 99988887765 7889
Q ss_pred hhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeCCCC----CCchhHHHHHHhccCcc
Q 007267 304 DRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYSSTD----DSTLPQDIYRMLSRPYA 379 (610)
Q Consensus 304 e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~~~----~~~l~~dl~~~l~~~~~ 379 (610)
||+++.++++.|++||++|++.|||||||+++.+|+|+|+++.+++.|||.+|+|..|. ..+|.+||.|.++++.|
T Consensus 580 ek~l~~pq~~~y~~LA~e~v~~g~svDlF~t~~ayvDvAtlg~v~~~TgG~vy~Y~~F~a~~D~~rl~nDL~~~vtk~~g 659 (1007)
T KOG1984|consen 580 EKNLLQPQDKTYTTLAKEFVESGCSVDLFLTPNAYVDVATLGVVPALTGGQVYKYYPFQALTDGPRLLNDLVRNVTKKQG 659 (1007)
T ss_pred hhhccCcchhHHHHHHHHHHHhCceEEEEEcccceeeeeeecccccccCceeEEecchhhcccHHHHHHHHHHhccccee
Confidence 99999999999999999999999999999999999999999999999999999999984 56899999999999999
Q ss_pred eeeEEEEEccCCeeeeeeeeccccCCCCCcceeeeecCCCccEEEEEEEecCCCcCCCCCCccEEEEEEEeeecCCcccc
Q 007267 380 FNCIMRLRTSSEFKPGHSYGHFFPDPQYENVQHIICCDSYATYAYDFDFANAAGFARHTSEQPMLQIAFQYTVVVPPEEL 459 (610)
Q Consensus 380 ~~a~lrvr~S~gl~v~~~~G~~~~~~~~~~~~~i~~~~~~~t~a~~fe~~~~~~l~~~~~~~~~iQ~a~~Yt~~~g~~~~ 459 (610)
|+|+||||||+||++.++|||+..++ ..-..++.+|.|+|+.++|++++ +|++ +.+++||+|++||+++|+||+
T Consensus 660 f~a~mrvRtStGirv~~f~Gnf~~~~--~tDiela~lD~dkt~~v~fkhDd--kLq~--~s~~~fQ~AlLYTti~G~RR~ 733 (1007)
T KOG1984|consen 660 FDAVMRVRTSTGIRVQDFYGNFLMRN--PTDIELAALDCDKTLTVEFKHDD--KLQD--GSDVHFQTALLYTTIDGQRRL 733 (1007)
T ss_pred eeeEEEEeecCceeeeeeechhhhcC--CCCccccccccCceeEEEEeccc--cccC--CcceeEEEEEEEeccCCceeE
Confidence 99999999999999999999999875 33468899999999998887775 7864 678999999999999999988
Q ss_pred c--ccc-----------------------cc--------------------------------------cc---------
Q 007267 460 S--SEG-----------------------LG--------------------------------------SV--------- 467 (610)
Q Consensus 460 ~--n~~-----------------------~~--------------------------------------s~--------- 467 (610)
| |.+ +| ++
T Consensus 734 Rv~Nlsl~~ts~l~~lyr~~~~d~l~a~maK~a~~~i~~~~lk~vre~l~~~~~~iL~~YRk~cas~~ssgQLILPeslK 813 (1007)
T KOG1984|consen 734 RVLNLSLAVTSQLSELYRSADTDPLIAIMAKQAAKAILDKPLKEVREQLVSQCAQILASYRKNCASPASSGQLILPESLK 813 (1007)
T ss_pred EEEecchhhhhhHHHHHHhcCccHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHhhcCCCCcccEechhhhH
Confidence 7 431 00 00
Q ss_pred -------------------------------cccCChhhhHhhhcccccccCCCCCCCc---ccccccchh-hhcCCCcE
Q 007267 468 -------------------------------SSALEPSSLQRAVYPLLTSYSTPDKQAF---PRHSLSRAA-LITSGSPI 512 (610)
Q Consensus 468 -------------------------------~~~~~~~~~~~~~yP~l~~~~spde~~~---~~~~l~r~~-~~~s~~~i 512 (610)
+++++++.++++||||+++.|+.|++.- ..+...|++ ..++.+||
T Consensus 814 LlPly~la~lKs~~l~~~~~~~DdRi~~~~~v~sl~v~~~~~~~YPrl~p~hdl~i~dtl~~~~p~~VraS~e~l~negi 893 (1007)
T KOG1984|consen 814 LLPLYMLALLKSSALRPQEIRTDDRIYQLQLVTSLSVEQLMPFFYPRLLPFHDLDIEDTLEFVLPKAVRASSEFLSNEGI 893 (1007)
T ss_pred HHHHHHHHHHHhhcccccccccchhHHHHHHhhcccHHhhhhhhccceeeeeccccccccccccccceecchhhccCCce
Confidence 6788899999999999999999886543 566667764 47889999
Q ss_pred EEEecCcEEEEEecCCCCCCCC---------------------CCCChhHHHHHHHHHHHhcCCCCceEEEEeCCC-CcH
Q 007267 513 FLLDAFTTIIVFYSSTADPTLP---------------------FPPPQDCLLRTTINKMKQERSITPKLIFIRGGQ-DDA 570 (610)
Q Consensus 513 yllD~g~~~~i~~G~~v~~~~~---------------------~~~~~~~~~~~~i~~i~~~r~~~p~l~~~~~~~-~~~ 570 (610)
||||||.+++||+|+.+++.|+ ++|+.+.++|++|+.|++.|....+++++++|. ..+
T Consensus 894 Yll~nG~~~ylwvg~sv~~~llQ~lf~V~s~~~i~s~~~~Lpe~dn~lS~k~r~~i~~i~~~r~~~l~v~~~k~g~~~~~ 973 (1007)
T KOG1984|consen 894 YLLDNGQKIYLWVGESVDPDLLQDLFSVSSFEQIDSQSGVLPELDNPLSRKVRNVISLIRRQRSSELPVVLVKQGLDGSE 973 (1007)
T ss_pred EEEecCcEEEEEecCCCCHHHHHHHhcCccccccccccccccccCcHHHHHHHHHHHHHHhccccccccEEEecCCCchh
Confidence 9999999999999999998555 469999999999999999999999999999995 455
Q ss_pred HHHHhhccCCCCCCCCCCcccccHHHHHHHHHHHHHHhhC
Q 007267 571 TIFENYLIEEQDVDGSGLTSVMGFVSFLEEISQSVVEYMK 610 (610)
Q Consensus 571 ~~f~~~LveD~~~~~~~~~~~~sy~dfl~~lh~~i~~~l~ 610 (610)
.+|.++|+||++.++ +||+||||.||++|+++|.
T Consensus 974 ~~~~~~lved~~~~~------~sY~dyL~~~H~ki~~~l~ 1007 (1007)
T KOG1984|consen 974 VEFSEYLVEDRGRNI------SSYVDYLCELHKKIQQKLS 1007 (1007)
T ss_pred hhhhhhhhcccccCc------cccchHHHHHHHHHHhhcC
Confidence 899999999999776 7999999999999999874
No 3
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.9e-109 Score=885.64 Aligned_cols=560 Identities=30% Similarity=0.502 Sum_probs=494.7
Q ss_pred CeeecccCccCCCHHHHHhcCCceeeEEccCCCCCCCCCCCcccCCCCCCCcCcCcCeeEecCceEeC--ceeEEcCCCC
Q 007267 1 MAVRATVSRFPSDPDAQEASGLPWGVTVTPFATKDENGAAPVYGSDGHMLPRCENCYAYFNTYCELEQ--WAWTCSLCGS 78 (610)
Q Consensus 1 ~~vR~t~~~~P~~~~~~~~~~lPlg~~v~Pf~~~~~~~~~~~~~~~~~~~~RC~~C~ayiNp~~~~~~--~~w~C~~C~~ 78 (610)
+++|+|.+++|.+.+++++++||||++|+||++..+. . +........++||++|++|||||+.|++ ++|+||+|+.
T Consensus 171 ~y~RsTl~~iP~t~sLl~kskLPlglvv~Pf~~~~d~-~-~~p~~~~~~IvRCr~CRtYiNPFV~fid~gr~WrCNlC~~ 248 (887)
T KOG1985|consen 171 SYVRSTLSAIPQTQSLLKKSKLPLGLVVHPFAHLDDI-D-PLPVITSTLIVRCRRCRTYINPFVEFIDQGRRWRCNLCGR 248 (887)
T ss_pred HHHHHHHHhCCccHHHHHhcCCCceEEEeeccccccc-C-CCCcccCCceeeehhhhhhcCCeEEecCCCceeeechhhh
Confidence 4689999999999999999999999999999987632 2 2223456789999999999999999984 6999999999
Q ss_pred CCCCChhhhcc-----cCCCcCccccccccEEEEecCCCCccccCCCCcEEEEEEeCCCCh---hHHHHHHHHHHHHHHh
Q 007267 79 LNGLSSQAIAR-----YTHPQSCAEMISSFIDLDLPLEGSEEETMQARPVYVAAVDLSSSE---EFLELTRSALQAALEA 150 (610)
Q Consensus 79 ~N~~p~~~~~~-----~~~~~~~pEL~~~tvey~~p~~y~~~~~~~~~p~~vFvID~s~~~---~~l~~l~~~l~~~l~~ 150 (610)
.|++|.++... |.+..+||||++++|||++|.+|+.+ +++|++|||+||||.++ |+|+.++++|++.|+.
T Consensus 249 ~NdvP~~f~~~~~t~~~~~~~~RpEl~~s~vE~iAP~eYmlR--~P~Pavy~FliDVS~~a~ksG~L~~~~~slL~~LD~ 326 (887)
T KOG1985|consen 249 VNDVPDDFDWDPLTGAYGDPYSRPELTSSVVEFIAPSEYMLR--PPQPAVYVFLIDVSISAIKSGYLETVARSLLENLDA 326 (887)
T ss_pred hcCCcHHhhcCccccccCCcccCccccceeEEEecCcccccC--CCCCceEEEEEEeehHhhhhhHHHHHHHHHHHhhhc
Confidence 99999997544 55578899999999999999999976 57899999999999975 8999999999999999
Q ss_pred CC--CCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccccc-Ccc-CcCccchHhHHHHHHHHHHhcCCCC
Q 007267 151 VP--SGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV-MPL-SQFLAPVETFKENITSALETLRPTT 226 (610)
Q Consensus 151 lp--~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~-~p~-~~~l~~~~e~~~~i~~~L~~L~~~~ 226 (610)
|| ++++|||||||+.||||++..+..++++ .++.|++|. +|. .+||+|++|||+.|+.+|+.|++++
T Consensus 327 lpgd~Rt~igfi~fDs~ihfy~~~~~~~qp~m---------m~vsdl~d~flp~pd~lLv~L~~ck~~i~~lL~~lp~~F 397 (887)
T KOG1985|consen 327 LPGDPRTRIGFITFDSTIHFYSVQGDLNQPQM---------MIVSDLDDPFLPMPDSLLVPLKECKDLIETLLKTLPEMF 397 (887)
T ss_pred CCCCCcceEEEEEeeceeeEEecCCCcCCCce---------eeeccccccccCCchhheeeHHHHHHHHHHHHHHHHHHH
Confidence 99 7899999999999999999887755555 355788884 454 6899999999999999999999999
Q ss_pred CcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecCCCCCCCcccccccCcCcccCCCcchhhc
Q 007267 227 SWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRA 306 (610)
Q Consensus 227 ~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~ 306 (610)
+|++. .++|+|+||++|.++|++.| |||++|.+++|+.|.|+++.|++.+. ++++++..
T Consensus 398 ~~~~~------------t~~alGpALkaaf~li~~~G------Gri~vf~s~lPnlG~G~L~~rEdp~~---~~s~~~~q 456 (887)
T KOG1985|consen 398 QDTRS------------TGSALGPALKAAFNLIGSTG------GRISVFQSTLPNLGAGKLKPREDPNV---RSSDEDSQ 456 (887)
T ss_pred hhccC------------cccccCHHHHHHHHHHhhcC------CeEEEEeccCCCCCcccccccccccc---ccchhhhh
Confidence 88764 46899999999999999986 89999999999999999999966543 35667788
Q ss_pred cCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeCCCCCC------chhHHHHHHhccCcce
Q 007267 307 LLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYSSTDDS------TLPQDIYRMLSRPYAF 380 (610)
Q Consensus 307 ~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~~~~~------~l~~dl~~~l~~~~~~ 380 (610)
++.+++.|||++|.+|++.+|+||+|+++.+|.|+|+|+.|++.|||.+|+|++|+.. +|.+||.|+|+|++||
T Consensus 457 lL~~~t~FYK~~a~~cs~~qI~VDlFl~s~qY~DlAsLs~LskySgG~~y~YP~f~~s~p~~~~Kf~~el~r~Ltr~~~f 536 (887)
T KOG1985|consen 457 LLSPATDFYKDLALECSKSQICVDLFLFSEQYTDLASLSCLSKYSGGQVYYYPSFDGSNPHDVLKFARELARYLTRKIGF 536 (887)
T ss_pred ccCCCchHHHHHHHHhccCceEEEEEeecccccchhhhhccccccCceeEEccCCCCCCHHHHHHHHHHHHHHhhhhhhh
Confidence 9999999999999999999999999999999999999999999999999999999865 7899999999999999
Q ss_pred eeEEEEEccCCeeeeeeeeccccCCCCCcceeeeecCCCccEEEEEEEecCCCcCCCCCCccEEEEEEEeeecCCccccc
Q 007267 381 NCIMRLRTSSEFKPGHSYGHFFPDPQYENVQHIICCDSYATYAYDFDFANAAGFARHTSEQPMLQIAFQYTVVVPPEELS 460 (610)
Q Consensus 381 ~a~lrvr~S~gl~v~~~~G~~~~~~~~~~~~~i~~~~~~~t~a~~fe~~~~~~l~~~~~~~~~iQ~a~~Yt~~~g~~~~~ 460 (610)
+|+||||||+|++++.+||||+.+. .++..++++++|++++|.+++++ .+ .....++|.|++||..+|+||+|
T Consensus 537 eaVmRiR~S~gl~~~~f~GnFF~RS--tDLla~~~v~~D~sy~~qisiEe--sl---~~~~~~fQvAlLyT~~~GERRIR 609 (887)
T KOG1985|consen 537 EAVMRIRCSTGLRMSSFFGNFFVRS--TDLLALPNVNPDQSYAFQISIEE--SL---TTGFCVFQVALLYTLSKGERRIR 609 (887)
T ss_pred heeEEeeccccccccceecccccCc--HHHhcccCCCCCccceEEEEeeh--hc---CCceeEEEeeeeecccCCceeEE
Confidence 9999999999999999999999986 67889999999999999988886 34 25678899999999999999987
Q ss_pred --ccc-------------------------------ccc----------------------------c------------
Q 007267 461 --SEG-------------------------------LGS----------------------------V------------ 467 (610)
Q Consensus 461 --n~~-------------------------------~~s----------------------------~------------ 467 (610)
+.+ +.| +
T Consensus 610 V~T~~lpt~~sl~evY~saD~~AI~~lla~~Av~ksl~ssL~dardal~~~~~D~l~aYk~~~~~~~~~~~~l~~p~~Lr 689 (887)
T KOG1985|consen 610 VHTLCLPTVSSLNEVYASADQEAIASLLAKKAVEKSLSSSLSDARDALTNAVVDILNAYKKLVSNQNGQGITLSLPASLR 689 (887)
T ss_pred EEEeeccccccHHHHHhhcCHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcccccCCcceecCcchh
Confidence 210 000 0
Q ss_pred --------------------------------cccCChhhhHhhhcccccccCCCCCCCccc---------ccccchhhh
Q 007267 468 --------------------------------SSALEPSSLQRAVYPLLTSYSTPDKQAFPR---------HSLSRAALI 506 (610)
Q Consensus 468 --------------------------------~~~~~~~~~~~~~yP~l~~~~spde~~~~~---------~~l~r~~~~ 506 (610)
++.+++..+++.+||.|+.+|+++..+... +.|.+....
T Consensus 690 llPllvlALlK~~~fr~g~~~~lD~R~~a~~~~~~lpl~~L~k~IYP~Lysl~~l~~ea~~~~~d~~~~~p~~L~ltae~ 769 (887)
T KOG1985|consen 690 LLPLLVLALLKHPAFRPGTGTRLDYRAYAMCLMSTLPLKYLMKYIYPTLYSLHDLDDEAGLPIHDQTVVLPPPLNLTAEL 769 (887)
T ss_pred hhHHHHHHHhcCCcccCCCCCCchHHHHHHHHhhcCCHHHHHhhhcccceeccccccccCcccccccccCCCccchHHHH
Confidence 567789999999999999999988766543 667777778
Q ss_pred cCCCcEEEEecCcEEEEEecCCCCCCCC---------------------CCCChhHHHHHHHHHHHhcCCCCceEEEEeC
Q 007267 507 TSGSPIFLLDAFTTIIVFYSSTADPTLP---------------------FPPPQDCLLRTTINKMKQERSITPKLIFIRG 565 (610)
Q Consensus 507 ~s~~~iyllD~g~~~~i~~G~~v~~~~~---------------------~~~~~~~~~~~~i~~i~~~r~~~p~l~~~~~ 565 (610)
++..|+||||+|.++|+|+|.+++|+++ .+++++++++++|+++|.+|..+|.++++|+
T Consensus 770 l~~~GlyL~D~g~~lfl~vg~~a~P~ll~~vfg~~~~adi~~~~~~lp~~~n~~s~r~~~fI~~lR~d~~~~p~~~ivr~ 849 (887)
T KOG1985|consen 770 LSRRGLYLMDTGTTLFLWVGSNADPSLLFDVFGVSTLADIPIGKYTLPELDNEESDRVRRFIKKLRDDRTYFPNLYIVRG 849 (887)
T ss_pred hccCceEEEecCcEEEEEEcCCCCccccccccCcchHhhcccccccCcccccchhHHHHHHHHHhhcCCcccceEEEEec
Confidence 8999999999999999999999999776 2488999999999999999999999999997
Q ss_pred CC--CcHHHHHhhccCCCCCCCCCCcccccHHHHHHHHHHHHHH
Q 007267 566 GQ--DDATIFENYLIEEQDVDGSGLTSVMGFVSFLEEISQSVVE 607 (610)
Q Consensus 566 ~~--~~~~~f~~~LveD~~~~~~~~~~~~sy~dfl~~lh~~i~~ 607 (610)
++ ....||.++||||++++. .||++||.|||++|++
T Consensus 850 ~~~s~~k~~f~~~lvEDrs~~~------~SY~efLq~lk~qv~~ 887 (887)
T KOG1985|consen 850 DDNSPLKAWFFSRLVEDRSENS------PSYYEFLQHLKAQVSK 887 (887)
T ss_pred CCCchHHHHHHHHHHhhhhcCc------HHHHHHHHHHHHHhcC
Confidence 63 455699999999999643 8999999999999974
No 4
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.1e-106 Score=854.43 Aligned_cols=574 Identities=24% Similarity=0.372 Sum_probs=504.5
Q ss_pred eeecccCccCCCHHHHHhcCCceeeEEccCCCCCCCCCCCcccCCCCCCCcCcCcCeeEecCceEeC--ceeEEcCCCCC
Q 007267 2 AVRATVSRFPSDPDAQEASGLPWGVTVTPFATKDENGAAPVYGSDGHMLPRCENCYAYFNTYCELEQ--WAWTCSLCGSL 79 (610)
Q Consensus 2 ~vR~t~~~~P~~~~~~~~~~lPlg~~v~Pf~~~~~~~~~~~~~~~~~~~~RC~~C~ayiNp~~~~~~--~~w~C~~C~~~ 79 (610)
|||+|||+||.++....++.+|++|+|+||.+.+. .|+. .++|+||.+|+||+||||++|- +.|.|+||.++
T Consensus 11 GvR~twnvwPs~~~~~~~~vvPla~lytPl~e~~~--~~~~----~y~P~~C~~C~AvlNPyc~vd~~a~~W~CpfC~qr 84 (745)
T KOG1986|consen 11 GVRFTWNVWPSTRAEASRTVVPLACLYTPLKERPD--LPPI----QYDPLRCSKCGAVLNPYCSVDFRAKSWICPFCNQR 84 (745)
T ss_pred CcccccccCCCcccccccccccHHHhccccccCCC--CCcc----CCCCchhccchhhcCcceeecccCceEeccccccC
Confidence 79999999999999999999999999999998754 2332 3589999999999999999993 68999999999
Q ss_pred CCCChhhhcccCC--CcCcc-cc--ccccEEEEecCCCCccccCCCCcEEEEEEeCCCChhHHHHHHHHHHHHHHhCCCC
Q 007267 80 NGLSSQAIARYTH--PQSCA-EM--ISSFIDLDLPLEGSEEETMQARPVYVAAVDLSSSEEFLELTRSALQAALEAVPSG 154 (610)
Q Consensus 80 N~~p~~~~~~~~~--~~~~p-EL--~~~tvey~~p~~y~~~~~~~~~p~~vFvID~s~~~~~l~~l~~~l~~~l~~lp~~ 154 (610)
|.+|++ |.. ..++| || ...||||.+++. ...||+|+||||+|..+++|+.+|++|+.+|+.||++
T Consensus 85 N~~p~~----Y~~is~~n~P~el~Pq~stvEy~l~~~------~~~ppvf~fVvDtc~~eeeL~~LkssL~~~l~lLP~~ 154 (745)
T KOG1986|consen 85 NPFPPH----YSGISENNLPPELLPQYSTVEYTLSPG------RVSPPVFVFVVDTCMDEEELQALKSSLKQSLSLLPEN 154 (745)
T ss_pred CCCChh----hcccCccCCChhhcCCcceeEEecCCC------CCCCceEEEEEeeccChHHHHHHHHHHHHHHhhCCCc
Confidence 999999 543 45666 88 589999999864 3458999999999999999999999999999999999
Q ss_pred cEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccccC--------------ccCcCccchHhHHHHHHHHHH
Q 007267 155 ALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDVM--------------PLSQFLAPVETFKENITSALE 220 (610)
Q Consensus 155 ~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~~--------------p~~~~l~~~~e~~~~i~~~L~ 220 (610)
++||||||++.|++|+++...+.+.+||. +.+++....+.+++ +.++||.|+++|...+.++|+
T Consensus 155 alvGlItfg~~v~v~el~~~~~sk~~VF~--G~ke~s~~q~~~~L~~~~~~~~~~~~~~~~~rFL~P~~~c~~~L~~lle 232 (745)
T KOG1986|consen 155 ALVGLITFGTMVQVHELGFEECSKSYVFS--GNKEYSAKQLLDLLGLSGGAGKGSENQSASNRFLLPAQECEFKLTNLLE 232 (745)
T ss_pred ceEEEEEecceEEEEEcCCCcccceeEEe--ccccccHHHHHHHhcCCcccccCCcccccchhhhccHHHHHHHHHHHHH
Confidence 99999999999999999999988999997 55555444454432 234799999999999999999
Q ss_pred hcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecCCCCCCCcccccccCcCcccCCC
Q 007267 221 TLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPPDHGAGQLDTRRYGEQYASKG 300 (610)
Q Consensus 221 ~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~ 300 (610)
+|+++ +|+++++. ++.||+|+||++|+.+|++..++. ++||++|++||||.|||++++++.++++|++.
T Consensus 233 ~L~~d-~wpV~~g~--------Rp~RcTG~Al~iA~~Ll~~c~p~~--g~rIv~f~gGPcT~GpG~vv~~el~~piRshh 301 (745)
T KOG1986|consen 233 ELQPD-PWPVPPGH--------RPLRCTGVALSIASGLLEGCFPNT--GARIVLFAGGPCTRGPGTVVSRELKEPIRSHH 301 (745)
T ss_pred HhcCC-CCCCCCCC--------CcccchhHHHHHHHHHhcccCCCC--cceEEEeccCCCCcCCceecchhhcCCCcCcc
Confidence 99998 89998865 478999999999999999887654 79999999999999999999999999999865
Q ss_pred -cc-hhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeCCCCCCchhHHHHHHhcc--
Q 007267 301 -ED-ADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYSSTDDSTLPQDIYRMLSR-- 376 (610)
Q Consensus 301 -~~-~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~~~~~~l~~dl~~~l~~-- 376 (610)
.+ ..++|++++.+||++||++++++|++||+|+++.+|+|+++|+++++.|||.+.+.++|+.+.|+++++|++++
T Consensus 302 di~~d~a~y~kKa~KfY~~La~r~~~~ghvlDifa~~lDQvGi~EMk~l~~~TGG~lvl~dsF~~s~Fk~sfqR~f~~d~ 381 (745)
T KOG1986|consen 302 DIEKDNAPYYKKAIKFYEKLAERLANQGHVLDIFAAALDQVGILEMKPLVESTGGVLVLGDSFNTSIFKQSFQRIFTRDG 381 (745)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHHhCCceEeeeeeeccccchHHHHHHhhcCCcEEEEecccchHHHHHHHHHHhcccc
Confidence 33 35689999999999999999999999999999999999999999999999999999999999999999999995
Q ss_pred ----CcceeeEEEEEccCCeeeeeeeeccccCCCCCc-------------ceeeeecCCCccEEEEEEEecCCCcCCCCC
Q 007267 377 ----PYAFNCIMRLRTSSEFKPGHSYGHFFPDPQYEN-------------VQHIICCDSYATYAYDFDFANAAGFARHTS 439 (610)
Q Consensus 377 ----~~~~~a~lrvr~S~gl~v~~~~G~~~~~~~~~~-------------~~~i~~~~~~~t~a~~fe~~~~~~l~~~~~ 439 (610)
.+||||.|+|+||++++|++++|++.+.+++++ .|+++.+++.+++++.||+......+ .+
T Consensus 382 ~~~l~~~fn~~leV~tSkdlkI~g~IGp~~Sl~~k~~~vsdt~ig~g~t~~wkm~~ls~~t~~s~~fei~~~~~~~--~~ 459 (745)
T KOG1986|consen 382 EGDLKMGFNGTLEVKTSKDLKIQGVIGPCVSLNKKGPNVSDTEIGEGNTSAWKMCGLSPSTTLSLFFEISNQHNIP--QS 459 (745)
T ss_pred ccchhhhcCceEEEEecCCcEEEecccccccccCCCCccccceeccccccceeeeccCCCceEEEEEEeccccCCC--CC
Confidence 479999999999999999999999998766432 49999999999999999999865432 35
Q ss_pred CccEEEEEEEeeecCCccccccc-------cc-----ccc----------------------------------------
Q 007267 440 EQPMLQIAFQYTVVVPPEELSSE-------GL-----GSV---------------------------------------- 467 (610)
Q Consensus 440 ~~~~iQ~a~~Yt~~~g~~~~~n~-------~~-----~s~---------------------------------------- 467 (610)
..+||||++.|.+.+|++|+|.+ +. ..+
T Consensus 460 ~~~~iQFiT~Yq~s~g~~riRVtT~~r~~~d~~~~~i~~~FDqEaaAV~mAR~~~~kae~e~~~d~~rwlDr~Lirlc~k 539 (745)
T KOG1986|consen 460 GQGYIQFITQYQHSSGQKRIRVTTLARPWADSGSPEISQSFDQEAAAVLMARLALLKAETEDGPDVLRWLDRNLIRLCQK 539 (745)
T ss_pred CeeEEEEEEEEEcCCCcEEEEEEEeehhhccccchHhhhccchHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHH
Confidence 68999999999999999877611 00 000
Q ss_pred ---cccCChhhhHh----hhccccc-----------ccCCCCCCCcccccccchhhhcCC--------------------
Q 007267 468 ---SSALEPSSLQR----AVYPLLT-----------SYSTPDKQAFPRHSLSRAALITSG-------------------- 509 (610)
Q Consensus 468 ---~~~~~~~~~~~----~~yP~l~-----------~~~spde~~~~~~~l~r~~~~~s~-------------------- 509 (610)
|.+.||.++++ ++||||| +|.|||||+|+||.|.|+++.++.
T Consensus 540 Fg~y~k~dPssf~l~~~fsl~PQfmfhLRRS~fLqvfNnSPDEt~~yrhll~~e~v~~sliMIqP~L~sySf~g~~epvl 619 (745)
T KOG1986|consen 540 FGDYRKDDPSSFRLSPNFSLYPQFMFHLRRSPFLQVFNNSPDETAYYRHLLNREDVDNSLIMIQPTLLSYSFNGPPEPVL 619 (745)
T ss_pred HhccCCCCchhhcCChhhhhhHHHHHhhccchhhhccCCCcchHHHHHHHHhhccchhhhheecceeeeeecCCCCceeE
Confidence 89999999998 8999999 489999999999999999886655
Q ss_pred --------CcEEEEecCcEEEEEecCCCCC--CCCCC-CChhHHHHHHH-------HHHHhcCCCCceEEEEeCCCCcHH
Q 007267 510 --------SPIFLLDAFTTIIVFYSSTADP--TLPFP-PPQDCLLRTTI-------NKMKQERSITPKLIFIRGGQDDAT 571 (610)
Q Consensus 510 --------~~iyllD~g~~~~i~~G~~v~~--~~~~~-~~~~~~~~~~i-------~~i~~~r~~~p~l~~~~~~~~~~~ 571 (610)
|.|+|||++|+|+||+|.++++ +++|+ .|+++.+++++ ++|..+|+|+||+++|+||+||+|
T Consensus 620 LD~~Si~~D~iLLlDt~f~i~i~hG~tIaqWR~~gy~~~pe~~~f~~LL~ap~~dA~el~~~RFP~PR~v~~~q~GSQAR 699 (745)
T KOG1986|consen 620 LDVASILADRILLLDTYFTIVIFHGSTIAQWRKAGYHEQPEYENFKELLEAPREDAQELLLERFPMPRYVVTDQGGSQAR 699 (745)
T ss_pred ecccccCCceEEEeecceEEEEECCchHHHHHhcccccChhhHHHHHHHHhHHHHHHHHHHhhCCCCeEEEecCCccHHH
Confidence 6999999999999999999998 77888 89999999988 577799999999999999999999
Q ss_pred HHHhhccCCCCC---C----CCCC-cccccHHHHHHHHHHHHH
Q 007267 572 IFENYLIEEQDV---D----GSGL-TSVMGFVSFLEEISQSVV 606 (610)
Q Consensus 572 ~f~~~LveD~~~---~----~~~~-~~~~sy~dfl~~lh~~i~ 606 (610)
|+++++++..+. . ++.+ +++.|+..|+.||+|-+.
T Consensus 700 FLlsklnPS~t~~~~~~~~~s~~I~TDDvSlq~fm~hLkklav 742 (745)
T KOG1986|consen 700 FLLSKLNPSETHNNLTAHGGSSIILTDDVSLQVFMEHLKKLAV 742 (745)
T ss_pred hhhhhcCcchhccchhhccCCCeeeeccccHHHHHHHHHhhcC
Confidence 999999996531 1 2222 568999999999998653
No 5
>PTZ00395 Sec24-related protein; Provisional
Probab=100.00 E-value=1.5e-97 Score=829.52 Aligned_cols=565 Identities=17% Similarity=0.270 Sum_probs=466.7
Q ss_pred eeecccCccCCCHHHHHhcCCceeeEEccCCCCCCCCCCCccc--------CCCCCCCcCcCcCeeEecCceEe-CceeE
Q 007267 2 AVRATVSRFPSDPDAQEASGLPWGVTVTPFATKDENGAAPVYG--------SDGHMLPRCENCYAYFNTYCELE-QWAWT 72 (610)
Q Consensus 2 ~vR~t~~~~P~~~~~~~~~~lPlg~~v~Pf~~~~~~~~~~~~~--------~~~~~~~RC~~C~ayiNp~~~~~-~~~w~ 72 (610)
.||+|||.+|.+.++++.+.||||++++||+.+.+.|..+.++ ..+.+|+||.+|++|+|+++.++ .++++
T Consensus 654 ~~r~tmY~iP~~~~~~~~~~iP~gi~v~Pfa~~~~~e~~~~~~~~~~~~d~~~~~~~~rc~~c~~y~~~~~~~~~~~~~~ 733 (1560)
T PTZ00395 654 FLKSTLYQIPLFSETLKLSQIPFGIIVNPFACLNEGEGIDKIDMKDIINDKEENIEILRCPKCLGYLHATILEDISSSVQ 733 (1560)
T ss_pred hhhhhhhcCcchHHHHHhcCCCceeecchhhhcCCCCCCcccchhhcccchhhccceeecchhHhhhcchheecccceEE
Confidence 5899999999999999999999999999999987655433332 12457899999999999999998 68999
Q ss_pred EcCCCCCCCCChhhh---cccC----CC--------cCccccccccEEEEecCCCCcc----------------------
Q 007267 73 CSLCGSLNGLSSQAI---ARYT----HP--------QSCAEMISSFIDLDLPLEGSEE---------------------- 115 (610)
Q Consensus 73 C~~C~~~N~~p~~~~---~~~~----~~--------~~~pEL~~~tvey~~p~~y~~~---------------------- 115 (610)
|+||++.+.+.+... .+|. +. ..+--|.+|+||+++|+-|..+
T Consensus 734 c~~c~~~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 813 (1560)
T PTZ00395 734 CVFCDTDFLINENVLFDIFQYNEKIGHKESDHNEHGNSLSPLLKGSVDIIIPPIYYHNVNKFKLTYTYLNKNINQTAFMI 813 (1560)
T ss_pred EEecCCcchhhHHHHHHHHHHhhhhccccccccccccccchhhcCceeEEccchhhccCCccceeeehhhcchhhhhhhh
Confidence 999999999865421 1232 11 1123577899999998754210
Q ss_pred --------------------------------------------------------------------------------
Q 007267 116 -------------------------------------------------------------------------------- 115 (610)
Q Consensus 116 -------------------------------------------------------------------------------- 115 (610)
T Consensus 814 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 893 (1560)
T PTZ00395 814 TNKIMSFTKHISNSLVANDSKGGNKATSASAFGDSGDANFLAGGGYTNYGGAGGYNTYDNQSGYNNHDVVNNRGGSGAGN 893 (1560)
T ss_pred hhhhhhhhhhhcchheecccccccccchhhhcccccccccccccccccccccccccccccccccccccccccccccCcCc
Confidence
Q ss_pred -----------------------------------------------------ccCCCCcEEEEEEeCCCCh---hHHHH
Q 007267 116 -----------------------------------------------------ETMQARPVYVAAVDLSSSE---EFLEL 139 (610)
Q Consensus 116 -----------------------------------------------------~~~~~~p~~vFvID~s~~~---~~l~~ 139 (610)
-..+.||+|+||||||..+ +.+.+
T Consensus 894 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~PP~YvFLIDVS~~AVkSGLl~t 973 (1560)
T PTZ00395 894 HLYGKDHDVQNFDNVMDNANFTIHDMKNLICEKNGEPDSAKIRRNSFLAKYPQVKNMLPPYFVFVVECSYNAIYNNITYT 973 (1560)
T ss_pred ccccCcccccchhhhccCCceeeecchhhhhcccCCchhhhhhccchhhccccccCCCCCEEEEEEECCHHHHhhChHHH
Confidence 0014679999999999986 89999
Q ss_pred HHHHHHHHHHhCC-CCcEEEEEeecceeEEEEecCCC-------------cceeeeeeCCCCCccccccccc-cCcc--C
Q 007267 140 TRSALQAALEAVP-SGALFGLATFSHKIGLYDVQGAI-------------PVVKNVFIPSDTEDTLSLELED-VMPL--S 202 (610)
Q Consensus 140 l~~~l~~~l~~lp-~~~~VglITf~~~V~~~~l~~~~-------------~~~~~v~~~~~~~~~~~~dl~~-~~p~--~ 202 (610)
++++|+++|+.|+ ++++|||||||+.||||+|+... .+++| +++.||+| |+|+ +
T Consensus 974 acesIK~sLDsL~dpRTRVGIITFDSsLHFYNLks~l~~~~~~~~~~~~l~qPQM---------LVVSDLDDPFLPlP~d 1044 (1560)
T PTZ00395 974 ILEGIRYAVQNVKCPQTKIAIITFNSSIYFYHCKGGKGVSGEEGDGGGGSGNHQV---------IVMSDVDDPFLPLPLE 1044 (1560)
T ss_pred HHHHHHHHHhcCCCCCcEEEEEEecCcEEEEecCcccccccccccccccCCCceE---------EeecCCccCcCCCCcc
Confidence 9999999999986 57999999999999999997642 23444 46789999 4786 5
Q ss_pred cCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecCCCCC
Q 007267 203 QFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPPDH 282 (610)
Q Consensus 203 ~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~pt~ 282 (610)
++|+++.|+++.|+++|+.|+.++.... ....|+|+||++|..+|+..|+ +|||++|++++|++
T Consensus 1045 dLLVnL~ESRevIe~LLDkLPemFt~t~------------~~esCLGSALqAA~~aLk~~GG----GGKIiVF~SSLPni 1108 (1560)
T PTZ00395 1045 DLFFGCVEEIDKINTLIDTIKSVSTTMQ------------SYGSCGNSALKIAMDMLKERNG----LGSICMFYTTTPNC 1108 (1560)
T ss_pred CeeechHHHHHHHHHHHHHHHHHhhccC------------CCcccHHHHHHHHHHHHHhcCC----CceEEEEEcCCCCC
Confidence 7999999999999999999998864332 2579999999999999999874 59999999999999
Q ss_pred CCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcC--hhcchhhhccCccEEEEeCC
Q 007267 283 GAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTD--LASLKFLSIESGGSLFLYSS 360 (610)
Q Consensus 283 GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~--l~~l~~l~~~TGG~v~~~~~ 360 (610)
|||+|+.++. +.+|+.++.++++||++||.+|++++|+||||+++.+++| +++|+.|++.|||++++|+.
T Consensus 1109 GpGaLK~Re~--------~~KEk~Ll~pqd~FYK~LA~ECsk~qISVDLFLfSsqYvDVDVATLg~Lsr~TGGqlyyYPn 1180 (1560)
T PTZ00395 1109 GIGAIKELKK--------DLQENFLEVKQKIFYDSLLLDLYAFNISVDIFIISSNNVRVCVPSLQYVAQNTGGKILFVEN 1180 (1560)
T ss_pred CCCccccccc--------ccccccccccchHHHHHHHHHHHhcCCceEEEEccCcccccccccccchhcccceeEEEeCC
Confidence 9999986542 2356778899999999999999999999999999998876 79999999999999999999
Q ss_pred CCC----CchhHHHHHHhcc-CcceeeEEEEEccCCeeeeeee--eccccCCCCCcceeeeecCCCccEEEEEEEecCCC
Q 007267 361 TDD----STLPQDIYRMLSR-PYAFNCIMRLRTSSEFKPGHSY--GHFFPDPQYENVQHIICCDSYATYAYDFDFANAAG 433 (610)
Q Consensus 361 ~~~----~~l~~dl~~~l~~-~~~~~a~lrvr~S~gl~v~~~~--G~~~~~~~~~~~~~i~~~~~~~t~a~~fe~~~~~~ 433 (610)
|+. .+|.+||.+.|++ ++||+|+||||||+||+|+.+| |+++......++..+|.+++|++|+|+|++++ +
T Consensus 1181 Fna~rD~~KL~~DL~r~LTre~iGyEAVMRVRCS~GLrVs~fyG~GnnF~s~rStDLLaLP~Id~DqSfaVeLk~DE--k 1258 (1560)
T PTZ00395 1181 FLWQKDYKEIYMNIMDTLTSEDIAYCCELKLRYSHHMSVKKLFCCNNNFNSIISVDTIKIPKIRHDQTFAFLLNYSD--I 1258 (1560)
T ss_pred CcccccHHHHHHHHHHHhhccceeeEEEEEEECCCCeEEEEEeccCCccccccccccccccccCCCceEEEEEEecc--c
Confidence 964 4789999999997 6999999999999999999999 44553211245678999999999999999886 5
Q ss_pred cCCCCCCccEEEEEEEeeecCCccccc--ccc-------------------------------ccc--------------
Q 007267 434 FARHTSEQPMLQIAFQYTVVVPPEELS--SEG-------------------------------LGS-------------- 466 (610)
Q Consensus 434 l~~~~~~~~~iQ~a~~Yt~~~g~~~~~--n~~-------------------------------~~s-------------- 466 (610)
|. ....+|||+|+|||+.+|+||+| |.. +.+
T Consensus 1259 L~--~~~~AYFQaALLYTSssGERRIRVHTLALPVTSsLseVFrsADqdAIvslLAK~AV~~aLsssdARe~L~dklVdI 1336 (1560)
T PTZ00395 1259 SE--SKKQIYFQCACIYTNLWGDRFVRLHTTHMNLTSSLSTVFRYTDAEALMNILIKQLCTNILHNDNYSKIIIDNLAAI 1336 (1560)
T ss_pred cC--CCCcEEEEEEEeeccCCCcEEEEEEeeeecccCCHHHHHHhhcHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence 64 25689999999999999999887 210 000
Q ss_pred --------------c---------------------------------------cccCChhhhHhhhcccccccCCC-CC
Q 007267 467 --------------V---------------------------------------SSALEPSSLQRAVYPLLTSYSTP-DK 492 (610)
Q Consensus 467 --------------~---------------------------------------~~~~~~~~~~~~~yP~l~~~~sp-de 492 (610)
+ ++++++..+..+|||+|+++|++ ++
T Consensus 1337 LtaYRK~CAsssssgQLILPESLKLLPLYILSLLKS~AfRt~I~sDeRVyaL~rL~SmPI~~Li~yLYPRLYpLHdL~~e 1416 (1560)
T PTZ00395 1337 LFSYRINCASSAHSGQLILPDTLKLLPLFTSSLLKHNVTKKEILHDLKVYSLIKLLSMPIISSLLYVYPVMYVIHIKGKT 1416 (1560)
T ss_pred HHHHHHHhhccCCCccccchhHHHHHHHHHHHHhccccccCCCCccHHHHHHHHHhCCCHHHHHhhhcCceEEccccccc
Confidence 0 57888889999999999999874 11
Q ss_pred ---------CCcccccccchh-hhcCCCcEEEEecCcEEEEEecCCCCCCCC------------------CCCChhHHHH
Q 007267 493 ---------QAFPRHSLSRAA-LITSGSPIFLLDAFTTIIVFYSSTADPTLP------------------FPPPQDCLLR 544 (610)
Q Consensus 493 ---------~~~~~~~l~r~~-~~~s~~~iyllD~g~~~~i~~G~~v~~~~~------------------~~~~~~~~~~ 544 (610)
.....+..+|.+ .+++.+||||||+|..|+||+|.+++++|+ ++++.+.+++
T Consensus 1417 ~e~d~~d~d~~ivLPp~LrLS~ErLesdGIYLLDNGe~IyLWVG~~V~PqLLqDLFGv~~~~~~~~eLPelDT~iS~RVr 1496 (1560)
T PTZ00395 1417 NEIDSMDVDDDLFIPKTIPSSAEKIYSNGIYLLDACTHFYLYFGFHSDANFAKEIVGDIPTEKNAHELNLTDTPNAQKVQ 1496 (1560)
T ss_pred ccCCccCCCCccccCCcccchHHHhcCCcEEEEECCCEEEEEECCCCCHHHHHHHcCCCccccccccccCCCCHHHHHHH
Confidence 122234555553 478889999999999999999999999665 2467899999
Q ss_pred HHHHHHHhcC--CCCceEEEEeCCCCcHHHHHhhccCCCCCCCCCCcccccHHHHHHHHHHHHHHhh
Q 007267 545 TTINKMKQER--SITPKLIFIRGGQDDATIFENYLIEEQDVDGSGLTSVMGFVSFLEEISQSVVEYM 609 (610)
Q Consensus 545 ~~i~~i~~~r--~~~p~l~~~~~~~~~~~~f~~~LveD~~~~~~~~~~~~sy~dfl~~lh~~i~~~l 609 (610)
++|+.||+.| .++++++++||++..|.+|+++||||++. ++ +||+||||+|||+|++.|
T Consensus 1497 nII~~LR~~r~~~~Y~pL~IVRqgDp~E~~F~s~LVEDRs~-g~-----~SYvDFLc~LHKqIq~kl 1557 (1560)
T PTZ00395 1497 RIIKNLSRIHHFNKYVPLVMVAPKSNEEEHLISLCVEDKAD-KE-----YSYVNFLCFIHKLVHKRI 1557 (1560)
T ss_pred HHHHHHHHhccCCCcceEEEEeCCCchHHHHHHhCeecCCC-CC-----CCHHHHHHHHHHHHHHhc
Confidence 9999999886 57888999999999999999999999985 44 899999999999999976
No 6
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=100.00 E-value=1.1e-98 Score=773.63 Aligned_cols=576 Identities=25% Similarity=0.380 Sum_probs=497.7
Q ss_pred eeecccCccCCCHHHHHhcCCceeeEEccCCCCCCCCCCCcccCCCCCCCcCcC-cCeeEecCceEeC--ceeEEcCCCC
Q 007267 2 AVRATVSRFPSDPDAQEASGLPWGVTVTPFATKDENGAAPVYGSDGHMLPRCEN-CYAYFNTYCELEQ--WAWTCSLCGS 78 (610)
Q Consensus 2 ~vR~t~~~~P~~~~~~~~~~lPlg~~v~Pf~~~~~~~~~~~~~~~~~~~~RC~~-C~ayiNp~~~~~~--~~w~C~~C~~ 78 (610)
|||+|||+||.|+.+++++.+|++|+|+||++.+. +++. .++|+.|.. |+||+||||.+|. +.|+|+||+.
T Consensus 11 gir~twnvfpat~~da~~~~iPia~lY~Pl~e~~~--~~v~----~yepv~C~~pC~avlnpyC~id~r~~~W~CpfCnq 84 (755)
T COG5047 11 GIRLTWNVFPATRGDATRTVIPIACLYTPLHEDDA--LTVN----YYEPVKCTAPCKAVLNPYCHIDERNQSWICPFCNQ 84 (755)
T ss_pred ceEEEEecccCCccccccccccHHHhccccccccc--cCcc----cCCCceecccchhhcCcceeeccCCceEecceecC
Confidence 89999999999999999999999999999999753 2222 258999999 9999999999994 5899999999
Q ss_pred CCCCChhhhcccCC--CcCcc-cc--ccccEEEEecCCCCccccCCCCcEEEEEEeCCCChhHHHHHHHHHHHHHHhCCC
Q 007267 79 LNGLSSQAIARYTH--PQSCA-EM--ISSFIDLDLPLEGSEEETMQARPVYVAAVDLSSSEEFLELTRSALQAALEAVPS 153 (610)
Q Consensus 79 ~N~~p~~~~~~~~~--~~~~p-EL--~~~tvey~~p~~y~~~~~~~~~p~~vFvID~s~~~~~l~~l~~~l~~~l~~lp~ 153 (610)
+|.+|++ |.+ ..++| || .+.||||++++. ..-||+|+||||++...++|.++|++|+..|+.+|+
T Consensus 85 rn~lp~q----y~~iS~~~LplellpqssTiey~lskp------~~~ppvf~fvvD~~~D~e~l~~Lkdslivslsllpp 154 (755)
T COG5047 85 RNTLPPQ----YRDISNANLPLELLPQSSTIEYTLSKP------VILPPVFFFVVDACCDEEELTALKDSLIVSLSLLPP 154 (755)
T ss_pred CCCCChh----hcCCCcccCCccccCCCceEEEEccCC------ccCCceEEEEEEeecCHHHHHHHHHHHHHHHhcCCc
Confidence 9999999 554 45666 98 689999999874 457899999999999999999999999999999999
Q ss_pred CcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccccC---------------c------cCcCccchHhHH
Q 007267 154 GALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDVM---------------P------LSQFLAPVETFK 212 (610)
Q Consensus 154 ~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~~---------------p------~~~~l~~~~e~~ 212 (610)
++.||||||++.|++|+++.....+++||. +.+++....|++++ + ..+|+.|+++|+
T Consensus 155 eaLvglItygt~i~v~el~ae~~~r~~VF~--g~~eyt~~~L~~ll~~~~~~~~~~~es~is~~~~~~~~rFl~p~q~ce 232 (755)
T COG5047 155 EALVGLITYGTSIQVHELNAENHRRSYVFS--GNKEYTKENLQELLALSKPTKSGGFESKISGIGQFASSRFLLPTQQCE 232 (755)
T ss_pred cceeeEEEecceeEEEeccccccCcceeec--chHHHHHHHHHHHhcccCCCCcchhhhhcccccccchhhhhccHHHHH
Confidence 999999999999999999988888889997 44444444443321 1 135999999999
Q ss_pred HHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecCCCCCCCcccccccC
Q 007267 213 ENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPPDHGAGQLDTRRY 292 (610)
Q Consensus 213 ~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~pt~GpG~l~~~~~ 292 (610)
..+.++|++|+++ +|++.++. ++.||+|+||.+|..+|+...++ .++||++|++||||+|||+|++++.
T Consensus 233 ~~L~n~le~L~pd-~~~v~~~~--------Rp~RCTGsAl~ias~Ll~~~~p~--~~~~i~lF~~GPcTvGpG~Vvs~el 301 (755)
T COG5047 233 FKLLNILEQLQPD-PWPVPAGK--------RPLRCTGSALNIASSLLEQCFPN--AGCHIVLFAGGPCTVGPGTVVSTEL 301 (755)
T ss_pred HHHHHHHHHhCCC-CccCCCCC--------CCccccchhHHHHHHHHHhhccC--cceeEEEEcCCCccccCceeeehhh
Confidence 9999999999999 79888764 48999999999999999988764 4899999999999999999999999
Q ss_pred cCcccCCCc-ch-hhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeCCCCCCchhHHH
Q 007267 293 GEQYASKGE-DA-DRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYSSTDDSTLPQDI 370 (610)
Q Consensus 293 ~~~~~~~~~-~~-e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~~~~~~l~~dl 370 (610)
++++|++.. +. .+++.+++.+||++||++.+++|+++|+|+.+.+|+|+.+|++|...|||.+.+.++|+.+.|++++
T Consensus 302 kEpmRshH~ie~d~aqh~kka~KFY~~laeR~a~~gh~~DifagcldqIGI~eM~~L~~sTgg~lvlsdsF~t~ifkqSf 381 (755)
T COG5047 302 KEPMRSHHDIESDSAQHSKKATKFYKGLAERVANQGHALDIFAGCLDQIGIMEMEPLTTSTGGALVLSDSFTTSIFKQSF 381 (755)
T ss_pred cccccccccccccchhhccchHHHHHHHHHHHhccchhHHHHHHHHHhhhhhcchhhccCCcceEEEeccccHHHHHHHH
Confidence 999998543 33 3789999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhccC------cceeeEEEEEccCCeeeeeeeeccccCCCCC-------------cceeeeecCCCccEEEEEEEecC
Q 007267 371 YRMLSRP------YAFNCIMRLRTSSEFKPGHSYGHFFPDPQYE-------------NVQHIICCDSYATYAYDFDFANA 431 (610)
Q Consensus 371 ~~~l~~~------~~~~a~lrvr~S~gl~v~~~~G~~~~~~~~~-------------~~~~i~~~~~~~t~a~~fe~~~~ 431 (610)
+|+|.++ +||||.|+|.||++++|++++|+...-+++. +.|++.++.|.++++++||+..+
T Consensus 382 qrif~~d~~g~l~~gfNa~m~V~TsKnl~~~g~ig~a~~~~k~~~ni~~~eigi~~t~swkm~slsPk~nyal~fei~~~ 461 (755)
T COG5047 382 QRIFNRDSEGYLKMGFNANMEVKTSKNLKIKGLIGHAVSVKKKANNISDSEIGIGATNSWKMASLSPKSNYALYFEIALG 461 (755)
T ss_pred HHHhCcCcccchhhhhccceeEeeccCceeeeeecceeeecccccccccccccccccccccccccCCCcceEEEEEeccc
Confidence 9999986 7999999999999999999999988755432 24999999999999999999875
Q ss_pred CCcC-CCCCCccEEEEEEEeeecCCccccccc---------c----------------------cccc------------
Q 007267 432 AGFA-RHTSEQPMLQIAFQYTVVVPPEELSSE---------G----------------------LGSV------------ 467 (610)
Q Consensus 432 ~~l~-~~~~~~~~iQ~a~~Yt~~~g~~~~~n~---------~----------------------~~s~------------ 467 (610)
.+-. .+....+||||.++|.+.+|.-|+|.+ + .+..
T Consensus 462 ~~~~~~~~~~~a~iQfiT~yQhss~t~riRVtTvar~f~~~~~p~i~~SFdqEaaaV~~aR~a~~K~~~ed~~Dv~rw~d 541 (755)
T COG5047 462 AASGSAQRPAEAYIQFITTYQHSSGTYRIRVTTVARMFTDGGLPKINRSFDQEAAAVFMARIAAFKAETEDIIDVFRWID 541 (755)
T ss_pred cCCCccCCcccchhhhhhhhhccCCcEEEEEeehhhhhccCCChhhhhcchhhHHHHHHHHHHHhhcccccchhHHHHHH
Confidence 4321 112357999999999999998555410 0 0000
Q ss_pred ------------cccCChhhhHh----hhccccc-----------ccCCCCCCCcccccccchhhhcCC-----------
Q 007267 468 ------------SSALEPSSLQR----AVYPLLT-----------SYSTPDKQAFPRHSLSRAALITSG----------- 509 (610)
Q Consensus 468 ------------~~~~~~~~~~~----~~yP~l~-----------~~~spde~~~~~~~l~r~~~~~s~----------- 509 (610)
|++.||.++++ .+||||+ +|.|||||+||||.|.++.+.++.
T Consensus 542 r~lirlcq~fa~y~k~dpssfrl~~~f~lypqf~y~lrRSpfL~vfNnSPDEt~fyrh~l~~~dv~~sLimiqPtL~Sys 621 (755)
T COG5047 542 RNLIRLCQKFADYRKDDPSSFRLDPNFTLYPQFMYHLRRSPFLSVFNNSPDETAFYRHMLNNADVNDSLIMIQPTLQSYS 621 (755)
T ss_pred HHHHHHHHHHHhcCCCCchhhcCCcchhhhhHHHhhhhccceeeccCCCcchHHHHHHHHhcccccchhhhhcchheeee
Confidence 89999999999 7999999 589999999999999999775544
Q ss_pred -----------------CcEEEEecCcEEEEEecCCCCC--CCCCC-CChhHHHHHHH-------HHHHhcCCCCceEEE
Q 007267 510 -----------------SPIFLLDAFTTIIVFYSSTADP--TLPFP-PPQDCLLRTTI-------NKMKQERSITPKLIF 562 (610)
Q Consensus 510 -----------------~~iyllD~g~~~~i~~G~~v~~--~~~~~-~~~~~~~~~~i-------~~i~~~r~~~p~l~~ 562 (610)
|.|+|||++++++||.|+.+++ ..+|+ .|++..++.++ .++..+|+|.|++++
T Consensus 622 ~~~~~~pVlLDs~svkpdviLLlDtff~Ili~hG~~iaqwr~agyq~qpey~~lK~Ll~~p~~ea~ell~dRfP~Prfi~ 701 (755)
T COG5047 622 FEKGGVPVLLDSVSVKPDVILLLDTFFHILIFHGSYIAQWRNAGYQEQPEYLNLKELLEAPRLEAAELLQDRFPIPRFIV 701 (755)
T ss_pred ccCCCceEEEeccccCCCeEEEeeceeEEEEECChHHHHHHhhhhhcCchhhhHHHHhhchhhHHHHHHHhhCCCCeEEE
Confidence 6899999999999999999998 77787 89999999999 567799999999999
Q ss_pred EeCCCCcHHHHHhhccCCCCC---CC--CCC--cccccHHHHHHHHHHHHH
Q 007267 563 IRGGQDDATIFENYLIEEQDV---DG--SGL--TSVMGFVSFLEEISQSVV 606 (610)
Q Consensus 563 ~~~~~~~~~~f~~~LveD~~~---~~--~~~--~~~~sy~dfl~~lh~~i~ 606 (610)
|+||+||+||+++++++..+. .+ ++. +++.+|..|..|+.+-+.
T Consensus 702 teqggSQaRfLlskinPsd~~~~~~~~~s~tilTddv~lq~fm~hl~~lav 752 (755)
T COG5047 702 TEQGGSQARFLLSKINPSDITNKMSGGGSETILTDDVNLQKFMNHLRKLAV 752 (755)
T ss_pred ecCCccHHHHHHhhcCccccccccccCccceeeecccCHHHHHHHHHHHhc
Confidence 999999999999999996432 12 111 468999999999998654
No 7
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=100.00 E-value=1.1e-96 Score=783.41 Aligned_cols=552 Identities=21% Similarity=0.406 Sum_probs=470.8
Q ss_pred eeecccCccCCCHHHHHhcCCceeeEEccCCCCCCCCCCCcccCCCCCCCcCcCcCeeEecCceEeC--ceeEEcCCCCC
Q 007267 2 AVRATVSRFPSDPDAQEASGLPWGVTVTPFATKDENGAAPVYGSDGHMLPRCENCYAYFNTYCELEQ--WAWTCSLCGSL 79 (610)
Q Consensus 2 ~vR~t~~~~P~~~~~~~~~~lPlg~~v~Pf~~~~~~~~~~~~~~~~~~~~RC~~C~ayiNp~~~~~~--~~w~C~~C~~~ 79 (610)
+||+|+|++|.+.+++++++||||++|+||.++.+.+-|++++ ....|+||++|++|+|||.+|+. ++|+||+|+..
T Consensus 152 yvrsT~yaiP~t~dl~~~skiPfgLVI~Pf~~l~~e~~~vpl~-~d~~ivRCrrCrsYiNPfv~fi~~g~kw~CNiC~~k 230 (861)
T COG5028 152 YVRSTMYAIPETNDLLKKSKIPFGLVIRPFLELYPEEDPVPLV-EDGSIVRCRRCRSYINPFVQFIEQGRKWRCNICRSK 230 (861)
T ss_pred HHHHHHhhCCCchhHHHhcCCCceEEeehhhhcCccCCCCccC-CCCcchhhhhhHhhcCceEEEecCCcEEEEeecccc
Confidence 5899999999999999999999999999999987644444433 33448999999999999999983 59999999999
Q ss_pred CCCChhhh-ccc-----CCCcCccccccccEEEEecCCCCccccCCCCcEEEEEEeCCCCh---hHHHHHHHHHHHHHHh
Q 007267 80 NGLSSQAI-ARY-----THPQSCAEMISSFIDLDLPLEGSEEETMQARPVYVAAVDLSSSE---EFLELTRSALQAALEA 150 (610)
Q Consensus 80 N~~p~~~~-~~~-----~~~~~~pEL~~~tvey~~p~~y~~~~~~~~~p~~vFvID~s~~~---~~l~~l~~~l~~~l~~ 150 (610)
|++|..+. ..+ .++.+||||.+++|||++|++|+.+ .+.||+|||+||||.++ +.+.++..+|++.|+.
T Consensus 231 N~vp~~~~~~~~~~~~r~d~~~r~El~~~vvdf~ap~~Y~~~--~p~P~~yvFlIDVS~~a~~~g~~~a~~r~Il~~l~~ 308 (861)
T COG5028 231 NDVPEGFDNPSGPNDPRSDRYSRPELKSGVVDFLAPKEYSLR--QPPPPVYVFLIDVSFEAIKNGLVKAAIRAILENLDQ 308 (861)
T ss_pred ccCcccccCcCCCCCccccccccchhhceeeEEecccceeec--cCCCCEEEEEEEeehHhhhcchHHHHHHHHHhhccC
Confidence 99998864 222 2256789999999999999999876 35589999999999986 7777788888888887
Q ss_pred CC---CCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccc-cCccC--cCccchHhHHHHHHHHHHhcCC
Q 007267 151 VP---SGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELED-VMPLS--QFLAPVETFKENITSALETLRP 224 (610)
Q Consensus 151 lp---~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~-~~p~~--~~l~~~~e~~~~i~~~L~~L~~ 224 (610)
+| +++||+||.||+.||+++++.+.. ..+..+.|+|+ ++|.. .|++|+.+|+..++.+|+.++.
T Consensus 309 ~~~~dpr~kIaii~fD~sl~ffk~s~d~~----------~~~~~vsdld~pFlPf~s~~fv~pl~~~k~~~etLl~~~~~ 378 (861)
T COG5028 309 IPNFDPRTKIAIICFDSSLHFFKLSPDLD----------EQMLIVSDLDEPFLPFPSGLFVLPLKSCKQIIETLLDRVPR 378 (861)
T ss_pred CCCCCCcceEEEEEEcceeeEEecCCCCc----------cceeeecccccccccCCcchhcccHHHHHHHHHHHHHHhhh
Confidence 75 589999999999999999987651 11245688888 47863 7999999999999999999999
Q ss_pred CCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecCCCCCCCcccccccCcCcccCCCcchh
Q 007267 225 TTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDAD 304 (610)
Q Consensus 225 ~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e 304 (610)
++.+.. .+..|+|+||++|..+++.+| |||++|.++.||.|.|+|..|++ +|
T Consensus 379 If~d~~------------~pk~~~G~aLk~a~~l~g~~G------Gkii~~~stlPn~G~Gkl~~r~d----------~e 430 (861)
T COG5028 379 IFQDNK------------SPKNALGPALKAAKSLIGGTG------GKIIVFLSTLPNMGIGKLQLRED----------KE 430 (861)
T ss_pred hhcccC------------CCccccCHHHHHHHHHhhccC------ceEEEEeecCCCccccccccccc----------ch
Confidence 976542 378999999999999998876 89999999999999999998765 35
Q ss_pred hccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeCCCCCCc------hhHHHHHHhccCc
Q 007267 305 RALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYSSTDDST------LPQDIYRMLSRPY 378 (610)
Q Consensus 305 ~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~~~~~~------l~~dl~~~l~~~~ 378 (610)
+.++++++.||+++|.+|++.||+||+|+++.+|+|++|++.|++.|||..++|++|+..+ |.+||.+++.++.
T Consensus 431 ~~ll~c~d~fYk~~a~e~~k~gIsvd~Flt~~~yidvaTls~l~~~T~G~~~~Yp~f~~~~~~d~~kl~~dL~~~ls~~~ 510 (861)
T COG5028 431 SSLLSCKDSFYKEFAIECSKVGISVDLFLTSEDYIDVATLSHLCRYTGGQTYFYPNFSATRPNDATKLANDLVSHLSMEI 510 (861)
T ss_pred hhhccccchHHHHHHHHHHHhcceEEEEeccccccchhhhcchhhccCcceEEcCCcccCCchhHHHHHHHHHHhhhhhh
Confidence 6689999999999999999999999999999999999999999999999999999998776 9999999999999
Q ss_pred ceeeEEEEEccCCeeeeeeeeccccCCCCCcceeeeecCCCccEEEEEEEecCCCcCCCCCCccEEEEEEEeeecCCccc
Q 007267 379 AFNCIMRLRTSSEFKPGHSYGHFFPDPQYENVQHIICCDSYATYAYDFDFANAAGFARHTSEQPMLQIAFQYTVVVPPEE 458 (610)
Q Consensus 379 ~~~a~lrvr~S~gl~v~~~~G~~~~~~~~~~~~~i~~~~~~~t~a~~fe~~~~~~l~~~~~~~~~iQ~a~~Yt~~~g~~~ 458 (610)
||+++||||||+|++++++|||++.+. .+++.++.+++|+|+.|+|++++ ++. ...+|||.|++||..+|+||
T Consensus 511 gy~~~~rvR~S~glr~s~fyGnf~~rs--~dl~~F~tm~rd~Sl~~~~sid~--~l~---~~~v~fQvAlL~T~~~GeRR 583 (861)
T COG5028 511 GYEAVMRVRCSTGLRVSSFYGNFFNRS--SDLCAFSTMPRDTSLLVEFSIDE--KLM---TSDVYFQVALLYTLNDGERR 583 (861)
T ss_pred hhheeeEeeccCceehhhhhccccccC--cccccccccCCCceEEEEEEecc--ccc---CCceEEEEEEEeeccCCceE
Confidence 999999999999999999999999876 67889999999999999999986 553 47999999999999999999
Q ss_pred cc--ccc------------------------------cc-cc--------------------------------------
Q 007267 459 LS--SEG------------------------------LG-SV-------------------------------------- 467 (610)
Q Consensus 459 ~~--n~~------------------------------~~-s~-------------------------------------- 467 (610)
+| |.+ +. +.
T Consensus 584 iRVvn~s~~~ss~~~evyasadq~aIa~~lak~a~~~~~~~s~~~~r~~i~~s~~~IL~~Ykk~~~~snt~tql~Lp~nL 663 (861)
T COG5028 584 IRVVNLSLPTSSSIREVYASADQLAIACILAKKASTKALNSSLKEARVLINKSMVDILKAYKKELVKSNTSTQLPLPANL 663 (861)
T ss_pred EEEEEeccccchhHHHHHHhccHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHhhccCCccccchhhh
Confidence 87 321 00 00
Q ss_pred --------------------------------cccCChhhhHhhhcccccccCCCCCCC-------cccccccchhh-hc
Q 007267 468 --------------------------------SSALEPSSLQRAVYPLLTSYSTPDKQA-------FPRHSLSRAAL-IT 507 (610)
Q Consensus 468 --------------------------------~~~~~~~~~~~~~yP~l~~~~spde~~-------~~~~~l~r~~~-~~ 507 (610)
+.++++..+++.|||++++.|+.-+++ ...+..+.++. .+
T Consensus 664 ~lLPll~lal~Ks~~~rs~~~~sD~r~~~L~~l~~~p~~~l~~~iYP~lyalHdm~~e~~l~~~~~~~~~~piNaT~s~l 743 (861)
T COG5028 664 KLLPLLMLALLKSSAFRSGSTPSDIRISALNRLTSLPLKQLMRNIYPTLYALHDMPIEAGLPDEGLLVLPSPINATSSLL 743 (861)
T ss_pred HHHHHHHHHHhhhcccccCCCccchhHHHHHHhhcCCHHHHHHhhccceeeecccccccCCCcccccccccchhhhHHHH
Confidence 567788899999999999998654433 22333333322 34
Q ss_pred CCCcEEEEecCcEEEEEecCCCCCCCC------------------CC---CChhHHHHHHHHHHHh-cCCCCceEEEEeC
Q 007267 508 SGSPIFLLDAFTTIIVFYSSTADPTLP------------------FP---PPQDCLLRTTINKMKQ-ERSITPKLIFIRG 565 (610)
Q Consensus 508 s~~~iyllD~g~~~~i~~G~~v~~~~~------------------~~---~~~~~~~~~~i~~i~~-~r~~~p~l~~~~~ 565 (610)
..+|+||+|+|.++|+|+|..+++.++ ++ ++.+.+++++|+++|+ .+-.++.++++|+
T Consensus 744 e~~GlYLidtg~~iflw~g~d~~p~Ll~dlf~~~~~~~I~~~k~~~p~~~n~~n~~v~~iI~~lrs~~~~~tl~lvlVR~ 823 (861)
T COG5028 744 ESGGLYLIDTGQKIFLWFGKDAVPSLLQDLFGVDSLSDIPSGKFTLPPTGNEFNERVRNIIGELRSVNDDSTLPLVLVRG 823 (861)
T ss_pred hcCCeEEEEcCCEEEEEecCCCCHHHHHHhcCcchhhhccccccccCCcCCHHHHHHHHHHHHHHhhCCCCccceEEEec
Confidence 668999999999999999999998554 22 6899999999999998 7777778999999
Q ss_pred CC-Cc-HHHHHhhccCCCCCCCCCCcccccHHHHHHHHHHHHHH
Q 007267 566 GQ-DD-ATIFENYLIEEQDVDGSGLTSVMGFVSFLEEISQSVVE 607 (610)
Q Consensus 566 ~~-~~-~~~f~~~LveD~~~~~~~~~~~~sy~dfl~~lh~~i~~ 607 (610)
|. +. +-||.+.||||++.|. +||.|||+.||+.|++
T Consensus 824 ~~d~s~~~~~~s~lVEDk~~n~------~SY~~yL~~lh~ki~~ 861 (861)
T COG5028 824 GGDPSLRLWFFSTLVEDKTLNI------PSYLDYLQILHEKIKS 861 (861)
T ss_pred CCCcchhhheehheecccccCC------ccHHHHHHHHHHHhcC
Confidence 94 44 7899999999999875 8999999999999874
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=4.3e-48 Score=389.49 Aligned_cols=241 Identities=28% Similarity=0.367 Sum_probs=208.0
Q ss_pred CCCcEEEEEEeCCCChhHHHHHHHHHHHHHHhCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccc-------
Q 007267 119 QARPVYVAAVDLSSSEEFLELTRSALQAALEAVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTL------- 191 (610)
Q Consensus 119 ~~~p~~vFvID~s~~~~~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~------- 191 (610)
|.||+|+||||+|..+.+++.+|++|+++|+.||++++|||||||++||||+|+...+.+++||.+ .+++.
T Consensus 1 p~pp~~vFviDvs~~~~el~~l~~sl~~~L~~lP~~a~VGlITfd~~V~~~~L~~~~~~~~~vf~g--~~~~~~~~~~~~ 78 (267)
T cd01478 1 TSPPVFLFVVDTCMDEEELDALKESLIMSLSLLPPNALVGLITFGTMVQVHELGFEECSKSYVFRG--NKDYTAKQIQDM 78 (267)
T ss_pred CCCCEEEEEEECccCHHHHHHHHHHHHHHHHhCCCCCEEEEEEECCEEEEEEcCCCcCceeeeccC--CccCCHHHHHHH
Confidence 458999999999999999999999999999999999999999999999999999877777888874 22221
Q ss_pred --------------ccccccc-Cc--cCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHH
Q 007267 192 --------------SLELEDV-MP--LSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMES 254 (610)
Q Consensus 192 --------------~~dl~~~-~p--~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~ 254 (610)
..++++. .| .++||+|++||++.|+++|++|+++ .|...++. ++.||+|+||++
T Consensus 79 l~~~~~~~~~~~~~~~~~~~~~~p~~~~~flvpl~e~~~~i~~lLe~L~~~-~~~~~~~~--------r~~r~~G~Al~~ 149 (267)
T cd01478 79 LGLGGPAMRPSASQHPGAGNPLPSAAASRFLLPVSQCEFTLTDLLEQLQPD-PWPVPAGH--------RPLRCTGVALSI 149 (267)
T ss_pred hccccccccccccCcCCccccccccccccEEEEHHHHHHHHHHHHHhCccc-ccccCCCC--------CCCCchHHHHHH
Confidence 1123442 34 3589999999999999999999987 46554332 478999999999
Q ss_pred HHHhhccccCCCcccceEEEEecCCCCCCCcccccccCcCcccCCC-cchh-hccCCcchHHHHHHHHHHHHcCcEEEEE
Q 007267 255 LFNYLGSEYGNTFALARVFAFLSGPPDHGAGQLDTRRYGEQYASKG-EDAD-RALLPEQTPFYKDLAAVAVQAGVCVDIF 332 (610)
Q Consensus 255 a~~lL~~~~~~~~~~GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~-~~~e-~~~~~~~~~fY~~la~~~~~~gisvDlf 332 (610)
|..+|+...++ .||||++|++|+||.|||+|+.++.++.+|++. ++++ .++++++.+||++||.+|+++||+||+|
T Consensus 150 A~~ll~~~~~~--~gGki~~F~sg~pT~GpG~l~~r~~~~~~r~~~d~~~~~~~~~~~a~~fY~~la~~~~~~~vsvDlF 227 (267)
T cd01478 150 AVGLLEACFPN--TGARIMLFAGGPCTVGPGAVVSTELKDPIRSHHDIDKDNAKYYKKAVKFYDSLAKRLAANGHAVDIF 227 (267)
T ss_pred HHHHHHhhcCC--CCcEEEEEECCCCCCCCceeeccccccccccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEE
Confidence 99999965432 369999999999999999999999888888754 4554 4799999999999999999999999999
Q ss_pred EecCCCcChhcchhhhccCccEEEEeCCCCCCchhHHHHH
Q 007267 333 AITNEYTDLASLKFLSIESGGSLFLYSSTDDSTLPQDIYR 372 (610)
Q Consensus 333 ~~~~~~~~l~~l~~l~~~TGG~v~~~~~~~~~~l~~dl~~ 372 (610)
+++.+|+|++||+.|++.|||.+++|++|+.+.|+++++|
T Consensus 228 ~~s~d~vglaem~~l~~~TGG~v~~~~~f~~~~f~~s~~~ 267 (267)
T cd01478 228 AGCLDQVGLLEMKVLVNSTGGHVVLSDSFTTSIFKQSFQR 267 (267)
T ss_pred eccccccCHHHHHHHHHhcCcEEEEeCCcchHHHHHHhcC
Confidence 9999999999999999999999999999999999998864
No 9
>cd01479 Sec24-like Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24
Probab=100.00 E-value=6.2e-46 Score=370.94 Aligned_cols=229 Identities=26% Similarity=0.455 Sum_probs=199.9
Q ss_pred CCCcEEEEEEeCCCCh---hHHHHHHHHHHHHHHhCCCC---cEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccc
Q 007267 119 QARPVYVAAVDLSSSE---EFLELTRSALQAALEAVPSG---ALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLS 192 (610)
Q Consensus 119 ~~~p~~vFvID~s~~~---~~l~~l~~~l~~~l~~lp~~---~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~ 192 (610)
|.||+|+||||+|..+ +.+++++++|+++|+.+|++ ++|||||||+.||||+++....++++. ++
T Consensus 1 p~pp~~~FvIDvs~~a~~~g~~~~~~~si~~~L~~lp~~~~~~~VgiITfd~~v~~y~l~~~~~~~q~~---------vv 71 (244)
T cd01479 1 PQPAVYVFLIDVSYNAIKSGLLATACEALLSNLDNLPGDDPRTRVGFITFDSTLHFFNLKSSLEQPQMM---------VV 71 (244)
T ss_pred CCCCEEEEEEEccHHHHhhChHHHHHHHHHHHHHhcCCCCCCeEEEEEEECCeEEEEECCCCCCCCeEE---------Ee
Confidence 4689999999999986 57999999999999999976 999999999999999998766544443 45
Q ss_pred ccccc-cCcc-CcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccc
Q 007267 193 LELED-VMPL-SQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALA 270 (610)
Q Consensus 193 ~dl~~-~~p~-~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~G 270 (610)
.|++| ++|+ ++||+|++|+++.|.++|++|+..+... .++.+|+|+||++|..+|+..| |
T Consensus 72 ~dl~d~f~P~~~~~lv~l~e~~~~i~~lL~~L~~~~~~~------------~~~~~c~G~Al~~A~~lL~~~G------G 133 (244)
T cd01479 72 SDLDDPFLPLPDGLLVNLKESRQVIEDLLDQIPEMFQDT------------KETESALGPALQAAFLLLKETG------G 133 (244)
T ss_pred eCcccccCCCCcceeecHHHHHHHHHHHHHHHHHHHhcC------------CCCcccHHHHHHHHHHHHHhcC------C
Confidence 68887 4677 6899999999999999999997653211 1378999999999999999654 9
Q ss_pred eEEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhcc
Q 007267 271 RVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIE 350 (610)
Q Consensus 271 kIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~ 350 (610)
||++|++|+||.|||+++.++.++.. ++++|+++++++++||++||.+|+++||+||+|+++.+++|+++|+.|++.
T Consensus 134 kIi~f~s~~pt~GpG~l~~~~~~~~~---~~~~e~~~~~p~~~fY~~la~~~~~~~isvDlF~~~~~~~dla~l~~l~~~ 210 (244)
T cd01479 134 KIIVFQSSLPTLGAGKLKSREDPKLL---STDKEKQLLQPQTDFYKKLALECVKSQISVDLFLFSNQYVDVATLGCLSRL 210 (244)
T ss_pred EEEEEeCCCCCcCCcccccCcccccc---CchhhhhhcCcchHHHHHHHHHHHHcCeEEEEEEccCcccChhhhhhhhhh
Confidence 99999999999999999998866533 344677899999999999999999999999999999999999999999999
Q ss_pred CccEEEEeC--CCC----CCchhHHHHHHhccC
Q 007267 351 SGGSLFLYS--STD----DSTLPQDIYRMLSRP 377 (610)
Q Consensus 351 TGG~v~~~~--~~~----~~~l~~dl~~~l~~~ 377 (610)
|||.+++|+ +|+ ..+|.+||+|.++|+
T Consensus 211 TGG~v~~y~~~~~~~~~d~~kl~~dl~~~ltr~ 243 (244)
T cd01479 211 TGGQVYYYPSFNFSAPNDVEKLVNELARYLTRK 243 (244)
T ss_pred cCceEEEECCccCCchhhHHHHHHHHHHHhccc
Confidence 999999999 553 458999999999986
No 10
>cd01468 trunk_domain trunk domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface. Some members of this family possess a partial MIDAS motif that is a characteristic feature of most vWA domain proteins.
Probab=100.00 E-value=5e-45 Score=364.71 Aligned_cols=228 Identities=34% Similarity=0.571 Sum_probs=200.3
Q ss_pred CCCcEEEEEEeCCCC---hhHHHHHHHHHHHHHHhCC--CCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccc
Q 007267 119 QARPVYVAAVDLSSS---EEFLELTRSALQAALEAVP--SGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSL 193 (610)
Q Consensus 119 ~~~p~~vFvID~s~~---~~~l~~l~~~l~~~l~~lp--~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~ 193 (610)
|+||+|+||||+|.. +++++.++++|+++|+.|| ++++|||||||+.||||+++....+.++ .++.
T Consensus 1 p~pp~~vFvID~s~~ai~~~~l~~~~~sl~~~l~~lp~~~~~~igiITf~~~V~~~~~~~~~~~~~~---------~v~~ 71 (239)
T cd01468 1 PQPPVFVFVIDVSYEAIKEGLLQALKESLLASLDLLPGDPRARVGLITYDSTVHFYNLSSDLAQPKM---------YVVS 71 (239)
T ss_pred CCCCEEEEEEEcchHhccccHHHHHHHHHHHHHHhCCCCCCcEEEEEEeCCeEEEEECCCCCCCCeE---------EEeC
Confidence 468999999999998 6899999999999999999 9999999999999999999876543333 3456
Q ss_pred ccccc-Ccc-CcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccce
Q 007267 194 ELEDV-MPL-SQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALAR 271 (610)
Q Consensus 194 dl~~~-~p~-~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~Gk 271 (610)
|++|. +|. .++|++++|+++.|.++|++|++++... .+ .++.||+|+||++|..+|+..+ .+||
T Consensus 72 dl~d~f~p~~~~~l~~~~e~~~~i~~~l~~l~~~~~~~-~~---------~~~~~~~G~Al~~A~~ll~~~~----~gGk 137 (239)
T cd01468 72 DLKDVFLPLPDRFLVPLSECKKVIHDLLEQLPPMFWPV-PT---------HRPERCLGPALQAAFLLLKGTF----AGGR 137 (239)
T ss_pred CCccCcCCCcCceeeeHHHHHHHHHHHHHhhhhhcccc-CC---------CCCcccHHHHHHHHHHHHhhcC----CCce
Confidence 77774 675 5799999999999999999999885321 01 1378999999999999999873 1499
Q ss_pred EEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccC
Q 007267 272 VFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIES 351 (610)
Q Consensus 272 Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~T 351 (610)
|++|++|+||.|||+++.+++++.+|++ +|+++++++.+||++||.+|+++||+||+|+++.+++|+++|++|++.|
T Consensus 138 I~~f~sg~pt~GpG~l~~~~~~~~~~~~---~e~~~~~~a~~fY~~la~~~~~~~isvdlF~~~~~~~dl~~l~~l~~~T 214 (239)
T cd01468 138 IIVFQGGLPTVGPGKLKSREDKEPIRSH---DEAQLLKPATKFYKSLAKECVKSGICVDLFAFSLDYVDVATLKQLAKST 214 (239)
T ss_pred EEEEECCCCCCCCCccccCcccccCCCc---cchhcccccHHHHHHHHHHHHHcCeEEEEEeccccccCHHHhhhhhhcC
Confidence 9999999999999999999888887654 6789999999999999999999999999999999999999999999999
Q ss_pred ccEEEEeCCC----CCCchhHHHHH
Q 007267 352 GGSLFLYSST----DDSTLPQDIYR 372 (610)
Q Consensus 352 GG~v~~~~~~----~~~~l~~dl~~ 372 (610)
||.+++|++| +.++|.+||+|
T Consensus 215 GG~v~~y~~f~~~~~~~~~~~~l~r 239 (239)
T cd01468 215 GGQVYLYDSFQAPNDGSKFKQDLQR 239 (239)
T ss_pred CceEEEeCCCCCcccHHHHHHHhcC
Confidence 9999999999 77788888764
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=4.7e-43 Score=351.80 Aligned_cols=230 Identities=29% Similarity=0.525 Sum_probs=181.0
Q ss_pred CCCcEEEEEEeCCCC---hhHHHHHHHHHHHHHHhCC--CCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccc
Q 007267 119 QARPVYVAAVDLSSS---EEFLELTRSALQAALEAVP--SGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSL 193 (610)
Q Consensus 119 ~~~p~~vFvID~s~~---~~~l~~l~~~l~~~l~~lp--~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~ 193 (610)
|+||+|+||||+|.. .+.++.++++|+++|+.|| ++++|||||||+.||+|+++......++ .++.
T Consensus 1 P~pp~y~FvID~s~~av~~g~~~~~~~sl~~~l~~l~~~~~~~vgiitfd~~V~~y~l~~~~~~~~~---------~v~~ 71 (243)
T PF04811_consen 1 PQPPVYVFVIDVSYEAVQSGLLQSLIESLKSALDSLPGDERTRVGIITFDSSVHFYNLSSSLSQPQM---------IVVS 71 (243)
T ss_dssp -S--EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTSSTSTT-EEEEEEESSSEEEEETTTTSSSTEE---------EEEH
T ss_pred CCCCEEEEEEECchhhhhccHHHHHHHHHHHHHHhccCCCCcEEEEEEeCCEEEEEECCCCcCCCcc---------cchH
Confidence 468999999999998 5999999999999999999 9999999999999999999876644444 3568
Q ss_pred ccccc-Ccc-CcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccce
Q 007267 194 ELEDV-MPL-SQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALAR 271 (610)
Q Consensus 194 dl~~~-~p~-~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~Gk 271 (610)
|++|+ +|. ++||++++|+++.|.++|++|++.++.... +.+.+|+|+||++|..+|++.+ .|||
T Consensus 72 dl~~~~~p~~~~llv~~~e~~~~i~~ll~~L~~~~~~~~~----------~~~~~c~G~Al~~A~~ll~~~~----~gGk 137 (243)
T PF04811_consen 72 DLDDPFIPLPDGLLVPLSECRDAIEELLESLPSIFPETAG----------KRPERCLGSALSAALSLLSSRN----TGGK 137 (243)
T ss_dssp HTTSHHSSTSSSSSEETTTCHHHHHHHHHHHHHHSTT-TT----------B-----HHHHHHHHHHHHHHHT----S-EE
T ss_pred HHhhcccCCcccEEEEhHHhHHHHHHHHHHhhhhcccccc----------cCccccHHHHHHHHHHHHhccc----cCCE
Confidence 88884 565 689999999999999999999875433211 1378999999999999999433 2599
Q ss_pred EEEEecCCCCCCC-cccccccCcCcccCCCcchh-hccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhc
Q 007267 272 VFAFLSGPPDHGA-GQLDTRRYGEQYASKGEDAD-RALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSI 349 (610)
Q Consensus 272 Ii~F~~g~pt~Gp-G~l~~~~~~~~~~~~~~~~e-~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~ 349 (610)
|++|++|+||.|| |++..+++.+. .++++| +.+++++.+||++||++|+++||+||+|+++.+++|+++|+.|++
T Consensus 138 I~~F~s~~pt~G~Gg~l~~~~~~~~---~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~tl~~l~~ 214 (243)
T PF04811_consen 138 ILVFTSGPPTYGPGGSLKKREDSSH---YDTEKEKALLLPPANEFYKKLAEECSKQGISVDLFVFSSDYVDLATLGPLAR 214 (243)
T ss_dssp EEEEESS---SSSTTSS-SBTTSCC---CCHCTTHHCHSHSSSHHHHHHHHHHHHCTEEEEEEEECSS--SHHHHTHHHH
T ss_pred EEEEeccCCCCCCCceecccccccc---cccccchhhhccccchHHHHHHHHHHhcCCEEEEEeecCCCCCcHhHHHHHH
Confidence 9999999999999 67666655422 344555 678889999999999999999999999999999999999999999
Q ss_pred cCccEEEEeCCCC----CCchhHHHHHHh
Q 007267 350 ESGGSLFLYSSTD----DSTLPQDIYRML 374 (610)
Q Consensus 350 ~TGG~v~~~~~~~----~~~l~~dl~~~l 374 (610)
.|||.+++|++|+ ..+|++||+|++
T Consensus 215 ~TGG~l~~y~~f~~~~~~~~l~~dl~r~~ 243 (243)
T PF04811_consen 215 YTGGSLYYYPNFNAERDGEKLRQDLKRLV 243 (243)
T ss_dssp CTT-EEEEETTTTCHHHHHHHHHHHHHHH
T ss_pred hCceeEEEeCCCCCchhHHHHHHHHHHhC
Confidence 9999999999999 667899998875
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=99.62 E-value=1.4e-15 Score=129.87 Aligned_cols=78 Identities=21% Similarity=0.389 Sum_probs=65.4
Q ss_pred ceeeEEEEEccCCeeeeeeeeccccCCCC-------Ccc--eeeeecCCCccEEEEEEEecCCCcCCCCCCccEEEEEEE
Q 007267 379 AFNCIMRLRTSSEFKPGHSYGHFFPDPQY-------ENV--QHIICCDSYATYAYDFDFANAAGFARHTSEQPMLQIAFQ 449 (610)
Q Consensus 379 ~~~a~lrvr~S~gl~v~~~~G~~~~~~~~-------~~~--~~i~~~~~~~t~a~~fe~~~~~~l~~~~~~~~~iQ~a~~ 449 (610)
||+|+||||||+|++|++++||+...... .++ |.++.++++++++|+|+++. .+. ..+.+|||+|++
T Consensus 1 g~~~~l~vr~S~gl~v~~~~G~~~~~~~~s~~~~g~~~~~~~~~~~l~~~~s~~~~~~~~~--~~~--~~~~~~iQ~~~~ 76 (96)
T PF08033_consen 1 GFNAVLRVRCSKGLKVSGVIGPCFNRSSVSDNEIGEGDTTRWKLPSLDPDTSFAFEFEIDE--DLP--NGSQAYIQFALL 76 (96)
T ss_dssp EEEEEEEEEE-TTEEEEEEESSSEESSTBESSECSBSSCSEEEEEEEETT--EEEEEEESS--BTB--TTSEEEEEEEEE
T ss_pred CceEEEEEEECCCeEEEEEEcCccccccccceeeccCCccEEEecccCCCCEEEEEEEECC--CCC--CCCeEEEEEEEE
Confidence 79999999999999999999999987521 344 99999999999999999975 343 367999999999
Q ss_pred eeecCCccccc
Q 007267 450 YTVVVPPEELS 460 (610)
Q Consensus 450 Yt~~~g~~~~~ 460 (610)
||+.+|+|++|
T Consensus 77 Yt~~~G~r~iR 87 (96)
T PF08033_consen 77 YTDSNGERRIR 87 (96)
T ss_dssp EEETTSEEEEE
T ss_pred EECCCCCEEEE
Confidence 99999999887
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=99.51 E-value=4.3e-15 Score=104.23 Aligned_cols=38 Identities=34% Similarity=0.943 Sum_probs=25.9
Q ss_pred CCCcCcCcCeeEecCceEeC--ceeEEcCCCCCCCCChhh
Q 007267 49 MLPRCENCYAYFNTYCELEQ--WAWTCSLCGSLNGLSSQA 86 (610)
Q Consensus 49 ~~~RC~~C~ayiNp~~~~~~--~~w~C~~C~~~N~~p~~~ 86 (610)
+|+||++|+||||||++|+. ++|+|+||++.|++|++|
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 47999999999999999994 699999999999999884
No 14
>PRK13685 hypothetical protein; Provisional
Probab=98.91 E-value=5.5e-08 Score=101.97 Aligned_cols=180 Identities=21% Similarity=0.288 Sum_probs=123.2
Q ss_pred cEEEEEEeCCCCh-------hHHHHHHHHHHHHHHhCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccc
Q 007267 122 PVYVAAVDLSSSE-------EFLELTRSALQAALEAVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLE 194 (610)
Q Consensus 122 p~~vFvID~s~~~-------~~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~d 194 (610)
...+|+||+|.++ ..++..|+++...++.++++.+||+|+|++..++.
T Consensus 89 ~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l~~~d~vglv~Fa~~a~~~------------------------- 143 (326)
T PRK13685 89 AVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELTPGINLGLIAFAGTATVL------------------------- 143 (326)
T ss_pred ceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhCCCCCeEEEEEEcCceeec-------------------------
Confidence 3589999999986 36899999999999999888999999999865420
Q ss_pred ccccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccc----cC-CCccc
Q 007267 195 LEDVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSE----YG-NTFAL 269 (610)
Q Consensus 195 l~~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~----~~-~~~~~ 269 (610)
+|+...++.+.+.|+.|... ..++.|.|+..|++.+... ++ .....
T Consensus 144 -----------~p~t~d~~~l~~~l~~l~~~------------------~~T~~g~al~~A~~~l~~~~~~~~~~~~~~~ 194 (326)
T PRK13685 144 -----------VSPTTNREATKNAIDKLQLA------------------DRTATGEAIFTALQAIATVGAVIGGGDTPPP 194 (326)
T ss_pred -----------CCCCCCHHHHHHHHHhCCCC------------------CCcchHHHHHHHHHHHHhhhcccccccCCCC
Confidence 01123456678888888643 2456899999998887631 10 01123
Q ss_pred ceEEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCC-----------
Q 007267 270 ARVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEY----------- 338 (610)
Q Consensus 270 GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~----------- 338 (610)
++|+++++|..+.|....... .. .+.++.+.+.||.|..+.++.+.
T Consensus 195 ~~IILlTDG~~~~~~~~~~~~---------------------~~--~~aa~~a~~~gi~i~~Ig~G~~~g~~~~~g~~~~ 251 (326)
T PRK13685 195 ARIVLMSDGKETVPTNPDNPR---------------------GA--YTAARTAKDQGVPISTISFGTPYGSVEINGQRQP 251 (326)
T ss_pred CEEEEEcCCCCCCCCCCCCcc---------------------cH--HHHHHHHHHcCCeEEEEEECCCCCCcCcCCceee
Confidence 789999999887663211000 00 13567778899999999988642
Q ss_pred --cChhcchhhhccCccEEEEeCCCCCCchhHHHHHHhccCccee
Q 007267 339 --TDLASLKFLSIESGGSLFLYSSTDDSTLPQDIYRMLSRPYAFN 381 (610)
Q Consensus 339 --~~l~~l~~l~~~TGG~v~~~~~~~~~~l~~dl~~~l~~~~~~~ 381 (610)
.|-.+|..+|+.|||..+..++- ..+ .++++.+.+..+|+
T Consensus 252 ~~~d~~~L~~iA~~tgG~~~~~~~~--~~L-~~if~~I~~~~~~~ 293 (326)
T PRK13685 252 VPVDDESLKKIAQLSGGEFYTAASL--EEL-RAVYATLQQQIGYE 293 (326)
T ss_pred ecCCHHHHHHHHHhcCCEEEEcCCH--HHH-HHHHHHHHHHhcee
Confidence 57789999999999987766542 223 23344444444443
No 15
>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=98.88 E-value=3.6e-08 Score=94.57 Aligned_cols=162 Identities=13% Similarity=0.159 Sum_probs=106.1
Q ss_pred EEEEEEeCCCCh-------hHHHHHHHHHHHHHHhC---CCCcEEEEEee-cceeEEEEecCCCcceeeeeeCCCCCccc
Q 007267 123 VYVAAVDLSSSE-------EFLELTRSALQAALEAV---PSGALFGLATF-SHKIGLYDVQGAIPVVKNVFIPSDTEDTL 191 (610)
Q Consensus 123 ~~vFvID~s~~~-------~~l~~l~~~l~~~l~~l---p~~~~VglITf-~~~V~~~~l~~~~~~~~~v~~~~~~~~~~ 191 (610)
-.+++||+|.++ ..|+..|..+...++.+ .+..+||||+| ++.-++ +
T Consensus 5 ~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~a~~--~-------------------- 62 (183)
T cd01453 5 HLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEK--L-------------------- 62 (183)
T ss_pred EEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCccEE--E--------------------
Confidence 368999999985 58999999999888754 45679999999 454332 1
Q ss_pred cccccccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccce
Q 007267 192 SLELEDVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALAR 271 (610)
Q Consensus 192 ~~dl~~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~Gk 271 (610)
+|+....+.+...|+.+... .+++.++.||..|...|+..... ..++
T Consensus 63 --------------~PlT~D~~~~~~~L~~~~~~-----------------~G~t~l~~aL~~A~~~l~~~~~~--~~~~ 109 (183)
T cd01453 63 --------------TDLTGNPRKHIQALKTAREC-----------------SGEPSLQNGLEMALESLKHMPSH--GSRE 109 (183)
T ss_pred --------------ECCCCCHHHHHHHhhcccCC-----------------CCchhHHHHHHHHHHHHhcCCcc--CceE
Confidence 11111122344444443110 13477999999999999753211 1257
Q ss_pred EEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccC
Q 007267 272 VFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIES 351 (610)
Q Consensus 272 Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~T 351 (610)
|++++++.-+.+|+. +.++++.+.+.||.|++..++. +...|+.+|+.|
T Consensus 110 iiil~sd~~~~~~~~----------------------------~~~~~~~l~~~~I~v~~IgiG~---~~~~L~~ia~~t 158 (183)
T cd01453 110 VLIIFSSLSTCDPGN----------------------------IYETIDKLKKENIRVSVIGLSA---EMHICKEICKAT 158 (183)
T ss_pred EEEEEcCCCcCChhh----------------------------HHHHHHHHHHcCcEEEEEEech---HHHHHHHHHHHh
Confidence 888877633322221 1357888999999999999864 467899999999
Q ss_pred ccEEEEeCCCCCCchhHHHHH
Q 007267 352 GGSLFLYSSTDDSTLPQDIYR 372 (610)
Q Consensus 352 GG~v~~~~~~~~~~l~~dl~~ 372 (610)
||+.|.-.+ ...|.+-+.+
T Consensus 159 gG~~~~~~~--~~~l~~~~~~ 177 (183)
T cd01453 159 NGTYKVILD--ETHLKELLLE 177 (183)
T ss_pred CCeeEeeCC--HHHHHHHHHh
Confidence 999665543 3345543333
No 16
>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=98.85 E-value=1.1e-07 Score=90.91 Aligned_cols=166 Identities=14% Similarity=0.128 Sum_probs=112.0
Q ss_pred EEEEEeCCCChh---HHHHHHHHHHHHHH-hCCCCcEEEEEeecce-eEEEEecCCCcceeeeeeCCCCCcccccccccc
Q 007267 124 YVAAVDLSSSEE---FLELTRSALQAALE-AVPSGALFGLATFSHK-IGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV 198 (610)
Q Consensus 124 ~vFvID~s~~~~---~l~~l~~~l~~~l~-~lp~~~~VglITf~~~-V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~ 198 (610)
++|+||+|.+.. .++.+|.++...+. .++++.+||+|+|++. .++. +
T Consensus 3 v~lvlD~SgSM~~~~rl~~ak~a~~~~~~~~~~~~d~v~lv~F~~~~~~~~-------------~--------------- 54 (178)
T cd01451 3 VIFVVDASGSMAARHRMAAAKGAVLSLLRDAYQRRDKVALIAFRGTEAEVL-------------L--------------- 54 (178)
T ss_pred EEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCceEE-------------e---------------
Confidence 679999999863 68888988888876 4567889999999864 2210 0
Q ss_pred CccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecC
Q 007267 199 MPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSG 278 (610)
Q Consensus 199 ~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g 278 (610)
| ....+..+...|+.++.. +.+.++.||..|...++...........|++++.|
T Consensus 55 -~-------~t~~~~~~~~~l~~l~~~------------------G~T~l~~aL~~a~~~l~~~~~~~~~~~~ivliTDG 108 (178)
T cd01451 55 -P-------PTRSVELAKRRLARLPTG------------------GGTPLAAGLLAAYELAAEQARDPGQRPLIVVITDG 108 (178)
T ss_pred -C-------CCCCHHHHHHHHHhCCCC------------------CCCcHHHHHHHHHHHHHHHhcCCCCceEEEEECCC
Confidence 0 001122344556655432 45679999999999982211110012589999999
Q ss_pred CCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEe
Q 007267 279 PPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLY 358 (610)
Q Consensus 279 ~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~ 358 (610)
.++.|...... --.++++++.+.||.+..+.+.....+-..|..||+.|||+.++.
T Consensus 109 ~~~~g~~~~~~------------------------~~~~~~~~l~~~gi~v~~I~~~~~~~~~~~l~~iA~~tgG~~~~~ 164 (178)
T cd01451 109 RANVGPDPTAD------------------------RALAAARKLRARGISALVIDTEGRPVRRGLAKDLARALGGQYVRL 164 (178)
T ss_pred CCCCCCCchhH------------------------HHHHHHHHHHhcCCcEEEEeCCCCccCccHHHHHHHHcCCeEEEc
Confidence 98876421100 004577888889988877766666667788999999999999988
Q ss_pred CCCCCCchh
Q 007267 359 SSTDDSTLP 367 (610)
Q Consensus 359 ~~~~~~~l~ 367 (610)
++.+...|.
T Consensus 165 ~d~~~~~~~ 173 (178)
T cd01451 165 PDLSADAIA 173 (178)
T ss_pred CcCCHHHHH
Confidence 877754444
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=98.83 E-value=8.9e-08 Score=93.72 Aligned_cols=169 Identities=24% Similarity=0.338 Sum_probs=110.3
Q ss_pred CCCcEEEEEEeCCCChh--------HHHHHHHHHHHHHHhCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcc
Q 007267 119 QARPVYVAAVDLSSSEE--------FLELTRSALQAALEAVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDT 190 (610)
Q Consensus 119 ~~~p~~vFvID~s~~~~--------~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~ 190 (610)
..+..++||||+|.++. .++.+|.++...++.++++.+|||++|++.++-. ... .+.++..
T Consensus 18 ~~~~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~l~~~~~v~lv~F~~~~~~~-----~~~--~~~~p~~---- 86 (206)
T cd01456 18 QLPPNVAIVLDNSGSMREVDGGGETRLDNAKAALDETANALPDGTRLGLWTFSGDGDNP-----LDV--RVLVPKG---- 86 (206)
T ss_pred CCCCcEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHhCCCCceEEEEEecCCCCCC-----ccc--ccccccc----
Confidence 45667999999999864 6889999999999999999999999999954210 000 0000000
Q ss_pred ccccccccCccCcCccchHhHHHHHHHHHHhcC-CCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCccc
Q 007267 191 LSLELEDVMPLSQFLAPVETFKENITSALETLR-PTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFAL 269 (610)
Q Consensus 191 ~~~dl~~~~p~~~~l~~~~e~~~~i~~~L~~L~-~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~ 269 (610)
.... ++..+. ...+..+.+.|+.|. .. ..+.++.||..|...+. .+. .
T Consensus 87 --~~~~---~~~~~~---~~~~~~l~~~i~~i~~~~------------------G~T~l~~aL~~a~~~l~-~~~----~ 135 (206)
T cd01456 87 --CLTA---PVNGFP---SAQRSALDAALNSLQTPT------------------GWTPLAAALAEAAAYVD-PGR----V 135 (206)
T ss_pred --cccc---ccCCCC---cccHHHHHHHHHhhcCCC------------------CcChHHHHHHHHHHHhC-CCC----c
Confidence 0000 001110 124566777888876 22 45679999999999986 221 2
Q ss_pred ceEEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHH-HHcCcEEEEEEecCCCcChhcchhhh
Q 007267 270 ARVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVA-VQAGVCVDIFAITNEYTDLASLKFLS 348 (610)
Q Consensus 270 GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~-~~~gisvDlf~~~~~~~~l~~l~~l~ 348 (610)
..|+++++|.++.|+... +..++++... ...++.|+.+.++.+ .|...|..+|
T Consensus 136 ~~iillTDG~~~~~~~~~-------------------------~~~~~~~~~~~~~~~i~i~~igiG~~-~~~~~l~~iA 189 (206)
T cd01456 136 NVVVLITDGEDTCGPDPC-------------------------EVARELAKRRTPAPPIKVNVIDFGGD-ADRAELEAIA 189 (206)
T ss_pred ceEEEEcCCCccCCCCHH-------------------------HHHHHHHHhcCCCCCceEEEEEecCc-ccHHHHHHHH
Confidence 689999999887653110 0001122110 125899999998765 6788999999
Q ss_pred ccCccEE
Q 007267 349 IESGGSL 355 (610)
Q Consensus 349 ~~TGG~v 355 (610)
..|||..
T Consensus 190 ~~tgG~~ 196 (206)
T cd01456 190 EATGGTY 196 (206)
T ss_pred HhcCCeE
Confidence 9999996
No 18
>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=98.82 E-value=1.4e-07 Score=88.02 Aligned_cols=149 Identities=23% Similarity=0.320 Sum_probs=105.2
Q ss_pred EEEEEeCCCChh--HHHHHHHHHHHHHHhCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccccCcc
Q 007267 124 YVAAVDLSSSEE--FLELTRSALQAALEAVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDVMPL 201 (610)
Q Consensus 124 ~vFvID~s~~~~--~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~~p~ 201 (610)
.+|+||+|.+.. .++.+++++...++.|+++.+||||+|++..+... |+
T Consensus 3 v~~vlD~S~SM~~~rl~~ak~a~~~l~~~l~~~~~~~li~F~~~~~~~~-----------------------------~~ 53 (155)
T cd01466 3 LVAVLDVSGSMAGDKLQLVKHALRFVISSLGDADRLSIVTFSTSAKRLS-----------------------------PL 53 (155)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcceEEEEEecCCccccC-----------------------------CC
Confidence 579999999863 58889999999999999999999999998654310 00
Q ss_pred CcCccch-HhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecCCC
Q 007267 202 SQFLAPV-ETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPP 280 (610)
Q Consensus 202 ~~~l~~~-~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~p 280 (610)
.+. ...+..+.++++.+.+. +.++++.||..|...+..... ......|+++++|.+
T Consensus 54 ----~~~~~~~~~~~~~~i~~~~~~------------------g~T~~~~al~~a~~~~~~~~~-~~~~~~iillTDG~~ 110 (155)
T cd01466 54 ----RRMTAKGKRSAKRVVDGLQAG------------------GGTNVVGGLKKALKVLGDRRQ-KNPVASIMLLSDGQD 110 (155)
T ss_pred ----cccCHHHHHHHHHHHHhccCC------------------CCccHHHHHHHHHHHHhhccc-CCCceEEEEEcCCCC
Confidence 001 12345566777776432 457799999999999875321 112368999999988
Q ss_pred CCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEe
Q 007267 281 DHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLY 358 (610)
Q Consensus 281 t~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~ 358 (610)
+.|+.. .++.+.++.|..+.++. ..+..+|..+|..|||+.++.
T Consensus 111 ~~~~~~---------------------------------~~~~~~~v~v~~igig~-~~~~~~l~~iA~~t~G~~~~~ 154 (155)
T cd01466 111 NHGAVV---------------------------------LRADNAPIPIHTFGLGA-SHDPALLAFIAEITGGTFSYV 154 (155)
T ss_pred Ccchhh---------------------------------hcccCCCceEEEEecCC-CCCHHHHHHHHhccCceEEEe
Confidence 765110 01123577888887754 468889999999999997763
No 19
>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=98.82 E-value=3.2e-07 Score=86.48 Aligned_cols=159 Identities=15% Similarity=0.169 Sum_probs=112.1
Q ss_pred EEEEEeCCCCh--hHHHHHHHHHHHHHHhCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccccCcc
Q 007267 124 YVAAVDLSSSE--EFLELTRSALQAALEAVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDVMPL 201 (610)
Q Consensus 124 ~vFvID~s~~~--~~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~~p~ 201 (610)
++|++|+|.+. ..++.+|+++...++.++++.+||+|+|++..+..- +.. +
T Consensus 3 ~~~vlD~S~SM~~~~~~~~k~a~~~~~~~l~~~~~v~li~f~~~~~~~~-----------------------~~~---~- 55 (170)
T cd01465 3 LVFVIDRSGSMDGPKLPLVKSALKLLVDQLRPDDRLAIVTYDGAAETVL-----------------------PAT---P- 55 (170)
T ss_pred EEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEecCCccEEe-----------------------cCc---c-
Confidence 68999999986 347889999999999999999999999998654311 000 0
Q ss_pred CcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecCCCC
Q 007267 202 SQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPPD 281 (610)
Q Consensus 202 ~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~pt 281 (610)
...+..+.+.|+.++.. +.+.++.||..|+..+...... ....+|++|++|.++
T Consensus 56 -------~~~~~~l~~~l~~~~~~------------------g~T~~~~al~~a~~~~~~~~~~-~~~~~ivl~TDG~~~ 109 (170)
T cd01465 56 -------VRDKAAILAAIDRLTAG------------------GSTAGGAGIQLGYQEAQKHFVP-GGVNRILLATDGDFN 109 (170)
T ss_pred -------cchHHHHHHHHHcCCCC------------------CCCCHHHHHHHHHHHHHhhcCC-CCeeEEEEEeCCCCC
Confidence 01224455566665432 3355899999999888653211 012679999999998
Q ss_pred CCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeCCC
Q 007267 282 HGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYSST 361 (610)
Q Consensus 282 ~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~~ 361 (610)
.|+... +-+.+....+.+.++.|+.+.++ +..+...|..+|+.++|..++.++.
T Consensus 110 ~~~~~~-------------------------~~~~~~~~~~~~~~v~i~~i~~g-~~~~~~~l~~ia~~~~g~~~~~~~~ 163 (170)
T cd01465 110 VGETDP-------------------------DELARLVAQKRESGITLSTLGFG-DNYNEDLMEAIADAGNGNTAYIDNL 163 (170)
T ss_pred CCCCCH-------------------------HHHHHHHHHhhcCCeEEEEEEeC-CCcCHHHHHHHHhcCCceEEEeCCH
Confidence 765311 11234555667789999999998 6788999999999999997776543
No 20
>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=98.76 E-value=6.3e-07 Score=86.53 Aligned_cols=168 Identities=18% Similarity=0.239 Sum_probs=108.3
Q ss_pred CcEEEEEEeCCCCh--hHHHHHHHHHHHHHHhCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccccc
Q 007267 121 RPVYVAAVDLSSSE--EFLELTRSALQAALEAVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV 198 (610)
Q Consensus 121 ~p~~vFvID~s~~~--~~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~ 198 (610)
|--.+|+||+|.+. ..++.+|.++...++.|+++.+||||+|++.++..--...
T Consensus 13 p~~vv~llD~SgSM~~~~l~~ak~~~~~ll~~l~~~d~v~lv~F~~~~~~~~~~~~------------------------ 68 (190)
T cd01463 13 PKDIVILLDVSGSMTGQRLHLAKQTVSSILDTLSDNDFFNIITFSNEVNPVVPCFN------------------------ 68 (190)
T ss_pred CceEEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCCCEEEEEEeCCCeeEEeeecc------------------------
Confidence 44689999999986 5688899999999999999999999999998765321000
Q ss_pred CccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccc---c---CCCcccceE
Q 007267 199 MPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSE---Y---GNTFALARV 272 (610)
Q Consensus 199 ~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~---~---~~~~~~GkI 272 (610)
..++....+.+..+.+.|+.|+.. +.+.++.||..|...|... . ........|
T Consensus 69 ---~~~~~~~~~~~~~~~~~l~~l~~~------------------G~T~~~~al~~a~~~l~~~~~~~~~~~~~~~~~~i 127 (190)
T cd01463 69 ---DTLVQATTSNKKVLKEALDMLEAK------------------GIANYTKALEFAFSLLLKNLQSNHSGSRSQCNQAI 127 (190)
T ss_pred ---cceEecCHHHHHHHHHHHhhCCCC------------------CcchHHHHHHHHHHHHHHhhhcccccccCCceeEE
Confidence 001111122445566666666543 3466999999999888751 1 001112479
Q ss_pred EEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHH-HHHHcCcEEEEEEecCCCcChhcchhhhccC
Q 007267 273 FAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAA-VAVQAGVCVDIFAITNEYTDLASLKFLSIES 351 (610)
Q Consensus 273 i~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~-~~~~~gisvDlf~~~~~~~~l~~l~~l~~~T 351 (610)
+++++|.++.+.. ....+.. .....++.|..|.++.+..|...|..||..+
T Consensus 128 illTDG~~~~~~~----------------------------~~~~~~~~~~~~~~v~i~tigiG~~~~d~~~L~~lA~~~ 179 (190)
T cd01463 128 MLITDGVPENYKE----------------------------IFDKYNWDKNSEIPVRVFTYLIGREVTDRREIQWMACEN 179 (190)
T ss_pred EEEeCCCCCcHhH----------------------------HHHHhcccccCCCcEEEEEEecCCccccchHHHHHHhhc
Confidence 9999998763210 0011100 0011245566666666656889999999999
Q ss_pred ccEEEEeCCC
Q 007267 352 GGSLFLYSST 361 (610)
Q Consensus 352 GG~v~~~~~~ 361 (610)
||..++.++-
T Consensus 180 ~G~~~~i~~~ 189 (190)
T cd01463 180 KGYYSHIQSL 189 (190)
T ss_pred CCeEEEcccC
Confidence 9998877653
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=98.65 E-value=1.6e-06 Score=82.60 Aligned_cols=155 Identities=19% Similarity=0.208 Sum_probs=104.6
Q ss_pred EEEEEEeCCCChh--------HHHHHHHHHHHHHHhCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccc
Q 007267 123 VYVAAVDLSSSEE--------FLELTRSALQAALEAVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLE 194 (610)
Q Consensus 123 ~~vFvID~s~~~~--------~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~d 194 (610)
-++|+||+|.+.. .++.++..+...++.. ++.+||+|+|++.++..-
T Consensus 4 ~vv~vlD~S~SM~~~~~~~~~r~~~a~~~~~~~~~~~-~~~~v~lv~f~~~~~~~~------------------------ 58 (180)
T cd01467 4 DIMIALDVSGSMLAQDFVKPSRLEAAKEVLSDFIDRR-ENDRIGLVVFAGAAFTQA------------------------ 58 (180)
T ss_pred eEEEEEECCcccccccCCCCCHHHHHHHHHHHHHHhC-CCCeEEEEEEcCCeeecc------------------------
Confidence 4789999999852 3677787777766654 577999999988654310
Q ss_pred ccccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEE
Q 007267 195 LEDVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFA 274 (610)
Q Consensus 195 l~~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~ 274 (610)
| +...+..+.++|+.|.... . ..++.++.||..|...+....+. ...|++
T Consensus 59 -----~-------~~~~~~~~~~~l~~l~~~~--~-------------~g~T~l~~al~~a~~~l~~~~~~---~~~iil 108 (180)
T cd01467 59 -----P-------LTLDRESLKELLEDIKIGL--A-------------GQGTAIGDAIGLAIKRLKNSEAK---ERVIVL 108 (180)
T ss_pred -----C-------CCccHHHHHHHHHHhhhcc--c-------------CCCCcHHHHHHHHHHHHHhcCCC---CCEEEE
Confidence 1 1112334556666665221 0 13467899999999998654321 257999
Q ss_pred EecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCC----------CcChhcc
Q 007267 275 FLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNE----------YTDLASL 344 (610)
Q Consensus 275 F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~----------~~~l~~l 344 (610)
++.|.++.|+-. ..+.+..+.+.||.|+.+.+... ..+...|
T Consensus 109 iTDG~~~~g~~~----------------------------~~~~~~~~~~~gi~i~~i~ig~~~~~~~~~~~~~~~~~~l 160 (180)
T cd01467 109 LTDGENNAGEID----------------------------PATAAELAKNKGVRIYTIGVGKSGSGPKPDGSTILDEDSL 160 (180)
T ss_pred EeCCCCCCCCCC----------------------------HHHHHHHHHHCCCEEEEEEecCCCCCcCCCCcccCCHHHH
Confidence 999987654210 01234556678999999988762 4678889
Q ss_pred hhhhccCccEEEEeCC
Q 007267 345 KFLSIESGGSLFLYSS 360 (610)
Q Consensus 345 ~~l~~~TGG~v~~~~~ 360 (610)
..||+.|||..++..+
T Consensus 161 ~~la~~tgG~~~~~~~ 176 (180)
T cd01467 161 VEIADKTGGRIFRALD 176 (180)
T ss_pred HHHHHhcCCEEEEecC
Confidence 9999999999888753
No 22
>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=98.63 E-value=1.3e-06 Score=83.46 Aligned_cols=145 Identities=19% Similarity=0.190 Sum_probs=101.5
Q ss_pred EEEEEEeCCCCh-------hHHHHHHHHHHHHH----HhCCCCcEEEEEeecc-eeEEEEecCCCcceeeeeeCCCCCcc
Q 007267 123 VYVAAVDLSSSE-------EFLELTRSALQAAL----EAVPSGALFGLATFSH-KIGLYDVQGAIPVVKNVFIPSDTEDT 190 (610)
Q Consensus 123 ~~vFvID~s~~~-------~~l~~l~~~l~~~l----~~lp~~~~VglITf~~-~V~~~~l~~~~~~~~~v~~~~~~~~~ 190 (610)
+-+++||+|.++ .+|++.|.++...+ +..| ..+||||+|.. ..++
T Consensus 5 a~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np-~~~vGlv~fag~~a~v---------------------- 61 (187)
T cd01452 5 ATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNP-ENNVGLMTMAGNSPEV---------------------- 61 (187)
T ss_pred EEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCC-CccEEEEEecCCceEE----------------------
Confidence 578999999874 57888898887664 4555 45999999987 3222
Q ss_pred ccccccccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccc
Q 007267 191 LSLELEDVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALA 270 (610)
Q Consensus 191 ~~~dl~~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~G 270 (610)
++|+......+...|+.+... ++..+|.||+.|...|+.... +....
T Consensus 62 --------------~~plT~D~~~~~~~L~~i~~~------------------g~~~l~~AL~~A~~~L~~~~~-~~~~~ 108 (187)
T cd01452 62 --------------LVTLTNDQGKILSKLHDVQPK------------------GKANFITGIQIAQLALKHRQN-KNQKQ 108 (187)
T ss_pred --------------EECCCCCHHHHHHHHHhCCCC------------------CcchHHHHHHHHHHHHhcCCC-cCCcc
Confidence 112222345566777766532 345699999999999975432 11125
Q ss_pred eEEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhcc
Q 007267 271 RVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIE 350 (610)
Q Consensus 271 kIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~ 350 (610)
||++|.+++-+.-||.+ .++++++.++||.||+..++...-+..-|..+.+.
T Consensus 109 rivi~v~S~~~~d~~~i----------------------------~~~~~~lkk~~I~v~vI~~G~~~~~~~~l~~~~~~ 160 (187)
T cd01452 109 RIVAFVGSPIEEDEKDL----------------------------VKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDA 160 (187)
T ss_pred eEEEEEecCCcCCHHHH----------------------------HHHHHHHHHcCCeEEEEEeCCCCCCHHHHHHHHHH
Confidence 99999998754433321 36899999999999999998877777777777666
Q ss_pred C
Q 007267 351 S 351 (610)
Q Consensus 351 T 351 (610)
.
T Consensus 161 ~ 161 (187)
T cd01452 161 V 161 (187)
T ss_pred h
Confidence 5
No 23
>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.
Probab=98.62 E-value=1.9e-06 Score=81.01 Aligned_cols=152 Identities=21% Similarity=0.213 Sum_probs=97.6
Q ss_pred EEEEEeCCCCh--hHHHHHHHHHHHHHHhCC---CCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccccc
Q 007267 124 YVAAVDLSSSE--EFLELTRSALQAALEAVP---SGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV 198 (610)
Q Consensus 124 ~vFvID~s~~~--~~l~~l~~~l~~~l~~lp---~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~ 198 (610)
.+|+||+|.+. ..++.+++++...++.|. ++.+||||+|++..+..- .+
T Consensus 3 vv~vlD~SgSm~~~~~~~~k~~~~~~~~~l~~~~~~~~~giv~Fs~~~~~~~-----------------------~~--- 56 (164)
T cd01472 3 IVFLVDGSESIGLSNFNLVKDFVKRVVERLDIGPDGVRVGVVQYSDDPRTEF-----------------------YL--- 56 (164)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHhhcccCCCCeEEEEEEEcCceeEEE-----------------------ec---
Confidence 57999999985 467888999998888774 568999999998765411 00
Q ss_pred CccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccc--cCCCcccceEEEEe
Q 007267 199 MPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSE--YGNTFALARVFAFL 276 (610)
Q Consensus 199 ~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~--~~~~~~~GkIi~F~ 276 (610)
.. . ..+..+.+.|+.++... ..+.+|.||..|...+... +........|++++
T Consensus 57 ---~~----~-~~~~~~~~~l~~l~~~~-----------------g~T~~~~al~~a~~~l~~~~~~~~~~~~~~iiliT 111 (164)
T cd01472 57 ---NT----Y-RSKDDVLEAVKNLRYIG-----------------GGTNTGKALKYVRENLFTEASGSREGVPKVLVVIT 111 (164)
T ss_pred ---CC----C-CCHHHHHHHHHhCcCCC-----------------CCchHHHHHHHHHHHhCCcccCCCCCCCEEEEEEc
Confidence 00 0 12344566677775431 3467999999999988752 11111235678888
Q ss_pred cCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCcc-EE
Q 007267 277 SGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGG-SL 355 (610)
Q Consensus 277 ~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG-~v 355 (610)
.|.++.+. ...+..+.+.||.+-.+.++. .|...|..+|..++| .+
T Consensus 112 DG~~~~~~-------------------------------~~~~~~l~~~gv~i~~ig~g~--~~~~~L~~ia~~~~~~~~ 158 (164)
T cd01472 112 DGKSQDDV-------------------------------EEPAVELKQAGIEVFAVGVKN--ADEEELKQIASDPKELYV 158 (164)
T ss_pred CCCCCchH-------------------------------HHHHHHHHHCCCEEEEEECCc--CCHHHHHHHHCCCchheE
Confidence 88543210 112334556777655555444 499999999999987 45
Q ss_pred EEeC
Q 007267 356 FLYS 359 (610)
Q Consensus 356 ~~~~ 359 (610)
+.+.
T Consensus 159 ~~~~ 162 (164)
T cd01472 159 FNVA 162 (164)
T ss_pred Eecc
Confidence 5443
No 24
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=98.58 E-value=3.2e-06 Score=97.17 Aligned_cols=155 Identities=18% Similarity=0.268 Sum_probs=105.2
Q ss_pred CcEEEEEEeCCCCh---hHHHHHHHHHHHHH-HhCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccc
Q 007267 121 RPVYVAAVDLSSSE---EFLELTRSALQAAL-EAVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELE 196 (610)
Q Consensus 121 ~p~~vFvID~s~~~---~~l~~l~~~l~~~l-~~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~ 196 (610)
+...++|||+|.++ ..++.++++++..| +.++++.+||||+|++..++.. ..
T Consensus 304 ~r~VVLVLDvSGSM~g~dRL~~lkqAA~~fL~~~l~~~DrVGLVtFsssA~vl~---pL--------------------- 359 (863)
T TIGR00868 304 QRIVCLVLDKSGSMTVEDRLKRMNQAAKLFLLQTVEKGSWVGMVTFDSAAYIKN---EL--------------------- 359 (863)
T ss_pred CceEEEEEECCccccccCHHHHHHHHHHHHHHHhCCCCCEEEEEEECCceeEee---cc---------------------
Confidence 34689999999996 35888888888765 4678899999999999765421 00
Q ss_pred ccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEe
Q 007267 197 DVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFL 276 (610)
Q Consensus 197 ~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~ 276 (610)
.++. + ...++.|.+.|. .. + .++++++.||..|+++|..... ...+..|++++
T Consensus 360 --t~It----s-~~dr~aL~~~L~---~~-A---------------~GGT~I~~GL~~Alq~L~~~~~-~~~~~~IILLT 412 (863)
T TIGR00868 360 --IQIT----S-SAERDALTANLP---TA-A---------------SGGTSICSGLKAAFQVIKKSYQ-STDGSEIVLLT 412 (863)
T ss_pred --ccCC----c-HHHHHHHHHhhc---cc-c---------------CCCCcHHHHHHHHHHHHHhccc-ccCCCEEEEEe
Confidence 0100 0 112333333332 11 0 1568899999999999986431 11246899998
Q ss_pred cCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEE
Q 007267 277 SGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLF 356 (610)
Q Consensus 277 ~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~ 356 (610)
+|.++.+ ..++..+.++|+.|..+.++.+. -..|..||+.|||..+
T Consensus 413 DGedn~~--------------------------------~~~l~~lk~~gVtI~TIg~G~da--d~~L~~IA~~TGG~~f 458 (863)
T TIGR00868 413 DGEDNTI--------------------------------SSCFEEVKQSGAIIHTIALGPSA--AKELEELSDMTGGLRF 458 (863)
T ss_pred CCCCCCH--------------------------------HHHHHHHHHcCCEEEEEEeCCCh--HHHHHHHHHhcCCEEE
Confidence 8865421 12445566789999999998764 2459999999999988
Q ss_pred EeCC
Q 007267 357 LYSS 360 (610)
Q Consensus 357 ~~~~ 360 (610)
+.++
T Consensus 459 ~asd 462 (863)
T TIGR00868 459 YASD 462 (863)
T ss_pred EeCC
Confidence 8864
No 25
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=98.50 E-value=2.4e-06 Score=79.43 Aligned_cols=150 Identities=24% Similarity=0.324 Sum_probs=100.2
Q ss_pred EEEEEeCCCCh-hHHHHHHHHHHHHHHhCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccccCccC
Q 007267 124 YVAAVDLSSSE-EFLELTRSALQAALEAVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDVMPLS 202 (610)
Q Consensus 124 ~vFvID~s~~~-~~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~~p~~ 202 (610)
.+|+||+|.++ +..+.+|+++..+|+.|+++.++.||+|++.+..+.- .
T Consensus 3 vvilvD~S~Sm~g~~~~~k~al~~~l~~L~~~d~fnii~f~~~~~~~~~--~---------------------------- 52 (155)
T PF13768_consen 3 VVILVDTSGSMSGEKELVKDALRAILRSLPPGDRFNIIAFGSSVRPLFP--G---------------------------- 52 (155)
T ss_pred EEEEEeCCCCCCCcHHHHHHHHHHHHHhCCCCCEEEEEEeCCEeeEcch--h----------------------------
Confidence 68999999986 3348899999999999999999999999997654331 0
Q ss_pred cCccchH-hHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecCCCC
Q 007267 203 QFLAPVE-TFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPPD 281 (610)
Q Consensus 203 ~~l~~~~-e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~pt 281 (610)
+++.+ +.++...+.|+.++.. .+++.+..||+.|+..+...+. .-.|+++++|.++
T Consensus 53 --~~~~~~~~~~~a~~~I~~~~~~-----------------~G~t~l~~aL~~a~~~~~~~~~----~~~IilltDG~~~ 109 (155)
T PF13768_consen 53 --LVPATEENRQEALQWIKSLEAN-----------------SGGTDLLAALRAALALLQRPGC----VRAIILLTDGQPV 109 (155)
T ss_pred --HHHHhHHHHHHHHHHHHHhccc-----------------CCCccHHHHHHHHHHhcccCCC----ccEEEEEEeccCC
Confidence 01111 2334445556555542 1456799999999988732221 3689999999874
Q ss_pred CCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEE
Q 007267 282 HGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLF 356 (610)
Q Consensus 282 ~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~ 356 (610)
.++- ... +....+. ..+.+..|.++. ..+-..|..||+.|||..+
T Consensus 110 ~~~~---------------------------~i~-~~v~~~~-~~~~i~~~~~g~-~~~~~~L~~LA~~~~G~~~ 154 (155)
T PF13768_consen 110 SGEE---------------------------EIL-DLVRRAR-GHIRIFTFGIGS-DADADFLRELARATGGSFH 154 (155)
T ss_pred CCHH---------------------------HHH-HHHHhcC-CCceEEEEEECC-hhHHHHHHHHHHcCCCEEE
Confidence 4320 011 1122221 456677777655 4567889999999999865
No 26
>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=98.50 E-value=3.2e-06 Score=81.29 Aligned_cols=159 Identities=12% Similarity=0.081 Sum_probs=103.0
Q ss_pred EEEEEEeCCCCh--hHHHHHHHHHHHHHHhC---------CCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccc
Q 007267 123 VYVAAVDLSSSE--EFLELTRSALQAALEAV---------PSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTL 191 (610)
Q Consensus 123 ~~vFvID~s~~~--~~l~~l~~~l~~~l~~l---------p~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~ 191 (610)
-.+|+||.|.+. ..++.+|+.++..++.| +++.+||+|+|++..++.-
T Consensus 4 dvv~vlD~S~Sm~~~~~~~~k~~~~~~~~~l~~~~~~~i~~~~~rvglv~fs~~~~~~~--------------------- 62 (186)
T cd01480 4 DITFVLDSSESVGLQNFDITKNFVKRVAERFLKDYYRKDPAGSWRVGVVQYSDQQEVEA--------------------- 62 (186)
T ss_pred eEEEEEeCCCccchhhHHHHHHHHHHHHHHHhhhhccCCCCCceEEEEEEecCCceeeE---------------------
Confidence 378999999985 46777888888877766 4568999999998754311
Q ss_pred cccccccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccce
Q 007267 192 SLELEDVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALAR 271 (610)
Q Consensus 192 ~~dl~~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~Gk 271 (610)
|+... ...+..+.+.|+.++... +++.+|.||..|...+.. +........
T Consensus 63 --------~l~~~----~~~~~~l~~~i~~l~~~g-----------------g~T~~~~AL~~a~~~l~~-~~~~~~~~~ 112 (186)
T cd01480 63 --------GFLRD----IRNYTSLKEAVDNLEYIG-----------------GGTFTDCALKYATEQLLE-GSHQKENKF 112 (186)
T ss_pred --------ecccc----cCCHHHHHHHHHhCccCC-----------------CCccHHHHHHHHHHHHhc-cCCCCCceE
Confidence 00000 013455677777775321 356799999999998875 111112357
Q ss_pred EEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccC
Q 007267 272 VFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIES 351 (610)
Q Consensus 272 Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~T 351 (610)
|++++.|.++.++. .-..+.+..+.+.||.|-.+..+. .+...|..++...
T Consensus 113 iillTDG~~~~~~~---------------------------~~~~~~~~~~~~~gi~i~~vgig~--~~~~~L~~IA~~~ 163 (186)
T cd01480 113 LLVITDGHSDGSPD---------------------------GGIEKAVNEADHLGIKIFFVAVGS--QNEEPLSRIACDG 163 (186)
T ss_pred EEEEeCCCcCCCcc---------------------------hhHHHHHHHHHHCCCEEEEEecCc--cchHHHHHHHcCC
Confidence 88888887642211 011345667778887766665544 7888899999888
Q ss_pred ccEEEEeCCCC
Q 007267 352 GGSLFLYSSTD 362 (610)
Q Consensus 352 GG~v~~~~~~~ 362 (610)
+|. ++.++|.
T Consensus 164 ~~~-~~~~~~~ 173 (186)
T cd01480 164 KSA-LYRENFA 173 (186)
T ss_pred cch-hhhcchh
Confidence 776 4445553
No 27
>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain. Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196.
Probab=98.44 E-value=6.8e-06 Score=85.08 Aligned_cols=171 Identities=18% Similarity=0.149 Sum_probs=104.1
Q ss_pred CCcEEEEEEeCCCCh-hHHHHHHHHHHHHHHh-CCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccc
Q 007267 120 ARPVYVAAVDLSSSE-EFLELTRSALQAALEA-VPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELED 197 (610)
Q Consensus 120 ~~p~~vFvID~s~~~-~~l~~l~~~l~~~l~~-lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~ 197 (610)
.|...+|+||+|.+. +.+..+++++...++. ++++.+||||+|++.+++..
T Consensus 52 ~p~~vvlvlD~SgSM~~~~~~a~~a~~~~l~~~l~~~d~v~lv~f~~~~~~~~--------------------------- 104 (296)
T TIGR03436 52 LPLTVGLVIDTSGSMRNDLDRARAAAIRFLKTVLRPNDRVFVVTFNTRLRLLQ--------------------------- 104 (296)
T ss_pred CCceEEEEEECCCCchHHHHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeEee---------------------------
Confidence 467899999999985 5677788888888876 78899999999998765411
Q ss_pred cCccCcCccchHhHHHHHHHHHHhcCCCCCc-ccccccccCCCCccCCCcchHHHHH-HHHHhhccccCCCcccceEEEE
Q 007267 198 VMPLSQFLAPVETFKENITSALETLRPTTSW-ERTAGAAQGLDGVLMGGRGFGLAME-SLFNYLGSEYGNTFALARVFAF 275 (610)
Q Consensus 198 ~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~-~~~~~~~~~~~~~~~~~~~~G~Al~-~a~~lL~~~~~~~~~~GkIi~F 275 (610)
| ....++.|.+.|+.+...... ....+. .....+++++..||. ++..++....+.......|++|
T Consensus 105 --~-------~t~~~~~l~~~l~~l~~~~~~~~~~~~~----~~~~~g~T~l~~al~~aa~~~~~~~~~~~p~rk~iIll 171 (296)
T TIGR03436 105 --D-------FTSDPRLLEAALNRLKPPLRTDYNSSGA----FVRDGGGTALYDAITLAALEQLANALAGIPGRKALIVI 171 (296)
T ss_pred --c-------CCCCHHHHHHHHHhccCCCccccccccc----cccCCCcchhHHHHHHHHHHHHHHhhcCCCCCeEEEEE
Confidence 0 011234566667776541000 000000 000024567888874 4455554432100001347777
Q ss_pred ecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCC------------cChhc
Q 007267 276 LSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEY------------TDLAS 343 (610)
Q Consensus 276 ~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~------------~~l~~ 343 (610)
++|..+. ...-++++...+.+++|.|..+.++... .+-.+
T Consensus 172 TDG~~~~----------------------------~~~~~~~~~~~~~~~~v~vy~I~~~~~~~~~~~~~~~~~~~~~~~ 223 (296)
T TIGR03436 172 SDGGDNR----------------------------SRDTLERAIDAAQRADVAIYSIDARGLRAPDLGAGAKAGLGGPEA 223 (296)
T ss_pred ecCCCcc----------------------------hHHHHHHHHHHHHHcCCEEEEeccCccccCCcccccccCCCcHHH
Confidence 7774321 1123467788888899988887765311 24568
Q ss_pred chhhhccCccEEEEe
Q 007267 344 LKFLSIESGGSLFLY 358 (610)
Q Consensus 344 l~~l~~~TGG~v~~~ 358 (610)
|..+|+.|||..++.
T Consensus 224 L~~iA~~TGG~~~~~ 238 (296)
T TIGR03436 224 LERLAEETGGRAFYV 238 (296)
T ss_pred HHHHHHHhCCeEecc
Confidence 999999999996554
No 28
>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=98.43 E-value=1.3e-05 Score=77.91 Aligned_cols=169 Identities=15% Similarity=0.214 Sum_probs=100.9
Q ss_pred EEEEEeCCCCh--hHHHHHHHHHHHHHHhCCC---CcEEEEEeecceeEEE-EecCCCcceeeeeeCCCCCccccccccc
Q 007267 124 YVAAVDLSSSE--EFLELTRSALQAALEAVPS---GALFGLATFSHKIGLY-DVQGAIPVVKNVFIPSDTEDTLSLELED 197 (610)
Q Consensus 124 ~vFvID~s~~~--~~l~~l~~~l~~~l~~lp~---~~~VglITf~~~V~~~-~l~~~~~~~~~v~~~~~~~~~~~~dl~~ 197 (610)
++|+||+|.+. ..++.+|.++...++.|+. +.+||||+|++.++.. .+..
T Consensus 3 i~~vlD~SgSM~~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~~~~~~~~~------------------------ 58 (198)
T cd01470 3 IYIALDASDSIGEEDFDEAKNAIKTLIEKISSYEVSPRYEIISYASDPKEIVSIRD------------------------ 58 (198)
T ss_pred EEEEEECCCCccHHHHHHHHHHHHHHHHHccccCCCceEEEEEecCCceEEEeccc------------------------
Confidence 68999999986 5688899999999988853 6899999999976542 2210
Q ss_pred cCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhcccc---CC--CcccceE
Q 007267 198 VMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEY---GN--TFALARV 272 (610)
Q Consensus 198 ~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~---~~--~~~~GkI 272 (610)
+ ....+..+.+.|+.++... .. . ..++.++.||..+...+.... +. ....-.|
T Consensus 59 ------~---~~~~~~~~~~~l~~~~~~~-~~--~----------~ggT~~~~Al~~~~~~l~~~~~~~~~~~~~~~~~i 116 (198)
T cd01470 59 ------F---NSNDADDVIKRLEDFNYDD-HG--D----------KTGTNTAAALKKVYERMALEKVRNKEAFNETRHVI 116 (198)
T ss_pred ------C---CCCCHHHHHHHHHhCCccc-cc--C----------ccchhHHHHHHHHHHHHHHHHhcCccchhhcceEE
Confidence 0 0011234555666664321 00 0 135678999998887663211 00 0001358
Q ss_pred EEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHH------HHHHcCcEEEEEEecCCCcChhcchh
Q 007267 273 FAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAA------VAVQAGVCVDIFAITNEYTDLASLKF 346 (610)
Q Consensus 273 i~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~------~~~~~gisvDlf~~~~~~~~l~~l~~ 346 (610)
++++.|.++.|..... ..+.++++.. .+...++.|..+.++. ..|-.+|..
T Consensus 117 illTDG~~~~g~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~v~i~~iGvG~-~~~~~~L~~ 173 (198)
T cd01470 117 ILFTDGKSNMGGSPLP----------------------TVDKIKNLVYKNNKSDNPREDYLDVYVFGVGD-DVNKEELND 173 (198)
T ss_pred EEEcCCCcCCCCChhH----------------------HHHHHHHHHhcccccccchhcceeEEEEecCc-ccCHHHHHH
Confidence 9999999987632110 0111112111 1133455555555543 478999999
Q ss_pred hhccCcc--EEEEeCCC
Q 007267 347 LSIESGG--SLFLYSST 361 (610)
Q Consensus 347 l~~~TGG--~v~~~~~~ 361 (610)
||..||| ++|...++
T Consensus 174 iA~~~~g~~~~f~~~~~ 190 (198)
T cd01470 174 LASKKDNERHFFKLKDY 190 (198)
T ss_pred HhcCCCCCceEEEeCCH
Confidence 9999999 45555544
No 29
>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=98.41 E-value=1.3e-05 Score=75.50 Aligned_cols=158 Identities=20% Similarity=0.257 Sum_probs=103.2
Q ss_pred cEEEEEEeCCCCh--hHHHHHHHHHHHHHHhCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccccC
Q 007267 122 PVYVAAVDLSSSE--EFLELTRSALQAALEAVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDVM 199 (610)
Q Consensus 122 p~~vFvID~s~~~--~~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~~ 199 (610)
.-++|++|+|.+. ..++.+++++...+..++++.+|++++|++.++.+- . . . .
T Consensus 3 ~~v~~vlD~S~SM~~~~~~~~~~al~~~l~~l~~~~~~~l~~Fs~~~~~~~--~-~----~----------~-------- 57 (171)
T cd01461 3 KEVVFVIDTSGSMSGTKIEQTKEALLTALKDLPPGDYFNIIGFSDTVEEFS--P-S----S----------V-------- 57 (171)
T ss_pred ceEEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEeCCCceeec--C-c----c----------e--------
Confidence 3588999999986 447889999999999999888999999998765421 0 0 0 0
Q ss_pred ccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecCC
Q 007267 200 PLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGP 279 (610)
Q Consensus 200 p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~ 279 (610)
+.+ .+....+.+.|+.+.+. +++.++.||..|...+....+ ....|++|+.|.
T Consensus 58 ~~~------~~~~~~~~~~l~~~~~~------------------g~T~l~~al~~a~~~l~~~~~---~~~~iillTDG~ 110 (171)
T cd01461 58 SAT------AENVAAAIEYVNRLQAL------------------GGTNMNDALEAALELLNSSPG---SVPQIILLTDGE 110 (171)
T ss_pred eCC------HHHHHHHHHHHHhcCCC------------------CCcCHHHHHHHHHHhhccCCC---CccEEEEEeCCC
Confidence 000 11122334445555432 345699999999998875211 136888888886
Q ss_pred CCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeC
Q 007267 280 PDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYS 359 (610)
Q Consensus 280 pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~ 359 (610)
++.+ .+.+ +.++++.+.++.|..+.++. ..+-..|..++..|||..++..
T Consensus 111 ~~~~----------------------------~~~~-~~~~~~~~~~i~i~~i~~g~-~~~~~~l~~ia~~~gG~~~~~~ 160 (171)
T cd01461 111 VTNE----------------------------SQIL-KNVREALSGRIRLFTFGIGS-DVNTYLLERLAREGRGIARRIY 160 (171)
T ss_pred CCCH----------------------------HHHH-HHHHHhcCCCceEEEEEeCC-ccCHHHHHHHHHcCCCeEEEec
Confidence 3210 1122 34444555577777766653 3567789999999999988876
Q ss_pred CC
Q 007267 360 ST 361 (610)
Q Consensus 360 ~~ 361 (610)
+-
T Consensus 161 ~~ 162 (171)
T cd01461 161 ET 162 (171)
T ss_pred Ch
Confidence 43
No 30
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=98.39 E-value=1.7e-06 Score=81.13 Aligned_cols=150 Identities=22% Similarity=0.275 Sum_probs=100.2
Q ss_pred EEEEEeCCCChh-------HHHHHHHHHHHHHHhCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccc
Q 007267 124 YVAAVDLSSSEE-------FLELTRSALQAALEAVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELE 196 (610)
Q Consensus 124 ~vFvID~s~~~~-------~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~ 196 (610)
++||||+|.+.. .++.++.++...++.+|.. +|||++|++..++. .
T Consensus 2 vv~v~D~SgSM~~~~~~~~~~~~~~~~~~~~~~~~~~~-~v~l~~f~~~~~~~-----------------------~--- 54 (172)
T PF13519_consen 2 VVFVLDNSGSMNGYDGNRTRIDQAKDALNELLANLPGD-RVGLVSFSDSSRTL-----------------------S--- 54 (172)
T ss_dssp EEEEEE-SGGGGTTTSSS-HHHHHHHHHHHHHHHHTTS-EEEEEEESTSCEEE-----------------------E---
T ss_pred EEEEEECCcccCCCCCCCcHHHHHHHHHHHHHHHCCCC-EEEEEEeccccccc-----------------------c---
Confidence 589999999862 4888999999999988844 99999999853210 0
Q ss_pred ccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEe
Q 007267 197 DVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFL 276 (610)
Q Consensus 197 ~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~ 276 (610)
| +...+..+.+.++.+..... . ....+++.|+..|..++..... ....|++|+
T Consensus 55 ---~-------~t~~~~~~~~~l~~~~~~~~---~-----------~~~t~~~~al~~a~~~~~~~~~---~~~~iv~iT 107 (172)
T PF13519_consen 55 ---P-------LTSDKDELKNALNKLSPQGM---P-----------GGGTNLYDALQEAAKMLASSDN---RRRAIVLIT 107 (172)
T ss_dssp ---E-------EESSHHHHHHHHHTHHHHG----------------SSS--HHHHHHHHHHHHHC-SS---EEEEEEEEE
T ss_pred ---c-------ccccHHHHHHHhhccccccc---C-----------ccCCcHHHHHHHHHHHHHhCCC---CceEEEEec
Confidence 0 11233445566666643210 0 1456799999999999986531 135778888
Q ss_pred cCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEE
Q 007267 277 SGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLF 356 (610)
Q Consensus 277 ~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~ 356 (610)
+|.++ . -..+.+..+.+.+|.+.++.++.+...-..|..+++.|||..+
T Consensus 108 DG~~~---------~----------------------~~~~~~~~~~~~~i~i~~v~~~~~~~~~~~l~~la~~tgG~~~ 156 (172)
T PF13519_consen 108 DGEDN---------S----------------------SDIEAAKALKQQGITIYTVGIGSDSDANEFLQRLAEATGGRYF 156 (172)
T ss_dssp S-TTH---------C----------------------HHHHHHHHHHCTTEEEEEEEES-TT-EHHHHHHHHHHTEEEEE
T ss_pred CCCCC---------c----------------------chhHHHHHHHHcCCeEEEEEECCCccHHHHHHHHHHhcCCEEE
Confidence 87543 0 0012667788999999999998877656789999999999977
Q ss_pred Ee
Q 007267 357 LY 358 (610)
Q Consensus 357 ~~ 358 (610)
..
T Consensus 157 ~~ 158 (172)
T PF13519_consen 157 HV 158 (172)
T ss_dssp EE
T ss_pred Ee
Confidence 76
No 31
>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax. ATR is the cellular receptor for the anthrax protective antigen and facilitates entry of the toxin into cells. The VWA domain in ATR contains the toxin binding site and mediates interaction with protective antigen. The binding is mediated by divalent cations that binds to the MIDAS motif. These proteins are a family of vertebrate ECM receptors expressed by endothelial cells.
Probab=98.28 E-value=3.6e-05 Score=73.90 Aligned_cols=158 Identities=16% Similarity=0.122 Sum_probs=90.4
Q ss_pred EEEEEEeCCCChh-HHHHHHHHHHHHHHhC-CCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccccCc
Q 007267 123 VYVAAVDLSSSEE-FLELTRSALQAALEAV-PSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDVMP 200 (610)
Q Consensus 123 ~~vFvID~s~~~~-~l~~l~~~l~~~l~~l-p~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~~p 200 (610)
-.+|+||+|.+.+ .....++.++..++.+ .++.+||+|+|++..+..- |
T Consensus 6 Dvv~llD~SgSm~~~~~~~~~~~~~l~~~~~~~~~rvglv~Fs~~~~~~~-----------------------------~ 56 (185)
T cd01474 6 DLYFVLDKSGSVAANWIEIYDFVEQLVDRFNSPGLRFSFITFSTRATKIL-----------------------------P 56 (185)
T ss_pred eEEEEEeCcCchhhhHHHHHHHHHHHHHHcCCCCcEEEEEEecCCceEEE-----------------------------e
Confidence 4789999999863 2222334455555443 4569999999998654311 1
Q ss_pred cCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhcc--ccCCCcccceEEEEecC
Q 007267 201 LSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGS--EYGNTFALARVFAFLSG 278 (610)
Q Consensus 201 ~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~--~~~~~~~~GkIi~F~~g 278 (610)
+.. ....+.+.++.|..... .+++++|.||..|...|.. .++.. ..-.|++++.|
T Consensus 57 l~~-------~~~~~~~~l~~l~~~~~---------------~g~T~~~~aL~~a~~~l~~~~~~~r~-~~~~villTDG 113 (185)
T cd01474 57 LTD-------DSSAIIKGLEVLKKVTP---------------SGQTYIHEGLENANEQIFNRNGGGRE-TVSVIIALTDG 113 (185)
T ss_pred ccc-------cHHHHHHHHHHHhccCC---------------CCCCcHHHHHHHHHHHHHhhccCCCC-CCeEEEEEcCC
Confidence 100 01123444544543311 1457899999999987732 22110 01348888889
Q ss_pred CCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEE-E
Q 007267 279 PPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLF-L 357 (610)
Q Consensus 279 ~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~-~ 357 (610)
.++...+.-. ...++.+.+.|+.|-.+.. ...+..+|..+|..++ .+| .
T Consensus 114 ~~~~~~~~~~---------------------------~~~a~~l~~~gv~i~~vgv--~~~~~~~L~~iA~~~~-~~f~~ 163 (185)
T cd01474 114 QLLLNGHKYP---------------------------EHEAKLSRKLGAIVYCVGV--TDFLKSQLINIADSKE-YVFPV 163 (185)
T ss_pred CcCCCCCcch---------------------------HHHHHHHHHcCCEEEEEee--chhhHHHHHHHhCCCC-eeEec
Confidence 8742111000 1235566778876555554 6678899999998875 444 3
Q ss_pred eCCCC
Q 007267 358 YSSTD 362 (610)
Q Consensus 358 ~~~~~ 362 (610)
..+|+
T Consensus 164 ~~~~~ 168 (185)
T cd01474 164 TSGFQ 168 (185)
T ss_pred CccHH
Confidence 33453
No 32
>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=98.27 E-value=3e-05 Score=74.43 Aligned_cols=150 Identities=17% Similarity=0.060 Sum_probs=94.0
Q ss_pred EEEEEeCCCCh--hH-HHHHHHHHHHHHHhCC---CCcEEEEEeecceeEE-EEecCCCcceeeeeeCCCCCcccccccc
Q 007267 124 YVAAVDLSSSE--EF-LELTRSALQAALEAVP---SGALFGLATFSHKIGL-YDVQGAIPVVKNVFIPSDTEDTLSLELE 196 (610)
Q Consensus 124 ~vFvID~s~~~--~~-l~~l~~~l~~~l~~lp---~~~~VglITf~~~V~~-~~l~~~~~~~~~v~~~~~~~~~~~~dl~ 196 (610)
++|+||+|.+. .. ++.+|..+...++.++ ++.+||+|+|++..+. +++...
T Consensus 3 v~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~~~~~l~~~---------------------- 60 (186)
T cd01471 3 LYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAKELIRLSSP---------------------- 60 (186)
T ss_pred EEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCceEEEECCCc----------------------
Confidence 68999999985 34 7889999999888774 6789999999987653 222110
Q ss_pred ccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccc-cCCCcccceEEEE
Q 007267 197 DVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSE-YGNTFALARVFAF 275 (610)
Q Consensus 197 ~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~-~~~~~~~GkIi~F 275 (610)
....+..+.++++.|.... . . .+.+.++.||..|.+.+... +........|+++
T Consensus 61 -----------~~~~~~~~~~~i~~l~~~~-~--~-----------~G~T~l~~aL~~a~~~l~~~~~~r~~~~~~vill 115 (186)
T cd01471 61 -----------NSTNKDLALNAIRALLSLY-Y--P-----------NGSTNTTSALLVVEKHLFDTRGNRENAPQLVIIM 115 (186)
T ss_pred -----------cccchHHHHHHHHHHHhCc-C--C-----------CCCccHHHHHHHHHHHhhccCCCcccCceEEEEE
Confidence 0112233334444443221 0 0 14577999999999999753 1111112478888
Q ss_pred ecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhcc
Q 007267 276 LSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIE 350 (610)
Q Consensus 276 ~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~ 350 (610)
++|.++.++.. .+.++++.+.|+.+-++.++ +..|...|..++..
T Consensus 116 TDG~~~~~~~~-----------------------------~~~a~~l~~~gv~v~~igiG-~~~d~~~l~~ia~~ 160 (186)
T cd01471 116 TDGIPDSKFRT-----------------------------LKEARKLRERGVIIAVLGVG-QGVNHEENRSLVGC 160 (186)
T ss_pred ccCCCCCCcch-----------------------------hHHHHHHHHCCCEEEEEEee-hhhCHHHHHHhcCC
Confidence 88987543110 13466677788776666664 34677777777764
No 33
>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=98.20 E-value=8.7e-05 Score=70.74 Aligned_cols=159 Identities=16% Similarity=0.174 Sum_probs=101.3
Q ss_pred EEEEEeCCCCh--hHHHHHHHHHHHHHHhCC---CCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccccc
Q 007267 124 YVAAVDLSSSE--EFLELTRSALQAALEAVP---SGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV 198 (610)
Q Consensus 124 ~vFvID~s~~~--~~l~~l~~~l~~~l~~lp---~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~ 198 (610)
.+|+||.|.+. ..++.++..+...++.+. +++|||+|+|++..++.- ++.+
T Consensus 3 i~fvlD~S~S~~~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~~~~~-----------------------~l~~- 58 (177)
T cd01469 3 IVFVLDGSGSIYPDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESFRTEF-----------------------TLNE- 58 (177)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCceeEEE-----------------------ecCc-
Confidence 58999999985 468889998988888774 478999999999765411 0111
Q ss_pred CccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhc--cccCCCcccceEEEEe
Q 007267 199 MPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLG--SEYGNTFALARVFAFL 276 (610)
Q Consensus 199 ~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~--~~~~~~~~~GkIi~F~ 276 (610)
+ . ....+.++++.++... +.+.+|.||..|...+- ..+.......-+++++
T Consensus 59 -----~----~-~~~~~~~~i~~~~~~~-----------------g~T~~~~AL~~a~~~l~~~~~g~R~~~~kv~illT 111 (177)
T cd01469 59 -----Y----R-TKEEPLSLVKHISQLL-----------------GLTNTATAIQYVVTELFSESNGARKDATKVLVVIT 111 (177)
T ss_pred -----c----C-CHHHHHHHHHhCccCC-----------------CCccHHHHHHHHHHHhcCcccCCCCCCCeEEEEEe
Confidence 0 0 1122445566554321 34679999999988762 2121111124588888
Q ss_pred cCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCC---cChhcchhhhccCcc
Q 007267 277 SGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEY---TDLASLKFLSIESGG 353 (610)
Q Consensus 277 ~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~---~~l~~l~~l~~~TGG 353 (610)
.|..+.|+-. +..+..+...|+.|-.+....+. .+..+|..+|..+++
T Consensus 112 DG~~~~~~~~-----------------------------~~~~~~~k~~gv~v~~Vgvg~~~~~~~~~~~L~~ias~p~~ 162 (177)
T cd01469 112 DGESHDDPLL-----------------------------KDVIPQAEREGIIRYAIGVGGHFQRENSREELKTIASKPPE 162 (177)
T ss_pred CCCCCCcccc-----------------------------HHHHHHHHHCCcEEEEEEecccccccccHHHHHHHhcCCcH
Confidence 8877543210 23556666788777666665532 347889999998874
Q ss_pred -EEEEeCCCC
Q 007267 354 -SLFLYSSTD 362 (610)
Q Consensus 354 -~v~~~~~~~ 362 (610)
++|..++|+
T Consensus 163 ~h~f~~~~~~ 172 (177)
T cd01469 163 EHFFNVTDFA 172 (177)
T ss_pred HhEEEecCHH
Confidence 566666664
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=98.18 E-value=0.00011 Score=68.95 Aligned_cols=151 Identities=25% Similarity=0.263 Sum_probs=93.4
Q ss_pred EEEEEeCCCCh--hHHHHHHHHHHHHHHhC---CCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccccc
Q 007267 124 YVAAVDLSSSE--EFLELTRSALQAALEAV---PSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV 198 (610)
Q Consensus 124 ~vFvID~s~~~--~~l~~l~~~l~~~l~~l---p~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~ 198 (610)
.+|++|.|.+. ..++.+++.+...++.+ +++.+||||+|++..+..- ++
T Consensus 3 v~~vlD~S~Sm~~~~~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~~~~~-----------------------~l--- 56 (164)
T cd01482 3 IVFLVDGSWSIGRSNFNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDPRTEF-----------------------DL--- 56 (164)
T ss_pred EEEEEeCCCCcChhhHHHHHHHHHHHHhheeeCCCceEEEEEEECCCeeEEE-----------------------ec---
Confidence 68999999986 46778888888887765 4689999999999754311 01
Q ss_pred CccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhh-ccccC-CCcccceEEEEe
Q 007267 199 MPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYL-GSEYG-NTFALARVFAFL 276 (610)
Q Consensus 199 ~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL-~~~~~-~~~~~GkIi~F~ 276 (610)
..+ . ..+.+.+.|++++.. .+++.+|.||..|...+ ....+ .......|++|+
T Consensus 57 ---~~~----~-~~~~l~~~l~~~~~~-----------------~g~T~~~~aL~~a~~~~~~~~~~~r~~~~k~iillT 111 (164)
T cd01482 57 ---NAY----T-SKEDVLAAIKNLPYK-----------------GGNTRTGKALTHVREKNFTPDAGARPGVPKVVILIT 111 (164)
T ss_pred ---CCC----C-CHHHHHHHHHhCcCC-----------------CCCChHHHHHHHHHHHhcccccCCCCCCCEEEEEEc
Confidence 110 0 123345556655422 13467999999777544 32111 111124688888
Q ss_pred cCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCcc-EE
Q 007267 277 SGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGG-SL 355 (610)
Q Consensus 277 ~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG-~v 355 (610)
.|.++.. .++.++++.+.||. +|+++....+...|..++..+.+ ++
T Consensus 112 DG~~~~~-------------------------------~~~~a~~lk~~gi~--i~~ig~g~~~~~~L~~ia~~~~~~~~ 158 (164)
T cd01482 112 DGKSQDD-------------------------------VELPARVLRNLGVN--VFAVGVKDADESELKMIASKPSETHV 158 (164)
T ss_pred CCCCCch-------------------------------HHHHHHHHHHCCCE--EEEEecCcCCHHHHHHHhCCCchheE
Confidence 8865310 13467778788865 44444444668889999988654 34
Q ss_pred EEe
Q 007267 356 FLY 358 (610)
Q Consensus 356 ~~~ 358 (610)
+..
T Consensus 159 ~~~ 161 (164)
T cd01482 159 FNV 161 (164)
T ss_pred EEc
Confidence 433
No 35
>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=98.12 E-value=9.6e-05 Score=73.28 Aligned_cols=156 Identities=22% Similarity=0.266 Sum_probs=100.1
Q ss_pred EEEEEEeCCCCh--hHHHHHHHHHHHHHHhC---CCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccc
Q 007267 123 VYVAAVDLSSSE--EFLELTRSALQAALEAV---PSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELED 197 (610)
Q Consensus 123 ~~vFvID~s~~~--~~l~~l~~~l~~~l~~l---p~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~ 197 (610)
-.+|+||.|.+. ..++.+|+.+...++.+ |+.++||+|+|++.+++.- ++.
T Consensus 4 DlvfllD~S~Sm~~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~~~~~-----------------------~l~- 59 (224)
T cd01475 4 DLVFLIDSSRSVRPENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTVKQEF-----------------------PLG- 59 (224)
T ss_pred cEEEEEeCCCCCCHHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCceeEEe-----------------------ccc-
Confidence 478999999985 46888999999988877 4578999999999865411 010
Q ss_pred cCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhh-ccccCCC-cc---cceE
Q 007267 198 VMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYL-GSEYGNT-FA---LARV 272 (610)
Q Consensus 198 ~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL-~~~~~~~-~~---~GkI 272 (610)
.+ ..+..+.+.|+.++... +++.+|.||..|...+ ....+.. .. ..-|
T Consensus 60 -----~~-----~~~~~l~~~i~~i~~~~-----------------~~t~tg~AL~~a~~~~~~~~~g~r~~~~~~~kvv 112 (224)
T cd01475 60 -----RF-----KSKADLKRAVRRMEYLE-----------------TGTMTGLAIQYAMNNAFSEAEGARPGSERVPRVG 112 (224)
T ss_pred -----cc-----CCHHHHHHHHHhCcCCC-----------------CCChHHHHHHHHHHHhCChhcCCCCCCCCCCeEE
Confidence 00 12344666677775431 3456899999888653 2211110 00 1246
Q ss_pred EEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCc
Q 007267 273 FAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESG 352 (610)
Q Consensus 273 i~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TG 352 (610)
+++++|.++.. ..+.+.++.+.||.| |+.+-...+..+|..+|..++
T Consensus 113 illTDG~s~~~-------------------------------~~~~a~~lk~~gv~i--~~VgvG~~~~~~L~~ias~~~ 159 (224)
T cd01475 113 IVVTDGRPQDD-------------------------------VSEVAAKARALGIEM--FAVGVGRADEEELREIASEPL 159 (224)
T ss_pred EEEcCCCCccc-------------------------------HHHHHHHHHHCCcEE--EEEeCCcCCHHHHHHHhCCCc
Confidence 78888764210 135677788888655 544444568899999998765
Q ss_pred c-EEEEeCCCC
Q 007267 353 G-SLFLYSSTD 362 (610)
Q Consensus 353 G-~v~~~~~~~ 362 (610)
+ .++..++|+
T Consensus 160 ~~~~f~~~~~~ 170 (224)
T cd01475 160 ADHVFYVEDFS 170 (224)
T ss_pred HhcEEEeCCHH
Confidence 4 666666664
No 36
>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=98.06 E-value=0.00012 Score=67.90 Aligned_cols=149 Identities=20% Similarity=0.251 Sum_probs=100.6
Q ss_pred EEEEEeCCCChh--HHHHHHHHHHHHHHhCC---CCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccccc
Q 007267 124 YVAAVDLSSSEE--FLELTRSALQAALEAVP---SGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV 198 (610)
Q Consensus 124 ~vFvID~s~~~~--~l~~l~~~l~~~l~~lp---~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~ 198 (610)
++|++|+|.+.. .++.++..+...+..+. ++.++||++|++.....- ++
T Consensus 3 i~~llD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~~~~-----------------------~~--- 56 (161)
T cd01450 3 IVFLLDGSESVGPENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVRVEF-----------------------SL--- 56 (161)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCceEEE-----------------------EC---
Confidence 578999999863 67888888888887764 488999999998543211 00
Q ss_pred CccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccC-CCcccceEEEEec
Q 007267 199 MPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYG-NTFALARVFAFLS 277 (610)
Q Consensus 199 ~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~-~~~~~GkIi~F~~ 277 (610)
... . .+..+.+.|+.+..... +.+.++.||..|...+....+ .......|++|++
T Consensus 57 ---~~~----~-~~~~~~~~i~~~~~~~~----------------~~t~~~~al~~a~~~~~~~~~~~~~~~~~iiliTD 112 (161)
T cd01450 57 ---NDY----K-SKDDLLKAVKNLKYLGG----------------GGTNTGKALQYALEQLFSESNARENVPKVIIVLTD 112 (161)
T ss_pred ---CCC----C-CHHHHHHHHHhcccCCC----------------CCccHHHHHHHHHHHhcccccccCCCCeEEEEECC
Confidence 000 0 13345556666543210 246799999999999976531 0112367999999
Q ss_pred CCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCcc
Q 007267 278 GPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGG 353 (610)
Q Consensus 278 g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG 353 (610)
|.++.++ + ..++.+.+.+.++.|..+.++. .+...|..++..||+
T Consensus 113 G~~~~~~------~-----------------------~~~~~~~~~~~~v~v~~i~~g~--~~~~~l~~la~~~~~ 157 (161)
T cd01450 113 GRSDDGG------D-----------------------PKEAAAKLKDEGIKVFVVGVGP--ADEEELREIASCPSE 157 (161)
T ss_pred CCCCCCc------c-----------------------hHHHHHHHHHCCCEEEEEeccc--cCHHHHHHHhCCCCC
Confidence 9887653 0 1356777777898888887766 788889999999843
No 37
>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein. Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092).
Probab=98.04 E-value=0.00026 Score=80.54 Aligned_cols=183 Identities=18% Similarity=0.229 Sum_probs=113.8
Q ss_pred CcEEEEEEeCCCCh--hHHHHHHHHHHHHHHhCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccccc
Q 007267 121 RPVYVAAVDLSSSE--EFLELTRSALQAALEAVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV 198 (610)
Q Consensus 121 ~p~~vFvID~s~~~--~~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~ 198 (610)
+.-++||||+|.++ ..++.+|+++..+|..|+++.+++||+|++.++.+.- .. .
T Consensus 271 p~~vvfvlD~SgSM~g~~i~~ak~al~~~l~~L~~~d~~~ii~F~~~~~~~~~--~~---------------~------- 326 (596)
T TIGR03788 271 PRELVFVIDTSGSMAGESIEQAKSALLLALDQLRPGDRFNIIQFDSDVTLLFP--VP---------------V------- 326 (596)
T ss_pred CceEEEEEECCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEECCcceEecc--cc---------------c-------
Confidence 44699999999986 4578899999999999999999999999998765311 00 0
Q ss_pred CccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecC
Q 007267 199 MPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSG 278 (610)
Q Consensus 199 ~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g 278 (610)
+. -.+....+.+.|+.|... +++.+..||..|+......... ....|+++++|
T Consensus 327 -~~------~~~~~~~a~~~i~~l~a~------------------GgT~l~~aL~~a~~~~~~~~~~--~~~~iillTDG 379 (596)
T TIGR03788 327 -PA------TAHNLARARQFVAGLQAD------------------GGTEMAGALSAALRDDGPESSG--ALRQVVFLTDG 379 (596)
T ss_pred -cC------CHHHHHHHHHHHhhCCCC------------------CCccHHHHHHHHHHhhcccCCC--ceeEEEEEeCC
Confidence 00 012333445556666532 3466999999998775332211 12479999998
Q ss_pred CCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEe
Q 007267 279 PPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLY 358 (610)
Q Consensus 279 ~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~ 358 (610)
..+. + ....+.+ . ....++.+..|.++.+ .+-..|..||+.+||..++.
T Consensus 380 ~~~~--------~--------------------~~~~~~~-~-~~~~~~ri~tvGiG~~-~n~~lL~~lA~~g~G~~~~i 428 (596)
T TIGR03788 380 AVGN--------E--------------------DALFQLI-R-TKLGDSRLFTVGIGSA-PNSYFMRKAAQFGRGSFTFI 428 (596)
T ss_pred CCCC--------H--------------------HHHHHHH-H-HhcCCceEEEEEeCCC-cCHHHHHHHHHcCCCEEEEC
Confidence 5310 0 0111222 1 1224566777766544 67788999999999986665
Q ss_pred CCCCCCchhH---HHHHHhccCcceeeEEEEE
Q 007267 359 SSTDDSTLPQ---DIYRMLSRPYAFNCIMRLR 387 (610)
Q Consensus 359 ~~~~~~~l~~---dl~~~l~~~~~~~a~lrvr 387 (610)
.+- ..+.. ++.+.+..+..-+..+++.
T Consensus 429 ~~~--~~~~~~~~~~l~~~~~p~l~~v~v~~~ 458 (596)
T TIGR03788 429 GST--DEVQRKMSQLFAKLEQPALTDIALTFD 458 (596)
T ss_pred CCH--HHHHHHHHHHHHhhcCeEEEEEEEEEc
Confidence 432 23332 3333345555566666664
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=98.04 E-value=0.00019 Score=69.40 Aligned_cols=154 Identities=18% Similarity=0.202 Sum_probs=90.7
Q ss_pred EEEEEEeCCCCh--hHHHHHHHHHHHHHHhC---------CCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccc
Q 007267 123 VYVAAVDLSSSE--EFLELTRSALQAALEAV---------PSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTL 191 (610)
Q Consensus 123 ~~vFvID~s~~~--~~l~~l~~~l~~~l~~l---------p~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~ 191 (610)
=.||+||.|.+. +.++.+|+.+...+..+ |..+|||+|+|++..++.-
T Consensus 21 DivfvlD~S~Sm~~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a~~~~--------------------- 79 (193)
T cd01477 21 DIVFVVDNSKGMTQGGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNATVVA--------------------- 79 (193)
T ss_pred eEEEEEeCCCCcchhhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCceEEEE---------------------
Confidence 489999999984 56888888887766543 4468999999999776521
Q ss_pred cccccccCccCcCccchHhHHHHHHHHHHh-cCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccc-cCCCccc
Q 007267 192 SLELEDVMPLSQFLAPVETFKENITSALET-LRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSE-YGNTFAL 269 (610)
Q Consensus 192 ~~dl~~~~p~~~~l~~~~e~~~~i~~~L~~-L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~-~~~~~~~ 269 (610)
+|.+. . ....+.+.|+. +..... ..++.+|.||..|.+++... .+.....
T Consensus 80 --~L~d~----------~-~~~~~~~ai~~~~~~~~~---------------~ggT~ig~aL~~A~~~l~~~~~~~R~~v 131 (193)
T cd01477 80 --DLNDL----------Q-SFDDLYSQIQGSLTDVSS---------------TNASYLDTGLQAAEQMLAAGKRTSRENY 131 (193)
T ss_pred --ecccc----------c-CHHHHHHHHHHHhhcccc---------------CCcchHHHHHHHHHHHHHhhhccccCCC
Confidence 11110 0 11223333433 111100 13467999999999999743 1100012
Q ss_pred ce-EEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhh
Q 007267 270 AR-VFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLS 348 (610)
Q Consensus 270 Gk-Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~ 348 (610)
.| ++++++|..+.+.+. ....|+++.+.||.|-.+.++. ..|...|..|+
T Consensus 132 ~kvvIllTDg~~~~~~~~----------------------------~~~~a~~l~~~GI~i~tVGiG~-~~d~~~~~~L~ 182 (193)
T cd01477 132 KKVVIVFASDYNDEGSND----------------------------PRPIAARLKSTGIAIITVAFTQ-DESSNLLDKLG 182 (193)
T ss_pred CeEEEEEecCccCCCCCC----------------------------HHHHHHHHHHCCCEEEEEEeCC-CCCHHHHHHHH
Confidence 45 666666633221110 1357888999999888888865 34444455555
Q ss_pred ccCccE
Q 007267 349 IESGGS 354 (610)
Q Consensus 349 ~~TGG~ 354 (610)
+..++.
T Consensus 183 ~ias~~ 188 (193)
T cd01477 183 KIASPG 188 (193)
T ss_pred HhcCCC
Confidence 554443
No 39
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=98.01 E-value=0.00025 Score=79.53 Aligned_cols=175 Identities=15% Similarity=0.127 Sum_probs=114.6
Q ss_pred CcEEEEEEeCCCCh--hHHHHHHHHHHHHHHh-CCCCcEEEEEeecce-eEEEEecCCCcceeeeeeCCCCCcccccccc
Q 007267 121 RPVYVAAVDLSSSE--EFLELTRSALQAALEA-VPSGALFGLATFSHK-IGLYDVQGAIPVVKNVFIPSDTEDTLSLELE 196 (610)
Q Consensus 121 ~p~~vFvID~s~~~--~~l~~l~~~l~~~l~~-lp~~~~VglITf~~~-V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~ 196 (610)
+-.++||||+|.++ ..+..+|.++...|.. +.++-+||||+|++. ..+ .+
T Consensus 401 ~~~vvfvvD~SGSM~~~rl~~aK~a~~~ll~~ay~~rD~v~lI~F~g~~a~~-------------~l------------- 454 (584)
T PRK13406 401 ETTTIFVVDASGSAALHRLAEAKGAVELLLAEAYVRRDQVALVAFRGRGAEL-------------LL------------- 454 (584)
T ss_pred CccEEEEEECCCCCcHhHHHHHHHHHHHHHHhhcCCCCEEEEEEECCCceeE-------------Ec-------------
Confidence 45789999999986 5788899998888864 567789999999664 321 00
Q ss_pred ccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEe
Q 007267 197 DVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFL 276 (610)
Q Consensus 197 ~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~ 276 (610)
| ...+...+...|+.|+.. +++.++.||..|..++...... ...-.|++++
T Consensus 455 ---p-------pT~~~~~~~~~L~~l~~g------------------GgTpL~~gL~~A~~~l~~~~~~-~~~~~iVLlT 505 (584)
T PRK13406 455 ---P-------PTRSLVRAKRSLAGLPGG------------------GGTPLAAGLDAAAALALQVRRK-GMTPTVVLLT 505 (584)
T ss_pred ---C-------CCcCHHHHHHHHhcCCCC------------------CCChHHHHHHHHHHHHHHhccC-CCceEEEEEe
Confidence 1 011222334556656432 4567999999999988653211 0125899999
Q ss_pred cCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEE
Q 007267 277 SGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLF 356 (610)
Q Consensus 277 ~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~ 356 (610)
.|-+|.|-+.-..+... ..+- ..++..+.+.||.+=++-+.... ...+..||+.+||..+
T Consensus 506 DG~~n~~~~~~~~~~~~-----------------~~~~-~~~a~~~~~~gi~~~vId~g~~~--~~~~~~LA~~~gg~y~ 565 (584)
T PRK13406 506 DGRANIARDGTAGRAQA-----------------EEDA-LAAARALRAAGLPALVIDTSPRP--QPQARALAEAMGARYL 565 (584)
T ss_pred CCCCCCCccccccccch-----------------hhHH-HHHHHHHHhcCCeEEEEecCCCC--cHHHHHHHHhcCCeEE
Confidence 99999875321111100 0000 34677888888776666655443 3457999999999999
Q ss_pred EeCCCCCCchhHHH
Q 007267 357 LYSSTDDSTLPQDI 370 (610)
Q Consensus 357 ~~~~~~~~~l~~dl 370 (610)
..+.-+...+.+-+
T Consensus 566 ~l~~~~a~~~~~~v 579 (584)
T PRK13406 566 PLPRADAGRLSQAV 579 (584)
T ss_pred ECCCCCHHHHHHHH
Confidence 99988876665433
No 40
>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=97.91 E-value=0.0004 Score=78.49 Aligned_cols=177 Identities=12% Similarity=0.084 Sum_probs=115.0
Q ss_pred CcEEEEEEeCCCCh--hHHHHHHHHHHHHHHh-CCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccc
Q 007267 121 RPVYVAAVDLSSSE--EFLELTRSALQAALEA-VPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELED 197 (610)
Q Consensus 121 ~p~~vFvID~s~~~--~~l~~l~~~l~~~l~~-lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~ 197 (610)
.-.++|+||+|.++ ..++.+|.++...+.. +.++.+||||+|++...-+-+
T Consensus 407 ~~~v~fvvD~SGSM~~~rl~~aK~av~~Ll~~~~~~~D~v~Li~F~~~~a~~~l-------------------------- 460 (589)
T TIGR02031 407 GRLLIFVVDASGSAAVARMSEAKGAVELLLGEAYVHRDQVSLIAFRGTAAEVLL-------------------------- 460 (589)
T ss_pred CceEEEEEECCCCCChHHHHHHHHHHHHHHHhhccCCCEEEEEEECCCCceEEC--------------------------
Confidence 34588999999987 3588899998888864 456679999999764311101
Q ss_pred cCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEec
Q 007267 198 VMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLS 277 (610)
Q Consensus 198 ~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~ 277 (610)
|. ......+...|+.|+.. +++.++.||..|...+....... ..-.|++++.
T Consensus 461 --p~-------t~~~~~~~~~L~~l~~g------------------GgTpL~~gL~~A~~~~~~~~~~~-~~~~ivllTD 512 (589)
T TIGR02031 461 --PP-------SRSVEQAKRRLDVLPGG------------------GGTPLAAGLAAAFQTALQARSSG-GTPTIVLITD 512 (589)
T ss_pred --CC-------CCCHHHHHHHHhcCCCC------------------CCCcHHHHHHHHHHHHHHhcccC-CceEEEEECC
Confidence 10 00122334556666532 34669999999999986432110 1147999999
Q ss_pred CCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEE
Q 007267 278 GPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFL 357 (610)
Q Consensus 278 g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~ 357 (610)
|.+|.|-+...... .. -..+..+-...++.++.+.||.+=++-+...+.+...+..||+..||..++
T Consensus 513 G~~nv~~~~~~~~~-~~------------~~~~~~~~~~~~a~~~~~~gi~~~vid~~~~~~~~~~~~~lA~~~~g~y~~ 579 (589)
T TIGR02031 513 GRGNIPLDGDPESI-KA------------DREQAAEEALALARKIREAGMPALVIDTAMRFVSTGFAQKLARKMGAHYIY 579 (589)
T ss_pred CCCCCCCCcccccc-cc------------cchhHHHHHHHHHHHHHhcCCeEEEEeCCCCCccchHHHHHHHhcCCcEEe
Confidence 99998753111000 00 001122333567888889998777776666666666789999999999998
Q ss_pred eCCCCCC
Q 007267 358 YSSTDDS 364 (610)
Q Consensus 358 ~~~~~~~ 364 (610)
.++-+..
T Consensus 580 l~~~~a~ 586 (589)
T TIGR02031 580 LPNATAA 586 (589)
T ss_pred CCCCChh
Confidence 8876654
No 41
>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=97.88 E-value=0.00086 Score=62.91 Aligned_cols=155 Identities=24% Similarity=0.233 Sum_probs=104.5
Q ss_pred EEEEEEeCCCCh--hHHHHHHHHHHHHHHhCCC---CcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccc
Q 007267 123 VYVAAVDLSSSE--EFLELTRSALQAALEAVPS---GALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELED 197 (610)
Q Consensus 123 ~~vFvID~s~~~--~~l~~l~~~l~~~l~~lp~---~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~ 197 (610)
-++|+||+|.+. ..++.+++.+...+..+.. +.+||+++|++..+.+.- +
T Consensus 3 ~v~l~vD~S~SM~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ii~f~~~~~~~~~-----------------------~-- 57 (177)
T smart00327 3 DVVFLLDGSGSMGPNRFEKAKEFVLKLVEQLDIGPDGDRVGLVTFSDDATVLFP-----------------------L-- 57 (177)
T ss_pred cEEEEEeCCCccchHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeCCCceEEEc-----------------------c--
Confidence 478999999986 5678888888888887765 899999999994432110 0
Q ss_pred cCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccC--CCcccceEEEE
Q 007267 198 VMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYG--NTFALARVFAF 275 (610)
Q Consensus 198 ~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~--~~~~~GkIi~F 275 (610)
. .....+.+.+.++.+... . .....++.|+..|...+..... .....-.|++|
T Consensus 58 ----~-----~~~~~~~~~~~i~~~~~~--~--------------~~~~~~~~al~~~~~~~~~~~~~~~~~~~~~ivii 112 (177)
T smart00327 58 ----N-----DSRSKDALLEALASLSYK--L--------------GGGTNLGAALQYALENLFSKSAGSRRGAPKVLILI 112 (177)
T ss_pred ----c-----ccCCHHHHHHHHHhcCCC--C--------------CCCchHHHHHHHHHHHhcCcCCCCCCCCCeEEEEE
Confidence 0 011234466667766541 0 0345599999999988852211 00002368888
Q ss_pred ecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEE
Q 007267 276 LSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSL 355 (610)
Q Consensus 276 ~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v 355 (610)
++|.++.+ ..+.+...++.+.++.+..+.++.+. +...+..++..++|..
T Consensus 113 tDg~~~~~-----------------------------~~~~~~~~~~~~~~i~i~~i~~~~~~-~~~~l~~~~~~~~~~~ 162 (177)
T smart00327 113 TDGESNDG-----------------------------GDLLKAAKELKRSGVKVFVVGVGNDV-DEEELKKLASAPGGVY 162 (177)
T ss_pred cCCCCCCC-----------------------------ccHHHHHHHHHHCCCEEEEEEccCcc-CHHHHHHHhCCCcceE
Confidence 88877644 12346777888888888888877543 7788999999999986
Q ss_pred EE
Q 007267 356 FL 357 (610)
Q Consensus 356 ~~ 357 (610)
.+
T Consensus 163 ~~ 164 (177)
T smart00327 163 VF 164 (177)
T ss_pred Ee
Confidence 54
No 42
>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=97.85 E-value=0.00028 Score=80.60 Aligned_cols=160 Identities=17% Similarity=0.180 Sum_probs=105.8
Q ss_pred CcEEEEEEeCCCCh---hHHHHHHHHHHHHHH-hCCCCcEEEEEeecce-eEEEEecCCCcceeeeeeCCCCCccccccc
Q 007267 121 RPVYVAAVDLSSSE---EFLELTRSALQAALE-AVPSGALFGLATFSHK-IGLYDVQGAIPVVKNVFIPSDTEDTLSLEL 195 (610)
Q Consensus 121 ~p~~vFvID~s~~~---~~l~~l~~~l~~~l~-~lp~~~~VglITf~~~-V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl 195 (610)
.-.++|+||+|.++ ..++.+|.++...+. .+..+.+||||+|+.. ..+ .+
T Consensus 465 ~~~vv~vvD~SgSM~~~~rl~~ak~a~~~ll~~a~~~~D~v~lI~F~g~~a~~-------------~~------------ 519 (633)
T TIGR02442 465 GNLVIFVVDASGSMAARGRMAAAKGAVLSLLRDAYQKRDKVALITFRGEEAEV-------------LL------------ 519 (633)
T ss_pred CceEEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCceE-------------Ec------------
Confidence 34688999999987 357778888777765 4566789999999753 211 00
Q ss_pred cccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccc---cCCCcccceE
Q 007267 196 EDVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSE---YGNTFALARV 272 (610)
Q Consensus 196 ~~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~---~~~~~~~GkI 272 (610)
| .......+...|+.|+.. +++.++.||..|..++... .+ ...+.|
T Consensus 520 ----p-------~t~~~~~~~~~L~~l~~g------------------G~Tpl~~aL~~A~~~l~~~~~~~~--~~~~~v 568 (633)
T TIGR02442 520 ----P-------PTSSVELAARRLEELPTG------------------GRTPLAAGLLKAAEVLSNELLRDD--DGRPLL 568 (633)
T ss_pred ----C-------CCCCHHHHHHHHHhCCCC------------------CCCCHHHHHHHHHHHHHHhhccCC--CCceEE
Confidence 1 111223344566666532 3466999999999988731 11 113689
Q ss_pred EEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCc
Q 007267 273 FAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESG 352 (610)
Q Consensus 273 i~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TG 352 (610)
+++++|.+|.|.+. .. +..+ -..+|.++.+.||.+.++-+....++...+..||+.+|
T Consensus 569 vliTDG~~n~~~~~---~~------------------~~~~-~~~~a~~l~~~~i~~~vIdt~~~~~~~~~~~~lA~~~g 626 (633)
T TIGR02442 569 VVITDGRANVADGG---EP------------------PTDD-ARTIAAKLAARGILFVVIDTESGFVRLGLAEDLARALG 626 (633)
T ss_pred EEECCCCCCCCCCC---CC------------------hHHH-HHHHHHHHHhcCCeEEEEeCCCCCcchhHHHHHHHhhC
Confidence 99999999886211 00 0001 13567777778877776666566677788999999999
Q ss_pred cEEEEe
Q 007267 353 GSLFLY 358 (610)
Q Consensus 353 G~v~~~ 358 (610)
|..+..
T Consensus 627 g~y~~l 632 (633)
T TIGR02442 627 GEYVRL 632 (633)
T ss_pred CeEEec
Confidence 997653
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=97.85 E-value=0.0013 Score=62.02 Aligned_cols=154 Identities=19% Similarity=0.209 Sum_probs=95.7
Q ss_pred EEEEEeCCCCh--hHHHHHHHHHHHHHHhC---CCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccccc
Q 007267 124 YVAAVDLSSSE--EFLELTRSALQAALEAV---PSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV 198 (610)
Q Consensus 124 ~vFvID~s~~~--~~l~~l~~~l~~~l~~l---p~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~ 198 (610)
.+|+||.|.+- ..++.+|+-++..++.+ |+.++||+|+|++..+.. + ++.+
T Consensus 3 ivfllD~S~Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~~~-~----------------------~l~~- 58 (165)
T cd01481 3 IVFLIDGSDNVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPRPE-F----------------------YLNT- 58 (165)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCeeEE-E----------------------eccc-
Confidence 58999999874 57888999898888877 467999999999865431 0 1111
Q ss_pred CccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhh-ccccCCCcc---cceEEE
Q 007267 199 MPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYL-GSEYGNTFA---LARVFA 274 (610)
Q Consensus 199 ~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL-~~~~~~~~~---~GkIi~ 274 (610)
+ . ++..+.+.|+.++-... ..+.+|.||..+...+ ....|.... .=.+++
T Consensus 59 -----~----~-~~~~l~~~i~~i~~~~g----------------~~t~t~~AL~~~~~~~f~~~~g~R~~~~~~kv~vv 112 (165)
T cd01481 59 -----H----S-TKADVLGAVRRLRLRGG----------------SQLNTGSALDYVVKNLFTKSAGSRIEEGVPQFLVL 112 (165)
T ss_pred -----c----C-CHHHHHHHHHhcccCCC----------------CcccHHHHHHHHHHhhcCccccCCccCCCCeEEEE
Confidence 0 0 23345666666643310 2345999999876544 332221100 113567
Q ss_pred EecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccE
Q 007267 275 FLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGS 354 (610)
Q Consensus 275 F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~ 354 (610)
+++|..+. -..+-|+.+.+.|| .+|+.+....+..+|..+|..- -.
T Consensus 113 iTdG~s~d-------------------------------~~~~~a~~lr~~gv--~i~~vG~~~~~~~eL~~ias~p-~~ 158 (165)
T cd01481 113 ITGGKSQD-------------------------------DVERPAVALKRAGI--VPFAIGARNADLAELQQIAFDP-SF 158 (165)
T ss_pred EeCCCCcc-------------------------------hHHHHHHHHHHCCc--EEEEEeCCcCCHHHHHHHhCCC-cc
Confidence 77775320 01346777778884 5677776668888999888665 35
Q ss_pred EEEeCCC
Q 007267 355 LFLYSST 361 (610)
Q Consensus 355 v~~~~~~ 361 (610)
++..++|
T Consensus 159 vf~v~~f 165 (165)
T cd01481 159 VFQVSDF 165 (165)
T ss_pred EEEecCC
Confidence 5554443
No 44
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=97.83 E-value=0.00076 Score=74.07 Aligned_cols=164 Identities=14% Similarity=0.086 Sum_probs=97.3
Q ss_pred cEEEEEEeCCCChh---HHHHHHHHHHHHHHhC---CCCcEEEEEeecceeEE-EEecCCCcceeeeeeCCCCCcccccc
Q 007267 122 PVYVAAVDLSSSEE---FLELTRSALQAALEAV---PSGALFGLATFSHKIGL-YDVQGAIPVVKNVFIPSDTEDTLSLE 194 (610)
Q Consensus 122 p~~vFvID~s~~~~---~l~~l~~~l~~~l~~l---p~~~~VglITf~~~V~~-~~l~~~~~~~~~v~~~~~~~~~~~~d 194 (610)
--.+|+||+|.+.+ .++.++..+..++..+ ++.++||+|+|++..+. +.+....
T Consensus 43 lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~r~vfpL~s~~------------------- 103 (576)
T PTZ00441 43 VDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNTTELIRLGSGA------------------- 103 (576)
T ss_pred ceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCceEEEecCCCc-------------------
Confidence 45899999999863 3466777777777766 35689999999987543 2221110
Q ss_pred ccccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEE
Q 007267 195 LEDVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFA 274 (610)
Q Consensus 195 l~~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~ 274 (610)
...+..+...|..|..... ..+.+.+|.||..|...+...+......+-||+
T Consensus 104 --------------s~Dk~~aL~~I~sL~~~~~--------------pgGgTnig~AL~~Aae~L~sr~~R~nvpKVVIL 155 (576)
T PTZ00441 104 --------------SKDKEQALIIVKSLRKTYL--------------PYGKTNMTDALLEVRKHLNDRVNRENAIQLVIL 155 (576)
T ss_pred --------------cccHHHHHHHHHHHHhhcc--------------CCCCccHHHHHHHHHHHHhhcccccCCceEEEE
Confidence 0011223333444322100 014567999999888888654321122468999
Q ss_pred EecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhh----cc
Q 007267 275 FLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLS----IE 350 (610)
Q Consensus 275 F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~----~~ 350 (610)
|+.|.++.+.. . .+.++++.+.||.|-++.++. ..+...+..++ ..
T Consensus 156 LTDG~sns~~d----------------------------v-leaAq~LR~~GVeI~vIGVG~-g~n~e~LrlIAgC~p~~ 205 (576)
T PTZ00441 156 MTDGIPNSKYR----------------------------A-LEESRKLKDRNVKLAVIGIGQ-GINHQFNRLLAGCRPRE 205 (576)
T ss_pred EecCCCCCccc----------------------------H-HHHHHHHHHCCCEEEEEEeCC-CcCHHHHHHHhccCCCC
Confidence 99987642100 0 134667777888766666643 46666666666 33
Q ss_pred CccEEEEeCCCC
Q 007267 351 SGGSLFLYSSTD 362 (610)
Q Consensus 351 TGG~v~~~~~~~ 362 (610)
++|.+|...+|+
T Consensus 206 g~c~~Y~vadf~ 217 (576)
T PTZ00441 206 GKCKFYSDADWE 217 (576)
T ss_pred CCCceEEeCCHH
Confidence 556777776774
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=97.81 E-value=0.00091 Score=62.50 Aligned_cols=108 Identities=19% Similarity=0.190 Sum_probs=67.9
Q ss_pred EEEEEeCCCCh-hHHHHHHHHHHHHHHhCC---CCcEEEEEeecce--eEEEEecCCCcceeeeeeCCCCCccccccccc
Q 007267 124 YVAAVDLSSSE-EFLELTRSALQAALEAVP---SGALFGLATFSHK--IGLYDVQGAIPVVKNVFIPSDTEDTLSLELED 197 (610)
Q Consensus 124 ~vFvID~s~~~-~~l~~l~~~l~~~l~~lp---~~~~VglITf~~~--V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~ 197 (610)
++|++|+|.+. +.++..++.++++++.+. +..+||+|+|++. .++.- .+.+
T Consensus 3 v~~llD~S~Sm~~~~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~~~~~~~~~~-----------------------~l~~ 59 (163)
T cd01476 3 LLFVLDSSGSVRGKFEKYKKYIERIVEGLEIGPTATRVALITYSGRGRQRVRF-----------------------NLPK 59 (163)
T ss_pred EEEEEeCCcchhhhHHHHHHHHHHHHHhcCCCCCCcEEEEEEEcCCCceEEEe-----------------------cCCC
Confidence 68999999985 445667888888887764 4789999999883 33210 0000
Q ss_pred cCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCC-CcccceEEEEe
Q 007267 198 VMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGN-TFALARVFAFL 276 (610)
Q Consensus 198 ~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~-~~~~GkIi~F~ 276 (610)
...++.+.+.|+.|+.. ...+.+|.||..|..++....+. ......|++++
T Consensus 60 -----------~~~~~~l~~~i~~l~~~-----------------gg~T~l~~aL~~a~~~l~~~~~~r~~~~~~villT 111 (163)
T cd01476 60 -----------HNDGEELLEKVDNLRFI-----------------GGTTATGAAIEVALQQLDPSEGRREGIPKVVVVLT 111 (163)
T ss_pred -----------CCCHHHHHHHHHhCccC-----------------CCCccHHHHHHHHHHHhccccCCCCCCCeEEEEEC
Confidence 01223455666666532 03467999999999999622111 11124688888
Q ss_pred cCCCCC
Q 007267 277 SGPPDH 282 (610)
Q Consensus 277 ~g~pt~ 282 (610)
+|.++.
T Consensus 112 DG~~~~ 117 (163)
T cd01476 112 DGRSHD 117 (163)
T ss_pred CCCCCC
Confidence 887653
No 46
>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=97.81 E-value=0.00033 Score=66.05 Aligned_cols=158 Identities=21% Similarity=0.266 Sum_probs=97.0
Q ss_pred EEEEEeCCCCh--hHHHHHHHHHHHHHHhC---CCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccccc
Q 007267 124 YVAAVDLSSSE--EFLELTRSALQAALEAV---PSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV 198 (610)
Q Consensus 124 ~vFvID~s~~~--~~l~~l~~~l~~~l~~l---p~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~ 198 (610)
.+|+||.|.+. ..++.+++.+...++.+ +++++||+|+|++..+.+- ++.+
T Consensus 2 ivflvD~S~sm~~~~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~~~~-----------------------~~~~- 57 (178)
T PF00092_consen 2 IVFLVDTSGSMSGDNFEKAKQFVKSIISRLSISNNGTRVGIVTFSDSARVLF-----------------------SLTD- 57 (178)
T ss_dssp EEEEEE-STTSCHHHHHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEEEEE-----------------------ETTS-
T ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHHhhhccccccccceeeeeccccccc-----------------------cccc-
Confidence 58999999986 35888999999999855 5789999999999876311 0000
Q ss_pred CccCcCccchHhHHHHHHHHH-HhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccc--cCCCcccceEEEE
Q 007267 199 MPLSQFLAPVETFKENITSAL-ETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSE--YGNTFALARVFAF 275 (610)
Q Consensus 199 ~p~~~~l~~~~e~~~~i~~~L-~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~--~~~~~~~GkIi~F 275 (610)
......+.+.+ ..++.. .+.+.+|.||..|...+... +.......-|+++
T Consensus 58 ----------~~~~~~~~~~i~~~~~~~-----------------~g~t~~~~aL~~a~~~l~~~~~~~r~~~~~~iili 110 (178)
T PF00092_consen 58 ----------YQSKNDLLNAINDSIPSS-----------------GGGTNLGAALKFAREQLFSSNNGGRPNSPKVIILI 110 (178)
T ss_dssp ----------HSSHHHHHHHHHTTGGCC-----------------BSSB-HHHHHHHHHHHTTSGGGTTGTTSEEEEEEE
T ss_pred ----------cccccccccccccccccc-----------------chhhhHHHHHhhhhhcccccccccccccccceEEE
Confidence 00112223333 333221 14567999999999998654 1111123468888
Q ss_pred ecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhcc--Ccc
Q 007267 276 LSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIE--SGG 353 (610)
Q Consensus 276 ~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~--TGG 353 (610)
++|.++.++-. ...+..+.+. ..|.+|+.+.+..+..+|..|+.. .+|
T Consensus 111 TDG~~~~~~~~-----------------------------~~~~~~~~~~-~~i~~~~ig~~~~~~~~l~~la~~~~~~~ 160 (178)
T PF00092_consen 111 TDGNSNDSDSP-----------------------------SEEAANLKKS-NGIKVIAIGIDNADNEELRELASCPTSEG 160 (178)
T ss_dssp ESSSSSSHSGH-----------------------------HHHHHHHHHH-CTEEEEEEEESCCHHHHHHHHSHSSTCHH
T ss_pred EeecccCCcch-----------------------------HHHHHHHHHh-cCcEEEEEecCcCCHHHHHHHhCCCCCCC
Confidence 88877553210 0112222222 457777777677888899999955 447
Q ss_pred EEEEeCCCC
Q 007267 354 SLFLYSSTD 362 (610)
Q Consensus 354 ~v~~~~~~~ 362 (610)
.+++..+++
T Consensus 161 ~~~~~~~~~ 169 (178)
T PF00092_consen 161 HVFYLADFS 169 (178)
T ss_dssp HEEEESSHH
T ss_pred cEEEcCCHH
Confidence 777776653
No 47
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=97.80 E-value=0.00061 Score=67.05 Aligned_cols=169 Identities=16% Similarity=0.133 Sum_probs=114.5
Q ss_pred cEEEEEEeCCCCh---hHHHHHHHHHHHHHH-hCCCCcEEEEEeecce-eEEEEecCCCcceeeeeeCCCCCcccccccc
Q 007267 122 PVYVAAVDLSSSE---EFLELTRSALQAALE-AVPSGALFGLATFSHK-IGLYDVQGAIPVVKNVFIPSDTEDTLSLELE 196 (610)
Q Consensus 122 p~~vFvID~s~~~---~~l~~l~~~l~~~l~-~lp~~~~VglITf~~~-V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~ 196 (610)
-.+|||||.|.+. ..++++|-++.+.|. .-..+-+|++|+|... -
T Consensus 79 ~lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~dAYq~RdkvavI~F~G~~A------------------------------ 128 (261)
T COG1240 79 NLIVFVVDASGSMAARRRMAAAKGAALSLLRDAYQRRDKVAVIAFRGEKA------------------------------ 128 (261)
T ss_pred CcEEEEEeCcccchhHHHHHHHHHHHHHHHHHHHHccceEEEEEecCCcc------------------------------
Confidence 3589999999996 457888888877775 3445789999999641 1
Q ss_pred ccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCC-cccceEEEE
Q 007267 197 DVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNT-FALARVFAF 275 (610)
Q Consensus 197 ~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~-~~~GkIi~F 275 (610)
.+++|...+-+.+.+.|+.|+... .+=+..||..|..++....... ..--.+++.
T Consensus 129 ------~lll~pT~sv~~~~~~L~~l~~GG------------------~TPL~~aL~~a~ev~~r~~r~~p~~~~~~vvi 184 (261)
T COG1240 129 ------ELLLPPTSSVELAERALERLPTGG------------------KTPLADALRQAYEVLAREKRRGPDRRPVMVVI 184 (261)
T ss_pred ------eEEeCCcccHHHHHHHHHhCCCCC------------------CCchHHHHHHHHHHHHHhhccCCCcceEEEEE
Confidence 112223334455677888887642 2339999999999997654100 112578999
Q ss_pred ecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEE
Q 007267 276 LSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSL 355 (610)
Q Consensus 276 ~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v 355 (610)
+.|.||.+.+.=...+ -...+.++...|+-+=+.-+-..++.+.-...||...||.+
T Consensus 185 TDGr~n~~~~~~~~~e-----------------------~~~~a~~~~~~g~~~lvid~e~~~~~~g~~~~iA~~~Gg~~ 241 (261)
T COG1240 185 TDGRANVPIPLGPKAE-----------------------TLEAASKLRLRGIQLLVIDTEGSEVRLGLAEEIARASGGEY 241 (261)
T ss_pred eCCccCCCCCCchHHH-----------------------HHHHHHHHhhcCCcEEEEecCCccccccHHHHHHHHhCCeE
Confidence 9999988764221100 02456666677766666666667777777799999999999
Q ss_pred EEeCCCCCCchh
Q 007267 356 FLYSSTDDSTLP 367 (610)
Q Consensus 356 ~~~~~~~~~~l~ 367 (610)
+..+......+.
T Consensus 242 ~~L~~l~~~~i~ 253 (261)
T COG1240 242 YHLDDLSDDSIV 253 (261)
T ss_pred EecccccchHHH
Confidence 999877665554
No 48
>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=97.74 E-value=0.0013 Score=60.17 Aligned_cols=149 Identities=23% Similarity=0.290 Sum_probs=98.3
Q ss_pred EEEEEEeCCCCh--hHHHHHHHHHHHHHHhCCC---CcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccc
Q 007267 123 VYVAAVDLSSSE--EFLELTRSALQAALEAVPS---GALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELED 197 (610)
Q Consensus 123 ~~vFvID~s~~~--~~l~~l~~~l~~~l~~lp~---~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~ 197 (610)
.++|+||+|.+. ..++.+++.+...+..++. ..++|++.|+...+.+- ++.+
T Consensus 2 ~v~~viD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~f~~~~~~~~-----------------------~~~~ 58 (161)
T cd00198 2 DIVFLLDVSGSMGGEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARVVL-----------------------PLTT 58 (161)
T ss_pred cEEEEEeCCCCcCcchHHHHHHHHHHHHHhcccCCCCcEEEEEEecCccceee-----------------------cccc
Confidence 378999999985 6788899999999988876 78999999998332211 0000
Q ss_pred cCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEec
Q 007267 198 VMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLS 277 (610)
Q Consensus 198 ~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~ 277 (610)
. ...+.+...++.+... . .....+..|+..+...+..... ......|++|++
T Consensus 59 ------~-----~~~~~~~~~~~~~~~~--~--------------~~~t~~~~al~~~~~~~~~~~~-~~~~~~lvvitD 110 (161)
T cd00198 59 ------D-----TDKADLLEAIDALKKG--L--------------GGGTNIGAALRLALELLKSAKR-PNARRVIILLTD 110 (161)
T ss_pred ------c-----CCHHHHHHHHHhcccC--C--------------CCCccHHHHHHHHHHHhcccCC-CCCceEEEEEeC
Confidence 0 0223455566666430 0 1345689999999999876310 012367888888
Q ss_pred CCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccC
Q 007267 278 GPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIES 351 (610)
Q Consensus 278 g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~T 351 (610)
|.++.++ .+ ..+..+.+.+.++.+.++.++. ..+-..+..++..|
T Consensus 111 g~~~~~~-----~~-----------------------~~~~~~~~~~~~v~v~~v~~g~-~~~~~~l~~l~~~~ 155 (161)
T cd00198 111 GEPNDGP-----EL-----------------------LAEAARELRKLGITVYTIGIGD-DANEDELKEIADKT 155 (161)
T ss_pred CCCCCCc-----ch-----------------------hHHHHHHHHHcCCEEEEEEcCC-CCCHHHHHHHhccc
Confidence 8765543 00 1245666777799998888876 34566788888887
No 49
>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=97.67 E-value=0.00031 Score=66.75 Aligned_cols=45 Identities=20% Similarity=0.169 Sum_probs=36.5
Q ss_pred EEEEEeCCCCh--hHHHHHHHHHHHHHHhCC------CCcEEEEEeecceeEE
Q 007267 124 YVAAVDLSSSE--EFLELTRSALQAALEAVP------SGALFGLATFSHKIGL 168 (610)
Q Consensus 124 ~vFvID~s~~~--~~l~~l~~~l~~~l~~lp------~~~~VglITf~~~V~~ 168 (610)
++|+||+|.+. ..++.+++++...++.+. ++.+||||+|++..+.
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 57999999985 567889999888888774 3569999999997654
No 50
>PF00626 Gelsolin: Gelsolin repeat; InterPro: IPR007123 Gelsolin is a cytoplasmic, calcium-regulated, actin-modulating protein that binds to the barbed ends of actin filaments, preventing monomer exchange (end-blocking or capping) []. It can promote nucleation (the assembly of monomers into filaments), as well as sever existing filaments. In addition, this protein binds with high affinity to fibronectin. Plasma gelsolin and cytoplasmic gelsolin are derived from a single gene by alternate initiation sites and differential splicing. Sequence comparisons indicate an evolutionary relationship between gelsolin, villin, fragmin and severin []. Six large repeating segments occur in gelsolin and villin, and 3 similar segments in severin and fragmin. While the multiple repeats have yet to be related to any known function of the actin-severing proteins, the superfamily appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues [].; PDB: 3FG6_F 1RGI_G 2FGH_A 1D0N_B 3EGD_B 2NUP_B 2NUT_B 3EGX_B 1JHW_A 1J72_A ....
Probab=97.66 E-value=6.5e-05 Score=60.78 Aligned_cols=60 Identities=18% Similarity=0.356 Sum_probs=47.7
Q ss_pred hcCCCcEEEEecCcEEEEEecCCCCCCCCCCCChhH-HHHHHHHHHH-hcCCCCceEEEEeCCCCcHHH
Q 007267 506 ITSGSPIFLLDAFTTIIVFYSSTADPTLPFPPPQDC-LLRTTINKMK-QERSITPKLIFIRGGQDDATI 572 (610)
Q Consensus 506 ~~s~~~iyllD~g~~~~i~~G~~v~~~~~~~~~~~~-~~~~~i~~i~-~~r~~~p~l~~~~~~~~~~~~ 572 (610)
.+..+++||||+|..+++|+|...+ .... .-..+.+.+. .+|...|++.++.+|...++|
T Consensus 14 ~L~s~~~yIld~~~~i~vW~G~~~~-------~~e~~~a~~~a~~~~~~~~~~~~~~~~~~eg~E~~~F 75 (76)
T PF00626_consen 14 SLNSDDCYILDCGYEIFVWVGKKSS-------PEEKAFAAQLAQELLSEERPPLPEVIRVEEGKEPAEF 75 (76)
T ss_dssp GEETTSEEEEEESSEEEEEEHTTSH-------HHHHHHHHHHHHHHHHHHTTTTSEEEEEETTHHHHHH
T ss_pred HcCCCCEEEEEeCCCcEEEEeccCC-------HHHHHHHHHHHHHhhhhcCCCCCEEEEecCCCCChHH
Confidence 4567899999999999999999944 2222 2346667788 899999999999999876665
No 51
>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=97.45 E-value=0.0062 Score=57.64 Aligned_cols=146 Identities=18% Similarity=0.165 Sum_probs=87.7
Q ss_pred EEEEEEeCCCCh---hHHHHHHHHHHHHHHhCCC-CcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccccc
Q 007267 123 VYVAAVDLSSSE---EFLELTRSALQAALEAVPS-GALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV 198 (610)
Q Consensus 123 ~~vFvID~s~~~---~~l~~l~~~l~~~l~~lp~-~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~ 198 (610)
.++|+||+|.+. ..++.+|+++...++.+.+ +.++|+++|++... ..... .... ..+.++
T Consensus 2 ~v~~llD~SgSM~~~~kl~~ak~a~~~l~~~l~~~~d~~~l~~F~~~~~------~~~~~-~~~~--------~~~~~~- 65 (174)
T cd01454 2 AVTLLLDLSGSMRSDRRIDVAKKAAVLLAEALEACGVPHAILGFTTDAG------GRERV-RWIK--------IKDFDE- 65 (174)
T ss_pred EEEEEEECCCCCCCCcHHHHHHHHHHHHHHHHHHcCCcEEEEEecCCCC------Cccce-EEEE--------ecCccc-
Confidence 478999999986 3688899888887777764 88999999988630 00000 0000 000100
Q ss_pred CccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecC
Q 007267 199 MPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSG 278 (610)
Q Consensus 199 ~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g 278 (610)
.+ ...+...|..+.+. ..+.+|.||..|...+..... ....|+++++|
T Consensus 66 -----~~------~~~~~~~l~~~~~~------------------g~T~~~~al~~a~~~l~~~~~---~~~~iiliTDG 113 (174)
T cd01454 66 -----SL------HERARKRLAALSPG------------------GNTRDGAAIRHAAERLLARPE---KRKILLVISDG 113 (174)
T ss_pred -----cc------chhHHHHHHccCCC------------------CCCcHHHHHHHHHHHHhcCCC---cCcEEEEEeCC
Confidence 00 11233445444332 346799999999999875322 13678999999
Q ss_pred CCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHH---HHHHHHHcCcEEEEEEecCCC
Q 007267 279 PPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKD---LAAVAVQAGVCVDIFAITNEY 338 (610)
Q Consensus 279 ~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~---la~~~~~~gisvDlf~~~~~~ 338 (610)
.|+.+...-.. ....++ .+.++.+.||.+..+.+..+.
T Consensus 114 ~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~~gi~v~~igig~~~ 154 (174)
T cd01454 114 EPNDLDYYEGN----------------------VFATEDALRAVIEARKLGIEVFGITIDRDA 154 (174)
T ss_pred CcCcccccCcc----------------------hhHHHHHHHHHHHHHhCCcEEEEEEecCcc
Confidence 99876421100 001112 377788889988877776553
No 52
>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=97.37 E-value=0.002 Score=61.63 Aligned_cols=164 Identities=13% Similarity=0.181 Sum_probs=106.4
Q ss_pred EEeCCCCh-------hHHHHHHHHHHHHHHhC---CCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccccccc
Q 007267 127 AVDLSSSE-------EFLELTRSALQAALEAV---PSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELE 196 (610)
Q Consensus 127 vID~s~~~-------~~l~~l~~~l~~~l~~l---p~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~ 196 (610)
|||.|... ..++.+...+...++.. .|=+.+|||+..+.+-- .+ .++
T Consensus 1 viD~S~~m~~~D~~PtRl~~~~~~l~~Fv~eff~qNPiSqlgii~~~~~~a~-~l---------------------s~l- 57 (193)
T PF04056_consen 1 VIDMSEAMREKDLKPTRLQCVLKALEEFVREFFDQNPISQLGIIVMRDGRAE-RL---------------------SEL- 57 (193)
T ss_pred CeechHhHHhCcCCccHHHHHHHHHHHHHHHHHhcCChhheeeeeeecceeE-Ee---------------------eec-
Confidence 57887764 56777777777776532 44579999988664311 00 111
Q ss_pred ccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEe
Q 007267 197 DVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFL 276 (610)
Q Consensus 197 ~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~ 276 (610)
+.+-....+.|.++.... + .+..++-.||+.|...|+...+.. .=.|+++.
T Consensus 58 ------------sgn~~~h~~~L~~~~~~~----~-----------~G~~SLqN~Le~A~~~L~~~p~~~--srEIlvi~ 108 (193)
T PF04056_consen 58 ------------SGNPQEHIEALKKLRKLE----P-----------SGEPSLQNGLEMARSSLKHMPSHG--SREILVIF 108 (193)
T ss_pred ------------CCCHHHHHHHHHHhccCC----C-----------CCChhHHHHHHHHHHHHhhCcccc--ceEEEEEE
Confidence 111122344555554221 1 145679999999999998653221 12788878
Q ss_pred cCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEE
Q 007267 277 SGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLF 356 (610)
Q Consensus 277 ~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~ 356 (610)
++.-|..||.+ .+..+.+.+.+|-|++..++. .+.-.+.+|+.|||...
T Consensus 109 gSl~t~Dp~di----------------------------~~ti~~l~~~~IrvsvI~laa---Ev~I~k~i~~~T~G~y~ 157 (193)
T PF04056_consen 109 GSLTTCDPGDI----------------------------HETIESLKKENIRVSVISLAA---EVYICKKICKETGGTYG 157 (193)
T ss_pred eecccCCchhH----------------------------HHHHHHHHHcCCEEEEEEEhH---HHHHHHHHHHhhCCEEE
Confidence 88888888744 257889999999999999876 46678999999999633
Q ss_pred EeCCCCCCchhHHHHHHhc
Q 007267 357 LYSSTDDSTLPQDIYRMLS 375 (610)
Q Consensus 357 ~~~~~~~~~l~~dl~~~l~ 375 (610)
.. .|...|++-|.....
T Consensus 158 V~--lde~H~~~lL~~~~~ 174 (193)
T PF04056_consen 158 VI--LDEDHFKELLMEHVP 174 (193)
T ss_pred Ee--cCHHHHHHHHHhhCC
Confidence 33 455567765555544
No 53
>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=97.28 E-value=0.013 Score=56.68 Aligned_cols=151 Identities=12% Similarity=0.036 Sum_probs=92.7
Q ss_pred EEEEEeCCCChh--HHH-HHHHHHHHHHHhC---CCCcEEEEEeecceeEEE-EecCCCcceeeeeeCCCCCcccccccc
Q 007267 124 YVAAVDLSSSEE--FLE-LTRSALQAALEAV---PSGALFGLATFSHKIGLY-DVQGAIPVVKNVFIPSDTEDTLSLELE 196 (610)
Q Consensus 124 ~vFvID~s~~~~--~l~-~l~~~l~~~l~~l---p~~~~VglITf~~~V~~~-~l~~~~~~~~~v~~~~~~~~~~~~dl~ 196 (610)
.+|+||.|.+.+ ..+ .+++-++..++.+ +.+++||+|+|++..+++ .+...
T Consensus 3 i~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~~~~~~~~~---------------------- 60 (192)
T cd01473 3 LTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNRDVVPFSDE---------------------- 60 (192)
T ss_pred EEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCceeEEecCcc----------------------
Confidence 589999999863 244 4777777777766 467999999999976542 11100
Q ss_pred ccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCC-cccceEEEE
Q 007267 197 DVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNT-FALARVFAF 275 (610)
Q Consensus 197 ~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~-~~~GkIi~F 275 (610)
....+..+.+.|+.+...... .+++.+|.||..|...+....+.. ...--++++
T Consensus 61 -----------~~~~~~~l~~~i~~l~~~~~~--------------~g~T~~~~AL~~a~~~~~~~~~~r~~~~kv~Ill 115 (192)
T cd01473 61 -----------ERYDKNELLKKINDLKNSYRS--------------GGETYIVEALKYGLKNYTKHGNRRKDAPKVTMLF 115 (192)
T ss_pred -----------cccCHHHHHHHHHHHHhccCC--------------CCcCcHHHHHHHHHHHhccCCCCcccCCeEEEEE
Confidence 011234456667776542110 145679999999988875432211 011237777
Q ss_pred ecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhcc
Q 007267 276 LSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIE 350 (610)
Q Consensus 276 ~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~ 350 (610)
|.|..+.+-- .--.+.++.+.+.||.+-.+..+. .+-.++..++..
T Consensus 116 TDG~s~~~~~---------------------------~~~~~~a~~lk~~gV~i~~vGiG~--~~~~el~~ia~~ 161 (192)
T cd01473 116 TDGNDTSASK---------------------------KELQDISLLYKEENVKLLVVGVGA--ASENKLKLLAGC 161 (192)
T ss_pred ecCCCCCcch---------------------------hhHHHHHHHHHHCCCEEEEEEecc--ccHHHHHHhcCC
Confidence 7776532100 001256778888998877777754 466788888864
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=97.24 E-value=0.0068 Score=59.77 Aligned_cols=158 Identities=16% Similarity=0.241 Sum_probs=88.5
Q ss_pred EEEEEEeCCCCh---------hHHHHHHHHHHHHHHhC---CCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcc
Q 007267 123 VYVAAVDLSSSE---------EFLELTRSALQAALEAV---PSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDT 190 (610)
Q Consensus 123 ~~vFvID~s~~~---------~~l~~l~~~l~~~l~~l---p~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~ 190 (610)
..+|+||+|.++ ..|+.+++.+...+... -++.+||+|.|++.-+-.. .. ...++
T Consensus 3 ~ivf~iDvS~SM~~~~~~~~~s~l~~a~~~i~~~~~~ki~~~~~D~vGlilf~t~~~~~~---~~--~~~i~-------- 69 (218)
T cd01458 3 SVVFLVDVSPSMFESKDGEYESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTEESKNP---VG--YENIY-------- 69 (218)
T ss_pred EEEEEEeCCHHHcCCCCCCCCChHHHHHHHHHHHHHhceeCCCCCeEEEEEEcccCCCCc---CC--CCceE--------
Confidence 578999998854 45777888888888752 4567999999987532110 00 00111
Q ss_pred ccccccccCccCcCccchHhHHHHHHHHHHhcCCCCC-cccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCccc
Q 007267 191 LSLELEDVMPLSQFLAPVETFKENITSALETLRPTTS-WERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFAL 269 (610)
Q Consensus 191 ~~~dl~~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~-~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~ 269 (610)
+..++. .| ....|..+++.+..... .....+ ...+..++.||.+|..++..... ....
T Consensus 70 v~~~l~---------~~---~~~~l~~l~~~~~~~~~~~~~~~~--------~~~~~~l~~aL~~a~~~~~~~~~-~~~~ 128 (218)
T cd01458 70 VLLDLD---------TP---GAERVEDLKELIEPGGLSFAGQVG--------DSGQVSLSDALWVCLDLFSKGKK-KKSH 128 (218)
T ss_pred EeecCC---------CC---CHHHHHHHHHHhhcchhhhcccCC--------CCCCccHHHHHHHHHHHHHhccc-cccc
Confidence 011110 01 12234444443332200 000000 01467799999999999986211 1123
Q ss_pred ceEEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCC
Q 007267 270 ARVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNE 337 (610)
Q Consensus 270 GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~ 337 (610)
-+|++||+|--..|.... ...-..+++.++.+.||.+.+|....+
T Consensus 129 k~IvL~TDg~~p~~~~~~-----------------------~~~~~~~~a~~l~~~gI~i~~i~i~~~ 173 (218)
T cd01458 129 KRIFLFTNNDDPHGGDSI-----------------------KDSQAAVKAEDLKDKGIELELFPLSSP 173 (218)
T ss_pred cEEEEECCCCCCCCCCHH-----------------------HHHHHHHHHHHHHhCCcEEEEEecCCC
Confidence 589999998654441110 011234678888888999999887544
No 55
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=97.23 E-value=0.0029 Score=59.10 Aligned_cols=49 Identities=22% Similarity=0.320 Sum_probs=40.3
Q ss_pred CcEEEEEEeCCCCh--hHHHHHHHHHHHHHHhCCC------CcEEEEEeecceeEEEE
Q 007267 121 RPVYVAAVDLSSSE--EFLELTRSALQAALEAVPS------GALFGLATFSHKIGLYD 170 (610)
Q Consensus 121 ~p~~vFvID~s~~~--~~l~~l~~~l~~~l~~lp~------~~~VglITf~~~V~~~~ 170 (610)
-|+| |++|+|.+. +.++++..+|+..++.|.. .+.++|||||+.+++|.
T Consensus 4 lP~~-lllDtSgSM~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~~a~~~~ 60 (207)
T COG4245 4 LPCY-LLLDTSGSMIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGPARVIQ 60 (207)
T ss_pred CCEE-EEEecCcccccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecCcceEEe
Confidence 4655 789999986 6799999999999988743 57999999999777654
No 56
>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=97.09 E-value=0.014 Score=53.89 Aligned_cols=130 Identities=14% Similarity=0.068 Sum_probs=77.3
Q ss_pred EEEEEeCCCChhH--HHHHHHHHHHHHHhCC-CCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccccCc
Q 007267 124 YVAAVDLSSSEEF--LELTRSALQAALEAVP-SGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDVMP 200 (610)
Q Consensus 124 ~vFvID~s~~~~~--l~~l~~~l~~~l~~lp-~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~~p 200 (610)
++|+||+|.+... ++..+..+...++.+. ++.+|++|+|++....+.+..
T Consensus 3 v~illD~SgSM~~~k~~~a~~~~~~l~~~~~~~~~~v~li~F~~~~~~~~~~~--------------------------- 55 (152)
T cd01462 3 VILLVDQSGSMYGAPEEVAKAVALALLRIALAENRDTYLILFDSEFQTKIVDK--------------------------- 55 (152)
T ss_pred EEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHcCCcEEEEEeCCCceEEecCC---------------------------
Confidence 6899999998642 5556666666666554 477999999998732211100
Q ss_pred cCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEecCCC
Q 007267 201 LSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPP 280 (610)
Q Consensus 201 ~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~p 280 (610)
. ..+..+++.|..... .+++.++.||..+...+..... ..+.|+++++|..
T Consensus 56 --------~---~~~~~~~~~l~~~~~---------------~ggT~l~~al~~a~~~l~~~~~---~~~~ivliTDG~~ 106 (152)
T cd01462 56 --------T---DDLEEPVEFLSGVQL---------------GGGTDINKALRYALELIERRDP---RKADIVLITDGYE 106 (152)
T ss_pred --------c---ccHHHHHHHHhcCCC---------------CCCcCHHHHHHHHHHHHHhcCC---CCceEEEECCCCC
Confidence 0 011223333322210 1456799999999999876432 1368999999853
Q ss_pred CCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCC
Q 007267 281 DHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNE 337 (610)
Q Consensus 281 t~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~ 337 (610)
+..+ .+.. +.+......++.|..+.++.+
T Consensus 107 ~~~~---------------------------~~~~-~~~~~~~~~~~~v~~~~~g~~ 135 (152)
T cd01462 107 GGVS---------------------------DELL-REVELKRSRVARFVALALGDH 135 (152)
T ss_pred CCCC---------------------------HHHH-HHHHHHHhcCcEEEEEEecCC
Confidence 2111 1111 234444566789999988764
No 57
>smart00262 GEL Gelsolin homology domain. Gelsolin/severin/villin homology domain. Calcium-binding and actin-binding. Both intra- and extracellular domains.
Probab=96.55 E-value=0.011 Score=49.44 Aligned_cols=62 Identities=8% Similarity=0.134 Sum_probs=43.3
Q ss_pred hcCCCcEEEEecCcEEEEEecCCCCCCCCCCCChhHHHHHHHHHHH-hcCCCCceEEEEeCCCCcHHHH
Q 007267 506 ITSGSPIFLLDAFTTIIVFYSSTADPTLPFPPPQDCLLRTTINKMK-QERSITPKLIFIRGGQDDATIF 573 (610)
Q Consensus 506 ~~s~~~iyllD~g~~~~i~~G~~v~~~~~~~~~~~~~~~~~i~~i~-~~r~~~p~l~~~~~~~~~~~~f 573 (610)
.+..+.+||||+|..|++|+|..+++ .+-.....+.+.+. ..+.+..++.+++||...+.|.
T Consensus 22 ~L~s~d~fild~~~~iyvW~G~~as~------~ek~~A~~~a~~~~~~~~~~~~~i~~v~eg~E~~~F~ 84 (90)
T smart00262 22 SLNSGDCYILDTGSEIYVWVGKKSSQ------DEKKKAAELAVELDDTLGPGPVQVRVVDEGKEPPEFW 84 (90)
T ss_pred HCCCCCEEEEECCCEEEEEECCCCCH------HHHHHHHHHHHHHHHhcCCCCceEEEEeCCCCCHHHH
Confidence 35678999999999999999999883 22333334444444 3445666899999998665443
No 58
>KOG2884 consensus 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=96.04 E-value=0.23 Score=47.56 Aligned_cols=155 Identities=15% Similarity=0.194 Sum_probs=94.7
Q ss_pred EEEEEEeCCCCh-------hHHHHHHHHHHHHHH-hC--CCCcEEEEEeecc-eeEEEEecCCCcceeeeeeCCCCCccc
Q 007267 123 VYVAAVDLSSSE-------EFLELTRSALQAALE-AV--PSGALFGLATFSH-KIGLYDVQGAIPVVKNVFIPSDTEDTL 191 (610)
Q Consensus 123 ~~vFvID~s~~~-------~~l~~l~~~l~~~l~-~l--p~~~~VglITf~~-~V~~~~l~~~~~~~~~v~~~~~~~~~~ 191 (610)
+-+.+||-|--+ ..+++=++++.-... .+ .+...|||||... .+.+.. +
T Consensus 5 atmi~iDNse~mrNgDy~PtRf~aQ~daVn~v~~~K~~snpEntvGiitla~a~~~vLs--T------------------ 64 (259)
T KOG2884|consen 5 ATMICIDNSEYMRNGDYLPTRFQAQKDAVNLVCQAKLRSNPENTVGIITLANASVQVLS--T------------------ 64 (259)
T ss_pred eEEEEEeChHHhhcCCCChHHHHHHHHHHHHHHHhhhcCCcccceeeEeccCCCceeee--e------------------
Confidence 356778876532 566666666654433 22 2334799999865 444311 0
Q ss_pred cccccccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccce
Q 007267 192 SLELEDVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALAR 271 (610)
Q Consensus 192 ~~dl~~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~Gk 271 (610)
+...+..|...+..++.. ++.-++.+|+.|.-+|+..-+ ++---|
T Consensus 65 ----------------~T~d~gkils~lh~i~~~------------------g~~~~~~~i~iA~lalkhRqn-k~~~~r 109 (259)
T KOG2884|consen 65 ----------------LTSDRGKILSKLHGIQPH------------------GKANFMTGIQIAQLALKHRQN-KNQKQR 109 (259)
T ss_pred ----------------ccccchHHHHHhcCCCcC------------------CcccHHHHHHHHHHHHHhhcC-CCcceE
Confidence 011234456666666543 345599999999999987532 212269
Q ss_pred EEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccC
Q 007267 272 VFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIES 351 (610)
Q Consensus 272 Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~T 351 (610)
|++|.++|-.. .|+ -.-++|+++.+++|.||++.|+-..-+-.-+......+
T Consensus 110 iVvFvGSpi~e--------------------~ek--------eLv~~akrlkk~~Vaidii~FGE~~~~~e~l~~fida~ 161 (259)
T KOG2884|consen 110 IVVFVGSPIEE--------------------SEK--------ELVKLAKRLKKNKVAIDIINFGEAENNTEKLFEFIDAL 161 (259)
T ss_pred EEEEecCcchh--------------------hHH--------HHHHHHHHHHhcCeeEEEEEeccccccHHHHHHHHHHh
Confidence 99999997422 111 12478999999999999999987655533344444444
Q ss_pred ccE-----EEEeCC
Q 007267 352 GGS-----LFLYSS 360 (610)
Q Consensus 352 GG~-----v~~~~~ 360 (610)
+|. +...+.
T Consensus 162 N~~~~gshlv~Vpp 175 (259)
T KOG2884|consen 162 NGKGDGSHLVSVPP 175 (259)
T ss_pred cCCCCCceEEEeCC
Confidence 443 555543
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=95.42 E-value=0.64 Score=47.11 Aligned_cols=46 Identities=22% Similarity=0.240 Sum_probs=34.0
Q ss_pred CCcEEEEEEeCCCCh-------hHHHHHHHHHHHHHHhCCCCcEEEEEeecceeE
Q 007267 120 ARPVYVAAVDLSSSE-------EFLELTRSALQAALEAVPSGALFGLATFSHKIG 167 (610)
Q Consensus 120 ~~p~~vFvID~s~~~-------~~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~ 167 (610)
...-++++||.|.+. ..++ .+..|..+++.++. -+||++.|+..+.
T Consensus 59 r~~qIvlaID~S~SM~~~~~~~~ale-ak~lIs~al~~Le~-g~vgVv~Fg~~~~ 111 (266)
T cd01460 59 RDYQILIAIDDSKSMSENNSKKLALE-SLCLVSKALTLLEV-GQLGVCSFGEDVQ 111 (266)
T ss_pred cCceEEEEEecchhcccccccccHHH-HHHHHHHHHHhCcC-CcEEEEEeCCCce
Confidence 346799999999985 2355 45566677777765 5999999998653
No 60
>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=94.93 E-value=1 Score=43.20 Aligned_cols=98 Identities=17% Similarity=0.047 Sum_probs=63.4
Q ss_pred HHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhc-cccCCCcccceEEEEecCCCCCCCccccccc
Q 007267 213 ENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLG-SEYGNTFALARVFAFLSGPPDHGAGQLDTRR 291 (610)
Q Consensus 213 ~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~-~~~~~~~~~GkIi~F~~g~pt~GpG~l~~~~ 291 (610)
..+..+|++++.... +..|..||..|++-|. .... ..--||+++.|--|.| .+.+
T Consensus 75 ~~l~~~l~~~q~g~a-----------------g~~TadAi~~av~rl~~~~~a---~~kvvILLTDG~n~~~--~i~P-- 130 (191)
T cd01455 75 ETLKMMHAHSQFCWS-----------------GDHTVEATEFAIKELAAKEDF---DEAIVIVLSDANLERY--GIQP-- 130 (191)
T ss_pred HHHHHHHHhcccCcc-----------------CccHHHHHHHHHHHHHhcCcC---CCcEEEEEeCCCcCCC--CCCh--
Confidence 567788887764321 1223388999998886 4321 1235677777765432 2221
Q ss_pred CcCcccCCCcchhhccCCcchHHHHHH-HHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeCC
Q 007267 292 YGEQYASKGEDADRALLPEQTPFYKDL-AAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYSS 360 (610)
Q Consensus 292 ~~~~~~~~~~~~e~~~~~~~~~fY~~l-a~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~ 360 (610)
.++ |+.+.+.||-|..+..+.. |-.++..+++.|||+-|...+
T Consensus 131 ------------------------~~aAa~lA~~~gV~iytIgiG~~--d~~~l~~iA~~tgG~~F~A~d 174 (191)
T cd01455 131 ------------------------KKLADALAREPNVNAFVIFIGSL--SDEADQLQRELPAGKAFVCMD 174 (191)
T ss_pred ------------------------HHHHHHHHHhCCCEEEEEEecCC--CHHHHHHHHhCCCCcEEEeCC
Confidence 234 4667788988888777653 667899999999999777654
No 61
>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=94.37 E-value=0.83 Score=44.16 Aligned_cols=43 Identities=19% Similarity=0.108 Sum_probs=31.3
Q ss_pred EEEEEEeCCCChh---------HHHHHHHHHHHHHHhCC--CCcEEEEEeecce
Q 007267 123 VYVAAVDLSSSEE---------FLELTRSALQAALEAVP--SGALFGLATFSHK 165 (610)
Q Consensus 123 ~~vFvID~s~~~~---------~l~~l~~~l~~~l~~lp--~~~~VglITf~~~ 165 (610)
-++|+||.|.++. .++.+++++...+..+. +...+++++|++.
T Consensus 4 dvv~~ID~SgSM~~~~~~~~~~k~~~ak~~~~~l~~~~~~~D~d~i~l~~f~~~ 57 (199)
T cd01457 4 DYTLLIDKSGSMAEADEAKERSRWEEAQESTRALARKCEEYDSDGITVYLFSGD 57 (199)
T ss_pred CEEEEEECCCcCCCCCCCCCchHHHHHHHHHHHHHHHHHhcCCCCeEEEEecCC
Confidence 4889999999873 36778888887766543 3456888888654
No 62
>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=93.05 E-value=15 Score=39.56 Aligned_cols=272 Identities=16% Similarity=0.135 Sum_probs=132.2
Q ss_pred EEEEEeCCCCh-hHH---HHHHHHHHHHHHhCCCCcEEEEEeec-ceeEEEEecCCCcceeeeeeCCCCCcccccccccc
Q 007267 124 YVAAVDLSSSE-EFL---ELTRSALQAALEAVPSGALFGLATFS-HKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV 198 (610)
Q Consensus 124 ~vFvID~s~~~-~~l---~~l~~~l~~~l~~lp~~~~VglITf~-~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~ 198 (610)
..|+.|+|+++ ..+ ..+-..|...|..+-.+.|+||=+|= +.|.=|-...+. ... .|-... ....+
T Consensus 102 LYyLMDlS~SM~ddl~~lk~lg~~L~~~m~~it~n~rlGfGsFVDK~v~P~~~t~p~----~l~-~PC~~~--~~~c~-- 172 (423)
T smart00187 102 LYYLMDLSYSMKDDLDNLKSLGDDLAREMKGLTSNFRLGFGSFVDKTVSPFVSTRPE----KLE-NPCPNY--NLTCE-- 172 (423)
T ss_pred eEEEEeCCccHHHHHHHHHHHHHHHHHHHHhcccCceeeEEEeecCccCCcccCCHH----Hhc-CCCcCC--CCCcC--
Confidence 66899999997 334 44555566667777889999998884 433222211000 000 000000 00000
Q ss_pred CccC-cCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEec
Q 007267 199 MPLS-QFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLS 277 (610)
Q Consensus 199 ~p~~-~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~ 277 (610)
-|.. +-..++.+....+.+.+....-.. +. | .|...+-+-+++|+-- +..|= +...-||++|++
T Consensus 173 p~f~f~~~L~LT~~~~~F~~~V~~~~iSg-N~------D------~PEgG~DAimQaaVC~-~~IGW-R~~a~rllv~~T 237 (423)
T smart00187 173 PPYGFKHVLSLTDDTDEFNEEVKKQRISG-NL------D------APEGGFDAIMQAAVCT-EQIGW-REDARRLLVFST 237 (423)
T ss_pred CCcceeeeccCCCCHHHHHHHHhhceeec-CC------c------CCcccHHHHHHHHhhc-ccccc-CCCceEEEEEEc
Confidence 1111 123566665556666666644321 11 1 1445566667777421 12220 001248999988
Q ss_pred CCCCC--CCcccccc---cCcC-cccCCCcchhhc-cCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhcc
Q 007267 278 GPPDH--GAGQLDTR---RYGE-QYASKGEDADRA-LLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIE 350 (610)
Q Consensus 278 g~pt~--GpG~l~~~---~~~~-~~~~~~~~~e~~-~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~ 350 (610)
-.+-. |-|+|... .+++ ++...+ +.. -..-...--.+|++++.+++|. =||+....+.+++ ..|+..
T Consensus 238 Da~fH~AGDGkLaGIv~PNDg~CHL~~~g---~Yt~s~~~DYPSi~ql~~kL~e~nI~-~IFAVT~~~~~~Y--~~Ls~l 311 (423)
T smart00187 238 DAGFHFAGDGKLAGIVQPNDGQCHLDNNG---EYTMSTTQDYPSIGQLNQKLAENNIN-PIFAVTKKQVSLY--KELSAL 311 (423)
T ss_pred CCCccccCCcceeeEecCCCCcceeCCCC---CcCccCcCCCCCHHHHHHHHHhcCce-EEEEEcccchhHH--HHHHHh
Confidence 76643 77876543 2211 221111 000 0001122345788888888875 4888888877765 555555
Q ss_pred CccEEEEeCCCCCCc---hhHHHHHHhccCcceeeEEEEEc-cCCeeeeeeeeccccCCCCCcceeeeecCCCccEEEEE
Q 007267 351 SGGSLFLYSSTDDST---LPQDIYRMLSRPYAFNCIMRLRT-SSEFKPGHSYGHFFPDPQYENVQHIICCDSYATYAYDF 426 (610)
Q Consensus 351 TGG~v~~~~~~~~~~---l~~dl~~~l~~~~~~~a~lrvr~-S~gl~v~~~~G~~~~~~~~~~~~~i~~~~~~~t~a~~f 426 (610)
-+|...=-=+-|... +..+-++.+ .-..+|+... +.+++++..- .|.........-...++...+++.|.+
T Consensus 312 ipgs~vg~Ls~DSsNIv~LI~~aY~~i----~S~V~l~~~~~p~~v~~~y~s-~C~~g~~~~~~~~C~~v~iG~~V~F~v 386 (423)
T smart00187 312 IPGSSVGVLSEDSSNVVELIKDAYNKI----SSRVELEDNSLPEGVSVTYTS-SCPGGVVGPGTRKCEGVKIGDTVSFEV 386 (423)
T ss_pred cCcceeeecccCcchHHHHHHHHHHhh----ceEEEEecCCCCCcEEEEEEe-eCCCCCcccCCcccCCcccCCEEEEEE
Confidence 555443221223332 223333333 2344555553 5577776443 433221111111234566677777777
Q ss_pred EEec
Q 007267 427 DFAN 430 (610)
Q Consensus 427 e~~~ 430 (610)
++.-
T Consensus 387 ~vta 390 (423)
T smart00187 387 TVTA 390 (423)
T ss_pred EEEe
Confidence 6664
No 63
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=91.94 E-value=5.6 Score=37.46 Aligned_cols=131 Identities=21% Similarity=0.259 Sum_probs=80.9
Q ss_pred EEEEEEeCCCCh-------hHHHHHHHHHHHHHHh-C--CCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCcccc
Q 007267 123 VYVAAVDLSSSE-------EFLELTRSALQAALEA-V--PSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLS 192 (610)
Q Consensus 123 ~~vFvID~s~~~-------~~l~~l~~~l~~~l~~-l--p~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~ 192 (610)
+-|.+||-|.-+ ..+++=|+++...++. . .+...||||+-... .+ .+
T Consensus 5 atvvliDNse~s~NgDy~ptRFeAQkd~ve~if~~K~ndnpEntiGli~~~~a---------~p---~v----------- 61 (243)
T COG5148 5 ATVVLIDNSEASQNGDYLPTRFEAQKDAVESIFSKKFNDNPENTIGLIPLVQA---------QP---NV----------- 61 (243)
T ss_pred eEEEEEeChhhhhcCCCCcHHHHHHHHHHHHHHHHHhcCCccceeeeeecccC---------Cc---ch-----------
Confidence 567888976643 5667777777766642 2 23347888875331 00 00
Q ss_pred ccccccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceE
Q 007267 193 LELEDVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARV 272 (610)
Q Consensus 193 ~dl~~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkI 272 (610)
|..+...+..|...|..++-. ++.-++.+|+.|..+|+... ++.-..||
T Consensus 62 ------------lsT~T~~~gkilt~lhd~~~~------------------g~a~~~~~lqiaql~lkhR~-nk~q~qri 110 (243)
T COG5148 62 ------------LSTPTKQRGKILTFLHDIRLH------------------GGADIMRCLQIAQLILKHRD-NKGQRQRI 110 (243)
T ss_pred ------------hccchhhhhHHHHHhcccccc------------------CcchHHHHHHHHHHHHhccc-CCccceEE
Confidence 111122345666777666532 23448999999999998653 22112699
Q ss_pred EEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEec
Q 007267 273 FAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAIT 335 (610)
Q Consensus 273 i~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~ 335 (610)
++|.++|-.. ++.+ .-.+|+.+.+++++||+..++
T Consensus 111 VaFvgSpi~e--------sede--------------------Lirlak~lkknnVAidii~fG 145 (243)
T COG5148 111 VAFVGSPIQE--------SEDE--------------------LIRLAKQLKKNNVAIDIIFFG 145 (243)
T ss_pred EEEecCcccc--------cHHH--------------------HHHHHHHHHhcCeeEEEEehh
Confidence 9999987421 1111 125899999999999998775
No 64
>KOG0443 consensus Actin regulatory proteins (gelsolin/villin family) [Cytoskeleton]
Probab=89.12 E-value=0.8 Score=52.00 Aligned_cols=64 Identities=16% Similarity=0.370 Sum_probs=41.9
Q ss_pred cCCCcEEEEecCcEEEEEecCCCCCCCCCCCChhHHHH---HHHHH-HHhcCCCCceEEEEeCCCCcHHHHHhh
Q 007267 507 TSGSPIFLLDAFTTIIVFYSSTADPTLPFPPPQDCLLR---TTINK-MKQERSITPKLIFIRGGQDDATIFENY 576 (610)
Q Consensus 507 ~s~~~iyllD~g~~~~i~~G~~v~~~~~~~~~~~~~~~---~~i~~-i~~~r~~~p~l~~~~~~~~~~~~f~~~ 576 (610)
+..+.|||||++..+|||+|++++++.. .++|. ..|+. +...|.+.-.+++++||+.. ++|..+
T Consensus 645 L~tdDi~lLDt~~evfvWvG~~a~~~eK-----~~Al~~~~~yl~~~~p~gr~~~TPI~vV~qG~EP-p~Ftg~ 712 (827)
T KOG0443|consen 645 LMTDDIMLLDTWSEVFVWVGQEANEKEK-----EEALTIGQKYLETDLPEGRDPRTPIYVVKQGHEP-PFFTGF 712 (827)
T ss_pred ccccceEEEecCceEEEEecCCCChhHH-----HHHHHHHHHHHhccCcccCCCCCceEEecCCCCC-Chhhcc
Confidence 4668999999999999999999985322 22332 33322 24556554458889999753 344433
No 65
>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=88.87 E-value=30 Score=35.39 Aligned_cols=98 Identities=20% Similarity=0.181 Sum_probs=62.5
Q ss_pred cchHHHHHHHHHhhccccC-----CCcccceEEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHH
Q 007267 246 RGFGLAMESLFNYLGSEYG-----NTFALARVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAA 320 (610)
Q Consensus 246 ~~~G~Al~~a~~lL~~~~~-----~~~~~GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~ 320 (610)
..+..||..|+-.+..... +....+||+++.++-+.. ..+.-=+-+..-
T Consensus 116 s~LagALS~ALCyINR~~~~~~~~~~~~~~RILv~~s~s~d~--------------------------~~QYi~~MN~iF 169 (276)
T PF03850_consen 116 SLLAGALSMALCYINRISRESPSGGTSLKSRILVIVSGSPDS--------------------------SSQYIPLMNCIF 169 (276)
T ss_pred hhhHHHHHHHHHHHhhhhhcccCCCCCcCccEEEEEecCCCc--------------------------cHHHHHHHHHHH
Confidence 6788999999887754411 012347999963332211 011112345677
Q ss_pred HHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeCCCCCCchhHHHHHH
Q 007267 321 VAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYSSTDDSTLPQDIYRM 373 (610)
Q Consensus 321 ~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~~~~~~l~~dl~~~ 373 (610)
.|.+.+|.||++..+. -+-.-|.+.+..|||.-...+.. +.|.+-|...
T Consensus 170 aAqk~~v~IDv~~L~~--~~s~fLqQa~d~T~G~y~~~~~~--~~l~q~L~~~ 218 (276)
T PF03850_consen 170 AAQKQKVPIDVCKLGG--KDSTFLQQASDITGGIYLKVSKP--EGLLQYLLTA 218 (276)
T ss_pred HHhcCCceeEEEEecC--CchHHHHHHHHHhCceeeccCcc--ccHHHHHHHh
Confidence 7889999999999876 45566899999999996666553 3354444433
No 66
>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=88.46 E-value=11 Score=42.91 Aligned_cols=73 Identities=12% Similarity=0.145 Sum_probs=44.0
Q ss_pred cchHHHHHHHHHhhccccCCCcccceEEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHc
Q 007267 246 RGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQA 325 (610)
Q Consensus 246 ~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~ 325 (610)
..+..||.+|..++...+.+ ...=||++||+--...+..+- ++ .-=...|..+...
T Consensus 117 ~~l~daL~~~~~~f~~~~~k-~~~kRI~lfTd~D~P~~~~~~---------------~~--------~~a~~~a~dl~~~ 172 (584)
T TIGR00578 117 YSLSEVLWVCANLFSDVQFR-MSHKRIMLFTNEDNPHGNDSA---------------KA--------SRARTKAGDLRDT 172 (584)
T ss_pred CcHHHHHHHHHHHHHhcchh-hcCcEEEEECCCCCCCCCchh---------------HH--------HHHHHHHHHHHhc
Confidence 47899999999999853321 112479999975433321100 00 0002357888899
Q ss_pred CcEEEEEEecC-CCcChh
Q 007267 326 GVCVDIFAITN-EYTDLA 342 (610)
Q Consensus 326 gisvDlf~~~~-~~~~l~ 342 (610)
||.+++|..+. +.+|..
T Consensus 173 gi~ielf~l~~~~~Fd~s 190 (584)
T TIGR00578 173 GIFLDLMHLKKPGGFDIS 190 (584)
T ss_pred CeEEEEEecCCCCCCChh
Confidence 99999996642 224444
No 67
>KOG2353 consensus L-type voltage-dependent Ca2+ channel, alpha2/delta subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=87.84 E-value=11 Score=45.44 Aligned_cols=203 Identities=18% Similarity=0.202 Sum_probs=113.2
Q ss_pred ccccEEEEecC---CCCccccCCCCcEEEEEEeCCCCh--hHHHHHHHHHHHHHHhCCCCcEEEEEeecceeEEEEecCC
Q 007267 100 ISSFIDLDLPL---EGSEEETMQARPVYVAAVDLSSSE--EFLELTRSALQAALEAVPSGALFGLATFSHKIGLYDVQGA 174 (610)
Q Consensus 100 ~~~tvey~~p~---~y~~~~~~~~~p~~vFvID~s~~~--~~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~~~l~~~ 174 (610)
...++|+-..+ -|.. ....|--.+|++|+|++. ..++..|..+.++|+.|.++..|-++||++.++.-.....
T Consensus 203 ~~~~idl~D~R~r~Wyi~--aAt~pKdiviLlD~SgSm~g~~~~lak~tv~~iLdtLs~~Dfvni~tf~~~~~~v~pc~~ 280 (1104)
T KOG2353|consen 203 TDNSIDLYDCRNRSWYIQ--AATSPKDIVILLDVSGSMSGLRLDLAKQTVNEILDTLSDNDFVNILTFNSEVNPVSPCFN 280 (1104)
T ss_pred CCCcceeeeccccccccc--ccCCccceEEEEeccccccchhhHHHHHHHHHHHHhcccCCeEEEEeeccccCccccccc
Confidence 44555554443 2332 123455689999999985 6688899999999999999999999999998764221110
Q ss_pred CcceeeeeeCCCCCccccccccccCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHH
Q 007267 175 IPVVKNVFIPSDTEDTLSLELEDVMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMES 254 (610)
Q Consensus 175 ~~~~~~v~~~~~~~~~~~~dl~~~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~ 254 (610)
..++.---..+..+.++++.|... ...-+-.|++.
T Consensus 281 ---------------------------~~lvqAt~~nk~~~~~~i~~l~~k------------------~~a~~~~~~e~ 315 (1104)
T KOG2353|consen 281 ---------------------------GTLVQATMRNKKVFKEAIETLDAK------------------GIANYTAALEY 315 (1104)
T ss_pred ---------------------------CceeecchHHHHHHHHHHhhhccc------------------cccchhhhHHH
Confidence 111111123456667777777632 11226677778
Q ss_pred HHHhhccccCCCc------ccceEEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcE
Q 007267 255 LFNYLGSEYGNTF------ALARVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVC 328 (610)
Q Consensus 255 a~~lL~~~~~~~~------~~GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gis 328 (610)
|+++|...+.+.. +.=-||+|+.|.+.. ++++-++=..-...
T Consensus 316 aF~lL~~~n~s~~~~~~~~C~~~iml~tdG~~~~--------------------------------~~~If~~yn~~~~~ 363 (1104)
T KOG2353|consen 316 AFSLLRDYNDSRANTQRSPCNQAIMLITDGVDEN--------------------------------AKEIFEKYNWPDKK 363 (1104)
T ss_pred HHHHHHHhccccccccccccceeeEEeecCCccc--------------------------------HHHHHHhhccCCCc
Confidence 8877764321100 111355555554311 11111111111333
Q ss_pred EEEEEe--cCCCcChhcchhhh-ccCccEEEEeCCCCCCchhHHHHHHhccCccee
Q 007267 329 VDIFAI--TNEYTDLASLKFLS-IESGGSLFLYSSTDDSTLPQDIYRMLSRPYAFN 381 (610)
Q Consensus 329 vDlf~~--~~~~~~l~~l~~l~-~~TGG~v~~~~~~~~~~l~~dl~~~l~~~~~~~ 381 (610)
|-+|.+ +..-.++..+..+| ..=|+.++..+--+......+..+++.|+.+..
T Consensus 364 Vrvftflig~~~~~~~~~~wmac~n~gyy~~I~~~~~v~~~~~~y~~vlsRp~vl~ 419 (1104)
T KOG2353|consen 364 VRVFTFLIGDEVYDLDEIQWMACANKGYYVHIISIADVRENVLEYLDVLSRPLVLQ 419 (1104)
T ss_pred eEEEEEEecccccccccchhhhhhCCCceEeccchhhcChHhhhhhhhhccceeec
Confidence 555544 44456666666644 444555554443334455567778888887766
No 68
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=86.01 E-value=13 Score=40.22 Aligned_cols=149 Identities=18% Similarity=0.165 Sum_probs=87.9
Q ss_pred CcEEEEEEeCCCCh-hHHHHHHHHHHHHHH--hCCCCcEEEEEeecceeEEEEecCCCcceeeeeeCCCCCccccccccc
Q 007267 121 RPVYVAAVDLSSSE-EFLELTRSALQAALE--AVPSGALFGLATFSHKIGLYDVQGAIPVVKNVFIPSDTEDTLSLELED 197 (610)
Q Consensus 121 ~p~~vFvID~s~~~-~~l~~l~~~l~~~l~--~lp~~~~VglITf~~~V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~ 197 (610)
.| ++.+||.|+++ |.-+....++..+|- .+-+|.++.++.||+.++=+.+....
T Consensus 273 Gp-villlD~SGSM~G~~e~~AKAvalAl~~~alaenR~~~~~lF~s~~~~~el~~k~---------------------- 329 (437)
T COG2425 273 GP-VILLLDKSGSMSGFKEQWAKAVALALMRIALAENRDCYVILFDSEVIEYELYEKK---------------------- 329 (437)
T ss_pred CC-EEEEEeCCCCcCCcHHHHHHHHHHHHHHHHHHhccceEEEEecccceeeeecCCc----------------------
Confidence 45 66799999996 544443334444442 56788999999999943333332110
Q ss_pred cCccCcCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcccceEEEEec
Q 007267 198 VMPLSQFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFALARVFAFLS 277 (610)
Q Consensus 198 ~~p~~~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~ 277 (610)
. .+.++|+.|...+. +++-+-.||..|+..++...- ..+.|++-|+
T Consensus 330 -----------~----~~~e~i~fL~~~f~----------------GGTD~~~~l~~al~~~k~~~~---~~adiv~ITD 375 (437)
T COG2425 330 -----------I----DIEELIEFLSYVFG----------------GGTDITKALRSALEDLKSREL---FKADIVVITD 375 (437)
T ss_pred -----------c----CHHHHHHHHhhhcC----------------CCCChHHHHHHHHHHhhcccc---cCCCEEEEec
Confidence 0 12344555543321 345688999999999986542 2378999888
Q ss_pred CCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEE
Q 007267 278 GPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFL 357 (610)
Q Consensus 278 g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~ 357 (610)
|-+-. ..+|-.+..+.......-+.-.+.+.. +-+++..++..+ ++.
T Consensus 376 g~~~~----------------------------~~~~~~~v~e~~k~~~~rl~aV~I~~~--~~~~l~~Isd~~---i~~ 422 (437)
T COG2425 376 GEDER----------------------------LDDFLRKVKELKKRRNARLHAVLIGGY--GKPGLMRISDHI---IYR 422 (437)
T ss_pred cHhhh----------------------------hhHHHHHHHHHHHHhhceEEEEEecCC--CCcccceeeeee---EEe
Confidence 75311 134555666666566666666666554 323444455444 555
Q ss_pred eC
Q 007267 358 YS 359 (610)
Q Consensus 358 ~~ 359 (610)
++
T Consensus 423 ~~ 424 (437)
T COG2425 423 VE 424 (437)
T ss_pred eC
Confidence 55
No 69
>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=83.22 E-value=37 Score=37.04 Aligned_cols=265 Identities=15% Similarity=0.121 Sum_probs=121.9
Q ss_pred EEEEEeCCCCh-hH---HHHHHHHHHHHHHhCCCCcEEEEEeecce-eEEEEecCCCcceeeeeeCCCCCcccccccccc
Q 007267 124 YVAAVDLSSSE-EF---LELTRSALQAALEAVPSGALFGLATFSHK-IGLYDVQGAIPVVKNVFIPSDTEDTLSLELEDV 198 (610)
Q Consensus 124 ~vFvID~s~~~-~~---l~~l~~~l~~~l~~lp~~~~VglITf~~~-V~~~~l~~~~~~~~~v~~~~~~~~~~~~dl~~~ 198 (610)
.-|++|+|++. .. |..+-..|...|..+-.+.|+||=+|=+. |.=| ... ....+.++
T Consensus 105 LYyLmDlS~Sm~ddl~~l~~lg~~l~~~~~~it~~~~~GfGsfvdK~~~P~--~~~----------------~p~~l~~p 166 (426)
T PF00362_consen 105 LYYLMDLSYSMKDDLENLKSLGQDLAEEMRNITSNFRLGFGSFVDKPVMPF--VST----------------TPEKLKNP 166 (426)
T ss_dssp EEEEEE-SGGGHHHHHHHCCCCHHHHHHHHTT-SSEEEEEEEESSSSSTTT--ST-----------------SSHCHHST
T ss_pred EEEEeechhhhhhhHHHHHHHHHHHHHHHHhcCccceEechhhcccccCCc--ccC----------------ChhhhcCc
Confidence 66899999986 33 44455678888888999999999888442 2100 000 00111111
Q ss_pred --------C-ccC-cCccchHhHHHHHHHHHHhcCCCCCcccccccccCCCCccCCCcchHHHHHHHHHhhccccCCCcc
Q 007267 199 --------M-PLS-QFLAPVETFKENITSALETLRPTTSWERTAGAAQGLDGVLMGGRGFGLAMESLFNYLGSEYGNTFA 268 (610)
Q Consensus 199 --------~-p~~-~~l~~~~e~~~~i~~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~G~Al~~a~~lL~~~~~~~~~ 268 (610)
. |.. +-..++.+....+.+.+.+..- ++..- .|...|-+-+++|+-- +..|= ...
T Consensus 167 c~~~~~~c~~~~~f~~~l~Lt~~~~~F~~~v~~~~i--s~n~D-----------~PEgg~dal~Qa~vC~-~~igW-r~~ 231 (426)
T PF00362_consen 167 CPSKNPNCQPPFSFRHVLSLTDDITEFNEEVNKQKI--SGNLD-----------APEGGLDALMQAAVCQ-EEIGW-RNE 231 (426)
T ss_dssp SCCTTS--B---SEEEEEEEES-HHHHHHHHHTS----B--SS-----------SSBSHHHHHHHHHH-H-HHHT---ST
T ss_pred ccccCCCCCCCeeeEEeecccchHHHHHHhhhhccc--cCCCC-----------CCccccchheeeeecc-cccCc-ccC
Confidence 0 111 1134566666666666665432 12111 1455566667766531 11110 001
Q ss_pred cceEEEEecCCC--CCCCcccccccCcCcccCCCcchhhcc---CCcchHHHHHHHHHHHHcCcEEEEEEecCCCcChhc
Q 007267 269 LARVFAFLSGPP--DHGAGQLDTRRYGEQYASKGEDADRAL---LPEQTPFYKDLAAVAVQAGVCVDIFAITNEYTDLAS 343 (610)
Q Consensus 269 ~GkIi~F~~g~p--t~GpG~l~~~~~~~~~~~~~~~~e~~~---~~~~~~fY~~la~~~~~~gisvDlf~~~~~~~~l~~ 343 (610)
.=||++|++-.+ ..|-|++...-..+....|-. ....| .........+|.+.+.+++|. =||+......+++
T Consensus 232 a~~llv~~TD~~fH~agDg~l~gi~~pnd~~Chl~-~~~~y~~~~~~DYPSv~ql~~~l~e~~i~-~IFAVt~~~~~~Y- 308 (426)
T PF00362_consen 232 ARRLLVFSTDAGFHFAGDGKLAGIVKPNDGKCHLD-DNGMYTASTEQDYPSVGQLVRKLSENNIN-PIFAVTKDVYSIY- 308 (426)
T ss_dssp SEEEEEEEESS-B--TTGGGGGT--S---SS--BS-TTSBBGGGGCS----HHHHHHHHHHTTEE-EEEEEEGGGHHHH-
T ss_pred ceEEEEEEcCCccccccccccceeeecCCCceEEC-CCCcccccccccCCCHHHHHHHHHHcCCE-EEEEEchhhhhHH-
Confidence 248999888665 458888765433322221111 01011 112344566788888888865 4888887766654
Q ss_pred chhhhccCccE-EEEeCCCCCCc---hhHHHHHHhccCcceeeEEEEEc-cCCeeeeeeeeccccCCCCCcceeeeecCC
Q 007267 344 LKFLSIESGGS-LFLYSSTDDST---LPQDIYRMLSRPYAFNCIMRLRT-SSEFKPGHSYGHFFPDPQYENVQHIICCDS 418 (610)
Q Consensus 344 l~~l~~~TGG~-v~~~~~~~~~~---l~~dl~~~l~~~~~~~a~lrvr~-S~gl~v~~~~G~~~~~~~~~~~~~i~~~~~ 418 (610)
..|+..-+|. +-.... |.+. +..+-++.+. -...|+... +.++++ .+..+|.........-...++..
T Consensus 309 -~~L~~~i~~s~vg~L~~-dSsNIv~LI~~aY~~i~----s~V~L~~~~~p~~v~v-~y~s~C~~~~~~~~~~~C~~V~i 381 (426)
T PF00362_consen 309 -EELSNLIPGSSVGELSS-DSSNIVQLIKEAYNKIS----SKVELKHDNAPDGVKV-SYTSNCPNGSTVPGTNECSNVKI 381 (426)
T ss_dssp -HHHHHHSTTEEEEEEST-TSHTHHHHHHHHHHHHC----TEEEEEECS--TTEEE-EEEEEESSSEEEECCEEECSE-T
T ss_pred -HHHhhcCCCceeccccc-CchhHHHHHHHHHHHHh----heEEEEecCCCCcEEE-EEEEEccCCcccCcCccccCEec
Confidence 4444444444 333332 3332 3333333332 234444333 345666 44445544211111123334556
Q ss_pred CccEEEEEEEecC
Q 007267 419 YATYAYDFDFANA 431 (610)
Q Consensus 419 ~~t~a~~fe~~~~ 431 (610)
.+++.|.+.+...
T Consensus 382 G~~V~F~VtVta~ 394 (426)
T PF00362_consen 382 GDTVTFNVTVTAK 394 (426)
T ss_dssp T-EEEEEEEEEES
T ss_pred CCEEEEEEEEEEe
Confidence 6776666666653
No 70
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=82.64 E-value=19 Score=36.96 Aligned_cols=98 Identities=17% Similarity=0.206 Sum_probs=65.8
Q ss_pred CCcchHHHHHHHHHhhccccCCCcccceEEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHHHH
Q 007267 244 GGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAVAV 323 (610)
Q Consensus 244 ~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~~~ 323 (610)
+..++-.||+.|...|+...+.. .-.|++..++..|.-||.+- +..+.+.
T Consensus 141 g~fSLqNaLe~a~~~Lk~~p~H~--sREVLii~sslsT~DPgdi~----------------------------~tI~~lk 190 (378)
T KOG2807|consen 141 GDFSLQNALELAREVLKHMPGHV--SREVLIIFSSLSTCDPGDIY----------------------------ETIDKLK 190 (378)
T ss_pred CChHHHHHHHHHHHHhcCCCccc--ceEEEEEEeeecccCcccHH----------------------------HHHHHHH
Confidence 34568899999999998763211 12577777888999888542 3566778
Q ss_pred HcCcEEEEEEecCCCcChhcchhhhccCccEEEEeCCCCCCchhHHHHHHhccC
Q 007267 324 QAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYSSTDDSTLPQDIYRMLSRP 377 (610)
Q Consensus 324 ~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~~~~~~l~~dl~~~l~~~ 377 (610)
+..|-|.++..+.+ +..-+.||+.|||. |+=..|...|+ +|.+-.+.+
T Consensus 191 ~~kIRvsvIgLsaE---v~icK~l~kaT~G~--Y~V~lDe~Hlk-eLl~e~~~P 238 (378)
T KOG2807|consen 191 AYKIRVSVIGLSAE---VFICKELCKATGGR--YSVALDEGHLK-ELLLEHTHP 238 (378)
T ss_pred hhCeEEEEEeechh---HHHHHHHHHhhCCe--EEEEeCHHHHH-HHHHhcCCC
Confidence 88999999887654 44558899999994 33345655554 443333333
No 71
>KOG0443 consensus Actin regulatory proteins (gelsolin/villin family) [Cytoskeleton]
Probab=82.17 E-value=3 Score=47.53 Aligned_cols=72 Identities=14% Similarity=0.252 Sum_probs=51.5
Q ss_pred cCCCcEEEEecC-cEEEEEecCCCCCCCCCCCChhHHHHHHHHHHH-hcCCCCceEEEEeCCCCcH---HHHHhhccCCC
Q 007267 507 TSGSPIFLLDAF-TTIIVFYSSTADPTLPFPPPQDCLLRTTINKMK-QERSITPKLIFIRGGQDDA---TIFENYLIEEQ 581 (610)
Q Consensus 507 ~s~~~iyllD~g-~~~~i~~G~~v~~~~~~~~~~~~~~~~~i~~i~-~~r~~~p~l~~~~~~~~~~---~~f~~~LveD~ 581 (610)
+..+..||||+| ..||||.|...+. .+.-+++....+-|+ +.|++.=.++++.+|...+ .+|.+-..+++
T Consensus 282 Ld~~dCYILD~g~~~IfVW~Gr~as~-----~ERkaAm~~AeeFlk~k~yP~~TqV~rv~EG~Esa~FKq~F~~W~~~~~ 356 (827)
T KOG0443|consen 282 LDTEDCYILDCGGGEIFVWKGRQASL-----DERKAAMSSAEEFLKKKKYPPNTQVVRVLEGAESAPFKQLFDSWPDKDQ 356 (827)
T ss_pred hccCCeEEEecCCceEEEEeCCCCCH-----HHHHHHHHHHHHHHHhccCCCCceEEEecCCCcchhHHHHHhhCccccc
Confidence 466899999999 9999999999874 233444555555666 4555666888888886554 36777777777
Q ss_pred CC
Q 007267 582 DV 583 (610)
Q Consensus 582 ~~ 583 (610)
+.
T Consensus 357 t~ 358 (827)
T KOG0443|consen 357 TN 358 (827)
T ss_pred cc
Confidence 73
No 72
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.78 E-value=14 Score=37.66 Aligned_cols=100 Identities=14% Similarity=0.117 Sum_probs=64.0
Q ss_pred CcchHHHHHHHHHhhcccc----CCCcccceEEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHH
Q 007267 245 GRGFGLAMESLFNYLGSEY----GNTFALARVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAA 320 (610)
Q Consensus 245 ~~~~G~Al~~a~~lL~~~~----~~~~~~GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~ 320 (610)
...+..||..|+..+.... ......+||+++..++- . ..+.-=+-+...
T Consensus 118 ~s~lagals~ALcyinr~~~~~~~~~~~~~RIlii~~s~~-----------~----------------~~qYi~~mn~If 170 (279)
T TIGR00627 118 RTVLAGALSDALGYINRSEQSETASEKLKSRILVISITPD-----------M----------------ALQYIPLMNCIF 170 (279)
T ss_pred cccchhHHHhhhhhhcccccccccCcCCcceEEEEECCCC-----------c----------------hHHHHHHHHHHH
Confidence 3457888888888875421 11112489999987531 0 011112347788
Q ss_pred HHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeCCCCCCchhHHHHHHh
Q 007267 321 VAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYSSTDDSTLPQDIYRML 374 (610)
Q Consensus 321 ~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~~~~~~l~~dl~~~l 374 (610)
.|.+.+|.||++..+.+ -+..-+++++..|||.-.... +...|.+-|...+
T Consensus 171 aaqk~~I~Idv~~L~~e-~~~~~lqQa~~~TgG~Y~~~~--~~~~L~q~L~~~~ 221 (279)
T TIGR00627 171 SAQKQNIPIDVVSIGGD-FTSGFLQQAADITGGSYLHVK--KPQGLLQYLMTNM 221 (279)
T ss_pred HHHHcCceEEEEEeCCc-cccHHHHHHHHHhCCEEeccC--CHhHHHHHHHHhc
Confidence 89999999999988643 356789999999999644333 3334555554444
No 73
>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=77.23 E-value=1.3 Score=33.30 Aligned_cols=32 Identities=25% Similarity=0.595 Sum_probs=22.7
Q ss_pred CCCcCcCcCeeEecCceEe--CceeEEcCCCCCC
Q 007267 49 MLPRCENCYAYFNTYCELE--QWAWTCSLCGSLN 80 (610)
Q Consensus 49 ~~~RC~~C~ayiNp~~~~~--~~~w~C~~C~~~N 80 (610)
.+.-|++|+.----+-+-+ .-+|+|+.|+..|
T Consensus 21 ~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 21 YALICSKCFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred eeEECcccchhhcccccccCCceEEEcCCCCCcC
Confidence 4567999998644442322 3599999999887
No 74
>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=77.16 E-value=74 Score=30.91 Aligned_cols=104 Identities=22% Similarity=0.267 Sum_probs=61.9
Q ss_pred CCcchHHHHHHHHHhhccccCCCcccceEEEEec--CCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHHH
Q 007267 244 GGRGFGLAMESLFNYLGSEYGNTFALARVFAFLS--GPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAAV 321 (610)
Q Consensus 244 ~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~--g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~~ 321 (610)
..++.|.||..+..+|...+. .+.|-++=.| |+.|.|+.-+ +..-..
T Consensus 93 ~~Taig~Al~~a~~ll~~~~~---~~~RrVIDvSGDG~~N~G~~p~----------------------------~~ard~ 141 (205)
T PF06707_consen 93 GRTAIGSALDFAAALLAQNPF---ECWRRVIDVSGDGPNNQGPRPV----------------------------TSARDA 141 (205)
T ss_pred CCchHHHHHHHHHHHHHhCCC---CCceEEEEECCCCCCCCCCCcc----------------------------HHHHHH
Confidence 348999999999999987542 1344444444 5556664322 112334
Q ss_pred HHHcCcEEEEEEecCCCc----ChhcchhhhccCccEEEEeCCCCCCchhHHHHHHhccCc
Q 007267 322 AVQAGVCVDIFAITNEYT----DLASLKFLSIESGGSLFLYSSTDDSTLPQDIYRMLSRPY 378 (610)
Q Consensus 322 ~~~~gisvDlf~~~~~~~----~l~~l~~l~~~TGG~v~~~~~~~~~~l~~dl~~~l~~~~ 378 (610)
+...||.|+=+......- ++...-.=+-.+|---|..+..+.+.|.+-++|-|.++.
T Consensus 142 ~~~~GitINgL~I~~~~~~~~~~L~~yy~~~VIgGpgAFV~~a~~~~df~~AirrKL~rEi 202 (205)
T PF06707_consen 142 AVAAGITINGLAILDDDPFGGADLDAYYRRCVIGGPGAFVETARGFEDFAEAIRRKLIREI 202 (205)
T ss_pred HHHCCeEEeeeEecCCCCCccccHHHHHhhhcccCCCceEEEcCCHHHHHHHHHHHHHHHh
Confidence 556899999998876544 454433333333333344444444577777877776654
No 75
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=77.15 E-value=1.4 Score=31.70 Aligned_cols=27 Identities=22% Similarity=0.469 Sum_probs=19.7
Q ss_pred CcCcCcCeeEecCceEeC--ceeEEcCCCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQ--WAWTCSLCGSLNG 81 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~--~~w~C~~C~~~N~ 81 (610)
.+|.+|++-+- ++. ..+.|+.||..-.
T Consensus 4 y~C~~CG~~~~----~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVE----LDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEE----ECCCCCceECCCCCCeEE
Confidence 58999999542 332 2799999997654
No 76
>PRK10997 yieM hypothetical protein; Provisional
Probab=77.11 E-value=21 Score=39.50 Aligned_cols=49 Identities=27% Similarity=0.309 Sum_probs=32.1
Q ss_pred EEEEEEeCCCChh-HHHHHHHHHHHHHH--hCCCCcEEEEEeecceeEEEEe
Q 007267 123 VYVAAVDLSSSEE-FLELTRSALQAALE--AVPSGALFGLATFSHKIGLYDV 171 (610)
Q Consensus 123 ~~vFvID~s~~~~-~l~~l~~~l~~~l~--~lp~~~~VglITf~~~V~~~~l 171 (610)
-++++||+|.+.. .-+....++..+|- .+.++-++++|.|++.+.-|.+
T Consensus 325 piII~VDtSGSM~G~ke~~AkalAaAL~~iAl~q~dr~~li~Fs~~i~~~~l 376 (487)
T PRK10997 325 PFIVCVDTSGSMGGFNEQCAKAFCLALMRIALAENRRCYIMLFSTEVVTYEL 376 (487)
T ss_pred cEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHhcCCCEEEEEecCCceeecc
Confidence 3889999999863 32222223333332 4567889999999997766543
No 77
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=76.90 E-value=6.4 Score=35.09 Aligned_cols=42 Identities=26% Similarity=0.185 Sum_probs=31.6
Q ss_pred EEEEeCCCCh--hHHHHHHHHHHHHHHhCCCCcEEEEEeecceeEE
Q 007267 125 VAAVDLSSSE--EFLELTRSALQAALEAVPSGALFGLATFSHKIGL 168 (610)
Q Consensus 125 vFvID~s~~~--~~l~~l~~~l~~~l~~lp~~~~VglITf~~~V~~ 168 (610)
+++||+|.+. ++|....+.+...++.. +.+|-+|.||..|+-
T Consensus 2 ~vaiDtSGSis~~~l~~fl~ev~~i~~~~--~~~v~vi~~D~~v~~ 45 (126)
T PF09967_consen 2 VVAIDTSGSISDEELRRFLSEVAGILRRF--PAEVHVIQFDAEVQD 45 (126)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHHhC--CCCEEEEEECCEeee
Confidence 6899999985 56666666666666666 556899999998764
No 78
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=68.53 E-value=3.6 Score=27.07 Aligned_cols=30 Identities=20% Similarity=0.399 Sum_probs=19.8
Q ss_pred CcCcCcCeeEecCceEeCceeEEcCCCCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQWAWTCSLCGSLNGL 82 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~ 82 (610)
+.|..|+..+--- -....++|..|+..|.+
T Consensus 2 ~~C~~C~t~L~yP--~gA~~vrCs~C~~vt~v 31 (31)
T TIGR01053 2 VVCGGCRTLLMYP--RGASSVRCALCQTVNLV 31 (31)
T ss_pred cCcCCCCcEeecC--CCCCeEECCCCCeEecC
Confidence 4688888865210 11268999999887753
No 79
>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=67.06 E-value=1.3 Score=34.54 Aligned_cols=31 Identities=26% Similarity=0.664 Sum_probs=19.8
Q ss_pred CCcCcCcCeeEecCceEeCceeEEcCCCCCCCCCh
Q 007267 50 LPRCENCYAYFNTYCELEQWAWTCSLCGSLNGLSS 84 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~p~ 84 (610)
+.|| +|+.++ |.+-..++-+| .||....+-.
T Consensus 3 ifrC-~Cgr~l--ya~e~~kTkkC-~CG~~l~vk~ 33 (68)
T PF09082_consen 3 IFRC-DCGRYL--YAKEGAKTKKC-VCGKTLKVKE 33 (68)
T ss_dssp EEEE-TTS--E--EEETT-SEEEE-TTTEEEE--S
T ss_pred EEEe-cCCCEE--EecCCcceeEe-cCCCeeeeee
Confidence 5799 799987 43333478999 9999887754
No 80
>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=66.15 E-value=1.5 Score=32.05 Aligned_cols=35 Identities=20% Similarity=0.477 Sum_probs=25.1
Q ss_pred CCcCcCcCeeEecCceEeCceeEEcCCCCCCCCCh
Q 007267 50 LPRCENCYAYFNTYCELEQWAWTCSLCGSLNGLSS 84 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~p~ 84 (610)
-+||.+|+-.+--.-.+..-.-+|+=|++.|.+-.
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA 38 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence 37999998766433233334689999999998743
No 81
>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=60.71 E-value=3.9 Score=30.13 Aligned_cols=28 Identities=25% Similarity=0.708 Sum_probs=19.4
Q ss_pred cCcCcCeeEecCc-----------eEeC--ceeEEcCCCCC
Q 007267 52 RCENCYAYFNTYC-----------ELEQ--WAWTCSLCGSL 79 (610)
Q Consensus 52 RC~~C~ayiNp~~-----------~~~~--~~w~C~~C~~~ 79 (610)
+|..|+=..+|-- .|++ ..|+|+.|+..
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 6888887777642 3432 57999999853
No 82
>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=60.07 E-value=5.7 Score=26.42 Aligned_cols=23 Identities=26% Similarity=0.875 Sum_probs=14.8
Q ss_pred cCcCcCeeEecCceEeCceeEEcCCCC
Q 007267 52 RCENCYAYFNTYCELEQWAWTCSLCGS 78 (610)
Q Consensus 52 RC~~C~ayiNp~~~~~~~~w~C~~C~~ 78 (610)
+|..|+=...+- ..-|.||.|+.
T Consensus 3 ~C~~CGy~y~~~----~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGE----EAPWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCC----cCCCcCcCCCC
Confidence 577777433321 15789999986
No 83
>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=59.75 E-value=3.8 Score=29.76 Aligned_cols=28 Identities=25% Similarity=0.731 Sum_probs=17.7
Q ss_pred cCcCcCeeEecCce-----------EeC--ceeEEcCCCCC
Q 007267 52 RCENCYAYFNTYCE-----------LEQ--WAWTCSLCGSL 79 (610)
Q Consensus 52 RC~~C~ayiNp~~~-----------~~~--~~w~C~~C~~~ 79 (610)
+|..|+-..+|--. |++ ..|+|+.|+..
T Consensus 3 ~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 3 QCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred CCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 58888877776653 332 57999999864
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=57.94 E-value=7.1 Score=26.61 Aligned_cols=27 Identities=19% Similarity=0.437 Sum_probs=22.1
Q ss_pred CCcCcCcCeeEecCceEeCceeEEcCCCCC
Q 007267 50 LPRCENCYAYFNTYCELEQWAWTCSLCGSL 79 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~ 79 (610)
..+|..|++. +...+++.|.|.=|++.
T Consensus 8 ~~~C~~C~~~---~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSR---WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCe---EeEccCCEEEhhhCceE
Confidence 3579999998 56666799999999875
No 85
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=56.92 E-value=6.2 Score=28.95 Aligned_cols=31 Identities=19% Similarity=0.444 Sum_probs=21.1
Q ss_pred cCcCcCeeEecCceEeC-ceeEEcCCCCCCCCC
Q 007267 52 RCENCYAYFNTYCELEQ-WAWTCSLCGSLNGLS 83 (610)
Q Consensus 52 RC~~C~ayiNp~~~~~~-~~w~C~~C~~~N~~p 83 (610)
.|..|+..+-+- ..++ ..|+|+-|+..-...
T Consensus 2 FCp~Cg~~l~~~-~~~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPK-EGKEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCccccc-cCCCCCEEECCcCCCeEECC
Confidence 589999976222 1222 489999999876554
No 86
>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=55.36 E-value=22 Score=34.77 Aligned_cols=67 Identities=12% Similarity=0.133 Sum_probs=37.2
Q ss_pred CcchHHHHHHHHHhhccc-cCCCcccceEEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHH-HHHHH
Q 007267 245 GRGFGLAMESLFNYLGSE-YGNTFALARVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKD-LAAVA 322 (610)
Q Consensus 245 ~~~~G~Al~~a~~lL~~~-~~~~~~~GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~-la~~~ 322 (610)
...+..||.+|..++... ...+...-||++||..--..+ ..+. . ..-.++ .+..+
T Consensus 104 ~~~l~~al~v~~~~~~~~~~~~k~~~krI~l~Td~d~p~~-----~~~~----------~--------~~~~~~l~~~Dl 160 (224)
T PF03731_consen 104 EGDLSDALWVASDMFRERTCKKKKNKKRIFLFTDNDGPHE-----DDDE----------L--------ERIIQKLKAKDL 160 (224)
T ss_dssp ---HHHHHHHHHHHHHCHCTTS-ECEEEEEEEES-SSTTT------CCC----------H--------HHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHHHHhhcccCCCcEEEEEeCCCCCCC-----CHHH----------H--------HHHHHhhccccc
Confidence 345899999999999752 222222358888886532221 1110 0 001111 26678
Q ss_pred HHcCcEEEEEEe
Q 007267 323 VQAGVCVDIFAI 334 (610)
Q Consensus 323 ~~~gisvDlf~~ 334 (610)
...+|.+++|..
T Consensus 161 ~~~~i~~~~~~l 172 (224)
T PF03731_consen 161 QDNGIEIELFFL 172 (224)
T ss_dssp HHHTEEEEEEEC
T ss_pred hhcCcceeEeec
Confidence 899999999987
No 87
>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]
Probab=54.34 E-value=24 Score=39.78 Aligned_cols=68 Identities=19% Similarity=0.220 Sum_probs=46.3
Q ss_pred CCCcEEEEecCcEEEEEecCCCCCCCCCCCChhHHHHHHHHHHH-hcCCCCceEEEEeCCCCcHHHHHhh-ccCCC
Q 007267 508 SGSPIFLLDAFTTIIVFYSSTADPTLPFPPPQDCLLRTTINKMK-QERSITPKLIFIRGGQDDATIFENY-LIEEQ 581 (610)
Q Consensus 508 s~~~iyllD~g~~~~i~~G~~v~~~~~~~~~~~~~~~~~i~~i~-~~r~~~p~l~~~~~~~~~~~~f~~~-LveD~ 581 (610)
+..-+||||.|.+++||-|...-. ..+.+-|=+.+.|. .+|--.-.+..++||.....|.... ..+|+
T Consensus 647 DPRf~FlLD~G~~IyiW~G~~s~~------t~~~KARLfAEkinK~eRKgK~EI~l~rQg~e~pEFWqaLgg~p~e 716 (1255)
T KOG0444|consen 647 DPRFCFLLDAGETIYIWSGYKSRI------TVSNKARLFAEKINKRERKGKSEIELCRQGREPPEFWQALGGNPDE 716 (1255)
T ss_pred CcceEEEEeCCceEEEEeccchhc------ccchHHHHHHHHhhhhhccCceeeehhhhcCCCHHHHHHhCCCCcc
Confidence 445699999999999999988552 33445555556665 4565566899999997655555443 33444
No 88
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=52.50 E-value=6.5 Score=34.51 Aligned_cols=26 Identities=23% Similarity=0.548 Sum_probs=19.4
Q ss_pred CcCcCcCeeEecCceEeCceeEEcCCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQWAWTCSLCGSLN 80 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N 80 (610)
.+|++|+....+ +...|.||-|+..+
T Consensus 71 ~~C~~Cg~~~~~----~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 71 CECEDCSEEVSP----EIDLYRCPKCHGIM 96 (115)
T ss_pred EEcccCCCEEec----CCcCccCcCCcCCC
Confidence 699999954432 23468999999876
No 89
>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=52.25 E-value=11 Score=32.22 Aligned_cols=28 Identities=25% Similarity=0.496 Sum_probs=21.2
Q ss_pred CCcCcCcCeeEecCceEeCceeEEcCCCCCC
Q 007267 50 LPRCENCYAYFNTYCELEQWAWTCSLCGSLN 80 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N 80 (610)
.|.|.+|.+ -|.--++..|+|+-|++.-
T Consensus 2 lp~CP~C~s---eytY~dg~~~iCpeC~~EW 29 (109)
T TIGR00686 2 LPPCPKCNS---EYTYHDGTQLICPSCLYEW 29 (109)
T ss_pred CCcCCcCCC---cceEecCCeeECccccccc
Confidence 467888886 3555567899999999754
No 90
>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=52.09 E-value=12 Score=26.82 Aligned_cols=27 Identities=19% Similarity=0.423 Sum_probs=19.7
Q ss_pred CCcCcCcCeeEecCceEe-CceeEEcCCCC
Q 007267 50 LPRCENCYAYFNTYCELE-QWAWTCSLCGS 78 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~-~~~w~C~~C~~ 78 (610)
.+.|.+|++- . +..+. .+.|.|.-|++
T Consensus 18 g~~CP~Cg~~-~-~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGST-K-HYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCe-e-eEEeCCCCeEECCCCCC
Confidence 3679999987 3 33333 47999999985
No 91
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=51.69 E-value=6.7 Score=34.32 Aligned_cols=27 Identities=19% Similarity=0.399 Sum_probs=19.0
Q ss_pred CcCcCcCeeEecCceEeCceeEEcCCCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQWAWTCSLCGSLNG 81 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~ 81 (610)
.||..|+.... .+...|.||-|+..+.
T Consensus 71 ~~C~~Cg~~~~----~~~~~~~CP~Cgs~~~ 97 (113)
T PRK12380 71 AWCWDCSQVVE----IHQHDAQCPHCHGERL 97 (113)
T ss_pred EEcccCCCEEe----cCCcCccCcCCCCCCc
Confidence 59999995332 2245678999997653
No 92
>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=50.49 E-value=35 Score=33.57 Aligned_cols=33 Identities=18% Similarity=0.218 Sum_probs=22.3
Q ss_pred CCcchHHHHHHHHHhhccccCCCcccceEEEEecCC
Q 007267 244 GGRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGP 279 (610)
Q Consensus 244 ~~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~ 279 (610)
+++..|.||..+...+....- ....|+++++|.
T Consensus 128 GgTdi~~aL~~~~~~~~~~~~---~~t~vvIiSDg~ 160 (222)
T PF05762_consen 128 GGTDIGQALREFLRQYARPDL---RRTTVVIISDGW 160 (222)
T ss_pred CccHHHHHHHHHHHHhhcccc---cCcEEEEEeccc
Confidence 566799999998888763210 124678887764
No 93
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=50.27 E-value=7.1 Score=23.74 Aligned_cols=21 Identities=33% Similarity=0.817 Sum_probs=11.0
Q ss_pred cCcCcCeeEecCceEeCceeEEcCCCC
Q 007267 52 RCENCYAYFNTYCELEQWAWTCSLCGS 78 (610)
Q Consensus 52 RC~~C~ayiNp~~~~~~~~w~C~~C~~ 78 (610)
+|.+|++-+.+-.+| |+-||+
T Consensus 1 ~Cp~CG~~~~~~~~f------C~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKF------CPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcc------hhhhCC
Confidence 466666655433333 666654
No 94
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.77 E-value=39 Score=39.33 Aligned_cols=114 Identities=18% Similarity=0.275 Sum_probs=68.2
Q ss_pred CcCcCcCeeE-ecCceE----e--CceeEEcCCCCCCCCChhhhcccCCCcCccccccccEEEEec-CCCCc---cccCC
Q 007267 51 PRCENCYAYF-NTYCEL----E--QWAWTCSLCGSLNGLSSQAIARYTHPQSCAEMISSFIDLDLP-LEGSE---EETMQ 119 (610)
Q Consensus 51 ~RC~~C~ayi-Np~~~~----~--~~~w~C~~C~~~N~~p~~~~~~~~~~~~~pEL~~~tvey~~p-~~y~~---~~~~~ 119 (610)
+.|+.|+-.. ||.|.. - .+.-.|..|++.-..|.. .|+--+..+-+.-+ .+-.. +.-.|
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~----------Cp~Cgs~~L~~~G~GterieeeL~~~FP 505 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQS----------CPECGSEHLRAVGPGTERIEEELKRLFP 505 (730)
T ss_pred eecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCC----------CCCCCCCeeEEecccHHHHHHHHHHHCC
Confidence 4666666553 455543 2 378999999999887755 56533332333221 00000 01236
Q ss_pred CCcEEEEEEeCCCChhHHHHHHHHHHH----------HHH---hCCCCcEEEEEeecceeEEEEecCC
Q 007267 120 ARPVYVAAVDLSSSEEFLELTRSALQA----------ALE---AVPSGALFGLATFSHKIGLYDVQGA 174 (610)
Q Consensus 120 ~~p~~vFvID~s~~~~~l~~l~~~l~~----------~l~---~lp~~~~VglITf~~~V~~~~l~~~ 174 (610)
..+++.|--|+....+.++.+-..+.. +|. ..|+-+.||++-=|..++.-|++..
T Consensus 506 ~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~ 573 (730)
T COG1198 506 GARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRAS 573 (730)
T ss_pred CCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchH
Confidence 678888888888876655554443332 111 2466689999999988888777654
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=48.89 E-value=9.5 Score=33.58 Aligned_cols=31 Identities=19% Similarity=0.510 Sum_probs=26.1
Q ss_pred CCcCcCcCeeEecCceEeC---ceeEEcCCCCCC
Q 007267 50 LPRCENCYAYFNTYCELEQ---WAWTCSLCGSLN 80 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~---~~w~C~~C~~~N 80 (610)
...|..|+-.++.-|.+.. ..|.|.+|....
T Consensus 71 ~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k~r 104 (118)
T PF02318_consen 71 GRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQKQR 104 (118)
T ss_dssp CEEETTTTEEEETTSEEETSSSCCEEEHHHHHHH
T ss_pred CCcCCcCCccccCccCCcCCCCCCEEChhhHHHH
Confidence 4789999999999999873 589999997644
No 96
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=47.31 E-value=26 Score=36.07 Aligned_cols=31 Identities=29% Similarity=0.434 Sum_probs=28.0
Q ss_pred hhHHHHHHHHHHHHHHhCCCCcEEEEEeecc
Q 007267 134 EEFLELTRSALQAALEAVPSGALFGLATFSH 164 (610)
Q Consensus 134 ~~~l~~l~~~l~~~l~~lp~~~~VglITf~~ 164 (610)
..+|+.++.+|.++++.|.++-|+++|||-+
T Consensus 217 NdEL~~L~~~L~~a~~~L~~gGRl~VIsFHS 247 (314)
T COG0275 217 NDELEELEEALEAALDLLKPGGRLAVISFHS 247 (314)
T ss_pred hhHHHHHHHHHHHHHHhhCCCcEEEEEEecc
Confidence 4789999999999999999999999999943
No 97
>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=44.92 E-value=25 Score=30.83 Aligned_cols=33 Identities=15% Similarity=0.287 Sum_probs=25.3
Q ss_pred hHHHHHHHHHHHHHHhCCC---CcEEEEEeecceeE
Q 007267 135 EFLELTRSALQAALEAVPS---GALFGLATFSHKIG 167 (610)
Q Consensus 135 ~~l~~l~~~l~~~l~~lp~---~~~VglITf~~~V~ 167 (610)
...+.+|++|..-+..-|. +++|-+++||+.|.
T Consensus 110 ~fAe~vkDAi~Dyi~T~P~PT~~~~Vt~~~Fd~~V~ 145 (146)
T PF02905_consen 110 LFAECVKDAIRDYIMTRPQPTCNTQVTVCSFDDGVM 145 (146)
T ss_dssp HHHHHHHHHHHHHHCTS-TTGGGEEEEEEEEEEEE-
T ss_pred HHHHHHHHHHHHHhcCCCCCCcceEEEEEeCCCCCc
Confidence 4457899999988876553 68999999998774
No 98
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=43.62 E-value=9.3 Score=33.48 Aligned_cols=26 Identities=27% Similarity=0.510 Sum_probs=18.3
Q ss_pred CcCcCcCeeEecCceEeCc-eeEEcCCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQW-AWTCSLCGSLN 80 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~~-~w~C~~C~~~N 80 (610)
.+|..|+.+. ..... .|.||-|+..+
T Consensus 71 ~~C~~Cg~~~----~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 71 CWCETCQQYV----TLLTQRVRRCPQCHGDM 97 (114)
T ss_pred EEcccCCCee----ecCCccCCcCcCcCCCC
Confidence 5999999632 22223 48899999776
No 99
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=43.57 E-value=14 Score=35.12 Aligned_cols=25 Identities=28% Similarity=0.638 Sum_probs=20.4
Q ss_pred CcCcCcCeeEecCceEeCceeEEcCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQWAWTCSLCGSL 79 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~~~w~C~~C~~~ 79 (610)
.||++|++-|=+ ++++-+|+-|+..
T Consensus 150 A~CsrC~~~L~~----~~~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK----KGNMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE----cCcEEECCCCCCE
Confidence 499999997633 6789999999964
No 100
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=43.56 E-value=9.1 Score=33.71 Aligned_cols=28 Identities=25% Similarity=0.452 Sum_probs=18.5
Q ss_pred CCcCcCcCeeEecCceEeCc-eeEEcCCCCCCC
Q 007267 50 LPRCENCYAYFNTYCELEQW-AWTCSLCGSLNG 81 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~~-~w~C~~C~~~N~ 81 (610)
..||..|+.+. ..+.. .+.||-|+..+.
T Consensus 71 ~~~C~~Cg~~~----~~~~~~~~~CP~Cgs~~~ 99 (117)
T PRK00564 71 ELECKDCSHVF----KPNALDYGVCEKCHSKNV 99 (117)
T ss_pred EEEhhhCCCcc----ccCCccCCcCcCCCCCce
Confidence 36999999432 22333 345999998763
No 101
>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=43.40 E-value=11 Score=40.27 Aligned_cols=28 Identities=29% Similarity=0.680 Sum_probs=20.8
Q ss_pred cCcCcCeeEecCceEeCceeEEcCCCCCCCCChh
Q 007267 52 RCENCYAYFNTYCELEQWAWTCSLCGSLNGLSSQ 85 (610)
Q Consensus 52 RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~p~~ 85 (610)
+|++|+.- .-...|+||-|+..|.+.++
T Consensus 2 ~c~~cg~~------~~~~~g~cp~c~~w~~~~e~ 29 (372)
T cd01121 2 VCSECGYV------SPKWLGKCPECGEWNTLVEE 29 (372)
T ss_pred CCCCCCCC------CCCccEECcCCCCceeeeeh
Confidence 68888851 11357999999999998653
No 102
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=43.35 E-value=20 Score=23.93 Aligned_cols=30 Identities=27% Similarity=0.396 Sum_probs=20.5
Q ss_pred CCCcCcCcCeeEecCceEeCceeEEcCCCCCC
Q 007267 49 MLPRCENCYAYFNTYCELEQWAWTCSLCGSLN 80 (610)
Q Consensus 49 ~~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N 80 (610)
.+.+|..|++-. -..-++...+|.+|+...
T Consensus 2 ~~~~C~~C~~~~--i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 2 NLKKCSKCGGNG--IVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred CceEcCCCCCCe--EEEecCCeEEcccCCcEe
Confidence 356899999854 111234689999999764
No 103
>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=43.02 E-value=12 Score=26.32 Aligned_cols=29 Identities=31% Similarity=0.606 Sum_probs=22.6
Q ss_pred CcCcCcCeeEecCceEeC-ceeEEcCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQ-WAWTCSLCGSL 79 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~-~~w~C~~C~~~ 79 (610)
-||..|+....-...+.+ ....|+-|+..
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGST 35 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCCC
Confidence 489999987776666654 68999999983
No 104
>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=42.56 E-value=13 Score=27.33 Aligned_cols=30 Identities=27% Similarity=0.517 Sum_probs=21.0
Q ss_pred CcCcCcCeeEecCceEe-CceeEEcCCCCCC
Q 007267 51 PRCENCYAYFNTYCELE-QWAWTCSLCGSLN 80 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~-~~~w~C~~C~~~N 80 (610)
-||.+|+....-+..+. .....|+-|+..+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGGEK 36 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCCCc
Confidence 48999998655554443 3567899999854
No 105
>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=42.37 E-value=17 Score=23.71 Aligned_cols=26 Identities=27% Similarity=0.639 Sum_probs=13.8
Q ss_pred CCcCcCcCeeEecCceEeCceeEEcCCCC
Q 007267 50 LPRCENCYAYFNTYCELEQWAWTCSLCGS 78 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~~~w~C~~C~~ 78 (610)
.+.|..|++=. .-.|+..++|+-|++
T Consensus 2 ~p~Cp~C~se~---~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 2 LPKCPLCGSEY---TYEDGELLVCPECGH 27 (30)
T ss_dssp S---TTT--------EE-SSSEEETTTTE
T ss_pred CCCCCCCCCcc---eeccCCEEeCCcccc
Confidence 36788888743 337778999999985
No 106
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=42.05 E-value=15 Score=27.00 Aligned_cols=26 Identities=23% Similarity=0.635 Sum_probs=18.9
Q ss_pred CcCcCcCeeEecCceEeCceeEEcCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQWAWTCSLCGSL 79 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~~~w~C~~C~~~ 79 (610)
..|.+|++ . ++.....+|.|.-|+..
T Consensus 21 ~fCP~Cg~--~-~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 21 KFCPRCGS--G-FMAEHLDRWHCGKCGYT 46 (50)
T ss_pred CcCcCCCc--c-hheccCCcEECCCcCCE
Confidence 47999997 1 44444579999999863
No 107
>PF11265 Med25_VWA: Mediator complex subunit 25 von Willebrand factor type A; InterPro: IPR021419 The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex [].
Probab=41.57 E-value=3.6e+02 Score=26.66 Aligned_cols=88 Identities=13% Similarity=0.093 Sum_probs=53.8
Q ss_pred chHHHHHHHHHhhcccc------CCCcccceEEEEecCCCCCCCcccccccCcCcccCCCcchhhccCCcchHHHHHHHH
Q 007267 247 GFGLAMESLFNYLGSEY------GNTFALARVFAFLSGPPDHGAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDLAA 320 (610)
Q Consensus 247 ~~G~Al~~a~~lL~~~~------~~~~~~GkIi~F~~g~pt~GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~la~ 320 (610)
+..-+|.+|+.++.... ++...-=+.|+.+.++|..=|= .+. ..-....++++|.
T Consensus 111 ~iaEGLa~AL~~fd~~~~~r~~~~~~~~~khcILI~nSpP~~~p~----~~~---------------~~~~~~~~d~la~ 171 (226)
T PF11265_consen 111 AIAEGLAEALQCFDDFKQMRQQQQQTDVQKHCILICNSPPYRLPV----NEC---------------PQYSGKTCDQLAV 171 (226)
T ss_pred hHHHHHHHHHHHhcchhhhccccCcccccceEEEEeCCCCccccc----cCC---------------CcccCCCHHHHHH
Confidence 36777888888887321 1000012567777777743221 110 1112345678999
Q ss_pred HHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEE
Q 007267 321 VAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFL 357 (610)
Q Consensus 321 ~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~ 357 (610)
.+.+++|.+.+++= . -+..+..|-+..+|....
T Consensus 172 ~~~~~~I~LSiisP--r--klP~l~~Lfeka~~~~~~ 204 (226)
T PF11265_consen 172 LISERNISLSIISP--R--KLPSLRSLFEKAKGNPRA 204 (226)
T ss_pred HHHhcCceEEEEcC--c--cCHHHHHHHHhcCCCccc
Confidence 99999999988852 2 456678888887877655
No 108
>PRK03954 ribonuclease P protein component 4; Validated
Probab=41.45 E-value=14 Score=32.76 Aligned_cols=33 Identities=21% Similarity=0.489 Sum_probs=24.6
Q ss_pred cCcCcCeeEecC--ceE--eCc-----eeEEcCCCCCCCCCh
Q 007267 52 RCENCYAYFNTY--CEL--EQW-----AWTCSLCGSLNGLSS 84 (610)
Q Consensus 52 RC~~C~ayiNp~--~~~--~~~-----~w~C~~C~~~N~~p~ 84 (610)
-|++|.+++=|- +.+ .++ .++|..||+..-+|-
T Consensus 66 ~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~P~ 107 (121)
T PRK03954 66 YCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRYPY 107 (121)
T ss_pred HhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEeecc
Confidence 499999999774 333 332 359999999988873
No 109
>PRK10220 hypothetical protein; Provisional
Probab=40.86 E-value=21 Score=30.63 Aligned_cols=29 Identities=24% Similarity=0.621 Sum_probs=20.9
Q ss_pred CCcCcCcCeeEecCceEeCceeEEcCCCCCCC
Q 007267 50 LPRCENCYAYFNTYCELEQWAWTCSLCGSLNG 81 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~ 81 (610)
.|.|.+|.+ -|.--|+..|+|+-|++.-.
T Consensus 3 lP~CP~C~s---eytY~d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 3 LPHCPKCNS---EYTYEDNGMYICPECAHEWN 31 (111)
T ss_pred CCcCCCCCC---cceEcCCCeEECCcccCcCC
Confidence 467888876 24445567999999998543
No 110
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=40.43 E-value=14 Score=38.29 Aligned_cols=28 Identities=25% Similarity=0.691 Sum_probs=21.3
Q ss_pred CCCcCcCcCeeEecCceEeC--ceeEEcCCCCCCCCCh
Q 007267 49 MLPRCENCYAYFNTYCELEQ--WAWTCSLCGSLNGLSS 84 (610)
Q Consensus 49 ~~~RC~~C~ayiNp~~~~~~--~~w~C~~C~~~N~~p~ 84 (610)
..-||.+|+ |.. -.|.||-|+..-.+-|
T Consensus 353 ~~YRC~~CG--------F~a~~l~W~CPsC~~W~TikP 382 (389)
T COG2956 353 PRYRCQNCG--------FTAHTLYWHCPSCRAWETIKP 382 (389)
T ss_pred CCceecccC--------CcceeeeeeCCCcccccccCC
Confidence 345999998 443 4799999998877654
No 111
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.18 E-value=12 Score=33.39 Aligned_cols=31 Identities=19% Similarity=0.438 Sum_probs=19.7
Q ss_pred CCcCcCcCeeEecC-ceEeCc--eeEEcCCCCCCC
Q 007267 50 LPRCENCYAYFNTY-CELEQW--AWTCSLCGSLNG 81 (610)
Q Consensus 50 ~~RC~~C~ayiNp~-~~~~~~--~w~C~~C~~~N~ 81 (610)
-.|| .|+.+..+- ...+.. .|.||-|+..+.
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~ 103 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRA 103 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCCCCCC
Confidence 3599 999764432 122222 378999997664
No 112
>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=39.83 E-value=19 Score=28.17 Aligned_cols=29 Identities=21% Similarity=0.377 Sum_probs=22.0
Q ss_pred CCcCcCcCeeEecCceEeCceeEEcCCCCCC
Q 007267 50 LPRCENCYAYFNTYCELEQWAWTCSLCGSLN 80 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N 80 (610)
--.|..|+...-- ....+.|+|+-||..-
T Consensus 28 Sq~C~~CG~~~~~--~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKK--RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCccccccc--ccccceEEcCCCCCEE
Confidence 3579999987655 3445899999999863
No 113
>PHA00626 hypothetical protein
Probab=37.83 E-value=25 Score=26.33 Aligned_cols=31 Identities=16% Similarity=0.267 Sum_probs=19.2
Q ss_pred cCcCcCe---eEecCceEeCceeEEcCCCCCCCC
Q 007267 52 RCENCYA---YFNTYCELEQWAWTCSLCGSLNGL 82 (610)
Q Consensus 52 RC~~C~a---yiNp~~~~~~~~w~C~~C~~~N~~ 82 (610)
.|.+|+. +-|..|+-....++|+-|+..-.-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeech
Confidence 3666665 233333333578999999987653
No 114
>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=37.35 E-value=17 Score=24.97 Aligned_cols=28 Identities=32% Similarity=0.650 Sum_probs=19.9
Q ss_pred CcCcCcCeeEecCceEe-CceeEEcCCCC
Q 007267 51 PRCENCYAYFNTYCELE-QWAWTCSLCGS 78 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~-~~~w~C~~C~~ 78 (610)
.||..|+.......... .....|+-|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 48888888666554443 45778888887
No 115
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=37.01 E-value=25 Score=25.09 Aligned_cols=26 Identities=19% Similarity=0.284 Sum_probs=14.0
Q ss_pred cCcCcCeeEecCceEeCceeEEcCCCCCC
Q 007267 52 RCENCYAYFNTYCELEQWAWTCSLCGSLN 80 (610)
Q Consensus 52 RC~~C~ayiNp~~~~~~~~w~C~~C~~~N 80 (610)
+|.+|++-...- ....-.|+-||++-
T Consensus 4 ~C~~Cg~~~~~~---~~~~irC~~CG~rI 29 (44)
T smart00659 4 ICGECGRENEIK---SKDVVRCRECGYRI 29 (44)
T ss_pred ECCCCCCEeecC---CCCceECCCCCceE
Confidence 566666643321 13456677776543
No 116
>PRK00420 hypothetical protein; Validated
Probab=36.96 E-value=21 Score=31.11 Aligned_cols=30 Identities=20% Similarity=0.363 Sum_probs=24.2
Q ss_pred CcCcCcCeeEecCceEeCceeEEcCCCCCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQWAWTCSLCGSLNGLS 83 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~p 83 (610)
-.|..|+ .|+.++.++.-.|+.|+..-.+.
T Consensus 24 ~~CP~Cg---~pLf~lk~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPVCG---LPLFELKDGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCCCC---CcceecCCCceECCCCCCeeeec
Confidence 5799999 47777777899999999966554
No 117
>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=36.51 E-value=14 Score=23.85 Aligned_cols=15 Identities=33% Similarity=0.742 Sum_probs=12.5
Q ss_pred ceeEEcCCCCCCCCC
Q 007267 69 WAWTCSLCGSLNGLS 83 (610)
Q Consensus 69 ~~w~C~~C~~~N~~p 83 (610)
+.|.|+.|...|..-
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 579999999999643
No 118
>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=36.40 E-value=18 Score=25.49 Aligned_cols=25 Identities=24% Similarity=0.604 Sum_probs=17.4
Q ss_pred cCcCcCeeEecCceEe--CceeEEcCCCCC
Q 007267 52 RCENCYAYFNTYCELE--QWAWTCSLCGSL 79 (610)
Q Consensus 52 RC~~C~ayiNp~~~~~--~~~w~C~~C~~~ 79 (610)
+|..|++-- ..+| .+.++|.-||..
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 688998832 3455 368999999864
No 119
>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=35.96 E-value=44 Score=34.63 Aligned_cols=30 Identities=27% Similarity=0.328 Sum_probs=27.4
Q ss_pred hHHHHHHHHHHHHHHhCCCCcEEEEEeecc
Q 007267 135 EFLELTRSALQAALEAVPSGALFGLATFSH 164 (610)
Q Consensus 135 ~~l~~l~~~l~~~l~~lp~~~~VglITf~~ 164 (610)
.+|+.++.+|.++.+.|.++-++++|||.+
T Consensus 214 ~EL~~L~~~L~~~~~~L~~gGrl~VISfHS 243 (305)
T TIGR00006 214 DELEELEEALQFAPNLLAPGGRLSIISFHS 243 (305)
T ss_pred HhHHHHHHHHHHHHHHhcCCCEEEEEecCc
Confidence 789999999999999999999999999954
No 120
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=35.43 E-value=25 Score=23.68 Aligned_cols=28 Identities=18% Similarity=0.438 Sum_probs=13.5
Q ss_pred cCcCcCeeEecCceE-eC-ceeEEcCCCCC
Q 007267 52 RCENCYAYFNTYCEL-EQ-WAWTCSLCGSL 79 (610)
Q Consensus 52 RC~~C~ayiNp~~~~-~~-~~w~C~~C~~~ 79 (610)
-|+.|++-+.--.-- |+ .+|+|+-|+..
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 388888865332221 22 48999999864
No 121
>COG4867 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=35.31 E-value=1.8e+02 Score=31.34 Aligned_cols=97 Identities=16% Similarity=0.172 Sum_probs=65.1
Q ss_pred CcchHHHHHHHHHhhccccCCCcccceEEEEecCCCCC----CCcccccccCcCcccCCCcchhhccCCcchHHHHHH--
Q 007267 245 GRGFGLAMESLFNYLGSEYGNTFALARVFAFLSGPPDH----GAGQLDTRRYGEQYASKGEDADRALLPEQTPFYKDL-- 318 (610)
Q Consensus 245 ~~~~G~Al~~a~~lL~~~~~~~~~~GkIi~F~~g~pt~----GpG~l~~~~~~~~~~~~~~~~e~~~~~~~~~fY~~l-- 318 (610)
++.+--||..|-.+|+...+.+ -.|++.+.|-||- |-|...-.+. ++|- ..-.+.+
T Consensus 532 gTNlhhaL~LA~r~l~Rh~~~~---~~il~vTDGePtAhle~~DG~~~~f~y-------p~DP--------~t~~~Tvr~ 593 (652)
T COG4867 532 GTNLHHALALAGRHLRRHAGAQ---PVVLVVTDGEPTAHLEDGDGTSVFFDY-------PPDP--------RTIAHTVRG 593 (652)
T ss_pred ccchHHHHHHHHHHHHhCcccC---ceEEEEeCCCccccccCCCCceEecCC-------CCCh--------hHHHHHHHH
Confidence 3457788999999998765432 6899999999974 3343322111 1111 1111112
Q ss_pred HHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeC
Q 007267 319 AAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYS 359 (610)
Q Consensus 319 a~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~ 359 (610)
-..|.+.|+-+.+|-...++-=..-+..+++.++|+++.-+
T Consensus 594 ~d~~~r~G~q~t~FrLg~DpgL~~Fv~qva~rv~G~vv~pd 634 (652)
T COG4867 594 FDDMARLGAQVTIFRLGSDPGLARFIDQVARRVQGRVVVPD 634 (652)
T ss_pred HHHHHhccceeeEEeecCCHhHHHHHHHHHHHhCCeEEecC
Confidence 24678899999999998887555668899999999988654
No 122
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=34.73 E-value=22 Score=36.14 Aligned_cols=30 Identities=13% Similarity=0.290 Sum_probs=19.6
Q ss_pred CCCcCcCcCeeEecCceEeCceeEEcCCCC
Q 007267 49 MLPRCENCYAYFNTYCELEQWAWTCSLCGS 78 (610)
Q Consensus 49 ~~~RC~~C~ayiNp~~~~~~~~w~C~~C~~ 78 (610)
..--|.+|++-|---..-....|.|+-|++
T Consensus 244 ~GepC~~CGt~I~k~~~~gR~t~~CP~CQ~ 273 (273)
T COG0266 244 AGEPCRRCGTPIEKIKLGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCCccCCEeEEEEEcCCcCEeCCCCCC
Confidence 345588999977322111136899999974
No 123
>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=34.73 E-value=20 Score=24.45 Aligned_cols=26 Identities=19% Similarity=0.522 Sum_probs=13.0
Q ss_pred CcCcCeeEecCceEeCceeEEcCCCC
Q 007267 53 CENCYAYFNTYCELEQWAWTCSLCGS 78 (610)
Q Consensus 53 C~~C~ayiNp~~~~~~~~w~C~~C~~ 78 (610)
|..|++..|-...--....+|..|+.
T Consensus 4 C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 4 CPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp ETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCCCCCccccccCCCCCCCccCCCCC
Confidence 56666666544433334455555554
No 124
>PF10138 vWA-TerF-like: vWA found in TerF C terminus ; InterPro: IPR019303 This entry represents the N-terminal domain of a family of proteins that confer resistance to the metalloid element tellurium and its salts.
Probab=34.09 E-value=4.5e+02 Score=25.52 Aligned_cols=42 Identities=14% Similarity=0.061 Sum_probs=26.4
Q ss_pred EEEEEEeCCCCh------hHHHHHHHHHHHHHHhCCCCcEEEEEeecc
Q 007267 123 VYVAAVDLSSSE------EFLELTRSALQAALEAVPSGALFGLATFSH 164 (610)
Q Consensus 123 ~~vFvID~s~~~------~~l~~l~~~l~~~l~~lp~~~~VglITf~~ 164 (610)
...+|||.|.++ +..+.+.+-+...=..+.++..|=+.+|++
T Consensus 3 rV~LVLD~SGSM~~~yk~G~vQ~~~Er~lalA~~~DdDG~i~v~~Fs~ 50 (200)
T PF10138_consen 3 RVYLVLDISGSMRPLYKDGTVQRVVERILALAAQFDDDGEIDVWFFST 50 (200)
T ss_pred EEEEEEeCCCCCchhhhCccHHHHHHHHHHHHhhcCCCCceEEEEeCC
Confidence 367899999986 445555555544434566766565555555
No 125
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=33.83 E-value=23 Score=31.89 Aligned_cols=33 Identities=24% Similarity=0.551 Sum_probs=22.3
Q ss_pred CcCcCcCeeEecCceEeC--ceeEEcCCCCCCCCChh
Q 007267 51 PRCENCYAYFNTYCELEQ--WAWTCSLCGSLNGLSSQ 85 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~--~~w~C~~C~~~N~~p~~ 85 (610)
++|--|+..- ....++ +.|.|+-|++.|.+...
T Consensus 1 v~C~fC~~~s--~~~~~~~~~~w~C~~C~q~N~f~e~ 35 (131)
T PF09779_consen 1 VNCWFCGQNS--KVPYDNRNSNWTCPHCEQYNGFDED 35 (131)
T ss_pred CeeccCCCCC--CCCCCCCCCeeECCCCCCccCcccc
Confidence 4677777642 222232 35999999999998765
No 126
>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=33.80 E-value=17 Score=23.37 Aligned_cols=27 Identities=19% Similarity=0.639 Sum_probs=14.0
Q ss_pred cCcCcCeeEecCceEeCceeEEcCCCC
Q 007267 52 RCENCYAYFNTYCELEQWAWTCSLCGS 78 (610)
Q Consensus 52 RC~~C~ayiNp~~~~~~~~w~C~~C~~ 78 (610)
.|.+|+.++-.-..-....+.|+-|..
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEecCCCCeECcCCcC
Confidence 689999885332221135799999964
No 127
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.60 E-value=23 Score=31.45 Aligned_cols=27 Identities=26% Similarity=0.739 Sum_probs=17.6
Q ss_pred cCcCcCeeEecCceEe-C-ceeEEcCCCCCCCC
Q 007267 52 RCENCYAYFNTYCELE-Q-WAWTCSLCGSLNGL 82 (610)
Q Consensus 52 RC~~C~ayiNp~~~~~-~-~~w~C~~C~~~N~~ 82 (610)
-|.+|++-+. .. + -+|+||+|...-++
T Consensus 91 ~CARCGGrv~----lrsNKv~wvcnlc~k~q~i 119 (169)
T KOG3799|consen 91 FCARCGGRVS----LRSNKVMWVCNLCRKQQEI 119 (169)
T ss_pred HHHhcCCeee----eccCceEEeccCCcHHHHH
Confidence 4677777432 22 2 38999999876543
No 128
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.45 E-value=21 Score=32.32 Aligned_cols=31 Identities=23% Similarity=0.485 Sum_probs=20.1
Q ss_pred CCcCcCcCeeEecCc-------------eEe----CceeEEcCCCCCC
Q 007267 50 LPRCENCYAYFNTYC-------------ELE----QWAWTCSLCGSLN 80 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~-------------~~~----~~~w~C~~C~~~N 80 (610)
..+|..|+.....-- .+. ...|.||-||..+
T Consensus 70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 358999996654431 010 3468899999775
No 129
>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]
Probab=32.44 E-value=85 Score=35.72 Aligned_cols=60 Identities=12% Similarity=0.303 Sum_probs=36.6
Q ss_pred CCCcEEEEecCcEEEEEecCCCCCCCCCCCChhHHHHHHH----HHHH--hcCCCCceEEEEeCCCCcHHHHHhhcc
Q 007267 508 SGSPIFLLDAFTTIIVFYSSTADPTLPFPPPQDCLLRTTI----NKMK--QERSITPKLIFIRGGQDDATIFENYLI 578 (610)
Q Consensus 508 s~~~iyllD~g~~~~i~~G~~v~~~~~~~~~~~~~~~~~i----~~i~--~~r~~~p~l~~~~~~~~~~~~f~~~Lv 578 (610)
..-++|+||+...+|+|+|.... ..+|..- .++- -+|+-+..+.-..+ +.....|+++..
T Consensus 765 ~sk~VyiLDc~sDiF~W~GkKs~----------RLvraAa~KL~~EL~~M~dRPdyA~V~R~~E-G~E~q~FrsKFa 830 (1255)
T KOG0444|consen 765 GSKGVYILDCNSDIFLWIGKKSN----------RLVRAAAQKLVVELHQMIDRPDYAQVYRETE-GEESQMFRSKFA 830 (1255)
T ss_pred cCCeEEEEecCCceEEEecccch----------HHHHHHHHHHHHHHHhhhcCcchhheeeccC-ccHHHHHHHhhC
Confidence 44699999999999999999854 2333222 2222 35655554443333 334567777764
No 130
>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=32.38 E-value=25 Score=32.17 Aligned_cols=31 Identities=26% Similarity=0.701 Sum_probs=21.4
Q ss_pred CCcCcCcCeeEecCceEe-------------CceeEEcCCCCCC
Q 007267 50 LPRCENCYAYFNTYCELE-------------QWAWTCSLCGSLN 80 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~-------------~~~w~C~~C~~~N 80 (610)
.-||..|.+-+-+-.+-+ +.-|+|+-|++.-
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 469999999664433210 1379999999864
No 131
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=31.91 E-value=56 Score=33.74 Aligned_cols=30 Identities=30% Similarity=0.434 Sum_probs=27.3
Q ss_pred hHHHHHHHHHHHHHHhCCCCcEEEEEeecc
Q 007267 135 EFLELTRSALQAALEAVPSGALFGLATFSH 164 (610)
Q Consensus 135 ~~l~~l~~~l~~~l~~lp~~~~VglITf~~ 164 (610)
.+|+.++..|.++.+.|.++.++++|||.+
T Consensus 210 ~El~~L~~~L~~~~~~L~~gGrl~visfHS 239 (296)
T PRK00050 210 DELEELERALEAALDLLKPGGRLAVISFHS 239 (296)
T ss_pred hhHHHHHHHHHHHHHHhcCCCEEEEEecCc
Confidence 788999999999999999999999999954
No 132
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=30.38 E-value=7.3 Score=28.76 Aligned_cols=33 Identities=18% Similarity=0.386 Sum_probs=20.6
Q ss_pred CCcCcCcCeeEecCceEeCceeEEcCCCCCCCC
Q 007267 50 LPRCENCYAYFNTYCELEQWAWTCSLCGSLNGL 82 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~ 82 (610)
-+||..|.-.+----..---.-+||-|+..|.+
T Consensus 4 tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 4 TIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred eeehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 379999976542111000125789999999975
No 133
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=30.30 E-value=25 Score=27.34 Aligned_cols=26 Identities=19% Similarity=0.452 Sum_probs=18.5
Q ss_pred CcCcCcCeeEecCceEeCceeEEcCCCCCCCCCh
Q 007267 51 PRCENCYAYFNTYCELEQWAWTCSLCGSLNGLSS 84 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~p~ 84 (610)
.-|++|+...+ .. +|+.|+..+..+.
T Consensus 6 ~AC~~C~~i~~------~~--~Cp~Cgs~~~S~~ 31 (64)
T PRK06393 6 RACKKCKRLTP------EK--TCPVHGDEKTTTE 31 (64)
T ss_pred hhHhhCCcccC------CC--cCCCCCCCcCCcC
Confidence 45999998762 22 9999999764443
No 134
>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=29.98 E-value=28 Score=29.65 Aligned_cols=27 Identities=19% Similarity=0.486 Sum_probs=21.6
Q ss_pred cCcCcCeeEecCceEeCceeEEcCCCCCCCC
Q 007267 52 RCENCYAYFNTYCELEQWAWTCSLCGSLNGL 82 (610)
Q Consensus 52 RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~ 82 (610)
.|.+|++.|.|- +..+.|+-|+.....
T Consensus 2 fC~~Cg~~l~~~----~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPK----NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccC----CCeEECcCCCCcccc
Confidence 599999999652 468999999987554
No 135
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=29.76 E-value=38 Score=25.69 Aligned_cols=25 Identities=28% Similarity=0.487 Sum_probs=19.4
Q ss_pred CCCcCcCcCeeEecCceEeCceeEEcCCCCCC
Q 007267 49 MLPRCENCYAYFNTYCELEQWAWTCSLCGSLN 80 (610)
Q Consensus 49 ~~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N 80 (610)
.+..|..|+.+.=| .-+|+.||..+
T Consensus 26 ~l~~C~~CG~~~~~-------H~vC~~CG~Y~ 50 (57)
T PRK12286 26 GLVECPNCGEPKLP-------HRVCPSCGYYK 50 (57)
T ss_pred cceECCCCCCccCC-------eEECCCCCcCC
Confidence 56789999997544 67899999655
No 136
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=29.68 E-value=32 Score=23.49 Aligned_cols=29 Identities=28% Similarity=0.575 Sum_probs=15.0
Q ss_pred CcCcCcCeeEecCc-eEe--CceeEEcCCCCC
Q 007267 51 PRCENCYAYFNTYC-ELE--QWAWTCSLCGSL 79 (610)
Q Consensus 51 ~RC~~C~ayiNp~~-~~~--~~~w~C~~C~~~ 79 (610)
++|.+|++-.+-=- ++. +++.+|+-|++.
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence 46666666544322 121 246666666654
No 137
>KOG3768 consensus DEAD box RNA helicase [General function prediction only]
Probab=29.55 E-value=90 Score=34.90 Aligned_cols=47 Identities=15% Similarity=0.284 Sum_probs=30.6
Q ss_pred cChhcchhhhccCccEEEEeCCCCCCchhHHHHHHhccCcceeeEEEEEc
Q 007267 339 TDLASLKFLSIESGGSLFLYSSTDDSTLPQDIYRMLSRPYAFNCIMRLRT 388 (610)
Q Consensus 339 ~~l~~l~~l~~~TGG~v~~~~~~~~~~l~~dl~~~l~~~~~~~a~lrvr~ 388 (610)
+|-.-+..+|+.|||+-|.. -+...+.+.|..++++ .-|..+++.-|
T Consensus 192 ~Dds~IermCevTGGRSysV--~Spr~lnqciesLvqk-vQ~gVvv~FE~ 238 (888)
T KOG3768|consen 192 IDDSVIERMCEVTGGRSYSV--VSPRQLNQCIESLVQK-VQYGVVVRFEC 238 (888)
T ss_pred CCchhhHHhhhhcCCceeee--eCHHHHHHHHHHHHHh-hccCeEEEeee
Confidence 45567899999999996655 3344566666666655 34555555544
No 138
>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=29.48 E-value=28 Score=20.21 Aligned_cols=13 Identities=23% Similarity=0.726 Sum_probs=7.8
Q ss_pred eEEcCCCCCCCCC
Q 007267 71 WTCSLCGSLNGLS 83 (610)
Q Consensus 71 w~C~~C~~~N~~p 83 (610)
|.|++|+....-.
T Consensus 1 ~~C~~C~~~~~~~ 13 (24)
T PF13894_consen 1 FQCPICGKSFRSK 13 (24)
T ss_dssp EE-SSTS-EESSH
T ss_pred CCCcCCCCcCCcH
Confidence 7899998766543
No 139
>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=28.70 E-value=25 Score=22.09 Aligned_cols=22 Identities=32% Similarity=0.537 Sum_probs=13.5
Q ss_pred cCcCcCeeEecCceEeCceeEEcCCCCC
Q 007267 52 RCENCYAYFNTYCELEQWAWTCSLCGSL 79 (610)
Q Consensus 52 RC~~C~ayiNp~~~~~~~~w~C~~C~~~ 79 (610)
+|..|++-++ ...-.|+.||+.
T Consensus 2 ~CP~C~~~V~------~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVP------ESAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCch------hhcCcCCCCCCC
Confidence 4777777552 234567778764
No 140
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=28.36 E-value=28 Score=25.54 Aligned_cols=26 Identities=35% Similarity=0.677 Sum_probs=17.2
Q ss_pred CcCcCcCeeEecCceEeC--ceeEEcCCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQ--WAWTCSLCGSLN 80 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~--~~w~C~~C~~~N 80 (610)
-+|.+|++-+ ..+. ..-.|+-|+++-
T Consensus 7 Y~C~~Cg~~~----~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 7 YKCARCGREV----ELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEhhhcCCee----ehhhccCceeCCCCCcEE
Confidence 3788888766 3232 567888888754
No 141
>COG1773 Rubredoxin [Energy production and conversion]
Probab=27.93 E-value=26 Score=26.36 Aligned_cols=14 Identities=36% Similarity=0.973 Sum_probs=10.5
Q ss_pred eEeC--ceeEEcCCCC
Q 007267 65 ELEQ--WAWTCSLCGS 78 (610)
Q Consensus 65 ~~~~--~~w~C~~C~~ 78 (610)
.|++ -.|.|+.|+.
T Consensus 29 ~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 29 PFEDLPDDWVCPECGV 44 (55)
T ss_pred chhhCCCccCCCCCCC
Confidence 3553 5899999996
No 142
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=27.32 E-value=27 Score=21.49 Aligned_cols=14 Identities=43% Similarity=0.850 Sum_probs=11.6
Q ss_pred eeEEcCCCCCCCCC
Q 007267 70 AWTCSLCGSLNGLS 83 (610)
Q Consensus 70 ~w~C~~C~~~N~~p 83 (610)
.|.|+-|...|...
T Consensus 2 ~W~C~~C~~~N~~~ 15 (26)
T smart00547 2 DWECPACTFLNFAS 15 (26)
T ss_pred cccCCCCCCcChhh
Confidence 69999999998643
No 143
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=26.12 E-value=30 Score=35.81 Aligned_cols=36 Identities=19% Similarity=0.354 Sum_probs=24.7
Q ss_pred CCcCcCcCeeEecCce--EeCceeEEcCCCCCCCCChh
Q 007267 50 LPRCENCYAYFNTYCE--LEQWAWTCSLCGSLNGLSSQ 85 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~--~~~~~w~C~~C~~~N~~p~~ 85 (610)
-.-|+.|+.==+.+-. +..-.|+|++|++.|+-...
T Consensus 220 ALIC~~C~~HNGla~~ee~~yi~F~C~~Cn~LN~~~k~ 257 (328)
T KOG2846|consen 220 ALICSQCHHHNGLARKEEYEYITFRCPHCNALNPAKKS 257 (328)
T ss_pred hhcchhhccccCcCChhhcCceEEECccccccCCCcCC
Confidence 3568888875444333 33368999999999986543
No 144
>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=25.45 E-value=54 Score=20.26 Aligned_cols=23 Identities=22% Similarity=0.609 Sum_probs=12.1
Q ss_pred CcCcCeeEecCceEeCceeEEcCCC
Q 007267 53 CENCYAYFNTYCELEQWAWTCSLCG 77 (610)
Q Consensus 53 C~~C~ayiNp~~~~~~~~w~C~~C~ 77 (610)
|.+|+.-|-|.-+ ...|.|+-||
T Consensus 1 C~sC~~~i~~r~~--~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQ--AVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCccc--CceEeCCCCC
Confidence 5566655543221 2357777776
No 145
>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=25.12 E-value=24 Score=25.88 Aligned_cols=10 Identities=30% Similarity=1.185 Sum_probs=4.0
Q ss_pred ceeEEcCCCC
Q 007267 69 WAWTCSLCGS 78 (610)
Q Consensus 69 ~~w~C~~C~~ 78 (610)
+.|.|++|++
T Consensus 40 ~~W~CPiC~~ 49 (50)
T PF02891_consen 40 PKWKCPICNK 49 (50)
T ss_dssp ---B-TTT--
T ss_pred CCeECcCCcC
Confidence 5799999986
No 146
>PRK12860 transcriptional activator FlhC; Provisional
Probab=24.79 E-value=34 Score=32.70 Aligned_cols=27 Identities=30% Similarity=0.794 Sum_probs=18.5
Q ss_pred CCCcCcCcCe-eEecCceEe-CceeEEcCCC
Q 007267 49 MLPRCENCYA-YFNTYCELE-QWAWTCSLCG 77 (610)
Q Consensus 49 ~~~RC~~C~a-yiNp~~~~~-~~~w~C~~C~ 77 (610)
...+|..|++ || -... + ...++|++|.
T Consensus 133 ~l~~C~~Cgg~fv-~~~~-e~~~~f~CplC~ 161 (189)
T PRK12860 133 QLARCCRCGGKFV-THAH-DLRHNFVCGLCQ 161 (189)
T ss_pred eeccCCCCCCCee-cccc-ccCCCCcCCCCC
Confidence 3569999987 33 1111 2 3689999999
No 147
>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=24.48 E-value=47 Score=22.03 Aligned_cols=14 Identities=21% Similarity=0.278 Sum_probs=10.0
Q ss_pred CCCCCcCcCcCeeE
Q 007267 47 GHMLPRCENCYAYF 60 (610)
Q Consensus 47 ~~~~~RC~~C~ayi 60 (610)
..+++||..|+.-|
T Consensus 14 ~~~~irC~~CG~RI 27 (32)
T PF03604_consen 14 PGDPIRCPECGHRI 27 (32)
T ss_dssp TSSTSSBSSSS-SE
T ss_pred CCCcEECCcCCCeE
Confidence 35789999998643
No 148
>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=24.44 E-value=21 Score=31.12 Aligned_cols=26 Identities=31% Similarity=0.945 Sum_probs=16.6
Q ss_pred CcCcCcCeeEecCceEeCceeEEcCCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQWAWTCSLCGSLN 80 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N 80 (610)
.||..|+.-..+ +...+.||.|+..+
T Consensus 71 ~~C~~Cg~~~~~----~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 71 ARCRDCGHEFEP----DEFDFSCPRCGSPD 96 (113)
T ss_dssp EEETTTS-EEEC----HHCCHH-SSSSSS-
T ss_pred EECCCCCCEEec----CCCCCCCcCCcCCC
Confidence 589999985443 23347799999986
No 149
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=24.35 E-value=38 Score=32.54 Aligned_cols=35 Identities=20% Similarity=0.338 Sum_probs=21.6
Q ss_pred CcCcCcCeeEecCceEe--CceeEEcCCCCCCCCChh
Q 007267 51 PRCENCYAYFNTYCELE--QWAWTCSLCGSLNGLSSQ 85 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~--~~~w~C~~C~~~N~~p~~ 85 (610)
+-|++|.-=-+.+---. -..|+|++|++.|..+.+
T Consensus 193 lIC~~C~hhngl~~~~ek~~~efiC~~Cn~~n~~~~~ 229 (251)
T COG5415 193 LICPQCHHHNGLYRLAEKPIIEFICPHCNHKNDEVKE 229 (251)
T ss_pred hccccccccccccccccccchheecccchhhcCcccc
Confidence 45666654332222111 137999999999987755
No 150
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.24 E-value=37 Score=37.91 Aligned_cols=35 Identities=17% Similarity=0.478 Sum_probs=22.9
Q ss_pred CcCcCcCee-EecCceEe------CceeEEcCCCCCCCCChh
Q 007267 51 PRCENCYAY-FNTYCELE------QWAWTCSLCGSLNGLSSQ 85 (610)
Q Consensus 51 ~RC~~C~ay-iNp~~~~~------~~~w~C~~C~~~N~~p~~ 85 (610)
+.|.+|+.. -+|.|..- .+.-+|..||..-.+|+.
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~ 255 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKT 255 (505)
T ss_pred eEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCC
Confidence 467777665 35566531 357888888888777654
No 151
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=24.11 E-value=45 Score=24.41 Aligned_cols=27 Identities=22% Similarity=0.580 Sum_probs=18.2
Q ss_pred CcCcCcCeeEecCceEeCceeEEcCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQWAWTCSLCGSL 79 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~~~w~C~~C~~~ 79 (610)
..|.+|++=. |+-.-..+|.|.=|+..
T Consensus 20 ~~CPrCG~gv--fmA~H~dR~~CGkCgyT 46 (51)
T COG1998 20 RFCPRCGPGV--FMADHKDRWACGKCGYT 46 (51)
T ss_pred ccCCCCCCcc--hhhhcCceeEeccccce
Confidence 5699999411 33333469999999864
No 152
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=23.97 E-value=31 Score=24.12 Aligned_cols=9 Identities=44% Similarity=1.198 Sum_probs=7.2
Q ss_pred CcCcCcCee
Q 007267 51 PRCENCYAY 59 (610)
Q Consensus 51 ~RC~~C~ay 59 (610)
+||.+|++|
T Consensus 2 ~kC~~CG~~ 10 (40)
T PF15288_consen 2 VKCKNCGAF 10 (40)
T ss_pred ccccccccc
Confidence 588889885
No 153
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=23.83 E-value=28 Score=35.09 Aligned_cols=34 Identities=26% Similarity=0.587 Sum_probs=26.2
Q ss_pred CCcCcCcCeeEecCce-EeCceeEEcCCCCCCCCChh
Q 007267 50 LPRCENCYAYFNTYCE-LEQWAWTCSLCGSLNGLSSQ 85 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~-~~~~~w~C~~C~~~N~~p~~ 85 (610)
-.+|..|+..+ |.+ +..+.|+|+-|++...+...
T Consensus 28 w~KCp~c~~~~--y~~eL~~n~~vcp~c~~h~ri~A~ 62 (294)
T COG0777 28 WTKCPSCGEML--YRKELESNLKVCPKCGHHMRISAR 62 (294)
T ss_pred eeECCCcccee--eHHHHHhhhhcccccCcccccCHH
Confidence 36999999977 322 33579999999999988654
No 154
>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=23.66 E-value=30 Score=28.30 Aligned_cols=16 Identities=19% Similarity=0.567 Sum_probs=7.2
Q ss_pred ceeEEcCCCCCCCCCh
Q 007267 69 WAWTCSLCGSLNGLSS 84 (610)
Q Consensus 69 ~~w~C~~C~~~N~~p~ 84 (610)
..|.|+||++.+.+.-
T Consensus 21 ~~F~CPfC~~~~sV~v 36 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSV 36 (81)
T ss_dssp S----TTT--SS-EEE
T ss_pred ceEcCCcCCCCCeEEE
Confidence 6899999999998753
No 155
>PF01795 Methyltransf_5: MraW methylase family; InterPro: IPR002903 This is a family of S-adenosyl-L-methionine-dependent methyltransferases, which are found primarily, though not exclusively, in bacteria. The Escherichia coli protein is essential and has been linked to peptidoglycan biosynthesis [, ].; GO: 0008168 methyltransferase activity; PDB: 1N2X_A 1M6Y_A 1WG8_A 3TKA_A.
Probab=23.14 E-value=57 Score=33.87 Aligned_cols=30 Identities=23% Similarity=0.301 Sum_probs=27.2
Q ss_pred hHHHHHHHHHHHHHHhCCCCcEEEEEeecc
Q 007267 135 EFLELTRSALQAALEAVPSGALFGLATFSH 164 (610)
Q Consensus 135 ~~l~~l~~~l~~~l~~lp~~~~VglITf~~ 164 (610)
.+|+.++.+|.++.+.|.++-++++|||.+
T Consensus 215 ~EL~~L~~~L~~a~~~L~~gGrl~VISFHS 244 (310)
T PF01795_consen 215 DELEELERGLEAAPDLLKPGGRLVVISFHS 244 (310)
T ss_dssp THHHHHHHHHHHHHHHEEEEEEEEEEESSH
T ss_pred cHHHHHHHHHHHHHHHhcCCcEEEEEEecc
Confidence 688999999999999999999999999954
No 156
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.13 E-value=44 Score=34.05 Aligned_cols=26 Identities=19% Similarity=0.353 Sum_probs=18.1
Q ss_pred CCcCcCcCeeEecCceEe--C-ceeEEcCCCC
Q 007267 50 LPRCENCYAYFNTYCELE--Q-WAWTCSLCGS 78 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~--~-~~w~C~~C~~ 78 (610)
.--|.+|++-| -+.. + ..|.|+-|+.
T Consensus 244 g~pCprCG~~I---~~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 244 GEPCLNCKTPI---RRVVVAGRSSHYCPHCQK 272 (272)
T ss_pred CCcCCCCCCee---EEEEECCCccEECcCCcC
Confidence 34599999866 2222 3 5899999974
No 157
>PF12773 DZR: Double zinc ribbon
Probab=22.73 E-value=42 Score=24.26 Aligned_cols=32 Identities=22% Similarity=0.326 Sum_probs=23.3
Q ss_pred CCCcCcCcCeeEecCceEeCceeEEcCCCCCCCCC
Q 007267 49 MLPRCENCYAYFNTYCELEQWAWTCSLCGSLNGLS 83 (610)
Q Consensus 49 ~~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~p 83 (610)
+-..|.+|++-+. .-+...++|+-|++.|...
T Consensus 11 ~~~fC~~CG~~l~---~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 11 DAKFCPHCGTPLP---PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cccCChhhcCChh---hccCCCCCCcCCcCCCcCC
Confidence 4468999998886 2234689999999986543
No 158
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.48 E-value=47 Score=34.40 Aligned_cols=25 Identities=24% Similarity=0.603 Sum_probs=20.5
Q ss_pred CCcCcCcCeeEecCceEeCceeEEcCCCCCCC
Q 007267 50 LPRCENCYAYFNTYCELEQWAWTCSLCGSLNG 81 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~ 81 (610)
-..|..|+. +..+.|.|+-||...+
T Consensus 309 S~~C~~cg~-------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 309 SKTCPCCGH-------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred cccccccCC-------ccceeEECCCCCCeeh
Confidence 368999998 5578999999998654
No 159
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=22.35 E-value=58 Score=27.95 Aligned_cols=32 Identities=22% Similarity=0.493 Sum_probs=25.0
Q ss_pred cCcCcCeeEecCceE----eCc--eeEEcCCCCCCCCC
Q 007267 52 RCENCYAYFNTYCEL----EQW--AWTCSLCGSLNGLS 83 (610)
Q Consensus 52 RC~~C~ayiNp~~~~----~~~--~w~C~~C~~~N~~p 83 (610)
-|++|.+++=|.... .++ .|+|.-||..--+|
T Consensus 58 ~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p 95 (105)
T COG2023 58 ICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYP 95 (105)
T ss_pred hccccCcccccCcceEEEEcCCeEEEEecCCCcEEEec
Confidence 499999998887543 333 79999999987766
No 160
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=22.13 E-value=53 Score=24.70 Aligned_cols=25 Identities=28% Similarity=0.554 Sum_probs=18.4
Q ss_pred CCCcCcCcCeeEecCceEeCceeEEcCCCCCC
Q 007267 49 MLPRCENCYAYFNTYCELEQWAWTCSLCGSLN 80 (610)
Q Consensus 49 ~~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N 80 (610)
.+..|..|+.+. ....+|+.||..+
T Consensus 25 ~l~~C~~cG~~~-------~~H~vc~~cG~Y~ 49 (55)
T TIGR01031 25 TLVVCPNCGEFK-------LPHRVCPSCGYYK 49 (55)
T ss_pred cceECCCCCCcc-------cCeeECCccCeEC
Confidence 567899999954 3457888888544
No 161
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.08 E-value=57 Score=29.19 Aligned_cols=25 Identities=20% Similarity=0.499 Sum_probs=18.9
Q ss_pred CcCcCcCeeEecCceEeCceeEEcCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQWAWTCSLCGSL 79 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~~~w~C~~C~~~ 79 (610)
-.|..|+.= ..+ -++.-.||.|++.
T Consensus 29 ~hCp~Cg~P---LF~-KdG~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGTP---LFR-KDGEVFCPVCGYR 53 (131)
T ss_pred hhCcccCCc---cee-eCCeEECCCCCce
Confidence 369999984 444 3588999999953
No 162
>KOG2487 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription; Replication, recombination and repair]
Probab=21.95 E-value=1.3e+02 Score=30.46 Aligned_cols=44 Identities=14% Similarity=0.222 Sum_probs=34.7
Q ss_pred HHHHHHHHHHcCcEEEEEEecCCCcChhcchhhhccCccEEEEeCCC
Q 007267 315 YKDLAAVAVQAGVCVDIFAITNEYTDLASLKFLSIESGGSLFLYSST 361 (610)
Q Consensus 315 Y~~la~~~~~~gisvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~~ 361 (610)
|-+.--.|.+++|.||++....+ -..|.+.|..|||.....++-
T Consensus 185 ~MNciFaAqKq~I~Idv~~l~~~---s~~LqQa~D~TGG~YL~v~~~ 228 (314)
T KOG2487|consen 185 YMNCIFAAQKQNIPIDVVSLGGD---SGFLQQACDITGGDYLHVEKP 228 (314)
T ss_pred HHHHHHHHHhcCceeEEEEecCC---chHHHHHHhhcCCeeEecCCc
Confidence 34566678899999999998776 345899999999997776654
No 163
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=21.43 E-value=36 Score=28.23 Aligned_cols=35 Identities=20% Similarity=0.266 Sum_probs=22.0
Q ss_pred CCCcCcCcCeeEecCceEeCceeEEcCCCCCCCCChh
Q 007267 49 MLPRCENCYAYFNTYCELEQWAWTCSLCGSLNGLSSQ 85 (610)
Q Consensus 49 ~~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~p~~ 85 (610)
.|+||++||--.++ .-...--.||-|+..-.-++.
T Consensus 57 ~Pa~CkkCGfef~~--~~ik~pSRCP~CKSE~Ie~pr 91 (97)
T COG3357 57 RPARCKKCGFEFRD--DKIKKPSRCPKCKSEWIEEPR 91 (97)
T ss_pred cChhhcccCccccc--cccCCcccCCcchhhcccCCc
Confidence 57899999854433 001235789999876554443
No 164
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=21.41 E-value=82 Score=24.05 Aligned_cols=14 Identities=21% Similarity=0.420 Sum_probs=9.1
Q ss_pred CCCcCcCcCeeEec
Q 007267 49 MLPRCENCYAYFNT 62 (610)
Q Consensus 49 ~~~RC~~C~ayiNp 62 (610)
.+++|..|+.-|-|
T Consensus 8 ~~~~CtSCg~~i~p 21 (61)
T COG2888 8 DPPVCTSCGREIAP 21 (61)
T ss_pred CCceeccCCCEecc
Confidence 35677777776644
No 165
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=21.38 E-value=1.4e+02 Score=27.04 Aligned_cols=66 Identities=18% Similarity=0.220 Sum_probs=35.7
Q ss_pred CCcCcCcCeeEecCceEeCceeEEcCCCCCCCCChhhhcccCCCcCccccccccEEEEecCCCCccccCCCCcEEEEEEe
Q 007267 50 LPRCENCYAYFNTYCELEQWAWTCSLCGSLNGLSSQAIARYTHPQSCAEMISSFIDLDLPLEGSEEETMQARPVYVAAVD 129 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~p~~~~~~~~~~~~~pEL~~~tvey~~p~~y~~~~~~~~~p~~vFvID 129 (610)
..||.+|+.+.=| -+-.|+-|+..+.+..-. . ..+-++..=|+-|..+... ...+|..|-+|+
T Consensus 29 g~kC~~CG~v~~P------Pr~~Cp~C~~~~~~E~ve---l---s~~G~V~t~Tv~~~~~~~~-----~~~~P~viaiV~ 91 (140)
T COG1545 29 GTKCKKCGRVYFP------PRAYCPKCGSETELEWVE---L---SGEGKVETYTVVYVKPPGF-----SLEEPYVIAIVE 91 (140)
T ss_pred EEEcCCCCeEEcC------CcccCCCCCCCCceEEEE---e---CCCeEEEEEEEEeeCCCCc-----ccCCCEEEEEEE
Confidence 3699999997533 456799999986321110 0 0011222233444444332 123677777777
Q ss_pred CCC
Q 007267 130 LSS 132 (610)
Q Consensus 130 ~s~ 132 (610)
.-.
T Consensus 92 l~~ 94 (140)
T COG1545 92 LEE 94 (140)
T ss_pred eCC
Confidence 654
No 166
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=21.35 E-value=51 Score=22.35 Aligned_cols=28 Identities=32% Similarity=0.609 Sum_probs=12.5
Q ss_pred CcCcCcCeeEecCce-Ee--CceeEEcCCCC
Q 007267 51 PRCENCYAYFNTYCE-LE--QWAWTCSLCGS 78 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~-~~--~~~w~C~~C~~ 78 (610)
++|.+|++-.+-=-. +- +.+.+|+-|++
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence 456666654332211 11 13566666654
No 167
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=21.31 E-value=67 Score=21.68 Aligned_cols=24 Identities=29% Similarity=0.415 Sum_probs=11.9
Q ss_pred CCcCcCcCeeEecCceEeCceeEEcCCCCC
Q 007267 50 LPRCENCYAYFNTYCELEQWAWTCSLCGSL 79 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~ 79 (610)
.-||..|+.+.= .-+-.|+-|+..
T Consensus 11 ~~rC~~Cg~~~~------pPr~~Cp~C~s~ 34 (37)
T PF12172_consen 11 GQRCRDCGRVQF------PPRPVCPHCGSD 34 (37)
T ss_dssp EEE-TTT--EEE------S--SEETTTT--
T ss_pred EEEcCCCCCEec------CCCcCCCCcCcc
Confidence 358999998732 234778888754
No 168
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=21.01 E-value=1e+02 Score=30.82 Aligned_cols=35 Identities=17% Similarity=0.455 Sum_probs=29.8
Q ss_pred CCCcCcCcCeeEecCceEeCceeEEcCCCCCCCCC
Q 007267 49 MLPRCENCYAYFNTYCELEQWAWTCSLCGSLNGLS 83 (610)
Q Consensus 49 ~~~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~p 83 (610)
..+.|+-|++.||---+.++...+|+-|+..+++-
T Consensus 64 p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr 98 (256)
T PF09788_consen 64 PVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIR 98 (256)
T ss_pred ceEEeecCCceecccCccceeeEECCCCCcccccc
Confidence 35699999999998877778899999999888763
No 169
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=20.97 E-value=46 Score=39.34 Aligned_cols=25 Identities=24% Similarity=0.660 Sum_probs=19.5
Q ss_pred CcCcCcCeeEecCceEeCceeEEcCCCCCCCCC
Q 007267 51 PRCENCYAYFNTYCELEQWAWTCSLCGSLNGLS 83 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~p 83 (610)
-||.+|+.| .-.++|+.||..+..+
T Consensus 626 RKCPkCG~y--------Tlk~rCP~CG~~Te~~ 650 (1095)
T TIGR00354 626 RKCPQCGKE--------SFWLKCPVCGELTEQL 650 (1095)
T ss_pred EECCCCCcc--------cccccCCCCCCccccc
Confidence 479999987 3468999999997543
No 170
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=20.89 E-value=50 Score=25.43 Aligned_cols=26 Identities=23% Similarity=0.501 Sum_probs=18.1
Q ss_pred cCcCcCeeEecCceEeCceeEEcCCCCCCCCChh
Q 007267 52 RCENCYAYFNTYCELEQWAWTCSLCGSLNGLSSQ 85 (610)
Q Consensus 52 RC~~C~ayiNp~~~~~~~~w~C~~C~~~N~~p~~ 85 (610)
-|.+|+.... .. +|+.|+...-..++
T Consensus 5 AC~~C~~i~~------~~--~CP~Cgs~~~T~~W 30 (61)
T PRK08351 5 ACRHCHYITT------ED--RCPVCGSRDLSDEW 30 (61)
T ss_pred hhhhCCcccC------CC--cCCCCcCCcccccc
Confidence 5999998762 22 69999997744433
No 171
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=20.83 E-value=55 Score=33.36 Aligned_cols=27 Identities=15% Similarity=0.415 Sum_probs=18.3
Q ss_pred CcCcCcCeeEecCceEeC-ceeEEcCCCC
Q 007267 51 PRCENCYAYFNTYCELEQ-WAWTCSLCGS 78 (610)
Q Consensus 51 ~RC~~C~ayiNp~~~~~~-~~w~C~~C~~ 78 (610)
--|.+|++-|-- ..+-+ ..|.||-|+.
T Consensus 246 ~pC~~Cg~~I~~-~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 246 EPCRRCGTPIEK-IKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCeeEE-EEECCCCcEECcCCCC
Confidence 349999987631 22223 5899999985
No 172
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=20.81 E-value=43 Score=20.85 Aligned_cols=8 Identities=50% Similarity=0.795 Sum_probs=5.0
Q ss_pred CcCcCcCe
Q 007267 51 PRCENCYA 58 (610)
Q Consensus 51 ~RC~~C~a 58 (610)
..|.+|++
T Consensus 3 ~~Cp~Cg~ 10 (26)
T PF13248_consen 3 MFCPNCGA 10 (26)
T ss_pred CCCcccCC
Confidence 45666666
No 173
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.68 E-value=47 Score=31.72 Aligned_cols=26 Identities=23% Similarity=0.687 Sum_probs=18.3
Q ss_pred CCcCcCcCeeEecCc-eE-e-CceeEEcCCCC
Q 007267 50 LPRCENCYAYFNTYC-EL-E-QWAWTCSLCGS 78 (610)
Q Consensus 50 ~~RC~~C~ayiNp~~-~~-~-~~~w~C~~C~~ 78 (610)
..+|..|++= |. .. + ...++|++|+-
T Consensus 134 l~~C~~Cgg~---fv~~~~e~~~~f~CplC~~ 162 (187)
T PRK12722 134 LSSCNCCGGH---FVTHAHDPVGSFVCGLCQP 162 (187)
T ss_pred eccCCCCCCC---eeccccccCCCCcCCCCCC
Confidence 5689999872 22 11 2 36899999987
No 174
>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=20.49 E-value=58 Score=22.80 Aligned_cols=25 Identities=24% Similarity=0.788 Sum_probs=13.5
Q ss_pred CcCcCeeEecCceEeC----ceeEEcCCCC
Q 007267 53 CENCYAYFNTYCELEQ----WAWTCSLCGS 78 (610)
Q Consensus 53 C~~C~ayiNp~~~~~~----~~w~C~~C~~ 78 (610)
|..|++ -.-|..+++ ..|+|+-|+.
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 666766 233333554 6899999943
No 175
>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=20.25 E-value=81 Score=21.68 Aligned_cols=25 Identities=32% Similarity=0.971 Sum_probs=15.9
Q ss_pred cCcCcCeeEecCceEeC----ceeEEcCCCC
Q 007267 52 RCENCYAYFNTYCELEQ----WAWTCSLCGS 78 (610)
Q Consensus 52 RC~~C~ayiNp~~~~~~----~~w~C~~C~~ 78 (610)
-|..|++ ---|- +++ ..|+|+-|+.
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 4677776 22222 543 5899999976
Done!