Query 005340
Match_columns 701
No_of_seqs 158 out of 760
Neff 8.0
Searched_HMMs 46136
Date Thu Mar 28 21:55:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005340.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005340hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00162 transport protein sec 100.0 2E-150 4E-155 1305.5 70.7 684 2-698 1-689 (761)
2 KOG1986 Vesicle coat complex C 100.0 4E-146 9E-151 1176.8 59.4 671 3-699 2-673 (745)
3 COG5047 SEC23 Vesicle coat com 100.0 2E-137 4E-142 1081.2 44.3 676 2-696 1-681 (755)
4 KOG1984 Vesicle coat complex C 100.0 1E-119 3E-124 985.5 48.6 607 6-690 283-927 (1007)
5 KOG1985 Vesicle coat complex C 100.0 9E-116 2E-120 955.5 45.7 586 6-675 166-794 (887)
6 COG5028 Vesicle coat complex C 100.0 3E-108 6E-113 889.3 47.8 601 6-697 146-807 (861)
7 PTZ00395 Sec24-related protein 100.0 2E-106 4E-111 918.6 50.2 606 6-683 648-1474(1560)
8 cd01478 Sec23-like Sec23-like: 100.0 1.5E-54 3.4E-59 445.8 28.4 264 128-395 2-267 (267)
9 cd01468 trunk_domain trunk dom 100.0 1.4E-43 3.1E-48 362.1 24.5 229 128-396 2-236 (239)
10 cd01479 Sec24-like Sec24-like: 100.0 3.7E-43 8E-48 358.8 22.8 227 128-398 2-241 (244)
11 PF04811 Sec23_trunk: Sec23/Se 100.0 5.2E-43 1.1E-47 359.4 19.5 230 128-396 2-238 (243)
12 PF08033 Sec23_BS: Sec23/Sec24 99.9 7.4E-22 1.6E-26 172.3 12.7 96 407-513 1-96 (96)
13 PF04815 Sec23_helical: Sec23/ 99.7 5E-18 1.1E-22 150.1 10.1 101 528-628 1-103 (103)
14 PF04810 zf-Sec23_Sec24: Sec23 99.6 2E-16 4.4E-21 113.4 2.1 40 57-96 1-40 (40)
15 cd01465 vWA_subgroup VWA subgr 98.6 4.5E-06 9.7E-11 80.5 17.9 159 131-384 2-163 (170)
16 cd01463 vWA_VGCC_like VWA Volt 98.5 4.8E-06 1E-10 82.2 17.5 166 128-384 12-189 (190)
17 cd01466 vWA_C3HC4_type VWA C3H 98.5 4.9E-06 1.1E-10 79.4 15.6 149 132-381 3-154 (155)
18 PRK13685 hypothetical protein; 98.5 6.8E-06 1.5E-10 88.2 18.2 161 129-383 88-275 (326)
19 cd01451 vWA_Magnesium_chelatas 98.5 1.1E-05 2.3E-10 78.9 18.0 163 132-389 3-172 (178)
20 cd01456 vWA_ywmD_type VWA ywmD 98.4 4.7E-06 1E-10 83.4 15.4 169 128-378 19-196 (206)
21 cd01453 vWA_transcription_fact 98.4 7.4E-06 1.6E-10 80.4 15.3 152 131-383 5-167 (183)
22 cd01467 vWA_BatA_type VWA BatA 98.2 6.8E-05 1.5E-09 73.1 17.0 156 130-383 3-176 (180)
23 cd01472 vWA_collagen von Wille 98.2 9.2E-05 2E-09 71.1 17.7 151 132-383 3-163 (164)
24 TIGR03436 acidobact_VWFA VWFA- 98.2 0.00025 5.3E-09 75.2 21.9 50 128-177 52-103 (296)
25 TIGR00868 hCaCC calcium-activa 98.1 0.00015 3.3E-09 85.5 21.0 154 128-383 303-462 (863)
26 cd01470 vWA_complement_factors 98.1 8.8E-05 1.9E-09 73.7 16.3 167 132-384 3-190 (198)
27 cd01452 VWA_26S_proteasome_sub 98.1 0.00012 2.5E-09 71.6 15.1 144 131-374 5-161 (187)
28 cd01461 vWA_interalpha_trypsin 98.1 0.00027 5.8E-09 68.1 17.5 159 129-384 2-162 (171)
29 cd01480 vWA_collagen_alpha_1-V 98.0 0.00017 3.7E-09 70.9 16.0 157 131-385 4-173 (186)
30 PF13519 VWA_2: von Willebrand 98.0 0.0001 2.2E-09 70.6 13.0 150 132-382 2-159 (172)
31 TIGR03788 marine_srt_targ mari 97.9 0.0082 1.8E-07 70.0 30.1 187 128-415 270-458 (596)
32 PF13768 VWA_3: von Willebrand 97.9 0.0003 6.4E-09 66.9 15.0 151 132-379 3-154 (155)
33 cd01469 vWA_integrins_alpha_su 97.9 0.00058 1.3E-08 66.6 16.6 156 132-385 3-172 (177)
34 cd01474 vWA_ATR ATR (Anthrax T 97.8 0.0004 8.6E-09 68.2 14.7 156 129-385 4-168 (185)
35 cd01482 vWA_collagen_alphaI-XI 97.8 0.0015 3.2E-08 62.8 17.6 45 132-176 3-52 (164)
36 cd01475 vWA_Matrilin VWA_Matri 97.8 0.00091 2E-08 67.8 16.9 155 130-385 3-170 (224)
37 cd01450 vWFA_subfamily_ECM Von 97.7 0.0018 3.9E-08 61.2 15.9 145 132-375 3-156 (161)
38 cd01471 vWA_micronemal_protein 97.5 0.003 6.4E-08 61.9 15.7 45 132-176 3-53 (186)
39 cd01477 vWA_F09G8-8_type VWA F 97.5 0.0038 8.2E-08 61.7 16.2 49 129-177 19-78 (193)
40 cd01481 vWA_collagen_alpha3-VI 97.5 0.005 1.1E-07 59.3 16.6 45 132-176 3-52 (165)
41 smart00327 VWA von Willebrand 97.5 0.009 2E-07 57.2 18.0 154 130-380 2-164 (177)
42 PF00092 VWA: von Willebrand f 97.5 0.0031 6.7E-08 60.8 14.7 156 132-386 2-170 (178)
43 TIGR02031 BchD-ChlD magnesium 97.4 0.0059 1.3E-07 70.7 18.8 176 128-387 406-586 (589)
44 PRK13406 bchD magnesium chelat 97.4 0.0085 1.8E-07 69.0 19.1 172 128-390 400-576 (584)
45 cd01476 VWA_integrin_invertebr 97.4 0.0089 1.9E-07 57.1 16.1 41 132-172 3-47 (163)
46 PF00626 Gelsolin: Gelsolin re 97.3 0.00016 3.4E-09 59.9 3.0 34 640-673 4-37 (76)
47 TIGR02442 Cob-chelat-sub cobal 97.2 0.0065 1.4E-07 71.2 15.7 161 128-381 464-632 (633)
48 COG1240 ChlD Mg-chelatase subu 97.2 0.015 3.3E-07 58.7 15.4 169 128-389 77-252 (261)
49 PF04056 Ssl1: Ssl1-like; Int 97.1 0.012 2.6E-07 57.7 13.5 95 267-397 78-173 (193)
50 PTZ00441 sporozoite surface pr 97.0 0.042 9.1E-07 62.0 19.1 165 128-386 41-218 (576)
51 cd00198 vWFA Von Willebrand fa 97.0 0.033 7E-07 51.9 16.1 148 131-374 2-155 (161)
52 cd01473 vWA_CTRP CTRP for CS 97.0 0.029 6.3E-07 55.4 16.0 149 132-373 3-161 (192)
53 cd01458 vWA_ku Ku70/Ku80 N-ter 96.4 0.23 4.9E-06 50.1 17.6 69 267-360 104-173 (218)
54 cd01454 vWA_norD_type norD typ 96.3 0.17 3.7E-06 48.9 15.7 43 131-173 2-48 (174)
55 cd01462 VWA_YIEM_type VWA YIEM 95.8 0.3 6.5E-06 45.9 14.5 43 132-174 3-48 (152)
56 KOG2884 26S proteasome regulat 95.6 0.55 1.2E-05 46.0 14.9 79 268-376 84-163 (259)
57 smart00262 GEL Gelsolin homolo 95.3 0.016 3.4E-07 49.6 3.4 32 643-674 15-46 (90)
58 cd01464 vWA_subfamily VWA subf 93.8 0.089 1.9E-06 51.0 5.1 45 132-176 6-58 (176)
59 TIGR00578 ku70 ATP-dependent D 93.8 1.5 3.2E-05 51.0 15.7 73 269-366 117-191 (584)
60 COG4245 TerY Uncharacterized p 93.1 0.15 3.3E-06 48.9 5.1 48 129-177 4-59 (207)
61 cd01460 vWA_midasin VWA_Midasi 92.2 11 0.00023 39.3 17.6 46 128-175 59-111 (266)
62 COG5148 RPN10 26S proteasome r 90.1 9.9 0.00022 36.6 13.5 59 269-358 85-145 (243)
63 KOG0443 Actin regulatory prote 89.7 0.34 7.4E-06 56.0 4.2 54 625-678 615-673 (827)
64 PF03850 Tfb4: Transcription f 86.9 28 0.0006 36.5 15.9 86 269-384 116-208 (276)
65 smart00187 INB Integrin beta s 85.9 61 0.0013 35.8 22.2 279 129-471 99-390 (423)
66 KOG0444 Cytoskeletal regulator 85.3 0.71 1.5E-05 52.2 3.4 43 631-673 623-668 (1255)
67 KOG2807 RNA polymerase II tran 84.4 20 0.00042 37.7 12.8 89 268-391 142-230 (378)
68 TIGR00627 tfb4 transcription f 80.9 18 0.0004 37.7 11.5 95 267-393 117-217 (279)
69 PF10058 DUF2296: Predicted in 79.8 1.3 2.7E-05 34.1 1.9 33 58-90 22-54 (54)
70 TIGR01053 LSD1 zinc finger dom 78.8 2.1 4.5E-05 28.9 2.4 30 59-92 2-31 (31)
71 PRK00398 rpoP DNA-directed RNA 77.3 1.8 3.9E-05 31.9 2.1 30 58-91 3-32 (46)
72 PF00362 Integrin_beta: Integr 76.8 1.3E+02 0.0029 33.6 20.9 281 128-472 101-394 (426)
73 KOG0444 Cytoskeletal regulator 75.4 2.9 6.4E-05 47.6 3.9 69 625-693 729-816 (1255)
74 PF09967 DUF2201: VWA-like dom 74.8 7.4 0.00016 35.5 5.8 42 133-176 2-45 (126)
75 KOG0443 Actin regulatory prote 72.0 3.3 7.1E-05 48.3 3.3 46 629-674 254-306 (827)
76 smart00661 RPOL9 RNA polymeras 66.0 4.1 8.9E-05 30.6 1.8 33 60-94 2-34 (52)
77 PF03731 Ku_N: Ku70/Ku80 N-ter 64.8 11 0.00023 38.0 5.1 42 131-172 1-53 (224)
78 KOG2487 RNA polymerase II tran 59.1 2.2E+02 0.0049 29.4 13.2 43 340-385 187-229 (314)
79 PF09723 Zn-ribbon_8: Zinc rib 57.8 4.9 0.00011 29.0 0.9 30 59-89 6-35 (42)
80 PF08271 TF_Zn_Ribbon: TFIIB z 56.9 13 0.00028 26.9 3.0 27 60-89 2-28 (43)
81 PF13719 zinc_ribbon_5: zinc-r 55.8 7.4 0.00016 27.3 1.5 32 59-90 3-35 (37)
82 cd00350 rubredoxin_like Rubred 55.7 7.9 0.00017 26.4 1.5 23 60-88 3-25 (33)
83 COG2888 Predicted Zn-ribbon RN 55.1 4.7 0.0001 31.2 0.4 23 57-89 37-59 (61)
84 PRK03954 ribonuclease P protei 53.7 8.5 0.00018 34.8 1.9 34 60-93 66-106 (121)
85 cd01457 vWA_ORF176_type VWA OR 52.4 17 0.00036 35.8 4.0 44 130-173 3-57 (199)
86 cd00730 rubredoxin Rubredoxin; 50.4 8.1 0.00018 29.2 1.0 30 60-89 3-43 (50)
87 KOG3799 Rab3 effector RIM1 and 50.3 7.9 0.00017 35.0 1.1 32 57-92 88-119 (169)
88 TIGR02605 CxxC_CxxC_SSSS putat 49.6 8.4 0.00018 29.0 1.0 31 59-90 6-36 (52)
89 PRK14890 putative Zn-ribbon RN 49.4 7 0.00015 30.4 0.5 22 58-89 36-57 (59)
90 PF14803 Nudix_N_2: Nudix N-te 49.3 4.4 9.5E-05 27.9 -0.5 30 60-89 2-31 (34)
91 PF13240 zinc_ribbon_2: zinc-r 48.3 8.7 0.00019 23.9 0.7 21 60-88 1-21 (23)
92 PRK12380 hydrogenase nickel in 48.2 11 0.00023 33.8 1.6 27 58-90 70-96 (113)
93 PF10122 Mu-like_Com: Mu-like 47.6 9.5 0.00021 28.7 1.0 34 58-93 4-37 (51)
94 TIGR00100 hypA hydrogenase nic 47.2 12 0.00025 33.7 1.7 27 58-90 70-96 (115)
95 PF09082 DUF1922: Domain of un 46.7 9.6 0.00021 30.6 0.9 30 58-93 3-32 (68)
96 PF13717 zinc_ribbon_4: zinc-r 45.7 14 0.00029 25.8 1.5 31 59-89 3-34 (36)
97 PRK00432 30S ribosomal protein 45.4 12 0.00026 28.2 1.3 25 59-89 21-46 (50)
98 PRK10997 yieM hypothetical pro 45.1 31 0.00067 39.0 5.0 50 131-180 325-377 (487)
99 COG1996 RPC10 DNA-directed RNA 44.8 12 0.00025 28.1 1.1 28 59-90 7-34 (49)
100 PF11781 RRN7: RNA polymerase 44.7 16 0.00035 25.5 1.7 27 58-89 8-34 (36)
101 COG1198 PriA Primosomal protei 43.6 82 0.0018 37.6 8.3 108 58-180 444-571 (730)
102 COG1096 Predicted RNA-binding 43.4 13 0.00029 36.0 1.5 25 59-89 150-174 (188)
103 smart00834 CxxC_CXXC_SSSS Puta 42.7 12 0.00026 26.5 0.9 29 59-88 6-34 (41)
104 PF08792 A2L_zn_ribbon: A2L zi 41.1 29 0.00064 23.7 2.5 29 58-90 3-31 (33)
105 PF05762 VWA_CoxE: VWA domain 40.9 47 0.001 33.4 5.2 44 128-174 55-100 (222)
106 PRK03681 hypA hydrogenase nick 39.7 18 0.00039 32.5 1.7 28 58-90 70-97 (114)
107 cd01455 vWA_F11C1-5a_type Von 39.5 2.7E+02 0.0059 27.4 10.0 97 245-383 75-174 (191)
108 PF07282 OrfB_Zn_ribbon: Putat 39.2 22 0.00047 28.5 2.0 28 59-90 29-56 (69)
109 COG5415 Predicted integral mem 37.9 23 0.0005 34.7 2.2 39 57-95 191-229 (251)
110 PF12773 DZR: Double zinc ribb 37.7 20 0.00042 26.7 1.4 32 57-93 11-42 (50)
111 PF02318 FYVE_2: FYVE-type zin 37.3 16 0.00034 33.0 1.0 32 58-89 71-103 (118)
112 PF12760 Zn_Tnp_IS1595: Transp 37.2 40 0.00087 24.7 3.0 27 59-88 19-45 (46)
113 COG2425 Uncharacterized protei 37.0 1.8E+02 0.004 32.4 9.3 49 131-179 274-325 (437)
114 PF09779 Ima1_N: Ima1 N-termin 36.7 25 0.00054 32.4 2.2 34 59-94 1-34 (131)
115 smart00659 RPOLCX RNA polymera 36.1 30 0.00065 25.3 2.1 26 60-90 4-29 (44)
116 smart00401 ZnF_GATA zinc finge 35.8 22 0.00048 27.0 1.4 32 58-89 3-34 (52)
117 COG2051 RPS27A Ribosomal prote 35.8 29 0.00064 27.6 2.1 34 57-93 18-51 (67)
118 PF00301 Rubredoxin: Rubredoxi 35.7 12 0.00025 27.9 -0.1 30 60-89 3-43 (47)
119 PF06943 zf-LSD1: LSD1 zinc fi 34.9 37 0.00081 21.7 2.1 24 61-88 1-24 (25)
120 PF10571 UPF0547: Uncharacteri 34.5 20 0.00043 23.1 0.8 23 60-90 2-24 (26)
121 PF07754 DUF1610: Domain of un 34.5 29 0.00063 21.9 1.5 24 61-88 1-24 (24)
122 PRK06393 rpoE DNA-directed RNA 34.2 23 0.0005 28.1 1.3 25 59-93 6-30 (64)
123 PRK00564 hypA hydrogenase nick 34.0 17 0.00036 32.8 0.6 30 57-91 70-99 (117)
124 COG3357 Predicted transcriptio 33.7 21 0.00045 30.3 1.0 36 57-96 57-92 (97)
125 TIGR02098 MJ0042_CXXC MJ0042 f 33.7 25 0.00053 24.5 1.3 31 59-89 3-34 (38)
126 smart00132 LIM Zinc-binding do 33.6 34 0.00073 23.3 2.0 29 60-88 1-35 (39)
127 PHA00626 hypothetical protein 32.6 41 0.00089 25.9 2.3 14 78-91 21-34 (59)
128 TIGR00416 sms DNA repair prote 32.1 25 0.00055 39.6 1.8 29 58-94 7-35 (454)
129 TIGR00686 phnA alkylphosphonat 31.3 40 0.00086 29.7 2.4 28 58-90 2-29 (109)
130 PF08274 PhnA_Zn_Ribbon: PhnA 31.0 23 0.0005 23.7 0.7 27 58-89 2-28 (30)
131 TIGR00311 aIF-2beta translatio 30.8 49 0.0011 30.5 3.1 32 58-92 97-130 (133)
132 PRK12286 rpmF 50S ribosomal pr 30.8 43 0.00093 26.0 2.3 26 57-91 26-51 (57)
133 TIGR01384 TFS_arch transcripti 30.6 33 0.00072 30.0 1.9 27 60-92 2-28 (104)
134 PRK11823 DNA repair protein Ra 30.4 27 0.00058 39.3 1.6 29 58-94 7-35 (446)
135 KOG2353 L-type voltage-depende 30.4 65 0.0014 40.2 4.9 50 128-177 224-275 (1104)
136 PRK00762 hypA hydrogenase nick 30.0 24 0.00052 32.1 0.9 33 58-91 70-103 (124)
137 cd01121 Sms Sms (bacterial rad 29.7 29 0.00062 38.0 1.6 27 60-94 2-28 (372)
138 COG1998 RPS31 Ribosomal protei 29.6 31 0.00068 25.8 1.2 25 59-89 20-46 (51)
139 PF01927 Mut7-C: Mut7-C RNAse 29.6 34 0.00073 32.1 1.9 33 58-90 91-134 (147)
140 PF00641 zf-RanBP: Zn-finger i 28.9 19 0.00041 23.8 0.0 14 79-92 3-16 (30)
141 cd01464 vWA_subfamily VWA subf 28.7 1.1E+02 0.0024 29.2 5.4 76 267-373 77-160 (176)
142 COG5242 TFB4 RNA polymerase II 28.7 1.1E+02 0.0024 30.5 5.2 86 268-384 128-215 (296)
143 PRK08351 DNA-directed RNA poly 28.6 36 0.00079 26.8 1.6 23 60-92 5-27 (61)
144 PRK03824 hypA hydrogenase nick 28.2 36 0.00077 31.5 1.7 34 57-90 69-117 (135)
145 COG0275 Predicted S-adenosylme 27.3 74 0.0016 33.5 4.0 27 144-170 219-245 (314)
146 PF01155 HypA: Hydrogenase exp 27.1 17 0.00036 32.5 -0.6 27 58-90 70-96 (113)
147 KOG2846 Predicted membrane pro 27.0 32 0.00069 36.4 1.3 36 58-93 220-255 (328)
148 COG1592 Rubrerythrin [Energy p 27.0 34 0.00074 32.8 1.4 15 77-91 131-145 (166)
149 PF13894 zf-C2H2_4: C2H2-type 26.5 35 0.00076 20.3 1.0 11 81-91 1-11 (24)
150 PF00320 GATA: GATA zinc finge 26.4 21 0.00046 24.8 -0.1 28 61-88 1-28 (36)
151 cd00729 rubredoxin_SM Rubredox 25.9 37 0.0008 23.3 1.0 11 80-90 2-12 (34)
152 PRK12722 transcriptional activ 25.6 32 0.0007 33.6 1.0 29 57-88 133-162 (187)
153 PRK10220 hypothetical protein; 25.1 68 0.0015 28.3 2.7 29 58-91 3-31 (111)
154 COG2956 Predicted N-acetylgluc 24.6 39 0.00085 35.8 1.4 29 57-93 353-381 (389)
155 smart00778 Prim_Zn_Ribbon Zinc 24.4 64 0.0014 22.7 2.0 27 60-88 5-33 (37)
156 PF14353 CpXC: CpXC protein 22.9 75 0.0016 28.8 2.9 35 59-93 2-51 (128)
157 PF05280 FlhC: Flagellar trans 22.8 33 0.00071 33.3 0.5 29 57-88 133-162 (175)
158 PF02891 zf-MIZ: MIZ/SP-RING z 22.6 31 0.00067 25.9 0.2 13 76-88 37-49 (50)
159 cd02342 ZZ_UBA_plant Zinc fing 22.4 65 0.0014 23.5 1.8 23 59-88 1-23 (43)
160 PF06707 DUF1194: Protein of u 22.3 7.9E+02 0.017 24.5 10.0 99 268-397 94-198 (205)
161 PF05907 DUF866: Eukaryotic pr 22.1 48 0.001 31.7 1.4 35 58-92 30-76 (161)
162 PF09297 zf-NADH-PPase: NADH p 22.0 84 0.0018 21.0 2.2 26 60-89 5-30 (32)
163 KOG0445 Actin regulatory prote 22.0 79 0.0017 36.6 3.2 29 645-673 362-390 (919)
164 smart00547 ZnF_RBZ Zinc finger 21.6 40 0.00087 21.2 0.6 14 80-93 2-15 (26)
165 PF02905 EBV-NA1: Epstein Barr 21.5 1E+02 0.0022 27.8 3.2 33 143-175 110-145 (146)
166 PF04032 Rpr2: RNAse P Rpr2/Rp 21.3 50 0.0011 27.5 1.2 30 59-88 47-85 (85)
167 PF15288 zf-CCHC_6: Zinc knuck 21.2 37 0.00081 24.3 0.4 9 59-67 2-10 (40)
168 PF05129 Elf1: Transcription e 21.1 35 0.00077 28.6 0.3 15 79-93 21-35 (81)
169 COG0675 Transposase and inacti 21.0 53 0.0011 34.9 1.7 25 58-91 309-333 (364)
170 PF03604 DNA_RNApol_7kD: DNA d 20.9 35 0.00076 23.2 0.2 12 55-66 14-25 (32)
171 COG1645 Uncharacterized Zn-fin 20.6 71 0.0015 29.3 2.1 25 59-89 29-53 (131)
172 PF06827 zf-FPG_IleRS: Zinc fi 20.6 67 0.0015 21.1 1.5 27 60-88 3-29 (30)
173 PRK12860 transcriptional activ 20.1 51 0.0011 32.3 1.2 28 57-87 133-161 (189)
174 TIGR00006 S-adenosyl-methyltra 20.1 1.1E+02 0.0024 32.5 3.8 27 144-170 215-241 (305)
175 COG1066 Sms Predicted ATP-depe 20.0 51 0.0011 36.2 1.3 27 59-95 8-36 (456)
No 1
>PLN00162 transport protein sec23; Provisional
Probab=100.00 E-value=1.9e-150 Score=1305.48 Aligned_cols=684 Identities=71% Similarity=1.191 Sum_probs=633.1
Q ss_pred CCcccccCCCeeeecCCCCCCCHHHhhcCCCCeEEEEccCCCCCCCCCCCCCCCCCccccCCCCceecCceEEEcCCceE
Q 005340 2 TEFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRTCRSILNPFSIVDFAAKIW 81 (701)
Q Consensus 2 ~~~~~~~~~~~iR~t~~~iP~~~~~~~~~~iPlg~~v~P~~~~~~~~~~vp~~~~~p~RC~~C~ayiNp~~~~~~~g~~w 81 (701)
|||++.|+.++||+|||+||.++.++++++|||||+|+||++.+ ++|+++++|+||++|+||+||||+|+.+|++|
T Consensus 1 ~~~~~~e~~~gvR~s~n~~P~t~~~~~~~~iPlg~v~tPl~~~~----~vp~v~~~pvRC~~CraylNPf~~~d~~~~~W 76 (761)
T PLN00162 1 MDFAELEAIDGVRMSWNVWPSSKIEASKCVIPLAALYTPLKPLP----ELPVLPYDPLRCRTCRAVLNPYCRVDFQAKIW 76 (761)
T ss_pred CchhhhcccCceEeeeecCCCCHHHHhcCCCCeEEEEecCCcCC----CCCcCCCCCCccCCCcCEECCceEEecCCCEE
Confidence 78999999999999999999999999999999999999999875 69999999999999999999999999999999
Q ss_pred EeCCCCCCCCCCccccCCCCCCCCccccCCCccEEEeCC---CCCCCCCCCcEEEEEEECCCchhhHHHHHHHHHHHhhc
Q 005340 82 ICPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPP---GPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDL 158 (701)
Q Consensus 82 ~C~~C~~~N~~p~~y~~~~~~~~~pEL~~~~~tvey~~~---~~~~~~~~~p~~vFvIDvs~~~~~l~~~~~~l~~~l~~ 158 (701)
+||||++.|.+|++|..+++.++||||+|+++||||++| +.++ .||+|+||||+|..+++++.++++|+++|+.
T Consensus 77 ~C~~C~~~N~~P~~Y~~~~~~~~p~EL~p~~~TvEY~~p~~~~~~~---~pp~fvFvID~s~~~~~l~~lk~sl~~~L~~ 153 (761)
T PLN00162 77 ICPFCFQRNHFPPHYSSISETNLPAELFPQYTTVEYTLPPGSGGAP---SPPVFVFVVDTCMIEEELGALKSALLQAIAL 153 (761)
T ss_pred EccCCCCCCCCchHhcccCccCCChhhcCCceeEEEECCCCCCCCC---CCcEEEEEEecchhHHHHHHHHHHHHHHHHh
Confidence 999999999999999988888999999999999999999 5555 7999999999999999999999999999999
Q ss_pred CCCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhHhhcccCCCCCCCccccCccCCCCccc-cccee
Q 005340 159 LPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDT-IARFL 237 (701)
Q Consensus 159 lp~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p-~~~~l 237 (701)
||++++|||||||+.||||+|+ .. .+|+++||+|+|+|+.+|+++++++.+....+... .++...+..+.| .++||
T Consensus 154 LP~~a~VGlITF~s~V~~~~L~-~~-~~~~~~Vf~g~k~~t~~~l~~~l~l~~~~~~~~~~-~~~~~~~~~~~p~~~~fL 230 (761)
T PLN00162 154 LPENALVGLITFGTHVHVHELG-FS-ECSKSYVFRGNKEVSKDQILEQLGLGGKKRRPAGG-GIAGARDGLSSSGVNRFL 230 (761)
T ss_pred CCCCCEEEEEEECCEEEEEEcC-CC-CCcceEEecCCccCCHHHHHHHhcccccccccccc-ccccccccccCCCcccee
Confidence 9999999999999999999999 66 68999999999999999999998775411101000 000000112344 58999
Q ss_pred EehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCc
Q 005340 238 VPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPI 317 (701)
Q Consensus 238 ~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~ 317 (701)
+|++||+..|+++|++|+++.|++++++|+.||+|+||++|..+|+.+.++.||||++|++||||.|||+|+.++.++++
T Consensus 231 vpl~e~~~~i~~lLe~L~~~~~~~~~~~rp~r~tG~AL~vA~~lL~~~~~~~gGrI~~F~sgppT~GpG~v~~r~~~~~~ 310 (761)
T PLN00162 231 LPASECEFTLNSALEELQKDPWPVPPGHRPARCTGAALSVAAGLLGACVPGTGARIMAFVGGPCTEGPGAIVSKDLSEPI 310 (761)
T ss_pred EEHHHHHHHHHHHHHhhhccccccCCCCCCCccHHHHHHHHHHHHhhccCCCceEEEEEeCCCCCCCCceeecccccccc
Confidence 99999999999999999998898888999999999999999999998888899999999999999999999999999999
Q ss_pred CCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhhhccccceEEEeCCCCchhhHHHHHHHh
Q 005340 318 RSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF 397 (701)
Q Consensus 318 ~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l 397 (701)
|+|+|++++++++++++.+||++||++|+++||+||+|+++.+|+||+||+.|++.|||.+++|++|+.+.|+++|+|+|
T Consensus 311 rsh~di~k~~~~~~~~a~~fY~~la~~~~~~gisvDlF~~s~dqvglaem~~l~~~TGG~v~~~~sF~~~~f~~~l~r~~ 390 (761)
T PLN00162 311 RSHKDLDKDAAPYYKKAVKFYEGLAKQLVAQGHVLDVFACSLDQVGVAEMKVAVERTGGLVVLAESFGHSVFKDSLRRVF 390 (761)
T ss_pred cCccccccchhhhcchHHHHHHHHHHHHHHcCceEEEEEccccccCHHHHhhhHhhcCcEEEEeCCcChHHHHHHHHHHh
Confidence 99999999888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred c-cCccCCcceeeEEEEEEecCCceEEEEEcCCcccCCCCCCcccccccCCCCCceEEecCCCCcEEEEEEEEecCCCCc
Q 005340 398 H-SGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPD 476 (701)
Q Consensus 398 ~-~~~~~~~~~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~ 476 (701)
+ +..+++.+||+|+||||||+|++|.+++||+++..++++++||+++|+|+++.|+++++++++||+|+|++++....
T Consensus 391 ~r~~~~~~~~gf~a~~~VrtS~glkv~g~~G~~~s~~~~~~~vsd~~iG~g~T~~w~l~~l~~~~t~av~f~~~~~~~~- 469 (761)
T PLN00162 391 ERDGEGSLGLSFNGTFEVNCSKDVKVQGAIGPCASLEKKGPSVSDTEIGEGGTTAWKLCGLDKKTSLAVFFEVANSGQS- 469 (761)
T ss_pred cccccccccccceeEEEEEecCCeEEeeeEcCcccccccCCccccccccCCCCceeeecCcCcCCEEEEEEEEcccccc-
Confidence 4 44445678999999999999999999999999887888889999999999999999999999999999999987510
Q ss_pred ccccCCCCeEEEEEEEEEEecCCcEEEEEEecceecccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCCchhHHHHHH
Q 005340 477 ATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKMEIEAEFDPIRWLD 556 (701)
Q Consensus 477 ~~~~~~~~~~~iQ~al~Yt~~~G~r~iRV~T~~l~vt~~~~~~~~~~~~~D~~a~~~~lak~~~~~~~~~~~~~~~~~l~ 556 (701)
.++ .+...+||||+++||+.+|+|||||||++++++.. +++.+++++||+||++++|||+++.++.+++..|+++||+
T Consensus 470 ~~~-~~~~~~~iQ~a~lYt~~~G~rRiRV~T~~~~~~~~-~~~~~v~~~fDqeA~a~llaR~av~k~~~~~~~d~~r~ld 547 (761)
T PLN00162 470 NPQ-PPGQQFFLQFLTRYQHSNGQTRLRVTTVTRRWVEG-SSSEELVAGFDQEAAAVVMARLASHKMETEEEFDATRWLD 547 (761)
T ss_pred CCC-CCCceEEEEEEEEEEcCCCCEEEEEEccccCccCC-CCHHHHHHhcCHHHHHHHHHHHHHHHHhhCCHHHHHHHHH
Confidence 001 23567999999999999999999999999997642 3688999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccccCCCCccccCccccchHHHHHHhhcccCcCCCCCChhHHHHHHHHHccCCHHHHHHhhcccceecc
Q 005340 557 KALIHMCSRFGDYQKDSPSSFSLSPRFSIFPQFMFHLRRSQFVQVFNNSPDETAYFRMILNRENVTNSVVMIQPSLISYS 636 (701)
Q Consensus 557 ~~lv~~~~~~~~y~~~~~~~l~lp~~l~~lP~~~~~l~ks~~l~~~~~s~D~r~~~~~~l~~~~~~~~~~~iyP~l~~~~ 636 (701)
++|+++|.+|+.|||+++++|+||++|++||+|||||+||++|+++|+|||||+++||.++++++++++.||||+|++||
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCcccccccccccCCeEEEEeCCcEEEEEECCChhHHHHcCCCCCCccHHHHHHhhhhc
Q 005340 637 FHSGPEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYHNQPEHQVVNFVVDFDF 698 (701)
Q Consensus 637 ~~~~p~~~~ls~~~l~~d~iyLlD~~~~i~i~~G~~v~~~~~~~~~~~~e~~~~~~~~~~~~ 698 (701)
+++.|+|++||+++|.+|+|||||+|++|+||+|++|++|+|+|||++|||++||++||+..
T Consensus 628 ~~~~P~pv~Ld~~si~~d~ilLLD~~f~vvi~~G~~ia~w~~~~~~~~~~~~~~~~~l~~p~ 689 (761)
T PLN00162 628 FNGPPEPVLLDVASIAADRILLLDSYFSVVIFHGSTIAQWRKAGYHNQPEHEAFAQLLEAPQ 689 (761)
T ss_pred CCCCCcceecchhhccCCceEEEeCCCEEEEEecCcccchhhcCCCCCcchhhHHHHHHhHH
Confidence 99999999999999999999999999999999999999999999999999999999998753
No 2
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.2e-146 Score=1176.80 Aligned_cols=671 Identities=58% Similarity=1.021 Sum_probs=638.7
Q ss_pred CcccccCCCeeeecCCCCCCCHHHhhcCCCCeEEEEccCCCCCCCCCCCCCCCCCccccCCCCceecCceEEEcCCceEE
Q 005340 3 EFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRTCRSILNPFSIVDFAAKIWI 82 (701)
Q Consensus 3 ~~~~~~~~~~iR~t~~~iP~~~~~~~~~~iPlg~~v~P~~~~~~~~~~vp~~~~~p~RC~~C~ayiNp~~~~~~~g~~w~ 82 (701)
.++++|+.++||+|||+||.++....++.+|++++|+||.+.. .+|+++|+|+||++|+||+||||.++.+.+.|.
T Consensus 2 ~~~~~e~~dGvR~twnvwPs~~~~~~~~vvPla~lytPl~e~~----~~~~~~y~P~~C~~C~AvlNPyc~vd~~a~~W~ 77 (745)
T KOG1986|consen 2 FIEDIEEIDGVRFTWNVWPSTRAEASRTVVPLACLYTPLKERP----DLPPIQYDPLRCSKCGAVLNPYCSVDFRAKSWI 77 (745)
T ss_pred cccccccCCCcccccccCCCcccccccccccHHHhccccccCC----CCCccCCCCchhccchhhcCcceeecccCceEe
Confidence 3668999999999999999999999999999999999999865 578899999999999999999999999999999
Q ss_pred eCCCCCCCCCCccccCCCCCCCCccccCCCccEEEeCCCCCCCCCCCcEEEEEEECCCchhhHHHHHHHHHHHhhcCCCC
Q 005340 83 CPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPGPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLPDN 162 (701)
Q Consensus 83 C~~C~~~N~~p~~y~~~~~~~~~pEL~~~~~tvey~~~~~~~~~~~~p~~vFvIDvs~~~~~l~~~~~~l~~~l~~lp~~ 162 (701)
|+||+++|.+|++|..+++.|.++||+|+++||||.++++.. .||+|+||||+|+.+++|+.++++|+.+|+.||++
T Consensus 78 CpfC~qrN~~p~~Y~~is~~n~P~el~Pq~stvEy~l~~~~~---~ppvf~fVvDtc~~eeeL~~LkssL~~~l~lLP~~ 154 (745)
T KOG1986|consen 78 CPFCNQRNPFPPHYSGISENNLPPELLPQYSTVEYTLSPGRV---SPPVFVFVVDTCMDEEELQALKSSLKQSLSLLPEN 154 (745)
T ss_pred ccccccCCCCChhhcccCccCCChhhcCCcceeEEecCCCCC---CCceEEEEEeeccChHHHHHHHHHHHHHHhhCCCc
Confidence 999999999999999999999999999999999999997666 79999999999999999999999999999999999
Q ss_pred cEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhHhhcccCCCCCCCccccCccCCCCcccccceeEehhh
Q 005340 163 SLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFD 242 (701)
Q Consensus 163 ~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~ 242 (701)
++||||||++.||+|+++ .. .++++|||+|+|||+.++++++++.+.. .+.+ . ....+..+||.|+++
T Consensus 155 alvGlItfg~~v~v~el~-~~-~~sk~~VF~G~ke~s~~q~~~~L~~~~~-~~~~------~---~~~~~~~rFL~P~~~ 222 (745)
T KOG1986|consen 155 ALVGLITFGTMVQVHELG-FE-ECSKSYVFSGNKEYSAKQLLDLLGLSGG-AGKG------S---ENQSASNRFLLPAQE 222 (745)
T ss_pred ceEEEEEecceEEEEEcC-CC-cccceeEEeccccccHHHHHHHhcCCcc-cccC------C---cccccchhhhccHHH
Confidence 999999999999999999 77 8899999999999999999999977541 1111 0 011235789999999
Q ss_pred hHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCC
Q 005340 243 CEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKD 322 (701)
Q Consensus 243 ~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d 322 (701)
|+..|.++|++|++|+|++++++|+.||||+||++|+.||+.+++++|+||++|++||||.|||+++++++++++|+|+|
T Consensus 223 c~~~L~~lle~L~~d~wpV~~g~Rp~RcTG~Al~iA~~Ll~~c~p~~g~rIv~f~gGPcT~GpG~vv~~el~~piRshhd 302 (745)
T KOG1986|consen 223 CEFKLTNLLEELQPDPWPVPPGHRPLRCTGVALSIASGLLEGCFPNTGARIVLFAGGPCTRGPGTVVSRELKEPIRSHHD 302 (745)
T ss_pred HHHHHHHHHHHhcCCCCCCCCCCCcccchhHHHHHHHHHhcccCCCCcceEEEeccCCCCcCCceecchhhcCCCcCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhhhccccceEEEeCCCCchhhHHHHHHHh-ccCc
Q 005340 323 LDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF-HSGD 401 (701)
Q Consensus 323 ~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l-~~~~ 401 (701)
+++++++|++++.+||++||++++.+|+++|+|+++.+++|+++|++|++.|||.+.+.++|+.+.|+++++|+| ++..
T Consensus 303 i~~d~a~y~kKa~KfY~~La~r~~~~ghvlDifa~~lDQvGi~EMk~l~~~TGG~lvl~dsF~~s~Fk~sfqR~f~~d~~ 382 (745)
T KOG1986|consen 303 IEKDNAPYYKKAIKFYEKLAERLANQGHVLDIFAAALDQVGILEMKPLVESTGGVLVLGDSFNTSIFKQSFQRIFTRDGE 382 (745)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHHhCCceEeeeeeeccccchHHHHHHhhcCCcEEEEecccchHHHHHHHHHHhccccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999 6777
Q ss_pred cCCcceeeEEEEEEecCCceEEEEEcCCcccCCCCCCcccccccCCCCCceEEecCCCCcEEEEEEEEecCCCCcccccC
Q 005340 402 YDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPDATLQS 481 (701)
Q Consensus 402 ~~~~~~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~ 481 (701)
+++.+||+|+|+|+||++++|++.+||+.+..+|++++||++||.|+|..|+++.+++.+++++.|++...... .
T Consensus 383 ~~l~~~fn~~leV~tSkdlkI~g~IGp~~Sl~~k~~~vsdt~ig~g~t~~wkm~~ls~~t~~s~~fei~~~~~~-----~ 457 (745)
T KOG1986|consen 383 GDLKMGFNGTLEVKTSKDLKIQGVIGPCVSLNKKGPNVSDTEIGEGNTSAWKMCGLSPSTTLSLFFEISNQHNI-----P 457 (745)
T ss_pred cchhhhcCceEEEEecCCcEEEecccccccccCCCCccccceeccccccceeeeccCCCceEEEEEEeccccCC-----C
Confidence 78899999999999999999999999999999999999999999999999999999999999999999876542 3
Q ss_pred CCCeEEEEEEEEEEecCCcEEEEEEecceecccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHH
Q 005340 482 TNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKMEIEAEFDPIRWLDKALIH 561 (701)
Q Consensus 482 ~~~~~~iQ~al~Yt~~~G~r~iRV~T~~l~vt~~~~~~~~~~~~~D~~a~~~~lak~~~~~~~~~~~~~~~~~l~~~lv~ 561 (701)
....+||||++.|.+.+|++|+||+|+++++++. ...++..+|||||++++|||.++.++..++..|+++|+|+.|++
T Consensus 458 ~~~~~~iQFiT~Yq~s~g~~riRVtT~~r~~~d~--~~~~i~~~FDqEaaAV~mAR~~~~kae~e~~~d~~rwlDr~Lir 535 (745)
T KOG1986|consen 458 QSGQGYIQFITQYQHSSGQKRIRVTTLARPWADS--GSPEISQSFDQEAAAVLMARLALLKAETEDGPDVLRWLDRNLIR 535 (745)
T ss_pred CCCeeEEEEEEEEEcCCCcEEEEEEEeehhhccc--cchHhhhccchHHHHHHHHHHHHHhhhccccchHHHHHHHHHHH
Confidence 3678999999999999999999999999999973 33789999999999999999999999999999999999999999
Q ss_pred HHHHhhccccCCCCccccCccccchHHHHHHhhcccCcCCCCCChhHHHHHHHHHccCCHHHHHHhhcccceecccCCCC
Q 005340 562 MCSRFGDYQKDSPSSFSLSPRFSIFPQFMFHLRRSQFVQVFNNSPDETAYFRMILNRENVTNSVVMIQPSLISYSFHSGP 641 (701)
Q Consensus 562 ~~~~~~~y~~~~~~~l~lp~~l~~lP~~~~~l~ks~~l~~~~~s~D~r~~~~~~l~~~~~~~~~~~iyP~l~~~~~~~~p 641 (701)
+|++|+.|+|++|+++.|+++|+++|+||||||||++|+++|.|||||+|+||+|++.++++++.||+|+|++|++++.|
T Consensus 536 lc~kFg~y~k~dPssf~l~~~fsl~PQfmfhLRRS~fLqvfNnSPDEt~~yrhll~~e~v~~sliMIqP~L~sySf~g~~ 615 (745)
T KOG1986|consen 536 LCQKFGDYRKDDPSSFRLSPNFSLYPQFMFHLRRSPFLQVFNNSPDETAYYRHLLNREDVDNSLIMIQPTLLSYSFNGPP 615 (745)
T ss_pred HHHHHhccCCCCchhhcCChhhhhhHHHHHhhccchhhhccCCCcchHHHHHHHHhhccchhhhheecceeeeeecCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccccCCeEEEEeCCcEEEEEECCChhHHHHcCCCCCCccHHHHHHhhhhcc
Q 005340 642 EPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYHNQPEHQVVNFVVDFDFN 699 (701)
Q Consensus 642 ~~~~ls~~~l~~d~iyLlD~~~~i~i~~G~~v~~~~~~~~~~~~e~~~~~~~~~~~~~ 699 (701)
+|+.||..||.+|.|+|||+++.|+||+|+++++|+++|||++|||++||+||++..+
T Consensus 616 epvlLD~~Si~~D~iLLlDt~f~i~i~hG~tIaqWR~~gy~~~pe~~~f~~LL~ap~~ 673 (745)
T KOG1986|consen 616 EPVLLDVASILADRILLLDTYFTIVIFHGSTIAQWRKAGYHEQPEYENFKELLEAPRE 673 (745)
T ss_pred ceeEecccccCCceEEEeecceEEEEECCchHHHHHhcccccChhhHHHHHHHHhHHH
Confidence 9999999999999999999999999999999999999999999999999999998754
No 3
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=100.00 E-value=1.7e-137 Score=1081.23 Aligned_cols=676 Identities=46% Similarity=0.853 Sum_probs=636.4
Q ss_pred CCcccccCCCeeeecCCCCCCCHHHhhcCCCCeEEEEccCCCCCCCCCCCCCCCCCccccCC-CCceecCceEEEcCCce
Q 005340 2 TEFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRT-CRSILNPFSIVDFAAKI 80 (701)
Q Consensus 2 ~~~~~~~~~~~iR~t~~~iP~~~~~~~~~~iPlg~~v~P~~~~~~~~~~vp~~~~~p~RC~~-C~ayiNp~~~~~~~g~~ 80 (701)
|+||.+||.++||+|||+||.|+.++..+.+|++|+|+||++.+ .+++..++|+.|.. |+||+||||.++.+.+.
T Consensus 1 m~fe~iee~dgir~twnvfpat~~da~~~~iPia~lY~Pl~e~~----~~~v~~yepv~C~~pC~avlnpyC~id~r~~~ 76 (755)
T COG5047 1 MNFEIIEENDGIRLTWNVFPATRGDATRTVIPIACLYTPLHEDD----ALTVNYYEPVKCTAPCKAVLNPYCHIDERNQS 76 (755)
T ss_pred CchhhhccccceEEEEecccCCccccccccccHHHhcccccccc----ccCcccCCCceecccchhhcCcceeeccCCce
Confidence 89999999999999999999999999999999999999999975 68888999999999 99999999999999999
Q ss_pred EEeCCCCCCCCCCccccCCCCCCCCccccCCCccEEEeCCCCCCCCCCCcEEEEEEECCCchhhHHHHHHHHHHHhhcCC
Q 005340 81 WICPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPGPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLP 160 (701)
Q Consensus 81 w~C~~C~~~N~~p~~y~~~~~~~~~pEL~~~~~tvey~~~~~~~~~~~~p~~vFvIDvs~~~~~l~~~~~~l~~~l~~lp 160 (701)
|+|+||++.|.+|++|..++..+.++||.|+++||||+++++.. .||+|+||||+++..++|..++++|+..|..+|
T Consensus 77 W~CpfCnqrn~lp~qy~~iS~~~LplellpqssTiey~lskp~~---~ppvf~fvvD~~~D~e~l~~Lkdslivslsllp 153 (755)
T COG5047 77 WICPFCNQRNTLPPQYRDISNANLPLELLPQSSTIEYTLSKPVI---LPPVFFFVVDACCDEEELTALKDSLIVSLSLLP 153 (755)
T ss_pred EecceecCCCCCChhhcCCCcccCCccccCCCceEEEEccCCcc---CCceEEEEEEeecCHHHHHHHHHHHHHHHhcCC
Confidence 99999999999999999999999999999999999999999887 899999999999999999999999999999999
Q ss_pred CCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhHhhcccCCCCC-CCccccCccCCC--Cccccccee
Q 005340 161 DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKP-STGVIAGVRDGL--SSDTIARFL 237 (701)
Q Consensus 161 ~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~l~~~~~~~~~-~~~~~~~~~~~~--~~~p~~~~l 237 (701)
+++.||||||++.|++|+++ .. ..+++|||+|+++|+.+.|++|+..+. -.++ +. ...+.. .+ ...+|+
T Consensus 154 peaLvglItygt~i~v~el~-ae-~~~r~~VF~g~~eyt~~~L~~ll~~~~-~~~~~~~----es~is~~~~~-~~~rFl 225 (755)
T COG5047 154 PEALVGLITYGTSIQVHELN-AE-NHRRSYVFSGNKEYTKENLQELLALSK-PTKSGGF----ESKISGIGQF-ASSRFL 225 (755)
T ss_pred ccceeeEEEecceeEEEecc-cc-ccCcceeecchHHHHHHHHHHHhcccC-CCCcchh----hhhccccccc-chhhhh
Confidence 99999999999999999999 76 778999999999999999999987752 1111 10 000000 01 125699
Q ss_pred EehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCc
Q 005340 238 VPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPI 317 (701)
Q Consensus 238 ~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~ 317 (701)
.|+++|+..|.++|++|++|+|+++.++|+.||||+||.+|+.||+.++++.|+||++|++||||.|||+|+++++++++
T Consensus 226 ~p~q~ce~~L~n~le~L~pd~~~v~~~~Rp~RCTGsAl~ias~Ll~~~~p~~~~~i~lF~~GPcTvGpG~Vvs~elkEpm 305 (755)
T COG5047 226 LPTQQCEFKLLNILEQLQPDPWPVPAGKRPLRCTGSALNIASSLLEQCFPNAGCHIVLFAGGPCTVGPGTVVSTELKEPM 305 (755)
T ss_pred ccHHHHHHHHHHHHHHhCCCCccCCCCCCCccccchhHHHHHHHHHhhccCcceeEEEEcCCCccccCceeeehhhcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhhhccccceEEEeCCCCchhhHHHHHHHh
Q 005340 318 RSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF 397 (701)
Q Consensus 318 ~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l 397 (701)
|+||+++++.+++.+++.+||++||++.+.+|+++|+|+.+.+++|+.+|.+|...|||.+.+.++|+.++|+++++|+|
T Consensus 306 RshH~ie~d~aqh~kka~KFY~~laeR~a~~gh~~DifagcldqIGI~eM~~L~~sTgg~lvlsdsF~t~ifkqSfqrif 385 (755)
T COG5047 306 RSHHDIESDSAQHSKKATKFYKGLAERVANQGHALDIFAGCLDQIGIMEMEPLTTSTGGALVLSDSFTTSIFKQSFQRIF 385 (755)
T ss_pred cccccccccchhhccchHHHHHHHHHHHhccchhHHHHHHHHHhhhhhcchhhccCCcceEEEeccccHHHHHHHHHHHh
Confidence 99999999989999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred -ccCccCCcceeeEEEEEEecCCceEEEEEcCCcccCCCCCCcccccccCCCCCceEEecCCCCcEEEEEEEEecCCCCc
Q 005340 398 -HSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPD 476 (701)
Q Consensus 398 -~~~~~~~~~~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~ 476 (701)
++..+++.+||+|.|+|.||++++|++.+|+..+.++++.++||.+||.|.|+.|++++++|.+++++.|++......+
T Consensus 386 ~~d~~g~l~~gfNa~m~V~TsKnl~~~g~ig~a~~~~k~~~ni~~~eigi~~t~swkm~slsPk~nyal~fei~~~~~~~ 465 (755)
T COG5047 386 NRDSEGYLKMGFNANMEVKTSKNLKIKGLIGHAVSVKKKANNISDSEIGIGATNSWKMASLSPKSNYALYFEIALGAASG 465 (755)
T ss_pred CcCcccchhhhhccceeEeeccCceeeeeecceeeecccccccccccccccccccccccccCCCcceEEEEEeccccCCC
Confidence 7777889999999999999999999999999999988999999999999999999999999999999999998765421
Q ss_pred ccccCCCCeEEEEEEEEEEecCCcEEEEEEecceecccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCCchhHHHHHH
Q 005340 477 ATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKMEIEAEFDPIRWLD 556 (701)
Q Consensus 477 ~~~~~~~~~~~iQ~al~Yt~~~G~r~iRV~T~~l~vt~~~~~~~~~~~~~D~~a~~~~lak~~~~~~~~~~~~~~~~~l~ 556 (701)
++ +....+|+||.+.|.+++|.-||||+|++..+++ .....+.++|||||+++++||.++.++..++..|+.+|+|
T Consensus 466 ~~--~~~~~a~iQfiT~yQhss~t~riRVtTvar~f~~--~~~p~i~~SFdqEaaaV~~aR~a~~K~~~ed~~Dv~rw~d 541 (755)
T COG5047 466 SA--QRPAEAYIQFITTYQHSSGTYRIRVTTVARMFTD--GGLPKINRSFDQEAAAVFMARIAAFKAETEDIIDVFRWID 541 (755)
T ss_pred cc--CCcccchhhhhhhhhccCCcEEEEEeehhhhhcc--CCChhhhhcchhhHHHHHHHHHHHhhcccccchhHHHHHH
Confidence 00 2346799999999999999999999999999997 4678899999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccccCCCCccccCccccchHHHHHHhhcccCcCCCCCChhHHHHHHHHHccCCHHHHHHhhcccceecc
Q 005340 557 KALIHMCSRFGDYQKDSPSSFSLSPRFSIFPQFMFHLRRSQFVQVFNNSPDETAYFRMILNRENVTNSVVMIQPSLISYS 636 (701)
Q Consensus 557 ~~lv~~~~~~~~y~~~~~~~l~lp~~l~~lP~~~~~l~ks~~l~~~~~s~D~r~~~~~~l~~~~~~~~~~~iyP~l~~~~ 636 (701)
+.|+++|+.|+.|+|++|+++.|+++|.++|+|||+|+||++|+++|.|||||++++|.|.+.++++++.||+|+|.+||
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCcccccccccccCCeEEEEeCCcEEEEEECCChhHHHHcCCCCCCccHHHHHHhhh
Q 005340 637 FHSGPEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYHNQPEHQVVNFVVDF 696 (701)
Q Consensus 637 ~~~~p~~~~ls~~~l~~d~iyLlD~~~~i~i~~G~~v~~~~~~~~~~~~e~~~~~~~~~~ 696 (701)
+++.+.||.||+-++++|.|+|||++++|+||.|+.+++|+++|||++|||+++|+||++
T Consensus 622 ~~~~~~pVlLDs~svkpdviLLlDtff~Ili~hG~~iaqwr~agyq~qpey~~lK~Ll~~ 681 (755)
T COG5047 622 FEKGGVPVLLDSVSVKPDVILLLDTFFHILIFHGSYIAQWRNAGYQEQPEYLNLKELLEA 681 (755)
T ss_pred ccCCCceEEEeccccCCCeEEEeeceeEEEEECChHHHHHHhhhhhcCchhhhHHHHhhc
Confidence 988899999999999999999999999999999999999999999999999999999964
No 4
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.5e-119 Score=985.55 Aligned_cols=607 Identities=20% Similarity=0.295 Sum_probs=545.0
Q ss_pred cccCCCeeeecCCCCCCCHHHhhcCCCCeEEEEccCCCCCCCCCCCCCCCC---CccccCCCCceecCceEEEcCCceEE
Q 005340 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPY---APLRCRTCRSILNPFSIVDFAAKIWI 82 (701)
Q Consensus 6 ~~~~~~~iR~t~~~iP~~~~~~~~~~iPlg~~v~P~~~~~~~~~~vp~~~~---~p~RC~~C~ayiNp~~~~~~~g~~w~ 82 (701)
.|++|+|||+|+|+||.|.+++++++||||++|+||+.+.++|+++|+++. +|+||+||+||+|||++|.++|++|+
T Consensus 283 GN~sPr~mr~T~Y~iP~T~Dl~~as~iPLalvIqPfa~l~p~E~~~~vVd~g~sgPvRC~RCkaYinPFmqF~~~gr~f~ 362 (1007)
T KOG1984|consen 283 GNCSPRFMRCTMYTIPCTNDLLKASQIPLALVIQPFATLTPNEAPVPVVDLGESGPVRCNRCKAYINPFMQFIDGGRKFI 362 (1007)
T ss_pred CCCCcchheeecccCCccHhHHHhcCCcceeEecccccCCcccCCCceecCCCCCCcchhhhhhhcCcceEEecCCceEE
Confidence 499999999999999999999999999999999999999999999999864 79999999999999999999999999
Q ss_pred eCCCCCCCCCCccccC-CC------CCCCCccccCCCccEEEeCCCC------CCCCCCCcEEEEEEECCCchhh---HH
Q 005340 83 CPFCFQRNHFPPHYAS-IT------DDNLPAELFPQYTTIEYEPPGP------GEKSSVPPVFMFVVDTCIIEEE---MS 146 (701)
Q Consensus 83 C~~C~~~N~~p~~y~~-~~------~~~~~pEL~~~~~tvey~~~~~------~~~~~~~p~~vFvIDvs~~~~~---l~ 146 (701)
||||+.+|++|.+|++ ++ +.+.|||| ..|||||++++. ++ .||+|||+||||+++++ +.
T Consensus 363 Cn~C~~~n~vp~~yf~~L~~~grr~D~~erpEL--~~Gt~dfvatk~Y~~~~k~p---~ppafvFmIDVSy~Ai~~G~~~ 437 (1007)
T KOG1984|consen 363 CNFCGSKNQVPDDYFNHLGPTGRRVDVEERPEL--CLGTVDFVATKDYCRKTKPP---KPPAFVFMIDVSYNAISNGAVK 437 (1007)
T ss_pred ecCCCccccCChhhcccCCCcccccccccCchh--cccccceeeehhhhhcCCCC---CCceEEEEEEeehhhhhcchHH
Confidence 9999999999999998 44 34789999 799999999842 44 79999999999999998 88
Q ss_pred HHHHHHHHHhhcCC---CCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhHhhcccCCCCCCCccccC
Q 005340 147 FLKSALSQAIDLLP---DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAG 223 (701)
Q Consensus 147 ~~~~~l~~~l~~lp---~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~l~~~~~~~~~~~~~~~~ 223 (701)
+++++|++.|+.++ ++.+|||||||++|||||++ +.|..|+++| ++|
T Consensus 438 a~ce~ik~~l~~lp~~~p~~~Vgivtfd~tvhFfnl~-s~L~qp~mli-----------------Vsd------------ 487 (1007)
T KOG1984|consen 438 AACEAIKSVLEDLPREEPNIRVGIVTFDKTVHFFNLS-SNLAQPQMLI-----------------VSD------------ 487 (1007)
T ss_pred HHHHHHHHHHhhcCccCCceEEEEEEecceeEeeccC-ccccCceEEE-----------------eec------------
Confidence 99999999999988 36899999999999999999 8877776655 222
Q ss_pred ccCCCCccc-ccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCC
Q 005340 224 VRDGLSSDT-IARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPST 302 (701)
Q Consensus 224 ~~~~~~~~p-~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~gg~Ii~F~~g~pt 302 (701)
+++.|+| +++++++..|++..|+.+|++|+. +| .+++.+++++|+||++|..+|+++ .|||+++|++..||
T Consensus 488 --v~dvfvPf~~g~~V~~~es~~~i~~lLd~Ip~-mf--~~sk~pes~~g~alqaa~lalk~~---~gGKl~vF~s~Lpt 559 (1007)
T KOG1984|consen 488 --VDDVFVPFLDGLFVNPNESRKVIELLLDSIPT-MF--QDSKIPESVFGSALQAAKLALKAA---DGGKLFVFHSVLPT 559 (1007)
T ss_pred --ccccccccccCeeccchHHHHHHHHHHHHhhh-hh--ccCCCCchhHHHHHHHHHHHHhcc---CCceEEEEeccccc
Confidence 2346788 488999999999999999999998 66 567889999999999999999953 29999999999999
Q ss_pred CCCc-ccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhhhccccceEEEe
Q 005340 303 EGPA-AIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLS 381 (701)
Q Consensus 303 ~GpG-~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~ 381 (701)
.|.| ++..|++...+. .+|| ++++.+++++|++||++|++.|+|||+|+++..|+|+|+++.+++.|||.+|+|
T Consensus 560 ~g~g~kl~~r~D~~l~~----t~ke-k~l~~pq~~~y~~LA~e~v~~g~svDlF~t~~ayvDvAtlg~v~~~TgG~vy~Y 634 (1007)
T KOG1984|consen 560 AGAGGKLSNRDDRRLIG----TDKE-KNLLQPQDKTYTTLAKEFVESGCSVDLFLTPNAYVDVATLGVVPALTGGQVYKY 634 (1007)
T ss_pred ccCcccccccchhhhhc----ccch-hhccCcchhHHHHHHHHHHHhCceEEEEEcccceeeeeeecccccccCceeEEe
Confidence 9988 888887655443 3565 489999999999999999999999999999999999999999999999999999
Q ss_pred CCCCchhhHHHHHHHh-ccCccCCcceeeEEEEEEecCCceEEEEEcCCcccCCCCCCcccccccCCCCCceEEecCCCC
Q 005340 382 DSFGHAVFKDSVRRVF-HSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKA 460 (701)
Q Consensus 382 ~~f~~~~~~~~l~~~l-~~~~~~~~~~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~ 460 (701)
.+|...++...|...| ++. .+..||+|.||||||.||++.+++||+.. +..++.+++.+|.|
T Consensus 635 ~~F~a~~D~~rl~nDL~~~v--tk~~gf~a~mrvRtStGirv~~f~Gnf~~---------------~~~tDiela~lD~d 697 (1007)
T KOG1984|consen 635 YPFQALTDGPRLLNDLVRNV--TKKQGFDAVMRVRTSTGIRVQDFYGNFLM---------------RNPTDIELAALDCD 697 (1007)
T ss_pred cchhhcccHHHHHHHHHHhc--ccceeeeeEEEEeecCceeeeeeechhhh---------------cCCCCccccccccC
Confidence 9998876555444444 222 34689999999999999999999999974 34678999999999
Q ss_pred cEEEEEEEEecCCCCcccccCCCCeEEEEEEEEEEecCCcEEEEEEecceecccCCCCHHHHHhccCHHHHHHHHHHHHH
Q 005340 461 TSLCLVFEIVKKEIPDATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVS 540 (701)
Q Consensus 461 ~s~~~~~~~~~~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~r~iRV~T~~l~vt~~~~~~~~~~~~~D~~a~~~~lak~~~ 540 (701)
++++++|+||++++. ...++||+|++||+.+|+||+||+|+++++|+ .+.++|+++|.|+++++|+|.|+
T Consensus 698 kt~~v~fkhDdkLq~-------~s~~~fQ~AlLYTti~G~RR~Rv~Nlsl~~ts---~l~~lyr~~~~d~l~a~maK~a~ 767 (1007)
T KOG1984|consen 698 KTLTVEFKHDDKLQD-------GSDVHFQTALLYTTIDGQRRLRVLNLSLAVTS---QLSELYRSADTDPLIAIMAKQAA 767 (1007)
T ss_pred ceeEEEEeccccccC-------CcceeEEEEEEEeccCCceeEEEEecchhhhh---hHHHHHHhcCccHHHHHHHHHHH
Confidence 999999999999963 67899999999999999999999999999995 89999999999999999999999
Q ss_pred HHhhcCCchhHHHHHHHHHHHHHHHhhccccCCC-----CccccCccccchHHHHHHhhcccCcCCCCCChhHHHHHHHH
Q 005340 541 FKMEIEAEFDPIRWLDKALIHMCSRFGDYQKDSP-----SSFSLSPRFSIFPQFMFHLRRSQFVQVFNNSPDETAYFRMI 615 (701)
Q Consensus 541 ~~~~~~~~~~~~~~l~~~lv~~~~~~~~y~~~~~-----~~l~lp~~l~~lP~~~~~l~ks~~l~~~~~s~D~r~~~~~~ 615 (701)
..+..+...++|+.+++.++++ |+.|||.|+ +||+|||+||+||+|+++++||.+|++..++.|+|+|.+.+
T Consensus 768 ~~i~~~~lk~vre~l~~~~~~i---L~~YRk~cas~~ssgQLILPeslKLlPly~la~lKs~~l~~~~~~~DdRi~~~~~ 844 (1007)
T KOG1984|consen 768 KAILDKPLKEVREQLVSQCAQI---LASYRKNCASPASSGQLILPESLKLLPLYMLALLKSSALRPQEIRTDDRIYQLQL 844 (1007)
T ss_pred HhcccccHHHHHHHHHHHHHHH---HHHHHHhhcCCCCcccEechhhhHHHHHHHHHHHHhhcccccccccchhHHHHHH
Confidence 9999999999999999988888 788888764 59999999999999999999999999999999999999999
Q ss_pred HccCCHHHHHHhhcccceeccc---C-----CCCcccccccccccCCeEEEEeCCcEEEEEECCChhHHHHcCCCCCCcc
Q 005340 616 LNRENVTNSVVMIQPSLISYSF---H-----SGPEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYHNQPEH 687 (701)
Q Consensus 616 l~~~~~~~~~~~iyP~l~~~~~---~-----~~p~~~~ls~~~l~~d~iyLlD~~~~i~i~~G~~v~~~~~~~~~~~~e~ 687 (701)
+.++++++++.++||+|+++|. + ..|.+|++|++.|..+||||||||..+|||+|++|.+.+.++++..++.
T Consensus 845 v~sl~v~~~~~~~YPrl~p~hdl~i~dtl~~~~p~~VraS~e~l~negiYll~nG~~~ylwvg~sv~~~llQ~lf~V~s~ 924 (1007)
T KOG1984|consen 845 VTSLSVEQLMPFFYPRLLPFHDLDIEDTLEFVLPKAVRASSEFLSNEGIYLLDNGQKIYLWVGESVDPDLLQDLFSVSSF 924 (1007)
T ss_pred hhcccHHhhhhhhccceeeeeccccccccccccccceecchhhccCCceEEEecCcEEEEEecCCCCHHHHHHHhcCccc
Confidence 9999999999999999999994 1 3599999999999999999999999999999999966555666655555
Q ss_pred HHH
Q 005340 688 QVV 690 (701)
Q Consensus 688 ~~~ 690 (701)
+++
T Consensus 925 ~~i 927 (1007)
T KOG1984|consen 925 EQI 927 (1007)
T ss_pred ccc
Confidence 444
No 5
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=8.7e-116 Score=955.55 Aligned_cols=586 Identities=21% Similarity=0.327 Sum_probs=524.5
Q ss_pred cccCCCeeeecCCCCCCCHHHhhcCCCCeEEEEccCCCCCCCCCCCCCC-CCCccccCCCCceecCceEEEcCCceEEeC
Q 005340 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPIL-PYAPLRCRTCRSILNPFSIVDFAAKIWICP 84 (701)
Q Consensus 6 ~~~~~~~iR~t~~~iP~~~~~~~~~~iPlg~~v~P~~~~~~~~~~vp~~-~~~p~RC~~C~ayiNp~~~~~~~g~~w~C~ 84 (701)
-|++|+|+|+|+++||++.+++++++||||++|+||+++. ...++|++ +..|+||++||+|||||+.|++.|++|+||
T Consensus 166 ~nc~p~y~RsTl~~iP~t~sLl~kskLPlglvv~Pf~~~~-d~~~~p~~~~~~IvRCr~CRtYiNPFV~fid~gr~WrCN 244 (887)
T KOG1985|consen 166 SNCSPSYVRSTLSAIPQTQSLLKKSKLPLGLVVHPFAHLD-DIDPLPVITSTLIVRCRRCRTYINPFVEFIDQGRRWRCN 244 (887)
T ss_pred cCCCHHHHHHHHHhCCccHHHHHhcCCCceEEEeeccccc-ccCCCCcccCCceeeehhhhhhcCCeEEecCCCceeeec
Confidence 4899999999999999999999999999999999999776 33467765 458999999999999999999999999999
Q ss_pred CCCCCCCCCccccC------CCCCCCCccccCCCccEEEeCCCC----CCCCCCCcEEEEEEECCCchhh---HHHHHHH
Q 005340 85 FCFQRNHFPPHYAS------ITDDNLPAELFPQYTTIEYEPPGP----GEKSSVPPVFMFVVDTCIIEEE---MSFLKSA 151 (701)
Q Consensus 85 ~C~~~N~~p~~y~~------~~~~~~~pEL~~~~~tvey~~~~~----~~~~~~~p~~vFvIDvs~~~~~---l~~~~~~ 151 (701)
+|+..|++|.+|.. -.+..+|||+ ++++|||++|.+ ++ +|++|+|+||||.++++ |+.++++
T Consensus 245 lC~~~NdvP~~f~~~~~t~~~~~~~~RpEl--~~s~vE~iAP~eYmlR~P---~Pavy~FliDVS~~a~ksG~L~~~~~s 319 (887)
T KOG1985|consen 245 LCGRVNDVPDDFDWDPLTGAYGDPYSRPEL--TSSVVEFIAPSEYMLRPP---QPAVYVFLIDVSISAIKSGYLETVARS 319 (887)
T ss_pred hhhhhcCCcHHhhcCccccccCCcccCccc--cceeEEEecCcccccCCC---CCceEEEEEEeehHhhhhhHHHHHHHH
Confidence 99999999998864 1245689999 899999999953 33 69999999999999988 8999999
Q ss_pred HHHHhhcCC--CCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhHhhcccCCCCCCCccccCccCCCC
Q 005340 152 LSQAIDLLP--DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLS 229 (701)
Q Consensus 152 l~~~l~~lp--~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~ 229 (701)
|+..|+.|| ++++|||||||+.||||++. .+++.|+ |++++| ++++
T Consensus 320 lL~~LD~lpgd~Rt~igfi~fDs~ihfy~~~-~~~~qp~-----------------mm~vsd--------------l~d~ 367 (887)
T KOG1985|consen 320 LLENLDALPGDPRTRIGFITFDSTIHFYSVQ-GDLNQPQ-----------------MMIVSD--------------LDDP 367 (887)
T ss_pred HHHhhhcCCCCCcceEEEEEeeceeeEEecC-CCcCCCc-----------------eeeecc--------------cccc
Confidence 999999999 67999999999999999998 5534443 333433 2345
Q ss_pred ccc-ccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCCccc
Q 005340 230 SDT-IARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAI 308 (701)
Q Consensus 230 ~~p-~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~gg~Ii~F~~g~pt~GpG~l 308 (701)
|+| .++||+|+++||+.|..+|++|+. +| ...+..++|+|+||++|..+|+ ..||||++|++++||.|.|+|
T Consensus 368 flp~pd~lLv~L~~ck~~i~~lL~~lp~-~F--~~~~~t~~alGpALkaaf~li~----~~GGri~vf~s~lPnlG~G~L 440 (887)
T KOG1985|consen 368 FLPMPDSLLVPLKECKDLIETLLKTLPE-MF--QDTRSTGSALGPALKAAFNLIG----STGGRISVFQSTLPNLGAGKL 440 (887)
T ss_pred ccCCchhheeeHHHHHHHHHHHHHHHHH-HH--hhccCcccccCHHHHHHHHHHh----hcCCeEEEEeccCCCCCcccc
Confidence 566 389999999999999999999998 66 5567789999999999999999 899999999999999999999
Q ss_pred ccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhhhccccceEEEeCCCCch-
Q 005340 309 VSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHA- 387 (701)
Q Consensus 309 ~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~- 387 (701)
+.||..+..++ ++...++.+++.|||++|.+|++.+|+||+|+++.+|.|+|+|+.|++.|||.+|+|++|+..
T Consensus 441 ~~rEdp~~~~s-----~~~~qlL~~~t~FYK~~a~~cs~~qI~VDlFl~s~qY~DlAsLs~LskySgG~~y~YP~f~~s~ 515 (887)
T KOG1985|consen 441 KPREDPNVRSS-----DEDSQLLSPATDFYKDLALECSKSQICVDLFLFSEQYTDLASLSCLSKYSGGQVYYYPSFDGSN 515 (887)
T ss_pred ccccccccccc-----hhhhhccCCCchHHHHHHHHhccCceEEEEEeecccccchhhhhccccccCceeEEccCCCCCC
Confidence 99976544332 233678999999999999999999999999999999999999999999999999999999976
Q ss_pred -----hhHHHHHHHhccCccCCcceeeEEEEEEecCCceEEEEEcCCcccCCCCCCcccccccCCCCCceEEecCCCCcE
Q 005340 388 -----VFKDSVRRVFHSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATS 462 (701)
Q Consensus 388 -----~~~~~l~~~l~~~~~~~~~~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~~s 462 (701)
+|.++|.|+|+ +++||+|+||||||+|+++..+|||++. +++++..++++.+|++
T Consensus 516 p~~~~Kf~~el~r~Lt-----r~~~feaVmRiR~S~gl~~~~f~GnFF~---------------RStDLla~~~v~~D~s 575 (887)
T KOG1985|consen 516 PHDVLKFARELARYLT-----RKIGFEAVMRIRCSTGLRMSSFFGNFFV---------------RSTDLLALPNVNPDQS 575 (887)
T ss_pred HHHHHHHHHHHHHHhh-----hhhhhheeEEeeccccccccceeccccc---------------CcHHHhcccCCCCCcc
Confidence 46777777774 4589999999999999999999999996 4688999999999999
Q ss_pred EEEEEEEecCCCCcccccCCCCeEEEEEEEEEEecCCcEEEEEEecceecccCCCCHHHHHhccCHHHHHHHHHHHHHHH
Q 005340 463 LCLVFEIVKKEIPDATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFK 542 (701)
Q Consensus 463 ~~~~~~~~~~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~r~iRV~T~~l~vt~~~~~~~~~~~~~D~~a~~~~lak~~~~~ 542 (701)
++|.+++++.+. ....+||.|++||...|||||||||+++|+++ ++.++|+++|++|++.+++++|+.+
T Consensus 576 y~~qisiEesl~--------~~~~~fQvAlLyT~~~GERRIRV~T~~lpt~~---sl~evY~saD~~AI~~lla~~Av~k 644 (887)
T KOG1985|consen 576 YAFQISIEESLT--------TGFCVFQVALLYTLSKGERRIRVHTLCLPTVS---SLNEVYASADQEAIASLLAKKAVEK 644 (887)
T ss_pred ceEEEEeehhcC--------CceeEEEeeeeecccCCceeEEEEEeeccccc---cHHHHHhhcCHHHHHHHHHHHHHHH
Confidence 999999999885 46778999999999999999999999999995 8999999999999999999999999
Q ss_pred hhcCCchhHHHHHHHHHHHHHHHhhccccCCC------CccccCccccchHHHHHHhhcccCcCC-CCCChhHHHHHHHH
Q 005340 543 MEIEAEFDPIRWLDKALIHMCSRFGDYQKDSP------SSFSLSPRFSIFPQFMFHLRRSQFVQV-FNNSPDETAYFRMI 615 (701)
Q Consensus 543 ~~~~~~~~~~~~l~~~lv~~~~~~~~y~~~~~------~~l~lp~~l~~lP~~~~~l~ks~~l~~-~~~s~D~r~~~~~~ 615 (701)
.++..+.|+|+.|.+.++++ ++.|++... ..+.+|.+|++||+|+++|.|++.|+. .+++.|+|+++++.
T Consensus 645 sl~ssL~dardal~~~~~D~---l~aYk~~~~~~~~~~~~l~~p~~LrllPllvlALlK~~~fr~g~~~~lD~R~~a~~~ 721 (887)
T KOG1985|consen 645 SLSSSLSDARDALTNAVVDI---LNAYKKLVSNQNGQGITLSLPASLRLLPLLVLALLKHPAFRPGTGTRLDYRAYAMCL 721 (887)
T ss_pred HHHhhhhhHHHHHHHHHHHH---HHHHHHHhcccccCCcceecCcchhhhHHHHHHHhcCCcccCCCCCCchHHHHHHHH
Confidence 99998999999999999988 777776432 379999999999999999999999995 59999999999999
Q ss_pred HccCCHHHHHHhhcccceeccc-C------------CCCcccccccccccCCeEEEEeCCcEEEEEECCChhH
Q 005340 616 LNRENVTNSVVMIQPSLISYSF-H------------SGPEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQ 675 (701)
Q Consensus 616 l~~~~~~~~~~~iyP~l~~~~~-~------------~~p~~~~ls~~~l~~d~iyLlD~~~~i~i~~G~~v~~ 675 (701)
+..+++..++++|||+||++|. + ..|++++|+.+.+++.|+||||+|..+++|+|+++++
T Consensus 722 ~~~lpl~~L~k~IYP~Lysl~~l~~ea~~~~~d~~~~~p~~L~ltae~l~~~GlyL~D~g~~lfl~vg~~a~P 794 (887)
T KOG1985|consen 722 MSTLPLKYLMKYIYPTLYSLHDLDDEAGLPIHDQTVVLPPPLNLTAELLSRRGLYLMDTGTTLFLWVGSNADP 794 (887)
T ss_pred hhcCCHHHHHhhhcccceeccccccccCcccccccccCCCccchHHHHhccCceEEEecCcEEEEEEcCCCCc
Confidence 9999999999999999999984 1 1478999999999999999999999999999999853
No 6
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=100.00 E-value=2.7e-108 Score=889.34 Aligned_cols=601 Identities=20% Similarity=0.331 Sum_probs=533.8
Q ss_pred cccCCCeeeecCCCCCCCHHHhhcCCCCeEEEEccCCCCCCCCCCCCCC-CCCccccCCCCceecCceEEEcCCceEEeC
Q 005340 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPIL-PYAPLRCRTCRSILNPFSIVDFAAKIWICP 84 (701)
Q Consensus 6 ~~~~~~~iR~t~~~iP~~~~~~~~~~iPlg~~v~P~~~~~~~~~~vp~~-~~~p~RC~~C~ayiNp~~~~~~~g~~w~C~ 84 (701)
.|++|+|||+|+|++|.+.+++++++||||++|+||.++.+.+.++|+. +..|+||++||+|+|||++|.++|++|+||
T Consensus 146 ~n~~p~yvrsT~yaiP~t~dl~~~skiPfgLVI~Pf~~l~~e~~~vpl~~d~~ivRCrrCrsYiNPfv~fi~~g~kw~CN 225 (861)
T COG5028 146 SNCSPKYVRSTMYAIPETNDLLKKSKIPFGLVIRPFLELYPEEDPVPLVEDGSIVRCRRCRSYINPFVQFIEQGRKWRCN 225 (861)
T ss_pred CCCCHHHHHHHHhhCCCchhHHHhcCCCceEEeehhhhcCccCCCCccCCCCcchhhhhhHhhcCceEEEecCCcEEEEe
Confidence 4899999999999999999999999999999999999988766677875 445899999999999999999999999999
Q ss_pred CCCCCCCCCccccC-------CCCCCCCccccCCCccEEEeCCCC----CCCCCCCcEEEEEEECCCchhh---HHHHHH
Q 005340 85 FCFQRNHFPPHYAS-------ITDDNLPAELFPQYTTIEYEPPGP----GEKSSVPPVFMFVVDTCIIEEE---MSFLKS 150 (701)
Q Consensus 85 ~C~~~N~~p~~y~~-------~~~~~~~pEL~~~~~tvey~~~~~----~~~~~~~p~~vFvIDvs~~~~~---l~~~~~ 150 (701)
+|+..|++|.+++. ..+.+.|+|| .+++|||++|.+ .+ .||+|||+||||.++.+ +.++.+
T Consensus 226 iC~~kN~vp~~~~~~~~~~~~r~d~~~r~El--~~~vvdf~ap~~Y~~~~p---~P~~yvFlIDVS~~a~~~g~~~a~~r 300 (861)
T COG5028 226 ICRSKNDVPEGFDNPSGPNDPRSDRYSRPEL--KSGVVDFLAPKEYSLRQP---PPPVYVFLIDVSFEAIKNGLVKAAIR 300 (861)
T ss_pred eccccccCcccccCcCCCCCccccccccchh--hceeeEEecccceeeccC---CCCEEEEEEEeehHhhhcchHHHHHH
Confidence 99999999998873 2235789999 799999999953 22 48999999999999987 789999
Q ss_pred HHHHHhhcCC---CCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhHhhcccCCCCCCCccccCccCC
Q 005340 151 ALSQAIDLLP---DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDG 227 (701)
Q Consensus 151 ~l~~~l~~lp---~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~ 227 (701)
+|++.|+.+| +++||+||.||+.||+++++ .+++ + .|+++++ ++
T Consensus 301 ~Il~~l~~~~~~dpr~kIaii~fD~sl~ffk~s-~d~~---------------~---~~~~vsd--------------ld 347 (861)
T COG5028 301 AILENLDQIPNFDPRTKIAIICFDSSLHFFKLS-PDLD---------------E---QMLIVSD--------------LD 347 (861)
T ss_pred HHHhhccCCCCCCCcceEEEEEEcceeeEEecC-CCCc---------------c---ceeeecc--------------cc
Confidence 9999999886 57999999999999999998 6521 0 2444443 34
Q ss_pred CCcccc--cceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCC
Q 005340 228 LSSDTI--ARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGP 305 (701)
Q Consensus 228 ~~~~p~--~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~gg~Ii~F~~g~pt~Gp 305 (701)
++|+|. ++|+.|+++++..++.||+.++. .| ..++.++.|+|.||++|..+++ .+||||++|.+..||.|.
T Consensus 348 ~pFlPf~s~~fv~pl~~~k~~~etLl~~~~~-If--~d~~~pk~~~G~aLk~a~~l~g----~~GGkii~~~stlPn~G~ 420 (861)
T COG5028 348 EPFLPFPSGLFVLPLKSCKQIIETLLDRVPR-IF--QDNKSPKNALGPALKAAKSLIG----GTGGKIIVFLSTLPNMGI 420 (861)
T ss_pred cccccCCcchhcccHHHHHHHHHHHHHHhhh-hh--cccCCCccccCHHHHHHHHHhh----ccCceEEEEeecCCCccc
Confidence 577884 57999999999988889999987 44 4578899999999999999998 899999999999999999
Q ss_pred cccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhhhccccceEEEeCCCC
Q 005340 306 AAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFG 385 (701)
Q Consensus 306 G~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~ 385 (701)
|+|..|+. ++ ..++++...||+++|.+|++.||+||+|+++.+++|++|++.|++.|||.+++|++|+
T Consensus 421 Gkl~~r~d-----------~e-~~ll~c~d~fYk~~a~e~~k~gIsvd~Flt~~~yidvaTls~l~~~T~G~~~~Yp~f~ 488 (861)
T COG5028 421 GKLQLRED-----------KE-SSLLSCKDSFYKEFAIECSKVGISVDLFLTSEDYIDVATLSHLCRYTGGQTYFYPNFS 488 (861)
T ss_pred cccccccc-----------ch-hhhccccchHHHHHHHHHHHhcceEEEEeccccccchhhhcchhhccCcceEEcCCcc
Confidence 99998874 22 3478999999999999999999999999999999999999999999999999999999
Q ss_pred chh------hHHHHHHHhccCccCCcceeeEEEEEEecCCceEEEEEcCCcccCCCCCCcccccccCCCCCceEEecCCC
Q 005340 386 HAV------FKDSVRRVFHSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDK 459 (701)
Q Consensus 386 ~~~------~~~~l~~~l~~~~~~~~~~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~ 459 (701)
.++ |.++|.+.+. ++.||++.||||||+|+++.++|||++.. +.+...++.++.
T Consensus 489 ~~~~~d~~kl~~dL~~~ls-----~~~gy~~~~rvR~S~glr~s~fyGnf~~r---------------s~dl~~F~tm~r 548 (861)
T COG5028 489 ATRPNDATKLANDLVSHLS-----MEIGYEAVMRVRCSTGLRVSSFYGNFFNR---------------SSDLCAFSTMPR 548 (861)
T ss_pred cCCchhHHHHHHHHHHhhh-----hhhhhheeeEeeccCceehhhhhcccccc---------------CcccccccccCC
Confidence 887 5566665553 45899999999999999999999999863 467899999999
Q ss_pred CcEEEEEEEEecCCCCcccccCCCCeEEEEEEEEEEecCCcEEEEEEecceecccCCCCHHHHHhccCHHHHHHHHHHHH
Q 005340 460 ATSLCLVFEIVKKEIPDATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLV 539 (701)
Q Consensus 460 ~~s~~~~~~~~~~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~r~iRV~T~~l~vt~~~~~~~~~~~~~D~~a~~~~lak~~ 539 (701)
|+|+.|+|++++++. ...+|||.|++||..+|+|||||.|+++++++ ++.++|+++|++|++.+|+|+|
T Consensus 549 d~Sl~~~~sid~~l~--------~~~v~fQvAlL~T~~~GeRRiRVvn~s~~~ss---~~~evyasadq~aIa~~lak~a 617 (861)
T COG5028 549 DTSLLVEFSIDEKLM--------TSDVYFQVALLYTLNDGERRIRVVNLSLPTSS---SIREVYASADQLAIACILAKKA 617 (861)
T ss_pred CceEEEEEEeccccc--------CCceEEEEEEEeeccCCceEEEEEEeccccch---hHHHHHHhccHHHHHHHHHHHH
Confidence 999999999999985 48899999999999999999999999999995 7999999999999999999999
Q ss_pred HHHhhcCCchhHHHHHHHHHHHHHHHhhccccC-----CCCccccCccccchHHHHHHhhcccCcCCCCCChhHHHHHHH
Q 005340 540 SFKMEIEAEFDPIRWLDKALIHMCSRFGDYQKD-----SPSSFSLSPRFSIFPQFMFHLRRSQFVQVFNNSPDETAYFRM 614 (701)
Q Consensus 540 ~~~~~~~~~~~~~~~l~~~lv~~~~~~~~y~~~-----~~~~l~lp~~l~~lP~~~~~l~ks~~l~~~~~s~D~r~~~~~ 614 (701)
+.++.+....++|+.|++.++++ +..|||. .+++++||++|++||++|++|.||.+|+...++.|.|++...
T Consensus 618 ~~~~~~~s~~~~r~~i~~s~~~I---L~~Ykk~~~~snt~tql~Lp~nL~lLPll~lal~Ks~~~rs~~~~sD~r~~~L~ 694 (861)
T COG5028 618 STKALNSSLKEARVLINKSMVDI---LKAYKKELVKSNTSTQLPLPANLKLLPLLMLALLKSSAFRSGSTPSDIRISALN 694 (861)
T ss_pred HHHhhhhhHHHHHHHHHHHHHHH---HHHHHHHHhhccCCccccchhhhHHHHHHHHHHhhhcccccCCCccchhHHHHH
Confidence 99999988899999999999998 6667763 467999999999999999999999999988899999999999
Q ss_pred HHccCCHHHHHHhhcccceeccc---C---------CCCcccccccccccCCeEEEEeCCcEEEEEECCChhHHHHcCCC
Q 005340 615 ILNRENVTNSVVMIQPSLISYSF---H---------SGPEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYH 682 (701)
Q Consensus 615 ~l~~~~~~~~~~~iyP~l~~~~~---~---------~~p~~~~ls~~~l~~d~iyLlD~~~~i~i~~G~~v~~~~~~~~~ 682 (701)
.+.++++.+.+..|||+||++|. + ..|+|+.++.+.+.+.|+||+|+|..+|+|+|+++.+-+.+.++
T Consensus 695 ~l~~~p~~~l~~~iYP~lyalHdm~~e~~l~~~~~~~~~~piNaT~s~le~~GlYLidtg~~iflw~g~d~~p~Ll~dlf 774 (861)
T COG5028 695 RLTSLPLKQLMRNIYPTLYALHDMPIEAGLPDEGLLVLPSPINATSSLLESGGLYLIDTGQKIFLWFGKDAVPSLLQDLF 774 (861)
T ss_pred HhhcCCHHHHHHhhccceeeecccccccCCCcccccccccchhhhHHHHhcCCeEEEEcCCEEEEEecCCCCHHHHHHhc
Confidence 99999999999999999999992 1 24889999999999999999999999999999998555545444
Q ss_pred CC------------------CccHHHHHHhhhh
Q 005340 683 NQ------------------PEHQVVNFVVDFD 697 (701)
Q Consensus 683 ~~------------------~e~~~~~~~~~~~ 697 (701)
+. |.++.+.++|+..
T Consensus 775 ~~~~~~~I~~~k~~~p~~~n~~n~~v~~iI~~l 807 (861)
T COG5028 775 GVDSLSDIPSGKFTLPPTGNEFNERVRNIIGEL 807 (861)
T ss_pred CcchhhhccccccccCCcCCHHHHHHHHHHHHH
Confidence 44 7778888888764
No 7
>PTZ00395 Sec24-related protein; Provisional
Probab=100.00 E-value=1.9e-106 Score=918.60 Aligned_cols=606 Identities=16% Similarity=0.197 Sum_probs=501.0
Q ss_pred cccCCCeeeecCCCCCCCHHHhhcCCCCeEEEEccCCCCCCCCCCCCCCC-----------CCccccCCCCceecCceEE
Q 005340 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILP-----------YAPLRCRTCRSILNPFSIV 74 (701)
Q Consensus 6 ~~~~~~~iR~t~~~iP~~~~~~~~~~iPlg~~v~P~~~~~~~~~~vp~~~-----------~~p~RC~~C~ayiNp~~~~ 74 (701)
.++||+|||+|||.||.+.++++.+.||||++++||+.+.++| +||.++ .+|+||.+|++|+|+++.+
T Consensus 648 gn~dP~~~r~tmY~iP~~~~~~~~~~iP~gi~v~Pfa~~~~~e-~~~~~~~~~~~~d~~~~~~~~rc~~c~~y~~~~~~~ 726 (1560)
T PTZ00395 648 GKADPRFLKSTLYQIPLFSETLKLSQIPFGIIVNPFACLNEGE-GIDKIDMKDIINDKEENIEILRCPKCLGYLHATILE 726 (1560)
T ss_pred CCCChhhhhhhhhcCcchHHHHHhcCCCceeecchhhhcCCCC-CCcccchhhcccchhhccceeecchhHhhhcchhee
Confidence 4999999999999999999999999999999999999987766 677642 3799999999999999999
Q ss_pred EcCCceEEeCCCCCCCCCCcc-------ccC-CCC----CC-----CCccccCCCccEEEeCCCC---------------
Q 005340 75 DFAAKIWICPFCFQRNHFPPH-------YAS-ITD----DN-----LPAELFPQYTTIEYEPPGP--------------- 122 (701)
Q Consensus 75 ~~~g~~w~C~~C~~~N~~p~~-------y~~-~~~----~~-----~~pEL~~~~~tvey~~~~~--------------- 122 (701)
+-. ++++|+||++.+.+... |.. +.. .+ ..|-| .|+||+++|..
T Consensus 727 ~~~-~~~~c~~c~~~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~ 802 (1560)
T PTZ00395 727 DIS-SSVQCVFCDTDFLINENVLFDIFQYNEKIGHKESDHNEHGNSLSPLL---KGSVDIIIPPIYYHNVNKFKLTYTYL 802 (1560)
T ss_pred ccc-ceEEEEecCCcchhhHHHHHHHHHHhhhhccccccccccccccchhh---cCceeEEccchhhccCCccceeeehh
Confidence 976 89999999999987422 111 111 01 11323 56666655410
Q ss_pred --------------------------------------------------------------------------------
Q 005340 123 -------------------------------------------------------------------------------- 122 (701)
Q Consensus 123 -------------------------------------------------------------------------------- 122 (701)
T Consensus 803 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 882 (1560)
T PTZ00395 803 NKNINQTAFMITNKIMSFTKHISNSLVANDSKGGNKATSASAFGDSGDANFLAGGGYTNYGGAGGYNTYDNQSGYNNHDV 882 (1560)
T ss_pred hcchhhhhhhhhhhhhhhhhhhcchheecccccccccchhhhcccccccccccccccccccccccccccccccccccccc
Confidence
Q ss_pred ----------C----------------------------------------------------C-CCCCCcEEEEEEECC
Q 005340 123 ----------G----------------------------------------------------E-KSSVPPVFMFVVDTC 139 (701)
Q Consensus 123 ----------~----------------------------------------------------~-~~~~~p~~vFvIDvs 139 (701)
+ + ...+||+|+||||||
T Consensus 883 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~PP~YvFLIDVS 962 (1560)
T PTZ00395 883 VNNRGGSGAGNHLYGKDHDVQNFDNVMDNANFTIHDMKNLICEKNGEPDSAKIRRNSFLAKYPQVKNMLPPYFVFVVECS 962 (1560)
T ss_pred cccccccCcCcccccCcccccchhhhccCCceeeecchhhhhcccCCchhhhhhccchhhccccccCCCCCEEEEEEECC
Confidence 0 0 003689999999999
Q ss_pred Cchhh---HHHHHHHHHHHhhcCC-CCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhHhhcccCCCC
Q 005340 140 IIEEE---MSFLKSALSQAIDLLP-DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPK 215 (701)
Q Consensus 140 ~~~~~---l~~~~~~l~~~l~~lp-~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~l~~~~~~~~ 215 (701)
..+++ +.+++++|+++|+.++ ++++|||||||+.||||+|+ +++....- .|+..-..++.+ |++++|
T Consensus 963 ~~AVkSGLl~tacesIK~sLDsL~dpRTRVGIITFDSsLHFYNLk-s~l~~~~~---~~~~~~~l~qPQ-MLVVSD---- 1033 (1560)
T PTZ00395 963 YNAIYNNITYTILEGIRYAVQNVKCPQTKIAIITFNSSIYFYHCK-GGKGVSGE---EGDGGGGSGNHQ-VIVMSD---- 1033 (1560)
T ss_pred HHHHhhChHHHHHHHHHHHHhcCCCCCcEEEEEEecCcEEEEecC-cccccccc---cccccccCCCce-EEeecC----
Confidence 99998 8999999999999997 56999999999999999997 53100000 000000112232 455554
Q ss_pred CCCccccCccCCCCcccc--cceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEE
Q 005340 216 PSTGVIAGVRDGLSSDTI--ARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARI 293 (701)
Q Consensus 216 ~~~~~~~~~~~~~~~~p~--~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~gg~I 293 (701)
++++|+|+ +++|+++.|+++.|+.+|+.|+. +| ........|+|+||++|..+|+.. +.||||
T Consensus 1034 ----------LDDPFLPlP~ddLLVnL~ESRevIe~LLDkLPe-mF--t~t~~~esCLGSALqAA~~aLk~~--GGGGKI 1098 (1560)
T PTZ00395 1034 ----------VDDPFLPLPLEDLFFGCVEEIDKINTLIDTIKS-VS--TTMQSYGSCGNSALKIAMDMLKER--NGLGSI 1098 (1560)
T ss_pred ----------CccCcCCCCccCeeechHHHHHHHHHHHHHHHH-Hh--hccCCCcccHHHHHHHHHHHHHhc--CCCceE
Confidence 44678884 78999999999999999999987 66 345567899999999999999942 335999
Q ss_pred EEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccC--hhcchhhh
Q 005340 294 LAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVG--VAELKVAV 371 (701)
Q Consensus 294 i~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~--l~~l~~l~ 371 (701)
++|++++|+.|||+|+.++. ..++ ..++.++.+||++||.+|++.+||||+|+++..++| |++|+.|+
T Consensus 1099 iVF~SSLPniGpGaLK~Re~---------~~KE-k~Ll~pqd~FYK~LA~ECsk~qISVDLFLfSsqYvDVDVATLg~Ls 1168 (1560)
T PTZ00395 1099 CMFYTTTPNCGIGAIKELKK---------DLQE-NFLEVKQKIFYDSLLLDLYAFNISVDIFIISSNNVRVCVPSLQYVA 1168 (1560)
T ss_pred EEEEcCCCCCCCCccccccc---------cccc-ccccccchHHHHHHHHHHHhcCCceEEEEccCcccccccccccchh
Confidence 99999999999999987641 1233 356788899999999999999999999999988876 79999999
Q ss_pred ccccceEEEeCCCCchhhH----HHHHHHhccCccCCcceeeEEEEEEecCCceEEEEEcC--CcccCCCCCCccccccc
Q 005340 372 EKTGGLVVLSDSFGHAVFK----DSVRRVFHSGDYDLGLSSNGIFEINCSKDIKVQGIIGP--CASLEKKGPLCSDAVVG 445 (701)
Q Consensus 372 ~~TGG~v~~~~~f~~~~~~----~~l~~~l~~~~~~~~~~~~~~l~vr~S~gl~v~~~~G~--~~~~~~~~~~~sd~~~g 445 (701)
+.|||++++|+.|+..++. .+|.+.|++ ..+||+|+||||||+||+|+.+||+ ++..
T Consensus 1169 r~TGGqlyyYPnFna~rD~~KL~~DL~r~LTr----e~iGyEAVMRVRCS~GLrVs~fyG~GnnF~s------------- 1231 (1560)
T PTZ00395 1169 QNTGGKILFVENFLWQKDYKEIYMNIMDTLTS----EDIAYCCELKLRYSHHMSVKKLFCCNNNFNS------------- 1231 (1560)
T ss_pred cccceeEEEeCCCcccccHHHHHHHHHHHhhc----cceeeEEEEEEECCCCeEEEEEeccCCcccc-------------
Confidence 9999999999999887544 445555532 1479999999999999999999954 3310
Q ss_pred CCCCCceEEecCCCCcEEEEEEEEecCCCCcccccCCCCeEEEEEEEEEEecCCcEEEEEEecceecccCCCCHHHHHhc
Q 005340 446 QGNTSAWKMCGLDKATSLCLVFEIVKKEIPDATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAG 525 (701)
Q Consensus 446 ~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~r~iRV~T~~l~vt~~~~~~~~~~~~ 525 (701)
.++++++.++.+++|+||+|+|++++++.. ...+|||+|++||+.+|+|||||||+++|||+ ++.++|++
T Consensus 1232 ~rStDLLaLP~Id~DqSfaVeLk~DEkL~~-------~~~AYFQaALLYTSssGERRIRVHTLALPVTS---sLseVFrs 1301 (1560)
T PTZ00395 1232 IISVDTIKIPKIRHDQTFAFLLNYSDISES-------KKQIYFQCACIYTNLWGDRFVRLHTTHMNLTS---SLSTVFRY 1301 (1560)
T ss_pred ccccccccccccCCCceEEEEEEeccccCC-------CCcEEEEEEEeeccCCCcEEEEEEeeeecccC---CHHHHHHh
Confidence 124678999999999999999999999853 56899999999999999999999999999994 89999999
Q ss_pred cCHHHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHHHHhhccccCC-----CCccccCccccchHHHHHHhhcccCcC
Q 005340 526 FDQEAAAVVMARLVSFKMEIEAEFDPIRWLDKALIHMCSRFGDYQKDS-----PSSFSLSPRFSIFPQFMFHLRRSQFVQ 600 (701)
Q Consensus 526 ~D~~a~~~~lak~~~~~~~~~~~~~~~~~l~~~lv~~~~~~~~y~~~~-----~~~l~lp~~l~~lP~~~~~l~ks~~l~ 600 (701)
+|++|++.+|+|+++.++++.. ++|+.|.+.++++ |.+||+.| ++||+||++||+||+|+++|+||.+|+
T Consensus 1302 ADqdAIvslLAK~AV~~aLsss--dARe~L~dklVdI---LtaYRK~CAsssssgQLILPESLKLLPLYILSLLKS~AfR 1376 (1560)
T PTZ00395 1302 TDAEALMNILIKQLCTNILHND--NYSKIIIDNLAAI---LFSYRINCASSAHSGQLILPDTLKLLPLFTSSLLKHNVTK 1376 (1560)
T ss_pred hcHHHHHHHHHHHHHHHhcccH--HHHHHHHHHHHHH---HHHHHHHhhccCCCccccchhHHHHHHHHHHHHhcccccc
Confidence 9999999999999999999874 8999999988888 77777765 458999999999999999999999998
Q ss_pred CCCCChhHHHHHHHHHccCCHHHHHHhhcccceeccc---C---------C---CCcccccccccccCCeEEEEeCCcEE
Q 005340 601 VFNNSPDETAYFRMILNRENVTNSVVMIQPSLISYSF---H---------S---GPEPALLDVAAIAADRILLLDSYFTV 665 (701)
Q Consensus 601 ~~~~s~D~r~~~~~~l~~~~~~~~~~~iyP~l~~~~~---~---------~---~p~~~~ls~~~l~~d~iyLlD~~~~i 665 (701)
..+++|+|++.+++++++++..++.++||+||++|. + + .|.+++||.++|.++||||||+|..+
T Consensus 1377 -t~I~sDeRVyaL~rL~SmPI~~Li~yLYPRLYpLHdL~~e~e~d~~d~d~~ivLPp~LrLS~ErLesdGIYLLDNGe~I 1455 (1560)
T PTZ00395 1377 -KEILHDLKVYSLIKLLSMPIISSLLYVYPVMYVIHIKGKTNEIDSMDVDDDLFIPKTIPSSAEKIYSNGIYLLDACTHF 1455 (1560)
T ss_pred -CCCCccHHHHHHHHHhCCCHHHHHhhhcCceEEcccccccccCCccCCCCccccCCcccchHHHhcCCcEEEEECCCEE
Confidence 478999999999999999999999999999999984 0 1 48999999999999999999999999
Q ss_pred EEEECCCh-hHHHHcCCCC
Q 005340 666 VIFHGATI-AQWRKAGYHN 683 (701)
Q Consensus 666 ~i~~G~~v-~~~~~~~~~~ 683 (701)
|||||++| ++|+++-+..
T Consensus 1456 yLWVG~~V~PqLLqDLFGv 1474 (1560)
T PTZ00395 1456 YLYFGFHSDANFAKEIVGD 1474 (1560)
T ss_pred EEEECCCCCHHHHHHHcCC
Confidence 99999999 6788776653
No 8
>cd01478 Sec23-like Sec23-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 23 is very similar to Sec24. The Sec23 and Sec24
Probab=100.00 E-value=1.5e-54 Score=445.82 Aligned_cols=264 Identities=55% Similarity=0.918 Sum_probs=238.6
Q ss_pred CCcEEEEEEECCCchhhHHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhHh
Q 005340 128 VPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQL 207 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~~l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~l 207 (701)
.||+|+||||+|..+++++.++++|+++|+.||++++|||||||++||||+|+ .. .+++++||+|+|+|+.+|+++++
T Consensus 2 ~pp~~vFviDvs~~~~el~~l~~sl~~~L~~lP~~a~VGlITfd~~V~~~~L~-~~-~~~~~~vf~g~~~~~~~~~~~~l 79 (267)
T cd01478 2 SPPVFLFVVDTCMDEEELDALKESLIMSLSLLPPNALVGLITFGTMVQVHELG-FE-ECSKSYVFRGNKDYTAKQIQDML 79 (267)
T ss_pred CCCEEEEEEECccCHHHHHHHHHHHHHHHHhCCCCCEEEEEEECCEEEEEEcC-CC-cCceeeeccCCccCCHHHHHHHh
Confidence 68999999999999999999999999999999999999999999999999999 76 78999999999999999999998
Q ss_pred hcccCCCCCCCccccCccCCCCccc--ccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhcc
Q 005340 208 NFFIKKPKPSTGVIAGVRDGLSSDT--IARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (701)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~~~~~~~p--~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~ 285 (701)
++.+.... ..+... .+.++.+.| .++|++|++||++.|+++|++|+++.|+.++++|+.||+|+||++|..+|+.+
T Consensus 80 ~~~~~~~~-~~~~~~-~~~~~~~~p~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~r~~r~~G~Al~~A~~ll~~~ 157 (267)
T cd01478 80 GLGGPAMR-PSASQH-PGAGNPLPSAAASRFLLPVSQCEFTLTDLLEQLQPDPWPVPAGHRPLRCTGVALSIAVGLLEAC 157 (267)
T ss_pred cccccccc-ccccCc-CCccccccccccccEEEEHHHHHHHHHHHHHhCcccccccCCCCCCCCchHHHHHHHHHHHHhh
Confidence 77541000 000000 012345555 37999999999999999999999988888888999999999999999999987
Q ss_pred CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccChh
Q 005340 286 VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVA 365 (701)
Q Consensus 286 ~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~ 365 (701)
.++.||||++|++|+||.|||+|+.|+.++++|+|.|++++++++++++.+||++||.+|+++||+||+|+++.+|+|++
T Consensus 158 ~~~~gGki~~F~sg~pT~GpG~l~~r~~~~~~r~~~d~~~~~~~~~~~a~~fY~~la~~~~~~~vsvDlF~~s~d~vgla 237 (267)
T cd01478 158 FPNTGARIMLFAGGPCTVGPGAVVSTELKDPIRSHHDIDKDNAKYYKKAVKFYDSLAKRLAANGHAVDIFAGCLDQVGLL 237 (267)
T ss_pred cCCCCcEEEEEECCCCCCCCceeeccccccccccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEEeccccccCHH
Confidence 77899999999999999999999999999999999999998888999999999999999999999999999999999999
Q ss_pred cchhhhccccceEEEeCCCCchhhHHHHHH
Q 005340 366 ELKVAVEKTGGLVVLSDSFGHAVFKDSVRR 395 (701)
Q Consensus 366 ~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~ 395 (701)
+|+.|++.|||.+++|++|+.+.|+++|+|
T Consensus 238 em~~l~~~TGG~v~~~~~f~~~~f~~s~~~ 267 (267)
T cd01478 238 EMKVLVNSTGGHVVLSDSFTTSIFKQSFQR 267 (267)
T ss_pred HHHHHHHhcCcEEEEeCCcchHHHHHHhcC
Confidence 999999999999999999999999998864
No 9
>cd01468 trunk_domain trunk domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface. Some members of this family possess a partial MIDAS motif that is a characteristic feature of most vWA domain proteins.
Probab=100.00 E-value=1.4e-43 Score=362.14 Aligned_cols=229 Identities=40% Similarity=0.592 Sum_probs=195.3
Q ss_pred CCcEEEEEEECCCchh---hHHHHHHHHHHHhhcCC--CCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHH
Q 005340 128 VPPVFMFVVDTCIIEE---EMSFLKSALSQAIDLLP--DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQ 202 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~---~l~~~~~~l~~~l~~lp--~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~ 202 (701)
+||+|+||||+|.+++ .+++++++|+++|+.|| ++++|||||||++||||+++ +....++++|+++.+
T Consensus 2 ~pp~~vFvID~s~~ai~~~~l~~~~~sl~~~l~~lp~~~~~~igiITf~~~V~~~~~~-~~~~~~~~~v~~dl~------ 74 (239)
T cd01468 2 QPPVFVFVIDVSYEAIKEGLLQALKESLLASLDLLPGDPRARVGLITYDSTVHFYNLS-SDLAQPKMYVVSDLK------ 74 (239)
T ss_pred CCCEEEEEEEcchHhccccHHHHHHHHHHHHHHhCCCCCCcEEEEEEeCCeEEEEECC-CCCCCCeEEEeCCCc------
Confidence 6999999999999954 49999999999999999 99999999999999999998 653346666644221
Q ss_pred HHhHhhcccCCCCCCCccccCccCCCCccc-ccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHH
Q 005340 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDT-IARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (701)
Q Consensus 203 l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p-~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~l 281 (701)
+.|+| .++++++++|+++.|.++|++|++..+.. +++++.||+|+||++|..+
T Consensus 75 -------------------------d~f~p~~~~~l~~~~e~~~~i~~~l~~l~~~~~~~-~~~~~~~~~G~Al~~A~~l 128 (239)
T cd01468 75 -------------------------DVFLPLPDRFLVPLSECKKVIHDLLEQLPPMFWPV-PTHRPERCLGPALQAAFLL 128 (239)
T ss_pred -------------------------cCcCCCcCceeeeHHHHHHHHHHHHHhhhhhcccc-CCCCCcccHHHHHHHHHHH
Confidence 23445 37899999999999999999999843321 3678899999999999999
Q ss_pred hhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCc
Q 005340 282 LGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (701)
Q Consensus 282 l~~~~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~ 361 (701)
|+.. ..||||++|++|+||.|||+|+.++.++++|+| + ++++++++.+||++||.+|+++||+||+|+++.++
T Consensus 129 l~~~--~~gGkI~~f~sg~pt~GpG~l~~~~~~~~~~~~----~-e~~~~~~a~~fY~~la~~~~~~~isvdlF~~~~~~ 201 (239)
T cd01468 129 LKGT--FAGGRIIVFQGGLPTVGPGKLKSREDKEPIRSH----D-EAQLLKPATKFYKSLAKECVKSGICVDLFAFSLDY 201 (239)
T ss_pred Hhhc--CCCceEEEEECCCCCCCCCccccCcccccCCCc----c-chhcccccHHHHHHHHHHHHHcCeEEEEEeccccc
Confidence 9932 139999999999999999999999988888876 2 36899999999999999999999999999999999
Q ss_pred cChhcchhhhccccceEEEeCCCCchhhHHHHHHH
Q 005340 362 VGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRV 396 (701)
Q Consensus 362 ~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~ 396 (701)
+|+++|+.|++.|||.+++|++|+..+..+.|.+.
T Consensus 202 ~dl~~l~~l~~~TGG~v~~y~~f~~~~~~~~~~~~ 236 (239)
T cd01468 202 VDVATLKQLAKSTGGQVYLYDSFQAPNDGSKFKQD 236 (239)
T ss_pred cCHHHhhhhhhcCCceEEEeCCCCCcccHHHHHHH
Confidence 99999999999999999999999655444444433
No 10
>cd01479 Sec24-like Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24
Probab=100.00 E-value=3.7e-43 Score=358.79 Aligned_cols=227 Identities=22% Similarity=0.318 Sum_probs=194.0
Q ss_pred CCcEEEEEEECCCchhh---HHHHHHHHHHHhhcCCCC---cEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChH
Q 005340 128 VPPVFMFVVDTCIIEEE---MSFLKSALSQAIDLLPDN---SLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~~---l~~~~~~l~~~l~~lp~~---~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~ 201 (701)
+||+|+||||+|..+++ +++++++|+++|+.+|++ ++|||||||+.||||+++ +.+..+++++
T Consensus 2 ~pp~~~FvIDvs~~a~~~g~~~~~~~si~~~L~~lp~~~~~~~VgiITfd~~v~~y~l~-~~~~~~q~~v---------- 70 (244)
T cd01479 2 QPAVYVFLIDVSYNAIKSGLLATACEALLSNLDNLPGDDPRTRVGFITFDSTLHFFNLK-SSLEQPQMMV---------- 70 (244)
T ss_pred CCCEEEEEEEccHHHHhhChHHHHHHHHHHHHHhcCCCCCCeEEEEEEECCeEEEEECC-CCCCCCeEEE----------
Confidence 69999999999999986 999999999999999977 999999999999999998 6534444433
Q ss_pred HHHhHhhcccCCCCCCCccccCccCCCCcccc-cceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHH
Q 005340 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTI-ARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAAS 280 (701)
Q Consensus 202 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~-~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ 280 (701)
++| ++++++|+ ++|++|++|+++.|.++|++|+. .| .+++++.+|+|+||++|..
T Consensus 71 -------v~d--------------l~d~f~P~~~~~lv~l~e~~~~i~~lL~~L~~-~~--~~~~~~~~c~G~Al~~A~~ 126 (244)
T cd01479 71 -------VSD--------------LDDPFLPLPDGLLVNLKESRQVIEDLLDQIPE-MF--QDTKETESALGPALQAAFL 126 (244)
T ss_pred -------eeC--------------cccccCCCCcceeecHHHHHHHHHHHHHHHHH-HH--hcCCCCcccHHHHHHHHHH
Confidence 222 12355664 78999999999999999999976 55 5678889999999999999
Q ss_pred HhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCC
Q 005340 281 LLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (701)
Q Consensus 281 ll~~~~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~ 360 (701)
+|+ +.||||++|++|+||.|||+|+.++.++ ++.+. ++ +++++++.+||+++|.+|+++||+||+|+++.+
T Consensus 127 lL~----~~GGkIi~f~s~~pt~GpG~l~~~~~~~-~~~~~---~e-~~~~~p~~~fY~~la~~~~~~~isvDlF~~~~~ 197 (244)
T cd01479 127 LLK----ETGGKIIVFQSSLPTLGAGKLKSREDPK-LLSTD---KE-KQLLQPQTDFYKKLALECVKSQISVDLFLFSNQ 197 (244)
T ss_pred HHH----hcCCEEEEEeCCCCCcCCcccccCcccc-ccCch---hh-hhhcCcchHHHHHHHHHHHHcCeEEEEEEccCc
Confidence 999 8999999999999999999999998654 34332 33 478999999999999999999999999999999
Q ss_pred ccChhcchhhhccccceEEEeC--CCCch----hhHHHHHHHhc
Q 005340 361 QVGVAELKVAVEKTGGLVVLSD--SFGHA----VFKDSVRRVFH 398 (701)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~~~~--~f~~~----~~~~~l~~~l~ 398 (701)
++|+++|+.|++.|||.+++|+ .|+.. ++..+++|.++
T Consensus 198 ~~dla~l~~l~~~TGG~v~~y~~~~~~~~~d~~kl~~dl~~~lt 241 (244)
T cd01479 198 YVDVATLGCLSRLTGGQVYYYPSFNFSAPNDVEKLVNELARYLT 241 (244)
T ss_pred ccChhhhhhhhhhcCceEEEECCccCCchhhHHHHHHHHHHHhc
Confidence 9999999999999999999999 66644 45556666663
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=5.2e-43 Score=359.39 Aligned_cols=230 Identities=32% Similarity=0.495 Sum_probs=179.1
Q ss_pred CCcEEEEEEECCCchhh---HHHHHHHHHHHhhcCC--CCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHH
Q 005340 128 VPPVFMFVVDTCIIEEE---MSFLKSALSQAIDLLP--DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQ 202 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~~---l~~~~~~l~~~l~~lp--~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~ 202 (701)
+||+|+||||+|.++++ ++.++++|+++|+.+| ++++|||||||+.||||+++ ..+..++++| +.+
T Consensus 2 ~pp~y~FvID~s~~av~~g~~~~~~~sl~~~l~~l~~~~~~~vgiitfd~~V~~y~l~-~~~~~~~~~v--------~~d 72 (243)
T PF04811_consen 2 QPPVYVFVIDVSYEAVQSGLLQSLIESLKSALDSLPGDERTRVGIITFDSSVHFYNLS-SSLSQPQMIV--------VSD 72 (243)
T ss_dssp S--EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTSSTSTT-EEEEEEESSSEEEEETT-TTSSSTEEEE--------EHH
T ss_pred CCCEEEEEEECchhhhhccHHHHHHHHHHHHHHhccCCCCcEEEEEEeCCEEEEEECC-CCcCCCcccc--------hHH
Confidence 69999999999999665 9999999999999999 89999999999999999998 6534455554 345
Q ss_pred HHhHhhcccCCCCCCCccccCccCCCCccc-ccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHH
Q 005340 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDT-IARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (701)
Q Consensus 203 l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p-~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~l 281 (701)
++++ +.| .++|++++.++++.|.++|++|++ .|+...++++.||+|+||++|..+
T Consensus 73 l~~~-----------------------~~p~~~~llv~~~e~~~~i~~ll~~L~~-~~~~~~~~~~~~c~G~Al~~A~~l 128 (243)
T PF04811_consen 73 LDDP-----------------------FIPLPDGLLVPLSECRDAIEELLESLPS-IFPETAGKRPERCLGSALSAALSL 128 (243)
T ss_dssp TTSH-----------------------HSSTSSSSSEETTTCHHHHHHHHHHHHH-HSTT-TTB-----HHHHHHHHHHH
T ss_pred Hhhc-----------------------ccCCcccEEEEhHHhHHHHHHHHHHhhh-hcccccccCccccHHHHHHHHHHH
Confidence 4443 233 288999999999999999999998 675555588999999999999999
Q ss_pred hhccCCCCCcEEEEEecCCCCCCC-cccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCC
Q 005340 282 LGACVPGSGARILAFVGGPSTEGP-AAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (701)
Q Consensus 282 l~~~~~~~gg~Ii~F~~g~pt~Gp-G~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~ 360 (701)
|+.. ..||||++|++|+||.|| |++..++.. .+.+.++++..+++++.+||++||++|+++||+||+|+++.+
T Consensus 129 l~~~--~~gGkI~~F~s~~pt~G~Gg~l~~~~~~----~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~ 202 (243)
T PF04811_consen 129 LSSR--NTGGKILVFTSGPPTYGPGGSLKKREDS----SHYDTEKEKALLLPPANEFYKKLAEECSKQGISVDLFVFSSD 202 (243)
T ss_dssp HHHH--TS-EEEEEEESS---SSSTTSS-SBTTS----CCCCHCTTHHCHSHSSSHHHHHHHHHHHHCTEEEEEEEECSS
T ss_pred Hhcc--ccCCEEEEEeccCCCCCCCceecccccc----cccccccchhhhccccchHHHHHHHHHHhcCCEEEEEeecCC
Confidence 9854 589999999999999999 676666543 456667776778889999999999999999999999999999
Q ss_pred ccChhcchhhhccccceEEEeCCCCchhhHHHHHHH
Q 005340 361 QVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRV 396 (701)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~ 396 (701)
++|+++|+.|++.|||.+++|++|+.+.+.+.|++.
T Consensus 203 ~~~l~tl~~l~~~TGG~l~~y~~f~~~~~~~~l~~d 238 (243)
T PF04811_consen 203 YVDLATLGPLARYTGGSLYYYPNFNAERDGEKLRQD 238 (243)
T ss_dssp --SHHHHTHHHHCTT-EEEEETTTTCHHHHHHHHHH
T ss_pred CCCcHhHHHHHHhCceeEEEeCCCCCchhHHHHHHH
Confidence 999999999999999999999999955444444433
No 12
>PF08033 Sec23_BS: Sec23/Sec24 beta-sandwich domain; InterPro: IPR012990 COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger (IPR006895 from INTERPRO), an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes part of the Sec23/24 beta-barrel domain, which is formed from approximately 180 residues from three segments of the polypeptide. The strands of the barrel are oriented roughly parallel to the membrane such that one end of the barrel forms part of the inner surface of the coat and the other end part of the membrane-distal surface. The barrel is constructed from two opposed sheets: a six-stranded beta sheet facing partly towards the zinc finger domain and partly towards the solvent, and a five-stranded beta sheet facing the helical domain.; PDB: 3EFO_B 3EG9_B 1PD0_A 1PD1_A 1M2V_B 1PCX_A 3EH2_C 3EGD_A 2NUP_A 3EGX_A ....
Probab=99.87 E-value=7.4e-22 Score=172.28 Aligned_cols=96 Identities=40% Similarity=0.672 Sum_probs=86.9
Q ss_pred eeeEEEEEEecCCceEEEEEcCCcccCCCCCCcccccccCCCCCceEEecCCCCcEEEEEEEEecCCCCcccccCCCCeE
Q 005340 407 SSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPDATLQSTNNQF 486 (701)
Q Consensus 407 ~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~~sd~~~g~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~ 486 (701)
||+|+||||||+|++|.+++||+... +++|+.++|.++++.|.+++++++++|+|+|++++++. ..+.+
T Consensus 1 g~~~~l~vr~S~gl~v~~~~G~~~~~----~~~s~~~~g~~~~~~~~~~~l~~~~s~~~~~~~~~~~~-------~~~~~ 69 (96)
T PF08033_consen 1 GFNAVLRVRCSKGLKVSGVIGPCFNR----SSVSDNEIGEGDTTRWKLPSLDPDTSFAFEFEIDEDLP-------NGSQA 69 (96)
T ss_dssp EEEEEEEEEE-TTEEEEEEESSSEES----STBESSECSBSSCSEEEEEEEETT--EEEEEEESSBTB-------TTSEE
T ss_pred CceEEEEEEECCCeEEEEEEcCcccc----ccccceeeccCCccEEEecccCCCCEEEEEEEECCCCC-------CCCeE
Confidence 79999999999999999999999975 36899999999999999999999999999999998774 36899
Q ss_pred EEEEEEEEEecCCcEEEEEEecceecc
Q 005340 487 YFQFLTYYQHNCGQMRLRVTTLSRRWV 513 (701)
Q Consensus 487 ~iQ~al~Yt~~~G~r~iRV~T~~l~vt 513 (701)
|||++++||+.+|+|||||+|+++|+|
T Consensus 70 ~iQ~~~~Yt~~~G~r~iRV~T~~l~vt 96 (96)
T PF08033_consen 70 YIQFALLYTDSNGERRIRVTTLSLPVT 96 (96)
T ss_dssp EEEEEEEEEETTSEEEEEEEEEEEEEE
T ss_pred EEEEEEEEECCCCCEEEEEEeeccccC
Confidence 999999999999999999999999986
No 13
>PF04815 Sec23_helical: Sec23/Sec24 helical domain; InterPro: IPR006900 COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger (IPR006895 from INTERPRO), an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region, and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes the all-helical domain, which forms an approximately 105-residue segment with the C-terminal 30 residues. The linker between alpha-M and alpha-N contacts Sar1.; GO: 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EGD_B 2NUP_B 2NUT_B 3EGX_B 3EH2_C 3EH1_A 3EFO_B 3EG9_B 2QTV_A 1M2O_C ....
Probab=99.75 E-value=5e-18 Score=150.07 Aligned_cols=101 Identities=24% Similarity=0.291 Sum_probs=88.8
Q ss_pred HHHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHHHHhhccccCC--CCccccCccccchHHHHHHhhcccCcCCCCCC
Q 005340 528 QEAAAVVMARLVSFKMEIEAEFDPIRWLDKALIHMCSRFGDYQKDS--PSSFSLSPRFSIFPQFMFHLRRSQFVQVFNNS 605 (701)
Q Consensus 528 ~~a~~~~lak~~~~~~~~~~~~~~~~~l~~~lv~~~~~~~~y~~~~--~~~l~lp~~l~~lP~~~~~l~ks~~l~~~~~s 605 (701)
|||++++++|+++.++.+++..++|+++++++++++..|+.+.... +++|+|||+||+||+|+++|+||++|++.+++
T Consensus 1 Qda~~~llak~ai~~~~~~~l~~~r~~l~~~~v~il~~Yr~~~~~~~~~~qLilPe~lklLPly~l~llKs~alr~~~v~ 80 (103)
T PF04815_consen 1 QDAITSLLAKQAIDKALSSSLKDARESLDNRLVDILAAYRKNCASSSSSGQLILPESLKLLPLYILALLKSPALRPTNVS 80 (103)
T ss_dssp HHHHHHHHHHHHHHHHCCS-HHHHHHHHHHHHHHHHHHHHHHCTTECCCTEEEEEGGGTTHHHHHHHHHTSTTTSCSTS-
T ss_pred CHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHhhccCCCCchhhhCCHHHHHHHHHHHHHHcchhhcCCCCC
Confidence 7999999999999999999999999999999999955555544432 35799999999999999999999999999999
Q ss_pred hhHHHHHHHHHccCCHHHHHHhh
Q 005340 606 PDETAYFRMILNRENVTNSVVMI 628 (701)
Q Consensus 606 ~D~r~~~~~~l~~~~~~~~~~~i 628 (701)
+|+|++.++++++++++.++.||
T Consensus 81 ~D~R~~~~~~~~~~~~~~~~~~i 103 (103)
T PF04815_consen 81 PDERAYAMHLLLSMPVDSLLRMI 103 (103)
T ss_dssp HHHHHHHHHHHHHS-HHHHHHHH
T ss_pred CcHHHHHHHHHHCCCHHHHHhhC
Confidence 99999999999999999999875
No 14
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=99.61 E-value=2e-16 Score=113.35 Aligned_cols=40 Identities=55% Similarity=1.250 Sum_probs=29.1
Q ss_pred CccccCCCCceecCceEEEcCCceEEeCCCCCCCCCCccc
Q 005340 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHY 96 (701)
Q Consensus 57 ~p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p~~y 96 (701)
+|+||++|+||||||++++.++++|+|+||++.|++|++|
T Consensus 1 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp~~Y 40 (40)
T PF04810_consen 1 GPVRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLPPHY 40 (40)
T ss_dssp -S-B-TTT--BS-TTSEEETTTTEEEETTT--EEE--GGG
T ss_pred CccccCCCCCEECCcceEcCCCCEEECcCCCCcCCCCCCC
Confidence 5899999999999999999999999999999999999887
No 15
>cd01465 vWA_subgroup VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if n
Probab=98.55 E-value=4.5e-06 Score=80.47 Aligned_cols=159 Identities=16% Similarity=0.189 Sum_probs=109.8
Q ss_pred EEEEEEECCCchhh--HHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhHhh
Q 005340 131 VFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLN 208 (701)
Q Consensus 131 ~~vFvIDvs~~~~~--l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~l~ 208 (701)
.++||+|+|.++.. ++.+++++...+..++++.+||+++|++..+..- . .. .
T Consensus 2 ~~~~vlD~S~SM~~~~~~~~k~a~~~~~~~l~~~~~v~li~f~~~~~~~~-~-~~-~----------------------- 55 (170)
T cd01465 2 NLVFVIDRSGSMDGPKLPLVKSALKLLVDQLRPDDRLAIVTYDGAAETVL-P-AT-P----------------------- 55 (170)
T ss_pred cEEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEecCCccEEe-c-Cc-c-----------------------
Confidence 36899999998754 7888899999999998888999999987654421 0 00 0
Q ss_pred cccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhccCC-
Q 005340 209 FFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVP- 287 (701)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~- 287 (701)
.. ....+...|+.+.. ...+.++.||..|...+.....
T Consensus 56 -------------------------------~~-~~~~l~~~l~~~~~---------~g~T~~~~al~~a~~~~~~~~~~ 94 (170)
T cd01465 56 -------------------------------VR-DKAAILAAIDRLTA---------GGSTAGGAGIQLGYQEAQKHFVP 94 (170)
T ss_pred -------------------------------cc-hHHHHHHHHHcCCC---------CCCCCHHHHHHHHHHHHHhhcCC
Confidence 00 01223344454432 1235778999999888864221
Q ss_pred CCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccChhcc
Q 005340 288 GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAEL 367 (701)
Q Consensus 288 ~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~l 367 (701)
..-.+|++|++|.++.|+.. .+-+.+....+...++.|+.+.++ ...+...|
T Consensus 95 ~~~~~ivl~TDG~~~~~~~~---------------------------~~~~~~~~~~~~~~~v~i~~i~~g-~~~~~~~l 146 (170)
T cd01465 95 GGVNRILLATDGDFNVGETD---------------------------PDELARLVAQKRESGITLSTLGFG-DNYNEDLM 146 (170)
T ss_pred CCeeEEEEEeCCCCCCCCCC---------------------------HHHHHHHHHHhhcCCeEEEEEEeC-CCcCHHHH
Confidence 11267999999998876411 112234455566789999999998 67899999
Q ss_pred hhhhccccceEEEeCCC
Q 005340 368 KVAVEKTGGLVVLSDSF 384 (701)
Q Consensus 368 ~~l~~~TGG~v~~~~~f 384 (701)
..++..++|..++.++.
T Consensus 147 ~~ia~~~~g~~~~~~~~ 163 (170)
T cd01465 147 EAIADAGNGNTAYIDNL 163 (170)
T ss_pred HHHHhcCCceEEEeCCH
Confidence 99999999998876543
No 16
>cd01463 vWA_VGCC_like VWA Voltage gated Calcium channel like: Voltage-gated calcium channels are a complex of five proteins: alpha 1, beta 1, gamma, alpha 2 and delta. The alpha 2 and delta subunits result from proteolytic processing of a single gene product and carries at its N-terminus the VWA and cache domains, The alpha 2 delta gene family has orthologues in D. melanogaster and C. elegans but none have been detected in aither A. thaliana or yeast. The exact biochemical function of the VWA domain is not known but the alpha 2 delta complex has been shown to regulate various functional properties of the channel complex.
Probab=98.52 E-value=4.8e-06 Score=82.20 Aligned_cols=166 Identities=16% Similarity=0.124 Sum_probs=106.6
Q ss_pred CCcEEEEEEECCCchhh--HHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEEE-cCCCCCCCCceeeecCCccCChHHHH
Q 005340 128 VPPVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHE-LGGFGQIIPKTYVFKGSKDVSKDQLL 204 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~~--l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~~-l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (701)
.|-.++||||+|.++.. ++.++++++..++.++++.+||||+|++.++..- .. ..
T Consensus 12 ~p~~vv~llD~SgSM~~~~l~~ak~~~~~ll~~l~~~d~v~lv~F~~~~~~~~~~~-~~--------------------- 69 (190)
T cd01463 12 SPKDIVILLDVSGSMTGQRLHLAKQTVSSILDTLSDNDFFNIITFSNEVNPVVPCF-ND--------------------- 69 (190)
T ss_pred CCceEEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCCCEEEEEEeCCCeeEEeeec-cc---------------------
Confidence 46789999999998753 8899999999999999999999999999877642 11 00
Q ss_pred hHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhc
Q 005340 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (701)
Q Consensus 205 ~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~ 284 (701)
.+.....+..+.+...|+.|+. . ..+.++.||..|...+..
T Consensus 70 ------------------------------~~~~~~~~~~~~~~~~l~~l~~------~---G~T~~~~al~~a~~~l~~ 110 (190)
T cd01463 70 ------------------------------TLVQATTSNKKVLKEALDMLEA------K---GIANYTKALEFAFSLLLK 110 (190)
T ss_pred ------------------------------ceEecCHHHHHHHHHHHhhCCC------C---CcchHHHHHHHHHHHHHH
Confidence 0000011122344455565543 1 246789999999988874
Q ss_pred c---C-----CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHH-HHHHcCcEEEEE
Q 005340 285 C---V-----PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSK-QLVHQGHVLDLF 355 (701)
Q Consensus 285 ~---~-----~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~-~~~~~~isvDlf 355 (701)
. . +.....|+++++|.++.+.-.+ +.+.. .....++.|..|
T Consensus 111 ~~~~~~~~~~~~~~~~iillTDG~~~~~~~~~------------------------------~~~~~~~~~~~~v~i~ti 160 (190)
T cd01463 111 NLQSNHSGSRSQCNQAIMLITDGVPENYKEIF------------------------------DKYNWDKNSEIPVRVFTY 160 (190)
T ss_pred hhhcccccccCCceeEEEEEeCCCCCcHhHHH------------------------------HHhcccccCCCcEEEEEE
Confidence 1 0 0122468999999775321100 11100 001124555555
Q ss_pred EecCCccChhcchhhhccccceEEEeCCC
Q 005340 356 ACALDQVGVAELKVAVEKTGGLVVLSDSF 384 (701)
Q Consensus 356 ~~~~~~~~l~~l~~l~~~TGG~v~~~~~f 384 (701)
.++.+..|...|..|+..+||..++.++.
T Consensus 161 giG~~~~d~~~L~~lA~~~~G~~~~i~~~ 189 (190)
T cd01463 161 LIGREVTDRREIQWMACENKGYYSHIQSL 189 (190)
T ss_pred ecCCccccchHHHHHHhhcCCeEEEcccC
Confidence 55555558889999999999999987653
No 17
>cd01466 vWA_C3HC4_type VWA C3HC4-type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most,
Probab=98.48 E-value=4.9e-06 Score=79.36 Aligned_cols=149 Identities=19% Similarity=0.182 Sum_probs=103.3
Q ss_pred EEEEEECCCchhh--HHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhHhhc
Q 005340 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNF 209 (701)
Q Consensus 132 ~vFvIDvs~~~~~--l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~l~~ 209 (701)
.+|+||+|.++.. ++.+++++...++.++++.+||||+|++..+.+ . +- .
T Consensus 3 v~~vlD~S~SM~~~rl~~ak~a~~~l~~~l~~~~~~~li~F~~~~~~~--~-~~-~------------------------ 54 (155)
T cd01466 3 LVAVLDVSGSMAGDKLQLVKHALRFVISSLGDADRLSIVTFSTSAKRL--S-PL-R------------------------ 54 (155)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcceEEEEEecCCcccc--C-CC-c------------------------
Confidence 5799999999764 888999999999999998999999999765432 1 00 0
Q ss_pred ccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhccC-CC
Q 005340 210 FIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACV-PG 288 (701)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~-~~ 288 (701)
+.. ...+..+.++++.+.. ...++++.||..|..++.... ..
T Consensus 55 ----------------------~~~------~~~~~~~~~~i~~~~~---------~g~T~~~~al~~a~~~~~~~~~~~ 97 (155)
T cd01466 55 ----------------------RMT------AKGKRSAKRVVDGLQA---------GGGTNVVGGLKKALKVLGDRRQKN 97 (155)
T ss_pred ----------------------ccC------HHHHHHHHHHHHhccC---------CCCccHHHHHHHHHHHHhhcccCC
Confidence 000 0122345566666543 235789999999999987321 12
Q ss_pred CCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccChhcch
Q 005340 289 SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELK 368 (701)
Q Consensus 289 ~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~l~ 368 (701)
....|+++++|.++.|+..+ ++.+.++.|..+.++. ..+..+|.
T Consensus 98 ~~~~iillTDG~~~~~~~~~-----------------------------------~~~~~~v~v~~igig~-~~~~~~l~ 141 (155)
T cd01466 98 PVASIMLLSDGQDNHGAVVL-----------------------------------RADNAPIPIHTFGLGA-SHDPALLA 141 (155)
T ss_pred CceEEEEEcCCCCCcchhhh-----------------------------------cccCCCceEEEEecCC-CCCHHHHH
Confidence 34689999999887661000 0112477888877753 46888999
Q ss_pred hhhccccceEEEe
Q 005340 369 VAVEKTGGLVVLS 381 (701)
Q Consensus 369 ~l~~~TGG~v~~~ 381 (701)
.++..|||..++.
T Consensus 142 ~iA~~t~G~~~~~ 154 (155)
T cd01466 142 FIAEITGGTFSYV 154 (155)
T ss_pred HHHhccCceEEEe
Confidence 9999999998863
No 18
>PRK13685 hypothetical protein; Provisional
Probab=98.47 E-value=6.8e-06 Score=88.23 Aligned_cols=161 Identities=20% Similarity=0.186 Sum_probs=112.8
Q ss_pred CcEEEEEEECCCchh-------hHHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChH
Q 005340 129 PPVFMFVVDTCIIEE-------EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (701)
Q Consensus 129 ~p~~vFvIDvs~~~~-------~l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~ 201 (701)
+...+||||+|.++. .++.++++++..++.++++.+||+|+|++..++.. |
T Consensus 88 ~~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l~~~d~vglv~Fa~~a~~~~--------p-------------- 145 (326)
T PRK13685 88 RAVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELTPGINLGLIAFAGTATVLV--------S-------------- 145 (326)
T ss_pred CceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhCCCCCeEEEEEEcCceeecC--------C--------------
Confidence 446899999999975 38999999999999998889999999987654320 0
Q ss_pred HHHhHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHH
Q 005340 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (701)
Q Consensus 202 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~l 281 (701)
+...++.+...|+.+... ..++.|.|+..|...
T Consensus 146 --------------------------------------~t~d~~~l~~~l~~l~~~---------~~T~~g~al~~A~~~ 178 (326)
T PRK13685 146 --------------------------------------PTTNREATKNAIDKLQLA---------DRTATGEAIFTALQA 178 (326)
T ss_pred --------------------------------------CCCCHHHHHHHHHhCCCC---------CCcchHHHHHHHHHH
Confidence 001123455677777541 235678999999888
Q ss_pred hhcc-------CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEE
Q 005340 282 LGAC-------VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDL 354 (701)
Q Consensus 282 l~~~-------~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDl 354 (701)
+... .....++|+++++|-.+.|..... . ... .+.++.+.+.||.|..
T Consensus 179 l~~~~~~~~~~~~~~~~~IILlTDG~~~~~~~~~~-------------~--------~~~----~~aa~~a~~~gi~i~~ 233 (326)
T PRK13685 179 IATVGAVIGGGDTPPPARIVLMSDGKETVPTNPDN-------------P--------RGA----YTAARTAKDQGVPIST 233 (326)
T ss_pred HHhhhcccccccCCCCCEEEEEcCCCCCCCCCCCC-------------c--------ccH----HHHHHHHHHcCCeEEE
Confidence 7521 012347899999998776631100 0 000 1346667788999999
Q ss_pred EEecCCc-------------cChhcchhhhccccceEEEeCC
Q 005340 355 FACALDQ-------------VGVAELKVAVEKTGGLVVLSDS 383 (701)
Q Consensus 355 f~~~~~~-------------~~l~~l~~l~~~TGG~v~~~~~ 383 (701)
+.++.+. .|-..|..+++.|||..++.++
T Consensus 234 Ig~G~~~g~~~~~g~~~~~~~d~~~L~~iA~~tgG~~~~~~~ 275 (326)
T PRK13685 234 ISFGTPYGSVEINGQRQPVPVDDESLKKIAQLSGGEFYTAAS 275 (326)
T ss_pred EEECCCCCCcCcCCceeeecCCHHHHHHHHHhcCCEEEEcCC
Confidence 9988642 5778999999999998887654
No 19
>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=98.47 E-value=1.1e-05 Score=78.90 Aligned_cols=163 Identities=19% Similarity=0.134 Sum_probs=108.8
Q ss_pred EEEEEECCCchh---hHHHHHHHHHHHhhc-CCCCcEEEEEEECCE-EEEEEcCCCCCCCCceeeecCCccCChHHHHhH
Q 005340 132 FMFVVDTCIIEE---EMSFLKSALSQAIDL-LPDNSLVGLITFGTL-VQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQ 206 (701)
Q Consensus 132 ~vFvIDvs~~~~---~l~~~~~~l~~~l~~-lp~~~~VgiItf~~~-V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~ 206 (701)
++|+||+|.++. .++.+++++...+.. ++++.+||+|+|++. .++. +. ..
T Consensus 3 v~lvlD~SgSM~~~~rl~~ak~a~~~~~~~~~~~~d~v~lv~F~~~~~~~~-~~-~t----------------------- 57 (178)
T cd01451 3 VIFVVDASGSMAARHRMAAAKGAVLSLLRDAYQRRDKVALIAFRGTEAEVL-LP-PT----------------------- 57 (178)
T ss_pred EEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCceEE-eC-CC-----------------------
Confidence 679999999975 478888888887764 567789999999854 2221 11 00
Q ss_pred hhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhccC
Q 005340 207 LNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACV 286 (701)
Q Consensus 207 l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~ 286 (701)
.....+...|+.++. ...+.++.||..|...++...
T Consensus 58 -----------------------------------~~~~~~~~~l~~l~~---------~G~T~l~~aL~~a~~~l~~~~ 93 (178)
T cd01451 58 -----------------------------------RSVELAKRRLARLPT---------GGGTPLAAGLLAAYELAAEQA 93 (178)
T ss_pred -----------------------------------CCHHHHHHHHHhCCC---------CCCCcHHHHHHHHHHHHHHHh
Confidence 001122344555532 134688999999999882111
Q ss_pred CCCC--cEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccCh
Q 005340 287 PGSG--ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGV 364 (701)
Q Consensus 287 ~~~g--g~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l 364 (701)
...+ ..|++++.|.++.|.... ... -.++++++...||.+..+.+.....+-
T Consensus 94 ~~~~~~~~ivliTDG~~~~g~~~~-----------------------~~~---~~~~~~~l~~~gi~v~~I~~~~~~~~~ 147 (178)
T cd01451 94 RDPGQRPLIVVITDGRANVGPDPT-----------------------ADR---ALAAARKLRARGISALVIDTEGRPVRR 147 (178)
T ss_pred cCCCCceEEEEECCCCCCCCCCch-----------------------hHH---HHHHHHHHHhcCCcEEEEeCCCCccCc
Confidence 1222 578999999888763100 000 145677788889888776665555677
Q ss_pred hcchhhhccccceEEEeCCCCchhh
Q 005340 365 AELKVAVEKTGGLVVLSDSFGHAVF 389 (701)
Q Consensus 365 ~~l~~l~~~TGG~v~~~~~f~~~~~ 389 (701)
..|..|++.|||..++.++.+...|
T Consensus 148 ~~l~~iA~~tgG~~~~~~d~~~~~~ 172 (178)
T cd01451 148 GLAKDLARALGGQYVRLPDLSADAI 172 (178)
T ss_pred cHHHHHHHHcCCeEEEcCcCCHHHH
Confidence 7899999999999999888776544
No 20
>cd01456 vWA_ywmD_type VWA ywmD type:Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=98.45 E-value=4.7e-06 Score=83.43 Aligned_cols=169 Identities=24% Similarity=0.275 Sum_probs=108.7
Q ss_pred CCcEEEEEEECCCchh--------hHHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCC
Q 005340 128 VPPVFMFVVDTCIIEE--------EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVS 199 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~--------~l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~ 199 (701)
.+..++||||+|.++. .++.+++++...++.++++.+||+++|++.++- . . ...
T Consensus 19 ~~~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~l~~~~~v~lv~F~~~~~~---~-~--~~~------------ 80 (206)
T cd01456 19 LPPNVAIVLDNSGSMREVDGGGETRLDNAKAALDETANALPDGTRLGLWTFSGDGDN---P-L--DVR------------ 80 (206)
T ss_pred CCCcEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHhCCCCceEEEEEecCCCCC---C-c--ccc------------
Confidence 5788999999999986 389999999999999998999999999985421 0 0 000
Q ss_pred hHHHHhHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHH
Q 005340 200 KDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAA 279 (701)
Q Consensus 200 ~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~ 279 (701)
..+-... ...+...+. ...+..+.+.|+.+.. + ...+.++.||..|.
T Consensus 81 -----~~~p~~~-----------------~~~~~~~~~---~~~~~~l~~~i~~i~~-----~---~G~T~l~~aL~~a~ 127 (206)
T cd01456 81 -----VLVPKGC-----------------LTAPVNGFP---SAQRSALDAALNSLQT-----P---TGWTPLAAALAEAA 127 (206)
T ss_pred -----ccccccc-----------------cccccCCCC---cccHHHHHHHHHhhcC-----C---CCcChHHHHHHHHH
Confidence 0000000 000000110 0234456677777751 1 12478899999999
Q ss_pred HHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHH-HHcCcEEEEEEec
Q 005340 280 SLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQL-VHQGHVLDLFACA 358 (701)
Q Consensus 280 ~ll~~~~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~-~~~~isvDlf~~~ 358 (701)
..+. ......|+++++|.++.|+.. .+..++++... ...+|.|+.+.++
T Consensus 128 ~~l~---~~~~~~iillTDG~~~~~~~~---------------------------~~~~~~~~~~~~~~~~i~i~~igiG 177 (206)
T cd01456 128 AYVD---PGRVNVVVLITDGEDTCGPDP---------------------------CEVARELAKRRTPAPPIKVNVIDFG 177 (206)
T ss_pred HHhC---CCCcceEEEEcCCCccCCCCH---------------------------HHHHHHHHHhcCCCCCceEEEEEec
Confidence 9985 133378999999987665300 00111222110 2258999999887
Q ss_pred CCccChhcchhhhccccceE
Q 005340 359 LDQVGVAELKVAVEKTGGLV 378 (701)
Q Consensus 359 ~~~~~l~~l~~l~~~TGG~v 378 (701)
.+ .+...|..+++.|||..
T Consensus 178 ~~-~~~~~l~~iA~~tgG~~ 196 (206)
T cd01456 178 GD-ADRAELEAIAEATGGTY 196 (206)
T ss_pred Cc-ccHHHHHHHHHhcCCeE
Confidence 64 67889999999999988
No 21
>cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.
Probab=98.41 E-value=7.4e-06 Score=80.37 Aligned_cols=152 Identities=13% Similarity=0.066 Sum_probs=99.5
Q ss_pred EEEEEEECCCchh-------hHHHHHHHHHHHhhcC---CCCcEEEEEEE-CCEEEEEEcCCCCCCCCceeeecCCccCC
Q 005340 131 VFMFVVDTCIIEE-------EMSFLKSALSQAIDLL---PDNSLVGLITF-GTLVQVHELGGFGQIIPKTYVFKGSKDVS 199 (701)
Q Consensus 131 ~~vFvIDvs~~~~-------~l~~~~~~l~~~l~~l---p~~~~VgiItf-~~~V~~~~l~~~~~~~~~~~v~~g~~~~~ 199 (701)
..+++||+|.++. +++.+++.+...++.+ .++.+||||+| ++.-++-. +
T Consensus 5 ~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~a~~~~---P----------------- 64 (183)
T cd01453 5 HLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLT---D----------------- 64 (183)
T ss_pred EEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCccEEEE---C-----------------
Confidence 4689999999976 3899999998888754 34579999999 44333321 0
Q ss_pred hHHHHhHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHH
Q 005340 200 KDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAA 279 (701)
Q Consensus 200 ~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~ 279 (701)
+....+.+...|+.+.. + ...+.++.||..|.
T Consensus 65 ----------------------------------------lT~D~~~~~~~L~~~~~-----~---~G~t~l~~aL~~A~ 96 (183)
T cd01453 65 ----------------------------------------LTGNPRKHIQALKTARE-----C---SGEPSLQNGLEMAL 96 (183)
T ss_pred ----------------------------------------CCCCHHHHHHHhhcccC-----C---CCchhHHHHHHHHH
Confidence 00000122233333311 1 12478999999999
Q ss_pred HHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecC
Q 005340 280 SLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACAL 359 (701)
Q Consensus 280 ~ll~~~~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~ 359 (701)
..++..-....++|++++++.-+.+| .-+.++++.+.+.||.|++..++.
T Consensus 97 ~~l~~~~~~~~~~iiil~sd~~~~~~------------------------------~~~~~~~~~l~~~~I~v~~IgiG~ 146 (183)
T cd01453 97 ESLKHMPSHGSREVLIIFSSLSTCDP------------------------------GNIYETIDKLKKENIRVSVIGLSA 146 (183)
T ss_pred HHHhcCCccCceEEEEEEcCCCcCCh------------------------------hhHHHHHHHHHHcCcEEEEEEech
Confidence 99974211234678888775221111 012457888889999999999864
Q ss_pred CccChhcchhhhccccceEEEeCC
Q 005340 360 DQVGVAELKVAVEKTGGLVVLSDS 383 (701)
Q Consensus 360 ~~~~l~~l~~l~~~TGG~v~~~~~ 383 (701)
+...|..+|+.|||+.|...+
T Consensus 147 ---~~~~L~~ia~~tgG~~~~~~~ 167 (183)
T cd01453 147 ---EMHICKEICKATNGTYKVILD 167 (183)
T ss_pred ---HHHHHHHHHHHhCCeeEeeCC
Confidence 467899999999999997543
No 22
>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=98.21 E-value=6.8e-05 Score=73.08 Aligned_cols=156 Identities=18% Similarity=0.209 Sum_probs=102.0
Q ss_pred cEEEEEEECCCchh--------hHHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChH
Q 005340 130 PVFMFVVDTCIIEE--------EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (701)
Q Consensus 130 p~~vFvIDvs~~~~--------~l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~ 201 (701)
.-++|+||+|.++. .++.++..+...+... ++.+||+|+|++.++..- . . .
T Consensus 3 ~~vv~vlD~S~SM~~~~~~~~~r~~~a~~~~~~~~~~~-~~~~v~lv~f~~~~~~~~-~-~--~---------------- 61 (180)
T cd01467 3 RDIMIALDVSGSMLAQDFVKPSRLEAAKEVLSDFIDRR-ENDRIGLVVFAGAAFTQA-P-L--T---------------- 61 (180)
T ss_pred ceEEEEEECCcccccccCCCCCHHHHHHHHHHHHHHhC-CCCeEEEEEEcCCeeecc-C-C--C----------------
Confidence 35789999999863 2567777777766654 467999999987664320 0 0 0
Q ss_pred HHHhHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHH
Q 005340 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (701)
Q Consensus 202 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~l 281 (701)
..+..+.++|+.|.. .. + ...+.++.||..|...
T Consensus 62 ----------------------------------------~~~~~~~~~l~~l~~-~~--~---~g~T~l~~al~~a~~~ 95 (180)
T cd01467 62 ----------------------------------------LDRESLKELLEDIKI-GL--A---GQGTAIGDAIGLAIKR 95 (180)
T ss_pred ----------------------------------------ccHHHHHHHHHHhhh-cc--c---CCCCcHHHHHHHHHHH
Confidence 001123345555542 11 1 2346788999999998
Q ss_pred hhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCC-
Q 005340 282 LGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD- 360 (701)
Q Consensus 282 l~~~~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~- 360 (701)
+... ......|+++++|.++.|+ . .+ .+.+..+.+.||.|+.+.++..
T Consensus 96 l~~~-~~~~~~iiliTDG~~~~g~--~-----------------------~~-----~~~~~~~~~~gi~i~~i~ig~~~ 144 (180)
T cd01467 96 LKNS-EAKERVIVLLTDGENNAGE--I-----------------------DP-----ATAAELAKNKGVRIYTIGVGKSG 144 (180)
T ss_pred HHhc-CCCCCEEEEEeCCCCCCCC--C-----------------------CH-----HHHHHHHHHCCCEEEEEEecCCC
Confidence 8632 1234678999999876552 0 00 1223445568999999988862
Q ss_pred ---------ccChhcchhhhccccceEEEeCC
Q 005340 361 ---------QVGVAELKVAVEKTGGLVVLSDS 383 (701)
Q Consensus 361 ---------~~~l~~l~~l~~~TGG~v~~~~~ 383 (701)
..+...|..|++.|||..++..+
T Consensus 145 ~~~~~~~~~~~~~~~l~~la~~tgG~~~~~~~ 176 (180)
T cd01467 145 SGPKPDGSTILDEDSLVEIADKTGGRIFRALD 176 (180)
T ss_pred CCcCCCCcccCCHHHHHHHHHhcCCEEEEecC
Confidence 46788899999999999998654
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=98.21 E-value=9.2e-05 Score=71.09 Aligned_cols=151 Identities=15% Similarity=0.173 Sum_probs=94.8
Q ss_pred EEEEEECCCchhh--HHHHHHHHHHHhhcCC---CCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhH
Q 005340 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQ 206 (701)
Q Consensus 132 ~vFvIDvs~~~~~--l~~~~~~l~~~l~~lp---~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~ 206 (701)
.+|+||+|.++.. ++.++++++..+..+. ++.++|+|+|++..+.. .. .. .
T Consensus 3 vv~vlD~SgSm~~~~~~~~k~~~~~~~~~l~~~~~~~~~giv~Fs~~~~~~-~~-~~-~--------------------- 58 (164)
T cd01472 3 IVFLVDGSESIGLSNFNLVKDFVKRVVERLDIGPDGVRVGVVQYSDDPRTE-FY-LN-T--------------------- 58 (164)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHhhcccCCCCeEEEEEEEcCceeEE-Ee-cC-C---------------------
Confidence 4899999998755 7888888888887764 46799999999876553 11 00 0
Q ss_pred hhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhcc-
Q 005340 207 LNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC- 285 (701)
Q Consensus 207 l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~- 285 (701)
. ..+..+.+.|+.++. . ...+.+|.||..|...+...
T Consensus 59 --~--------------------------------~~~~~~~~~l~~l~~-----~---~g~T~~~~al~~a~~~l~~~~ 96 (164)
T cd01472 59 --Y--------------------------------RSKDDVLEAVKNLRY-----I---GGGTNTGKALKYVRENLFTEA 96 (164)
T ss_pred --C--------------------------------CCHHHHHHHHHhCcC-----C---CCCchHHHHHHHHHHHhCCcc
Confidence 0 001233445565543 1 22468999999999988742
Q ss_pred ---CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCcc
Q 005340 286 ---VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (701)
Q Consensus 286 ---~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~ 362 (701)
-+.....|++++.|.++.+. ...+..+.+.||.+-.+..+ ..
T Consensus 97 ~~~~~~~~~~iiliTDG~~~~~~---------------------------------~~~~~~l~~~gv~i~~ig~g--~~ 141 (164)
T cd01472 97 SGSREGVPKVLVVITDGKSQDDV---------------------------------EEPAVELKQAGIEVFAVGVK--NA 141 (164)
T ss_pred cCCCCCCCEEEEEEcCCCCCchH---------------------------------HHHHHHHHHCCCEEEEEECC--cC
Confidence 11234457888887432110 01223444567755555444 34
Q ss_pred Chhcchhhhccccc-eEEEeCC
Q 005340 363 GVAELKVAVEKTGG-LVVLSDS 383 (701)
Q Consensus 363 ~l~~l~~l~~~TGG-~v~~~~~ 383 (701)
|...|..++..+|| .++.+.+
T Consensus 142 ~~~~L~~ia~~~~~~~~~~~~~ 163 (164)
T cd01472 142 DEEELKQIASDPKELYVFNVAD 163 (164)
T ss_pred CHHHHHHHHCCCchheEEeccC
Confidence 99999999999987 5555443
No 24
>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=98.18 E-value=0.00025 Score=75.19 Aligned_cols=50 Identities=22% Similarity=0.247 Sum_probs=42.5
Q ss_pred CCcEEEEEEECCCchhh-HHHHHHHHHHHhhc-CCCCcEEEEEEECCEEEEE
Q 005340 128 VPPVFMFVVDTCIIEEE-MSFLKSALSQAIDL-LPDNSLVGLITFGTLVQVH 177 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~~-l~~~~~~l~~~l~~-lp~~~~VgiItf~~~V~~~ 177 (701)
.|...+||||+|.++.. +..+++++...++. ++++.+||||+|++.+++.
T Consensus 52 ~p~~vvlvlD~SgSM~~~~~~a~~a~~~~l~~~l~~~d~v~lv~f~~~~~~~ 103 (296)
T TIGR03436 52 LPLTVGLVIDTSGSMRNDLDRARAAAIRFLKTVLRPNDRVFVVTFNTRLRLL 103 (296)
T ss_pred CCceEEEEEECCCCchHHHHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeEe
Confidence 47899999999998766 77888888888876 7888999999999877653
No 25
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=98.15 E-value=0.00015 Score=85.45 Aligned_cols=154 Identities=16% Similarity=0.207 Sum_probs=103.9
Q ss_pred CCcEEEEEEECCCchh---hHHHHHHHHHHHh-hcCCCCcEEEEEEECCEEEEEE-cCCCCCCCCceeeecCCccCChHH
Q 005340 128 VPPVFMFVVDTCIIEE---EMSFLKSALSQAI-DLLPDNSLVGLITFGTLVQVHE-LGGFGQIIPKTYVFKGSKDVSKDQ 202 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~---~l~~~~~~l~~~l-~~lp~~~~VgiItf~~~V~~~~-l~~~~~~~~~~~v~~g~~~~~~~~ 202 (701)
.++..++|||+|.++. .++.++++++..| +.++++.+||||+|++..++.. +. .
T Consensus 303 ~~r~VVLVLDvSGSM~g~dRL~~lkqAA~~fL~~~l~~~DrVGLVtFsssA~vl~pLt-~-------------------- 361 (863)
T TIGR00868 303 RQRIVCLVLDKSGSMTVEDRLKRMNQAAKLFLLQTVEKGSWVGMVTFDSAAYIKNELI-Q-------------------- 361 (863)
T ss_pred CCceEEEEEECCccccccCHHHHHHHHHHHHHHHhCCCCCEEEEEEECCceeEeeccc-c--------------------
Confidence 4566999999999985 3888888887765 4578889999999998876531 11 0
Q ss_pred HHhHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHh
Q 005340 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (701)
Q Consensus 203 l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll 282 (701)
+ .. ...++.|... |.. .+ ...+++|.||..|..+|
T Consensus 362 ------I------------------------ts-----~~dr~aL~~~---L~~----~A---~GGT~I~~GL~~Alq~L 396 (863)
T TIGR00868 362 ------I------------------------TS-----SAERDALTAN---LPT----AA---SGGTSICSGLKAAFQVI 396 (863)
T ss_pred ------C------------------------Cc-----HHHHHHHHHh---hcc----cc---CCCCcHHHHHHHHHHHH
Confidence 0 00 0011122222 221 01 23689999999999999
Q ss_pred hccCC-CCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCc
Q 005340 283 GACVP-GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (701)
Q Consensus 283 ~~~~~-~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~ 361 (701)
..... ..++.|+++++|-++.+ ..++..+.+.||.|..+.++.+.
T Consensus 397 ~~~~~~~~~~~IILLTDGedn~~----------------------------------~~~l~~lk~~gVtI~TIg~G~da 442 (863)
T TIGR00868 397 KKSYQSTDGSEIVLLTDGEDNTI----------------------------------SSCFEEVKQSGAIIHTIALGPSA 442 (863)
T ss_pred HhcccccCCCEEEEEeCCCCCCH----------------------------------HHHHHHHHHcCCEEEEEEeCCCh
Confidence 85321 24678999988854311 12344556689999999988654
Q ss_pred cChhcchhhhccccceEEEeCC
Q 005340 362 VGVAELKVAVEKTGGLVVLSDS 383 (701)
Q Consensus 362 ~~l~~l~~l~~~TGG~v~~~~~ 383 (701)
- ..|..|++.|||..++.++
T Consensus 443 d--~~L~~IA~~TGG~~f~asd 462 (863)
T TIGR00868 443 A--KELEELSDMTGGLRFYASD 462 (863)
T ss_pred H--HHHHHHHHhcCCEEEEeCC
Confidence 2 4689999999999998764
No 26
>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=98.13 E-value=8.8e-05 Score=73.70 Aligned_cols=167 Identities=15% Similarity=0.098 Sum_probs=99.5
Q ss_pred EEEEEECCCchhh--HHHHHHHHHHHhhcCC---CCcEEEEEEECCEEEEE-EcCCCCCCCCceeeecCCccCChHHHHh
Q 005340 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (701)
Q Consensus 132 ~vFvIDvs~~~~~--l~~~~~~l~~~l~~lp---~~~~VgiItf~~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (701)
++||||+|.++.. ++.+++++...++.++ .+.+||+|+|++..+.. .+. .. .
T Consensus 3 i~~vlD~SgSM~~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~~~~~~~~-~~-~-------------------- 60 (198)
T cd01470 3 IYIALDASDSIGEEDFDEAKNAIKTLIEKISSYEVSPRYEIISYASDPKEIVSIR-DF-N-------------------- 60 (198)
T ss_pred EEEEEECCCCccHHHHHHHHHHHHHHHHHccccCCCceEEEEEecCCceEEEecc-cC-C--------------------
Confidence 6899999999754 8899999999998875 36799999999876543 222 10 0
Q ss_pred HhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhcc
Q 005340 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (701)
Q Consensus 206 ~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~ 285 (701)
......+...|+.+.... ......+.++.||..|...+...
T Consensus 61 -----------------------------------~~~~~~~~~~l~~~~~~~----~~~~ggT~~~~Al~~~~~~l~~~ 101 (198)
T cd01470 61 -----------------------------------SNDADDVIKRLEDFNYDD----HGDKTGTNTAAALKKVYERMALE 101 (198)
T ss_pred -----------------------------------CCCHHHHHHHHHhCCccc----ccCccchhHHHHHHHHHHHHHHH
Confidence 000112334555554311 11123567888888887765310
Q ss_pred C-C-C-----CCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHH------HHHHcCcEE
Q 005340 286 V-P-G-----SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSK------QLVHQGHVL 352 (701)
Q Consensus 286 ~-~-~-----~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~------~~~~~~isv 352 (701)
. . . ..-.|++++.|.+|.|... ..+.+.++++.. .+...+|.|
T Consensus 102 ~~~~~~~~~~~~~~iillTDG~~~~g~~~------------------------~~~~~~~~~~~~~~~~~~~~~~~~v~i 157 (198)
T cd01470 102 KVRNKEAFNETRHVIILFTDGKSNMGGSP------------------------LPTVDKIKNLVYKNNKSDNPREDYLDV 157 (198)
T ss_pred HhcCccchhhcceEEEEEcCCCcCCCCCh------------------------hHHHHHHHHHHhcccccccchhcceeE
Confidence 0 0 0 1124789999998876310 011122222211 123345555
Q ss_pred EEEEecCCccChhcchhhhccccc--eEEEeCCC
Q 005340 353 DLFACALDQVGVAELKVAVEKTGG--LVVLSDSF 384 (701)
Q Consensus 353 Dlf~~~~~~~~l~~l~~l~~~TGG--~v~~~~~f 384 (701)
..+.++ +..+-.+|..++..||| +++...+|
T Consensus 158 ~~iGvG-~~~~~~~L~~iA~~~~g~~~~f~~~~~ 190 (198)
T cd01470 158 YVFGVG-DDVNKEELNDLASKKDNERHFFKLKDY 190 (198)
T ss_pred EEEecC-cccCHHHHHHHhcCCCCCceEEEeCCH
Confidence 555544 35789999999999999 46766655
No 27
>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=98.06 E-value=0.00012 Score=71.64 Aligned_cols=144 Identities=20% Similarity=0.200 Sum_probs=94.4
Q ss_pred EEEEEEECCCchhh-------HHHHHHHHHHHh----hcCCCCcEEEEEEECC-EEEEEEcCCCCCCCCceeeecCCccC
Q 005340 131 VFMFVVDTCIIEEE-------MSFLKSALSQAI----DLLPDNSLVGLITFGT-LVQVHELGGFGQIIPKTYVFKGSKDV 198 (701)
Q Consensus 131 ~~vFvIDvs~~~~~-------l~~~~~~l~~~l----~~lp~~~~VgiItf~~-~V~~~~l~~~~~~~~~~~v~~g~~~~ 198 (701)
+.+++||+|..+.+ ++..++++...+ +..|+ .+||||+|.+ .-++.-
T Consensus 5 a~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np~-~~vGlv~fag~~a~v~~-------------------- 63 (187)
T cd01452 5 ATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPE-NNVGLMTMAGNSPEVLV-------------------- 63 (187)
T ss_pred EEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCCC-ccEEEEEecCCceEEEE--------------------
Confidence 57899999998754 888888877664 55555 5999999875 322211
Q ss_pred ChHHHHhHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHH
Q 005340 199 SKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIA 278 (701)
Q Consensus 199 ~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A 278 (701)
|+......+...|+.+.. .....+|.||+.|
T Consensus 64 ----------------------------------------plT~D~~~~~~~L~~i~~---------~g~~~l~~AL~~A 94 (187)
T cd01452 64 ----------------------------------------TLTNDQGKILSKLHDVQP---------KGKANFITGIQIA 94 (187)
T ss_pred ----------------------------------------CCCCCHHHHHHHHHhCCC---------CCcchHHHHHHHH
Confidence 111112244456665542 1345799999999
Q ss_pred HHHhhccCCCC-CcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEe
Q 005340 279 ASLLGACVPGS-GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFAC 357 (701)
Q Consensus 279 ~~ll~~~~~~~-gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~ 357 (701)
...|+..-... ..||++|.+++-+.=| .+ ..++++++.++||.||++.+
T Consensus 95 ~~~L~~~~~~~~~~rivi~v~S~~~~d~-----------------------------~~-i~~~~~~lkk~~I~v~vI~~ 144 (187)
T cd01452 95 QLALKHRQNKNQKQRIVAFVGSPIEEDE-----------------------------KD-LVKLAKRLKKNNVSVDIINF 144 (187)
T ss_pred HHHHhcCCCcCCcceEEEEEecCCcCCH-----------------------------HH-HHHHHHHHHHcCCeEEEEEe
Confidence 99998543232 3599999987432111 11 23688999999999999999
Q ss_pred cCCccChhcchhhhccc
Q 005340 358 ALDQVGVAELKVAVEKT 374 (701)
Q Consensus 358 ~~~~~~l~~l~~l~~~T 374 (701)
+...-+..-+..+.+..
T Consensus 145 G~~~~~~~~l~~~~~~~ 161 (187)
T cd01452 145 GEIDDNTEKLTAFIDAV 161 (187)
T ss_pred CCCCCCHHHHHHHHHHh
Confidence 87655555555555544
No 28
>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=98.05 E-value=0.00027 Score=68.05 Aligned_cols=159 Identities=20% Similarity=0.198 Sum_probs=102.9
Q ss_pred CcEEEEEEECCCchhh--HHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhH
Q 005340 129 PPVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQ 206 (701)
Q Consensus 129 ~p~~vFvIDvs~~~~~--l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~ 206 (701)
|.-++||+|+|.++.. ++.+++++...+..+++..+|++++|++.++.+ . .. ..+
T Consensus 2 ~~~v~~vlD~S~SM~~~~~~~~~~al~~~l~~l~~~~~~~l~~Fs~~~~~~--~-~~-~~~------------------- 58 (171)
T cd01461 2 PKEVVFVIDTSGSMSGTKIEQTKEALLTALKDLPPGDYFNIIGFSDTVEEF--S-PS-SVS------------------- 58 (171)
T ss_pred CceEEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEeCCCceee--c-Cc-cee-------------------
Confidence 5678999999999853 888999999999999988899999999876544 1 10 000
Q ss_pred hhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhccC
Q 005340 207 LNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACV 286 (701)
Q Consensus 207 l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~ 286 (701)
.+ .+....+.+.|+.+.. ...+.++.||..|...+...
T Consensus 59 --------------------------~~------~~~~~~~~~~l~~~~~---------~g~T~l~~al~~a~~~l~~~- 96 (171)
T cd01461 59 --------------------------AT------AENVAAAIEYVNRLQA---------LGGTNMNDALEAALELLNSS- 96 (171)
T ss_pred --------------------------CC------HHHHHHHHHHHHhcCC---------CCCcCHHHHHHHHHHhhccC-
Confidence 00 0011122344444432 12457889999999888631
Q ss_pred CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccChhc
Q 005340 287 PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAE 366 (701)
Q Consensus 287 ~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~ 366 (701)
+.....|++|++|.++. ..+.+ +.++++.+.++.|..+.++. ..+-..
T Consensus 97 ~~~~~~iillTDG~~~~------------------------------~~~~~-~~~~~~~~~~i~i~~i~~g~-~~~~~~ 144 (171)
T cd01461 97 PGSVPQIILLTDGEVTN------------------------------ESQIL-KNVREALSGRIRLFTFGIGS-DVNTYL 144 (171)
T ss_pred CCCccEEEEEeCCCCCC------------------------------HHHHH-HHHHHhcCCCceEEEEEeCC-ccCHHH
Confidence 12346778888875210 11222 23344444577777776653 456788
Q ss_pred chhhhccccceEEEeCCC
Q 005340 367 LKVAVEKTGGLVVLSDSF 384 (701)
Q Consensus 367 l~~l~~~TGG~v~~~~~f 384 (701)
|..++..|||...+..+-
T Consensus 145 l~~ia~~~gG~~~~~~~~ 162 (171)
T cd01461 145 LERLAREGRGIARRIYET 162 (171)
T ss_pred HHHHHHcCCCeEEEecCh
Confidence 999999999999987653
No 29
>cd01480 vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=98.04 E-value=0.00017 Score=70.91 Aligned_cols=157 Identities=15% Similarity=0.121 Sum_probs=99.1
Q ss_pred EEEEEEECCCchhh--HHHHHHHHHHHhhcC---------CCCcEEEEEEECCEEEEE-EcCCCCCCCCceeeecCCccC
Q 005340 131 VFMFVVDTCIIEEE--MSFLKSALSQAIDLL---------PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDV 198 (701)
Q Consensus 131 ~~vFvIDvs~~~~~--l~~~~~~l~~~l~~l---------p~~~~VgiItf~~~V~~~-~l~~~~~~~~~~~v~~g~~~~ 198 (701)
-.+|+||.|.+... ++.+++.++..++.+ +++.+||+|+|++..++. .+. .
T Consensus 4 dvv~vlD~S~Sm~~~~~~~~k~~~~~~~~~l~~~~~~~i~~~~~rvglv~fs~~~~~~~~l~-~---------------- 66 (186)
T cd01480 4 DITFVLDSSESVGLQNFDITKNFVKRVAERFLKDYYRKDPAGSWRVGVVQYSDQQEVEAGFL-R---------------- 66 (186)
T ss_pred eEEEEEeCCCccchhhHHHHHHHHHHHHHHHhhhhccCCCCCceEEEEEEecCCceeeEecc-c----------------
Confidence 46899999998763 777777777777766 346899999999765432 111 0
Q ss_pred ChHHHHhHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHH
Q 005340 199 SKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIA 278 (701)
Q Consensus 199 ~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A 278 (701)
. ...+..+.+.|++++. . ...+.+|.||..|
T Consensus 67 -------------------------------------~----~~~~~~l~~~i~~l~~-----~---gg~T~~~~AL~~a 97 (186)
T cd01480 67 -------------------------------------D----IRNYTSLKEAVDNLEY-----I---GGGTFTDCALKYA 97 (186)
T ss_pred -------------------------------------c----cCCHHHHHHHHHhCcc-----C---CCCccHHHHHHHH
Confidence 0 0012344566666642 1 1257899999999
Q ss_pred HHHhhccC-CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEe
Q 005340 279 ASLLGACV-PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFAC 357 (701)
Q Consensus 279 ~~ll~~~~-~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~ 357 (701)
...+.... +.....|++++.|.++.++. .-..+.+.++...||.+-.+..
T Consensus 98 ~~~l~~~~~~~~~~~iillTDG~~~~~~~-----------------------------~~~~~~~~~~~~~gi~i~~vgi 148 (186)
T cd01480 98 TEQLLEGSHQKENKFLLVITDGHSDGSPD-----------------------------GGIEKAVNEADHLGIKIFFVAV 148 (186)
T ss_pred HHHHhccCCCCCceEEEEEeCCCcCCCcc-----------------------------hhHHHHHHHHHHCCCEEEEEec
Confidence 99987411 13335678888876532210 0113345667777888666655
Q ss_pred cCCccChhcchhhhccccceEEEeCCCC
Q 005340 358 ALDQVGVAELKVAVEKTGGLVVLSDSFG 385 (701)
Q Consensus 358 ~~~~~~l~~l~~l~~~TGG~v~~~~~f~ 385 (701)
+. .+...|..++...+|. ++.++|.
T Consensus 149 g~--~~~~~L~~IA~~~~~~-~~~~~~~ 173 (186)
T cd01480 149 GS--QNEEPLSRIACDGKSA-LYRENFA 173 (186)
T ss_pred Cc--cchHHHHHHHcCCcch-hhhcchh
Confidence 43 7888899999888776 4444443
No 30
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=97.98 E-value=0.0001 Score=70.60 Aligned_cols=150 Identities=23% Similarity=0.220 Sum_probs=96.3
Q ss_pred EEEEEECCCchhh-------HHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEE-EcCCCCCCCCceeeecCCccCChHHH
Q 005340 132 FMFVVDTCIIEEE-------MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQL 203 (701)
Q Consensus 132 ~vFvIDvs~~~~~-------l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l 203 (701)
++||||+|.++.. ++.+++++...++.+|. .+|||++|++..++. .+.
T Consensus 2 vv~v~D~SgSM~~~~~~~~~~~~~~~~~~~~~~~~~~-~~v~l~~f~~~~~~~~~~t----------------------- 57 (172)
T PF13519_consen 2 VVFVLDNSGSMNGYDGNRTRIDQAKDALNELLANLPG-DRVGLVSFSDSSRTLSPLT----------------------- 57 (172)
T ss_dssp EEEEEE-SGGGGTTTSSS-HHHHHHHHHHHHHHHHTT-SEEEEEEESTSCEEEEEEE-----------------------
T ss_pred EEEEEECCcccCCCCCCCcHHHHHHHHHHHHHHHCCC-CEEEEEEeccccccccccc-----------------------
Confidence 5899999998753 78889999998888875 499999998643211 111
Q ss_pred HhHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhh
Q 005340 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG 283 (701)
Q Consensus 204 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~ 283 (701)
..+..+.+.++++.... ......+++.|+..|..++.
T Consensus 58 --------------------------------------~~~~~~~~~l~~~~~~~-----~~~~~t~~~~al~~a~~~~~ 94 (172)
T PF13519_consen 58 --------------------------------------SDKDELKNALNKLSPQG-----MPGGGTNLYDALQEAAKMLA 94 (172)
T ss_dssp --------------------------------------SSHHHHHHHHHTHHHHG-------SSS--HHHHHHHHHHHHH
T ss_pred --------------------------------------ccHHHHHHHhhcccccc-----cCccCCcHHHHHHHHHHHHH
Confidence 11122334444443210 01234788999999999998
Q ss_pred ccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccC
Q 005340 284 ACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVG 363 (701)
Q Consensus 284 ~~~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~ 363 (701)
... .....|++|++|.++ . . ..+.++.+.+.+|.+.++.++.+...
T Consensus 95 ~~~-~~~~~iv~iTDG~~~--------~-----------------~--------~~~~~~~~~~~~i~i~~v~~~~~~~~ 140 (172)
T PF13519_consen 95 SSD-NRRRAIVLITDGEDN--------S-----------------S--------DIEAAKALKQQGITIYTVGIGSDSDA 140 (172)
T ss_dssp C-S-SEEEEEEEEES-TTH--------C-----------------H--------HHHHHHHHHCTTEEEEEEEES-TT-E
T ss_pred hCC-CCceEEEEecCCCCC--------c-----------------c--------hhHHHHHHHHcCCeEEEEEECCCccH
Confidence 431 134566777776433 0 0 01266678889999999999887766
Q ss_pred hhcchhhhccccceEEEeC
Q 005340 364 VAELKVAVEKTGGLVVLSD 382 (701)
Q Consensus 364 l~~l~~l~~~TGG~v~~~~ 382 (701)
-..+..+++.|||..+...
T Consensus 141 ~~~l~~la~~tgG~~~~~~ 159 (172)
T PF13519_consen 141 NEFLQRLAEATGGRYFHVD 159 (172)
T ss_dssp HHHHHHHHHHTEEEEEEE-
T ss_pred HHHHHHHHHhcCCEEEEec
Confidence 6789999999999988763
No 31
>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein. Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092).
Probab=97.94 E-value=0.0082 Score=70.00 Aligned_cols=187 Identities=17% Similarity=0.128 Sum_probs=115.7
Q ss_pred CCcEEEEEEECCCchhh--HHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHh
Q 005340 128 VPPVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~~--l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (701)
.|..++||||+|.++.. ++.+++++..+|..|+++.+++||+|++.++.+. . . ..+ ++
T Consensus 270 ~p~~vvfvlD~SgSM~g~~i~~ak~al~~~l~~L~~~d~~~ii~F~~~~~~~~-~--~-~~~----------~~------ 329 (596)
T TIGR03788 270 LPRELVFVIDTSGSMAGESIEQAKSALLLALDQLRPGDRFNIIQFDSDVTLLF-P--V-PVP----------AT------ 329 (596)
T ss_pred CCceEEEEEECCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEECCcceEec-c--c-ccc----------CC------
Confidence 45679999999999753 8889999999999999999999999999887652 1 1 000 00
Q ss_pred HhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhcc
Q 005340 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (701)
Q Consensus 206 ~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~ 285 (701)
.+....+.+.|+.|..+ ..+.+..||..|.......
T Consensus 330 -----------------------------------~~~~~~a~~~i~~l~a~---------GgT~l~~aL~~a~~~~~~~ 365 (596)
T TIGR03788 330 -----------------------------------AHNLARARQFVAGLQAD---------GGTEMAGALSAALRDDGPE 365 (596)
T ss_pred -----------------------------------HHHHHHHHHHHhhCCCC---------CCccHHHHHHHHHHhhccc
Confidence 01112333456665431 2467889999988765321
Q ss_pred CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccChh
Q 005340 286 VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVA 365 (701)
Q Consensus 286 ~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~ 365 (701)
....-.+|+++++|..+- .....+.+. ....++.+..|.++. ..+-.
T Consensus 366 ~~~~~~~iillTDG~~~~------------------------------~~~~~~~~~--~~~~~~ri~tvGiG~-~~n~~ 412 (596)
T TIGR03788 366 SSGALRQVVFLTDGAVGN------------------------------EDALFQLIR--TKLGDSRLFTVGIGS-APNSY 412 (596)
T ss_pred CCCceeEEEEEeCCCCCC------------------------------HHHHHHHHH--HhcCCceEEEEEeCC-CcCHH
Confidence 112224789999984210 011222221 122356677666654 46778
Q ss_pred cchhhhccccceEEEeCCCCchhhHHHHHHHhccCccCCcceeeEEEEEE
Q 005340 366 ELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVFHSGDYDLGLSSNGIFEIN 415 (701)
Q Consensus 366 ~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l~~~~~~~~~~~~~~l~vr 415 (701)
.|..|++.+||..++..+ .+...+.+.+++.... .+...+..+++.
T Consensus 413 lL~~lA~~g~G~~~~i~~--~~~~~~~~~~~l~~~~--~p~l~~v~v~~~ 458 (596)
T TIGR03788 413 FMRKAAQFGRGSFTFIGS--TDEVQRKMSQLFAKLE--QPALTDIALTFD 458 (596)
T ss_pred HHHHHHHcCCCEEEECCC--HHHHHHHHHHHHHhhc--CeEEEEEEEEEc
Confidence 899999999998776543 3344455566664331 244566666653
No 32
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=97.93 E-value=0.0003 Score=66.86 Aligned_cols=151 Identities=20% Similarity=0.205 Sum_probs=100.8
Q ss_pred EEEEEECCCchhh-HHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHhHhhcc
Q 005340 132 FMFVVDTCIIEEE-MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFF 210 (701)
Q Consensus 132 ~vFvIDvs~~~~~-l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~l~~~ 210 (701)
.+||||+|.++.. .+.++++|+..++.|+++.++.||+|++.+..|. . . ....+
T Consensus 3 vvilvD~S~Sm~g~~~~~k~al~~~l~~L~~~d~fnii~f~~~~~~~~-~--~----------------------~~~~~ 57 (155)
T PF13768_consen 3 VVILVDTSGSMSGEKELVKDALRAILRSLPPGDRFNIIAFGSSVRPLF-P--G----------------------LVPAT 57 (155)
T ss_pred EEEEEeCCCCCCCcHHHHHHHHHHHHHhCCCCCEEEEEEeCCEeeEcc-h--h----------------------HHHHh
Confidence 5899999998765 4899999999999999999999999999876552 1 1 00000
Q ss_pred cCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCC
Q 005340 211 IKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSG 290 (701)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~g 290 (701)
.+..+...+.|+.+..+ ...+.++.||+.|...+.. ++.-
T Consensus 58 ------------------------------~~~~~~a~~~I~~~~~~--------~G~t~l~~aL~~a~~~~~~--~~~~ 97 (155)
T PF13768_consen 58 ------------------------------EENRQEALQWIKSLEAN--------SGGTDLLAALRAALALLQR--PGCV 97 (155)
T ss_pred ------------------------------HHHHHHHHHHHHHhccc--------CCCccHHHHHHHHHHhccc--CCCc
Confidence 01122333555555431 2357889999999988621 2456
Q ss_pred cEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccChhcchhh
Q 005340 291 ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVA 370 (701)
Q Consensus 291 g~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~l~~l 370 (701)
-.|+++++|.|+.++ ....+.+. .+. ..+.+..|.++. ..+-..|..|
T Consensus 98 ~~IilltDG~~~~~~-----------------------------~~i~~~v~-~~~-~~~~i~~~~~g~-~~~~~~L~~L 145 (155)
T PF13768_consen 98 RAIILLTDGQPVSGE-----------------------------EEILDLVR-RAR-GHIRIFTFGIGS-DADADFLREL 145 (155)
T ss_pred cEEEEEEeccCCCCH-----------------------------HHHHHHHH-hcC-CCceEEEEEECC-hhHHHHHHHH
Confidence 788999998764332 11111121 111 457777777754 4567889999
Q ss_pred hccccceEE
Q 005340 371 VEKTGGLVV 379 (701)
Q Consensus 371 ~~~TGG~v~ 379 (701)
++.|||...
T Consensus 146 A~~~~G~~~ 154 (155)
T PF13768_consen 146 ARATGGSFH 154 (155)
T ss_pred HHcCCCEEE
Confidence 999999875
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=97.89 E-value=0.00058 Score=66.55 Aligned_cols=156 Identities=16% Similarity=0.147 Sum_probs=98.1
Q ss_pred EEEEEECCCchh--hHHHHHHHHHHHhhcCC---CCcEEEEEEECCEEEEE-EcCCCCCCCCceeeecCCccCChHHHHh
Q 005340 132 FMFVVDTCIIEE--EMSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (701)
Q Consensus 132 ~vFvIDvs~~~~--~l~~~~~~l~~~l~~lp---~~~~VgiItf~~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (701)
.+|+||.|.+.. +++.+++.++..++.+. ++.|||+|+|++..++. .+. .- .
T Consensus 3 i~fvlD~S~S~~~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~~~~~~l~-~~---~------------------ 60 (177)
T cd01469 3 IVFVLDGSGSIYPDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESFRTEFTLN-EY---R------------------ 60 (177)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCceeEEEecC-cc---C------------------
Confidence 589999999865 48888888888887764 46899999999876543 222 00 0
Q ss_pred HhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhcc
Q 005340 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (701)
Q Consensus 206 ~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~ 285 (701)
+...+.+.++.++. .. ..+.+|.||..|...+-..
T Consensus 61 -------------------------------------~~~~~~~~i~~~~~-----~~---g~T~~~~AL~~a~~~l~~~ 95 (177)
T cd01469 61 -------------------------------------TKEEPLSLVKHISQ-----LL---GLTNTATAIQYVVTELFSE 95 (177)
T ss_pred -------------------------------------CHHHHHHHHHhCcc-----CC---CCccHHHHHHHHHHHhcCc
Confidence 00112244555443 11 2378999999998876210
Q ss_pred ---CC-CCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCc
Q 005340 286 ---VP-GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (701)
Q Consensus 286 ---~~-~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~ 361 (701)
.+ ....-+++++.|..+.|+ . . +..++.+...||.|-.+..+...
T Consensus 96 ~~g~R~~~~kv~illTDG~~~~~~-----------------------~-------~-~~~~~~~k~~gv~v~~Vgvg~~~ 144 (177)
T cd01469 96 SNGARKDATKVLVVITDGESHDDP-----------------------L-------L-KDVIPQAEREGIIRYAIGVGGHF 144 (177)
T ss_pred ccCCCCCCCeEEEEEeCCCCCCcc-----------------------c-------c-HHHHHHHHHCCcEEEEEEecccc
Confidence 01 122347888888665432 0 0 23455566778877777665432
Q ss_pred ---cChhcchhhhccccc-eEEEeCCCC
Q 005340 362 ---VGVAELKVAVEKTGG-LVVLSDSFG 385 (701)
Q Consensus 362 ---~~l~~l~~l~~~TGG-~v~~~~~f~ 385 (701)
.+..+|..++..+++ +++..++|+
T Consensus 145 ~~~~~~~~L~~ias~p~~~h~f~~~~~~ 172 (177)
T cd01469 145 QRENSREELKTIASKPPEEHFFNVTDFA 172 (177)
T ss_pred cccccHHHHHHHhcCCcHHhEEEecCHH
Confidence 347889999988864 677666664
No 34
>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax. ATR is the cellular receptor for the anthrax protective antigen and facilitates entry of the toxin into cells. The VWA domain in ATR contains the toxin binding site and mediates interaction with protective antigen. The binding is mediated by divalent cations that binds to the MIDAS motif. These proteins are a family of vertebrate ECM receptors expressed by endothelial cells.
Probab=97.85 E-value=0.0004 Score=68.22 Aligned_cols=156 Identities=17% Similarity=0.104 Sum_probs=89.2
Q ss_pred CcEEEEEEECCCchhh-HHHHHHHHHHHhhcC-CCCcEEEEEEECCEEEEE-EcCCCCCCCCceeeecCCccCChHHHHh
Q 005340 129 PPVFMFVVDTCIIEEE-MSFLKSALSQAIDLL-PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (701)
Q Consensus 129 ~p~~vFvIDvs~~~~~-l~~~~~~l~~~l~~l-p~~~~VgiItf~~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (701)
+.-.+|+||.|.++.. .....+.++..++.+ .++.+||+|+|++..++. .+. ..
T Consensus 4 ~~Dvv~llD~SgSm~~~~~~~~~~~~~l~~~~~~~~~rvglv~Fs~~~~~~~~l~-~~---------------------- 60 (185)
T cd01474 4 HFDLYFVLDKSGSVAANWIEIYDFVEQLVDRFNSPGLRFSFITFSTRATKILPLT-DD---------------------- 60 (185)
T ss_pred ceeEEEEEeCcCchhhhHHHHHHHHHHHHHHcCCCCcEEEEEEecCCceEEEecc-cc----------------------
Confidence 4457999999999764 333334455554443 356899999999765432 111 00
Q ss_pred HhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhcc
Q 005340 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (701)
Q Consensus 206 ~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~ 285 (701)
...+.+.++.|.. .. + ...+++|.||..|...+...
T Consensus 61 --------------------------------------~~~~~~~l~~l~~-~~--~---~g~T~~~~aL~~a~~~l~~~ 96 (185)
T cd01474 61 --------------------------------------SSAIIKGLEVLKK-VT--P---SGQTYIHEGLENANEQIFNR 96 (185)
T ss_pred --------------------------------------HHHHHHHHHHHhc-cC--C---CCCCcHHHHHHHHHHHHHhh
Confidence 0012233333432 11 1 24689999999999877311
Q ss_pred CCCCC-----cEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCC
Q 005340 286 VPGSG-----ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (701)
Q Consensus 286 ~~~~g-----g~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~ 360 (701)
..| ..|++++.|.++...+. . + ...++.+.+.|+.|-.+.. .
T Consensus 97 --~~~~r~~~~~villTDG~~~~~~~~---------------------~---~-----~~~a~~l~~~gv~i~~vgv--~ 143 (185)
T cd01474 97 --NGGGRETVSVIIALTDGQLLLNGHK---------------------Y---P-----EHEAKLSRKLGAIVYCVGV--T 143 (185)
T ss_pred --ccCCCCCCeEEEEEcCCCcCCCCCc---------------------c---h-----HHHHHHHHHcCCEEEEEee--c
Confidence 222 34788888876311000 0 0 1124456667886555544 6
Q ss_pred ccChhcchhhhccccceEE-EeCCCC
Q 005340 361 QVGVAELKVAVEKTGGLVV-LSDSFG 385 (701)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~-~~~~f~ 385 (701)
..+..+|..++..++ .+| ...+|+
T Consensus 144 ~~~~~~L~~iA~~~~-~~f~~~~~~~ 168 (185)
T cd01474 144 DFLKSQLINIADSKE-YVFPVTSGFQ 168 (185)
T ss_pred hhhHHHHHHHhCCCC-eeEecCccHH
Confidence 678899999998875 444 334454
No 35
>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=97.80 E-value=0.0015 Score=62.78 Aligned_cols=45 Identities=24% Similarity=0.462 Sum_probs=36.3
Q ss_pred EEEEEECCCchhh--HHHHHHHHHHHhhcC---CCCcEEEEEEECCEEEE
Q 005340 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLL---PDNSLVGLITFGTLVQV 176 (701)
Q Consensus 132 ~vFvIDvs~~~~~--l~~~~~~l~~~l~~l---p~~~~VgiItf~~~V~~ 176 (701)
.+|++|.|.+... ++.+++.++..++.+ +++.+||+|+|++..++
T Consensus 3 v~~vlD~S~Sm~~~~~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~~~ 52 (164)
T cd01482 3 IVFLVDGSWSIGRSNFNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDPRT 52 (164)
T ss_pred EEEEEeCCCCcChhhHHHHHHHHHHHHhheeeCCCceEEEEEEECCCeeE
Confidence 6899999998754 888888888777765 46789999999986544
No 36
>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
Probab=97.80 E-value=0.00091 Score=67.83 Aligned_cols=155 Identities=19% Similarity=0.297 Sum_probs=95.8
Q ss_pred cEEEEEEECCCchh--hHHHHHHHHHHHhhcC---CCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHH
Q 005340 130 PVFMFVVDTCIIEE--EMSFLKSALSQAIDLL---PDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (701)
Q Consensus 130 p~~vFvIDvs~~~~--~l~~~~~~l~~~l~~l---p~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (701)
--.+|+||.|.+.. +++.+++.++..++.+ |+..+||+|+|++.+++. +. .. .
T Consensus 3 ~DlvfllD~S~Sm~~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~~~~-~~-l~-~------------------- 60 (224)
T cd01475 3 TDLVFLIDSSRSVRPENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTVKQE-FP-LG-R------------------- 60 (224)
T ss_pred ccEEEEEeCCCCCCHHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCceeEE-ec-cc-c-------------------
Confidence 34799999999865 4889999999888876 356899999999877553 11 00 0
Q ss_pred hHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhc
Q 005340 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (701)
Q Consensus 205 ~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~ 284 (701)
+ ..++.+.+.|+.++. . ...+.+|.||..|...+-.
T Consensus 61 -------------------------------~-----~~~~~l~~~i~~i~~-~-------~~~t~tg~AL~~a~~~~~~ 96 (224)
T cd01475 61 -------------------------------F-----KSKADLKRAVRRMEY-L-------ETGTMTGLAIQYAMNNAFS 96 (224)
T ss_pred -------------------------------c-----CCHHHHHHHHHhCcC-C-------CCCChHHHHHHHHHHHhCC
Confidence 0 011223345555543 1 1245789999988865321
Q ss_pred -c--CCC-C---CcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEe
Q 005340 285 -C--VPG-S---GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFAC 357 (701)
Q Consensus 285 -~--~~~-~---gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~ 357 (701)
. .+. . -..|+++++|.++.. .++.+.++...||.| |+.
T Consensus 97 ~~~g~r~~~~~~~kvvillTDG~s~~~---------------------------------~~~~a~~lk~~gv~i--~~V 141 (224)
T cd01475 97 EAEGARPGSERVPRVGIVVTDGRPQDD---------------------------------VSEVAAKARALGIEM--FAV 141 (224)
T ss_pred hhcCCCCCCCCCCeEEEEEcCCCCccc---------------------------------HHHHHHHHHHCCcEE--EEE
Confidence 0 001 1 123578888753210 134567777778655 555
Q ss_pred cCCccChhcchhhhcccc-ceEEEeCCCC
Q 005340 358 ALDQVGVAELKVAVEKTG-GLVVLSDSFG 385 (701)
Q Consensus 358 ~~~~~~l~~l~~l~~~TG-G~v~~~~~f~ 385 (701)
+....+..+|..++..++ +.++..++|+
T Consensus 142 gvG~~~~~~L~~ias~~~~~~~f~~~~~~ 170 (224)
T cd01475 142 GVGRADEEELREIASEPLADHVFYVEDFS 170 (224)
T ss_pred eCCcCCHHHHHHHhCCCcHhcEEEeCCHH
Confidence 545568899999998765 4677766665
No 37
>cd01450 vWFA_subfamily_ECM Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A
Probab=97.68 E-value=0.0018 Score=61.21 Aligned_cols=145 Identities=19% Similarity=0.188 Sum_probs=96.6
Q ss_pred EEEEEECCCchhh--HHHHHHHHHHHhhcCC---CCcEEEEEEECCEEEEE-EcCCCCCCCCceeeecCCccCChHHHHh
Q 005340 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (701)
Q Consensus 132 ~vFvIDvs~~~~~--l~~~~~~l~~~l~~lp---~~~~VgiItf~~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (701)
++|++|+|.++.. ++.+++.+...+..+. ++.++|+++|++..+.. ++. ..
T Consensus 3 i~~llD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~~~~~~~-~~---------------------- 59 (161)
T cd01450 3 IVFLLDGSESVGPENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVRVEFSLN-DY---------------------- 59 (161)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCceEEEECC-CC----------------------
Confidence 4799999998764 7788888888877664 47899999999754332 111 00
Q ss_pred HhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhcc
Q 005340 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (701)
Q Consensus 206 ~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~ 285 (701)
. ....+.+.++.+.. . .+ ..+.++.||..|...+...
T Consensus 60 ----------------------------~--------~~~~~~~~i~~~~~-~----~~--~~t~~~~al~~a~~~~~~~ 96 (161)
T cd01450 60 ----------------------------K--------SKDDLLKAVKNLKY-L----GG--GGTNTGKALQYALEQLFSE 96 (161)
T ss_pred ----------------------------C--------CHHHHHHHHHhccc-C----CC--CCccHHHHHHHHHHHhccc
Confidence 0 11233345555543 1 11 3578899999999998743
Q ss_pred C---CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCcc
Q 005340 286 V---PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (701)
Q Consensus 286 ~---~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~ 362 (701)
. ...-..|++|++|.++.++ -..++.+++.+.++.+..+..+. .
T Consensus 97 ~~~~~~~~~~iiliTDG~~~~~~-------------------------------~~~~~~~~~~~~~v~v~~i~~g~--~ 143 (161)
T cd01450 97 SNARENVPKVIIVLTDGRSDDGG-------------------------------DPKEAAAKLKDEGIKVFVVGVGP--A 143 (161)
T ss_pred ccccCCCCeEEEEECCCCCCCCc-------------------------------chHHHHHHHHHCCCEEEEEeccc--c
Confidence 1 1334578999999776553 01334566667788888887765 6
Q ss_pred Chhcchhhhcccc
Q 005340 363 GVAELKVAVEKTG 375 (701)
Q Consensus 363 ~l~~l~~l~~~TG 375 (701)
+...|..++..||
T Consensus 144 ~~~~l~~la~~~~ 156 (161)
T cd01450 144 DEEELREIASCPS 156 (161)
T ss_pred CHHHHHHHhCCCC
Confidence 8888999998883
No 38
>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell. In association with invasion, T. gondii sequentially discharges three sets of secretory organelles beginning with the micronemes, which contain adhesive proteins involved in parasite attachment to a host cell. Deployed as protein complexes, several micronemal proteins possess vertebrate-derived adhesive sequences that function in binding receptors. The VWA domain likely mediates the protein-protein interactions of these with their interacting partners.
Probab=97.54 E-value=0.003 Score=61.94 Aligned_cols=45 Identities=20% Similarity=0.190 Sum_probs=36.8
Q ss_pred EEEEEECCCchh--h-HHHHHHHHHHHhhcCC---CCcEEEEEEECCEEEE
Q 005340 132 FMFVVDTCIIEE--E-MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQV 176 (701)
Q Consensus 132 ~vFvIDvs~~~~--~-l~~~~~~l~~~l~~lp---~~~~VgiItf~~~V~~ 176 (701)
++||||.|.++. + ++.+++.+...++.++ ++.+||+|+|++..+.
T Consensus 3 v~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~~ 53 (186)
T cd01471 3 LYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAKE 53 (186)
T ss_pred EEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCceE
Confidence 689999999865 3 7788888888888764 5789999999987653
No 39
>cd01477 vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of mo
Probab=97.53 E-value=0.0038 Score=61.73 Aligned_cols=49 Identities=22% Similarity=0.264 Sum_probs=37.7
Q ss_pred CcEEEEEEECCCchh--hHHHHHHHHHHHhhcC---------CCCcEEEEEEECCEEEEE
Q 005340 129 PPVFMFVVDTCIIEE--EMSFLKSALSQAIDLL---------PDNSLVGLITFGTLVQVH 177 (701)
Q Consensus 129 ~p~~vFvIDvs~~~~--~l~~~~~~l~~~l~~l---------p~~~~VgiItf~~~V~~~ 177 (701)
+-=.|||||.|.+.. +++.+++.++..+..+ |+.+|||+|+|++..++.
T Consensus 19 ~~DivfvlD~S~Sm~~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a~~~ 78 (193)
T cd01477 19 WLDIVFVVDNSKGMTQGGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNATVV 78 (193)
T ss_pred eeeEEEEEeCCCCcchhhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCceEEE
Confidence 455799999999864 4888888887766543 345899999999876553
No 40
>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=97.52 E-value=0.005 Score=59.31 Aligned_cols=45 Identities=13% Similarity=0.271 Sum_probs=36.5
Q ss_pred EEEEEECCCchh--hHHHHHHHHHHHhhcCC---CCcEEEEEEECCEEEE
Q 005340 132 FMFVVDTCIIEE--EMSFLKSALSQAIDLLP---DNSLVGLITFGTLVQV 176 (701)
Q Consensus 132 ~vFvIDvs~~~~--~l~~~~~~l~~~l~~lp---~~~~VgiItf~~~V~~ 176 (701)
.+|+||.|.+-. +++.+++.++..++.++ +.++||+|+|++..+.
T Consensus 3 ivfllD~S~Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~~ 52 (165)
T cd01481 3 IVFLIDGSDNVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPRP 52 (165)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCeeE
Confidence 589999999854 48888888888888774 5689999999976543
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=97.48 E-value=0.009 Score=57.23 Aligned_cols=154 Identities=21% Similarity=0.160 Sum_probs=100.5
Q ss_pred cEEEEEEECCCch-hh-HHHHHHHHHHHhhcCCC---CcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHH
Q 005340 130 PVFMFVVDTCIIE-EE-MSFLKSALSQAIDLLPD---NSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (701)
Q Consensus 130 p~~vFvIDvs~~~-~~-l~~~~~~l~~~l~~lp~---~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (701)
.-++|+||+|.++ .. ++.+++.+...+..+.. +.+||+++|++..+.+.-- .
T Consensus 2 ~~v~l~vD~S~SM~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ii~f~~~~~~~~~~-~---------------------- 58 (177)
T smart00327 2 LDVVFLLDGSGSMGPNRFEKAKEFVLKLVEQLDIGPDGDRVGLVTFSDDATVLFPL-N---------------------- 58 (177)
T ss_pred ccEEEEEeCCCccchHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeCCCceEEEcc-c----------------------
Confidence 3578999999998 33 78888888888877765 7899999999854333100 0
Q ss_pred hHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhc
Q 005340 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (701)
Q Consensus 205 ~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~ 284 (701)
.....+.+...++.+... ......++.|+..|...+..
T Consensus 59 -----------------------------------~~~~~~~~~~~i~~~~~~-------~~~~~~~~~al~~~~~~~~~ 96 (177)
T smart00327 59 -----------------------------------DSRSKDALLEALASLSYK-------LGGGTNLGAALQYALENLFS 96 (177)
T ss_pred -----------------------------------ccCCHHHHHHHHHhcCCC-------CCCCchHHHHHHHHHHHhcC
Confidence 000112333455555420 12346778899988888752
Q ss_pred cCCCC----CcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCC
Q 005340 285 CVPGS----GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (701)
Q Consensus 285 ~~~~~----gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~ 360 (701)
..... .-.|++|++|.++.+ ..+.+...++.+.+|.+..+.++.+
T Consensus 97 ~~~~~~~~~~~~iviitDg~~~~~-------------------------------~~~~~~~~~~~~~~i~i~~i~~~~~ 145 (177)
T smart00327 97 KSAGSRRGAPKVLILITDGESNDG-------------------------------GDLLKAAKELKRSGVKVFVVGVGND 145 (177)
T ss_pred cCCCCCCCCCeEEEEEcCCCCCCC-------------------------------ccHHHHHHHHHHCCCEEEEEEccCc
Confidence 11111 346788888866543 1234566777788888888887754
Q ss_pred ccChhcchhhhccccceEEE
Q 005340 361 QVGVAELKVAVEKTGGLVVL 380 (701)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~~ 380 (701)
. +-..+..++..++|...+
T Consensus 146 ~-~~~~l~~~~~~~~~~~~~ 164 (177)
T smart00327 146 V-DEEELKKLASAPGGVYVF 164 (177)
T ss_pred c-CHHHHHHHhCCCcceEEe
Confidence 3 778899999999987765
No 42
>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=97.48 E-value=0.0031 Score=60.76 Aligned_cols=156 Identities=21% Similarity=0.241 Sum_probs=95.3
Q ss_pred EEEEEECCCchhh--HHHHHHHHHHHhhcC---CCCcEEEEEEECCEEEEE-EcCCCCCCCCceeeecCCccCChHHHHh
Q 005340 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLL---PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (701)
Q Consensus 132 ~vFvIDvs~~~~~--l~~~~~~l~~~l~~l---p~~~~VgiItf~~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (701)
.+|+||.|..... ++.+++.+...++.+ ++..+||+|+|++..+.+ .+. .. .
T Consensus 2 ivflvD~S~sm~~~~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~~~~~~~-~~-~-------------------- 59 (178)
T PF00092_consen 2 IVFLVDTSGSMSGDNFEKAKQFVKSIISRLSISNNGTRVGIVTFSDSARVLFSLT-DY-Q-------------------- 59 (178)
T ss_dssp EEEEEE-STTSCHHHHHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEEEEEETT-SH-S--------------------
T ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHHhhhccccccccceeeeecccccccccc-cc-c--------------------
Confidence 5899999998765 888888888888854 567999999999877543 222 10 0
Q ss_pred HhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHH-HHccCCCCCCCCCCCCccchhHHHHHHHHHhhc
Q 005340 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVL-EELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (701)
Q Consensus 206 ~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL-~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~ 284 (701)
....+.+.+ ..++. ....+.+|.||..|...+..
T Consensus 60 -------------------------------------~~~~~~~~i~~~~~~--------~~g~t~~~~aL~~a~~~l~~ 94 (178)
T PF00092_consen 60 -------------------------------------SKNDLLNAINDSIPS--------SGGGTNLGAALKFAREQLFS 94 (178)
T ss_dssp -------------------------------------SHHHHHHHHHTTGGC--------CBSSB-HHHHHHHHHHHTTS
T ss_pred -------------------------------------ccccccccccccccc--------cchhhhHHHHHhhhhhcccc
Confidence 000111222 22222 22356799999999999874
Q ss_pred c---C-CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCC
Q 005340 285 C---V-PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (701)
Q Consensus 285 ~---~-~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~ 360 (701)
. . +..-.-|+++++|.++.++- ... .+..+.+. ..+.+|+.+.+
T Consensus 95 ~~~~~r~~~~~~iiliTDG~~~~~~~--------------------------~~~-----~~~~~~~~-~~i~~~~ig~~ 142 (178)
T PF00092_consen 95 SNNGGRPNSPKVIILITDGNSNDSDS--------------------------PSE-----EAANLKKS-NGIKVIAIGID 142 (178)
T ss_dssp GGGTTGTTSEEEEEEEESSSSSSHSG--------------------------HHH-----HHHHHHHH-CTEEEEEEEES
T ss_pred cccccccccccceEEEEeecccCCcc--------------------------hHH-----HHHHHHHh-cCcEEEEEecC
Confidence 2 1 12233578888886654420 000 11111111 56677777767
Q ss_pred ccChhcchhhhcc--ccceEEEeCCCCc
Q 005340 361 QVGVAELKVAVEK--TGGLVVLSDSFGH 386 (701)
Q Consensus 361 ~~~l~~l~~l~~~--TGG~v~~~~~f~~ 386 (701)
..+..++..|+.. .+|.+++..+++.
T Consensus 143 ~~~~~~l~~la~~~~~~~~~~~~~~~~~ 170 (178)
T PF00092_consen 143 NADNEELRELASCPTSEGHVFYLADFSD 170 (178)
T ss_dssp CCHHHHHHHHSHSSTCHHHEEEESSHHH
T ss_pred cCCHHHHHHHhCCCCCCCcEEEcCCHHH
Confidence 7888899999955 4477887777654
No 43
>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=97.44 E-value=0.0059 Score=70.73 Aligned_cols=176 Identities=17% Similarity=0.071 Sum_probs=115.6
Q ss_pred CCcEEEEEEECCCchhh--HHHHHHHHHHHhhcC-CCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHH
Q 005340 128 VPPVFMFVVDTCIIEEE--MSFLKSALSQAIDLL-PDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~~--l~~~~~~l~~~l~~l-p~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (701)
..-.++||||+|.++.. ++.++.++...+... .+..+||+|+|++...-+-+. ..
T Consensus 406 ~~~~v~fvvD~SGSM~~~rl~~aK~av~~Ll~~~~~~~D~v~Li~F~~~~a~~~lp-~t--------------------- 463 (589)
T TIGR02031 406 SGRLLIFVVDASGSAAVARMSEAKGAVELLLGEAYVHRDQVSLIAFRGTAAEVLLP-PS--------------------- 463 (589)
T ss_pred cCceEEEEEECCCCCChHHHHHHHHHHHHHHHhhccCCCEEEEEEECCCCceEECC-CC---------------------
Confidence 35568899999999854 889999988888754 456699999997543111111 10
Q ss_pred hHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhc
Q 005340 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (701)
Q Consensus 205 ~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~ 284 (701)
.+...+...|+.|+. ...+.++.||..|...+..
T Consensus 464 -------------------------------------~~~~~~~~~L~~l~~---------gGgTpL~~gL~~A~~~~~~ 497 (589)
T TIGR02031 464 -------------------------------------RSVEQAKRRLDVLPG---------GGGTPLAAGLAAAFQTALQ 497 (589)
T ss_pred -------------------------------------CCHHHHHHHHhcCCC---------CCCCcHHHHHHHHHHHHHH
Confidence 011122244555543 1246889999999999874
Q ss_pred cCCCCC--cEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCcc
Q 005340 285 CVPGSG--ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (701)
Q Consensus 285 ~~~~~g--g~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~ 362 (701)
.. ..+ -+|+++++|.+|.|-+...... ..-..+..+-...++.++...||.+-++-+...+.
T Consensus 498 ~~-~~~~~~~ivllTDG~~nv~~~~~~~~~---------------~~~~~~~~~~~~~~a~~~~~~gi~~~vid~~~~~~ 561 (589)
T TIGR02031 498 AR-SSGGTPTIVLITDGRGNIPLDGDPESI---------------KADREQAAEEALALARKIREAGMPALVIDTAMRFV 561 (589)
T ss_pred hc-ccCCceEEEEECCCCCCCCCCcccccc---------------cccchhHHHHHHHHHHHHHhcCCeEEEEeCCCCCc
Confidence 22 123 3699999999998753110000 00012234455677888999998877776666666
Q ss_pred ChhcchhhhccccceEEEeCCCCch
Q 005340 363 GVAELKVAVEKTGGLVVLSDSFGHA 387 (701)
Q Consensus 363 ~l~~l~~l~~~TGG~v~~~~~f~~~ 387 (701)
+..-+..|++..||..++.++-+.+
T Consensus 562 ~~~~~~~lA~~~~g~y~~l~~~~a~ 586 (589)
T TIGR02031 562 STGFAQKLARKMGAHYIYLPNATAA 586 (589)
T ss_pred cchHHHHHHHhcCCcEEeCCCCChh
Confidence 6667899999999999998876653
No 44
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=97.39 E-value=0.0085 Score=68.96 Aligned_cols=172 Identities=14% Similarity=0.090 Sum_probs=111.3
Q ss_pred CCcEEEEEEECCCchh--hHHHHHHHHHHHhhc-CCCCcEEEEEEECCE-EEEEEcCCCCCCCCceeeecCCccCChHHH
Q 005340 128 VPPVFMFVVDTCIIEE--EMSFLKSALSQAIDL-LPDNSLVGLITFGTL-VQVHELGGFGQIIPKTYVFKGSKDVSKDQL 203 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~--~l~~~~~~l~~~l~~-lp~~~~VgiItf~~~-V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l 203 (701)
.+-.++||||+|.++. .+..+|.++...|.. +.+.-+||+|+|++. ..+- +. ..
T Consensus 400 ~~~~vvfvvD~SGSM~~~rl~~aK~a~~~ll~~ay~~rD~v~lI~F~g~~a~~~-lp-pT-------------------- 457 (584)
T PRK13406 400 SETTTIFVVDASGSAALHRLAEAKGAVELLLAEAYVRRDQVALVAFRGRGAELL-LP-PT-------------------- 457 (584)
T ss_pred CCccEEEEEECCCCCcHhHHHHHHHHHHHHHHhhcCCCCEEEEEEECCCceeEE-cC-CC--------------------
Confidence 4678999999999985 388999998888865 456679999999643 3221 11 10
Q ss_pred HhHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhh
Q 005340 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG 283 (701)
Q Consensus 204 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~ 283 (701)
.+...+...|+.|+. ...+.++.||..|..++.
T Consensus 458 --------------------------------------~~~~~~~~~L~~l~~---------gGgTpL~~gL~~A~~~l~ 490 (584)
T PRK13406 458 --------------------------------------RSLVRAKRSLAGLPG---------GGGTPLAAGLDAAAALAL 490 (584)
T ss_pred --------------------------------------cCHHHHHHHHhcCCC---------CCCChHHHHHHHHHHHHH
Confidence 011123345555543 135788999999998876
Q ss_pred ccCC-CCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCcc
Q 005340 284 ACVP-GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (701)
Q Consensus 284 ~~~~-~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~ 362 (701)
.... +.--+|+++|.|-+|.|.+.-..+. .....+ ..++..+...||.+-++-+....
T Consensus 491 ~~~~~~~~~~iVLlTDG~~n~~~~~~~~~~----------------~~~~~~----~~~a~~~~~~gi~~~vId~g~~~- 549 (584)
T PRK13406 491 QVRRKGMTPTVVLLTDGRANIARDGTAGRA----------------QAEEDA----LAAARALRAAGLPALVIDTSPRP- 549 (584)
T ss_pred HhccCCCceEEEEEeCCCCCCCcccccccc----------------chhhHH----HHHHHHHHhcCCeEEEEecCCCC-
Confidence 4311 1235889999999988753211110 000111 34577788888776665555433
Q ss_pred ChhcchhhhccccceEEEeCCCCchhhH
Q 005340 363 GVAELKVAVEKTGGLVVLSDSFGHAVFK 390 (701)
Q Consensus 363 ~l~~l~~l~~~TGG~v~~~~~f~~~~~~ 390 (701)
...+..|++.+||..+..+.-+.+.+.
T Consensus 550 -~~~~~~LA~~~gg~y~~l~~~~a~~~~ 576 (584)
T PRK13406 550 -QPQARALAEAMGARYLPLPRADAGRLS 576 (584)
T ss_pred -cHHHHHHHHhcCCeEEECCCCCHHHHH
Confidence 345899999999999999988776543
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=97.36 E-value=0.0089 Score=57.06 Aligned_cols=41 Identities=22% Similarity=0.332 Sum_probs=33.1
Q ss_pred EEEEEECCCchhh-HHHHHHHHHHHhhcCC---CCcEEEEEEECC
Q 005340 132 FMFVVDTCIIEEE-MSFLKSALSQAIDLLP---DNSLVGLITFGT 172 (701)
Q Consensus 132 ~vFvIDvs~~~~~-l~~~~~~l~~~l~~lp---~~~~VgiItf~~ 172 (701)
++|++|+|.+... ++..++.++..+..+. +..+||+|+|++
T Consensus 3 v~~llD~S~Sm~~~~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~~ 47 (163)
T cd01476 3 LLFVLDSSGSVRGKFEKYKKYIERIVEGLEIGPTATRVALITYSG 47 (163)
T ss_pred EEEEEeCCcchhhhHHHHHHHHHHHHHhcCCCCCCcEEEEEEEcC
Confidence 5899999998765 6667777777777664 478999999987
No 46
>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=97.33 E-value=0.00016 Score=59.88 Aligned_cols=34 Identities=21% Similarity=0.441 Sum_probs=31.7
Q ss_pred CCcccccccccccCCeEEEEeCCcEEEEEECCCh
Q 005340 640 GPEPALLDVAAIAADRILLLDSYFTVVIFHGATI 673 (701)
Q Consensus 640 ~p~~~~ls~~~l~~d~iyLlD~~~~i~i~~G~~v 673 (701)
.|++++++.++|.++++||||+|..||+|+|++.
T Consensus 4 ~~~~~~~s~~~L~s~~~yIld~~~~i~vW~G~~~ 37 (76)
T PF00626_consen 4 RPEQVPLSQSSLNSDDCYILDCGYEIFVWVGKKS 37 (76)
T ss_dssp EEEEESSSGGGEETTSEEEEEESSEEEEEEHTTS
T ss_pred cCCcCCCCHHHcCCCCEEEEEeCCCcEEEEeccC
Confidence 3678899999999999999999999999999994
No 47
>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=97.20 E-value=0.0065 Score=71.15 Aligned_cols=161 Identities=19% Similarity=0.149 Sum_probs=104.0
Q ss_pred CCcEEEEEEECCCchh---hHHHHHHHHHHHhhc-CCCCcEEEEEEECCE-EEEEEcCCCCCCCCceeeecCCccCChHH
Q 005340 128 VPPVFMFVVDTCIIEE---EMSFLKSALSQAIDL-LPDNSLVGLITFGTL-VQVHELGGFGQIIPKTYVFKGSKDVSKDQ 202 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~---~l~~~~~~l~~~l~~-lp~~~~VgiItf~~~-V~~~~l~~~~~~~~~~~v~~g~~~~~~~~ 202 (701)
....++||||+|.++. .+..++.++...+.. .....+||+|+|++. ..+. +. .
T Consensus 464 ~~~~vv~vvD~SgSM~~~~rl~~ak~a~~~ll~~a~~~~D~v~lI~F~g~~a~~~-~p-~-------------------- 521 (633)
T TIGR02442 464 AGNLVIFVVDASGSMAARGRMAAAKGAVLSLLRDAYQKRDKVALITFRGEEAEVL-LP-P-------------------- 521 (633)
T ss_pred CCceEEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCceEE-cC-C--------------------
Confidence 3557889999999984 377888887777654 456689999999742 2211 11 0
Q ss_pred HHhHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHh
Q 005340 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (701)
Q Consensus 203 l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll 282 (701)
..+...+...|+.|+. ...+.++.||..|..++
T Consensus 522 --------------------------------------t~~~~~~~~~L~~l~~---------gG~Tpl~~aL~~A~~~l 554 (633)
T TIGR02442 522 --------------------------------------TSSVELAARRLEELPT---------GGRTPLAAGLLKAAEVL 554 (633)
T ss_pred --------------------------------------CCCHHHHHHHHHhCCC---------CCCCCHHHHHHHHHHHH
Confidence 0111223345555543 12467889999999888
Q ss_pred hc---cCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecC
Q 005340 283 GA---CVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACAL 359 (701)
Q Consensus 283 ~~---~~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~ 359 (701)
.. ..+...+.|+++++|.+|.|.+. .. + ..+ -..++.++...||.+.++-+..
T Consensus 555 ~~~~~~~~~~~~~vvliTDG~~n~~~~~---~~---~-----------------~~~-~~~~a~~l~~~~i~~~vIdt~~ 610 (633)
T TIGR02442 555 SNELLRDDDGRPLLVVITDGRANVADGG---EP---P-----------------TDD-ARTIAAKLAARGILFVVIDTES 610 (633)
T ss_pred HHhhccCCCCceEEEEECCCCCCCCCCC---CC---h-----------------HHH-HHHHHHHHHhcCCeEEEEeCCC
Confidence 73 11234577999999999886211 00 0 011 1446777777787776665555
Q ss_pred CccChhcchhhhccccceEEEe
Q 005340 360 DQVGVAELKVAVEKTGGLVVLS 381 (701)
Q Consensus 360 ~~~~l~~l~~l~~~TGG~v~~~ 381 (701)
..++..-+..|++.+||..+..
T Consensus 611 ~~~~~~~~~~lA~~~gg~y~~l 632 (633)
T TIGR02442 611 GFVRLGLAEDLARALGGEYVRL 632 (633)
T ss_pred CCcchhHHHHHHHhhCCeEEec
Confidence 6677788999999999998863
No 48
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=97.15 E-value=0.015 Score=58.65 Aligned_cols=169 Identities=16% Similarity=0.101 Sum_probs=113.4
Q ss_pred CCcEEEEEEECCCchhh---HHHHHHHHHHHhhcCC-CCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHH
Q 005340 128 VPPVFMFVVDTCIIEEE---MSFLKSALSQAIDLLP-DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQL 203 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~~---l~~~~~~l~~~l~~lp-~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l 203 (701)
...-+|||||.|.++.- ++.++-++.+.|..-. ..-+|++|+|.. .. +
T Consensus 77 ~g~lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~dAYq~RdkvavI~F~G---------~~---A---------------- 128 (261)
T COG1240 77 AGNLIVFVVDASGSMAARRRMAAAKGAALSLLRDAYQRRDKVAVIAFRG---------EK---A---------------- 128 (261)
T ss_pred cCCcEEEEEeCcccchhHHHHHHHHHHHHHHHHHHHHccceEEEEEecC---------Cc---c----------------
Confidence 35678999999999764 7888888887776543 456999998751 11 1
Q ss_pred HhHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhh
Q 005340 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG 283 (701)
Q Consensus 204 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~ 283 (701)
.+++|...+-+.+.+.|+.|+. .+ .+-+..||..|..++.
T Consensus 129 -------------------------------~lll~pT~sv~~~~~~L~~l~~------GG---~TPL~~aL~~a~ev~~ 168 (261)
T COG1240 129 -------------------------------ELLLPPTSSVELAERALERLPT------GG---KTPLADALRQAYEVLA 168 (261)
T ss_pred -------------------------------eEEeCCcccHHHHHHHHHhCCC------CC---CCchHHHHHHHHHHHH
Confidence 1222222333455677777764 23 3456899999999998
Q ss_pred ccCC---CCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCC
Q 005340 284 ACVP---GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (701)
Q Consensus 284 ~~~~---~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~ 360 (701)
...+ ..--.+++.+.|.||.+++.=+. ... ...+.++...|+-+=+.-+-..
T Consensus 169 r~~r~~p~~~~~~vviTDGr~n~~~~~~~~---------------------~e~----~~~a~~~~~~g~~~lvid~e~~ 223 (261)
T COG1240 169 REKRRGPDRRPVMVVITDGRANVPIPLGPK---------------------AET----LEAASKLRLRGIQLLVIDTEGS 223 (261)
T ss_pred HhhccCCCcceEEEEEeCCccCCCCCCchH---------------------HHH----HHHHHHHhhcCCcEEEEecCCc
Confidence 5432 23457899999998877522100 011 1245556666776666666667
Q ss_pred ccChhcchhhhccccceEEEeCCCCchhh
Q 005340 361 QVGVAELKVAVEKTGGLVVLSDSFGHAVF 389 (701)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~~~~~f~~~~~ 389 (701)
++.+.-...||...||.+++.+..+....
T Consensus 224 ~~~~g~~~~iA~~~Gg~~~~L~~l~~~~i 252 (261)
T COG1240 224 EVRLGLAEEIARASGGEYYHLDDLSDDSI 252 (261)
T ss_pred cccccHHHHHHHHhCCeEEecccccchHH
Confidence 77788889999999999999998877544
No 49
>PF04056 Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like proteins are 40 kDa subunits of the transcription factor II H complex. This domain is often found associated with the C2H2 type Zn-finger (IPR007087 from INTERPRO).; GO: 0008270 zinc ion binding, 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent
Probab=97.07 E-value=0.012 Score=57.71 Aligned_cols=95 Identities=21% Similarity=0.232 Sum_probs=67.3
Q ss_pred CccchhHHHHHHHHHhhccCCCCCc-EEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHH
Q 005340 267 STRCTGTALSIAASLLGACVPGSGA-RILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQL 345 (701)
Q Consensus 267 ~~~~~G~Al~~A~~ll~~~~~~~gg-~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~ 345 (701)
...++-.||+.|...|+..- ..|. .|+++.++.-|.-||.+ .+..+.+
T Consensus 78 G~~SLqN~Le~A~~~L~~~p-~~~srEIlvi~gSl~t~Dp~di------------------------------~~ti~~l 126 (193)
T PF04056_consen 78 GEPSLQNGLEMARSSLKHMP-SHGSREILVIFGSLTTCDPGDI------------------------------HETIESL 126 (193)
T ss_pred CChhHHHHHHHHHHHHhhCc-cccceEEEEEEeecccCCchhH------------------------------HHHHHHH
Confidence 35688899999999998653 2344 56666666555555433 2457788
Q ss_pred HHcCcEEEEEEecCCccChhcchhhhccccceEEEeCCCCchhhHHHHHHHh
Q 005340 346 VHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF 397 (701)
Q Consensus 346 ~~~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l 397 (701)
.+.+|-|++..++. .+.-.+.+|+.|||.... ..++.+|++-+....
T Consensus 127 ~~~~IrvsvI~laa---Ev~I~k~i~~~T~G~y~V--~lde~H~~~lL~~~~ 173 (193)
T PF04056_consen 127 KKENIRVSVISLAA---EVYICKKICKETGGTYGV--ILDEDHFKELLMEHV 173 (193)
T ss_pred HHcCCEEEEEEEhH---HHHHHHHHHHhhCCEEEE--ecCHHHHHHHHHhhC
Confidence 88999999999886 566789999999995543 345667766554443
No 50
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=97.03 E-value=0.042 Score=62.04 Aligned_cols=165 Identities=13% Similarity=0.052 Sum_probs=95.7
Q ss_pred CCcEEEEEEECCCchhh---HHHHHHHHHHHhhcC---CCCcEEEEEEECCEEE-EEEcCCCCCCCCceeeecCCccCCh
Q 005340 128 VPPVFMFVVDTCIIEEE---MSFLKSALSQAIDLL---PDNSLVGLITFGTLVQ-VHELGGFGQIIPKTYVFKGSKDVSK 200 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~~---l~~~~~~l~~~l~~l---p~~~~VgiItf~~~V~-~~~l~~~~~~~~~~~v~~g~~~~~~ 200 (701)
..--++|+||+|.+... ++.++..+...+..+ ++..+||+++|++..+ ++.+. .. . .++
T Consensus 41 ~~lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~r~vfpL~-s~-~-----------s~D- 106 (576)
T PTZ00441 41 EEVDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNTTELIRLG-SG-A-----------SKD- 106 (576)
T ss_pred CCceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCceEEEecC-CC-c-----------ccc-
Confidence 35678999999998754 466777777777766 3467999999998654 33343 21 0 000
Q ss_pred HHHHhHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHH
Q 005340 201 DQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAAS 280 (701)
Q Consensus 201 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ 280 (701)
+..+...|..|..... + ...+.+|.||..|..
T Consensus 107 -------------------------------------------k~~aL~~I~sL~~~~~--p---gGgTnig~AL~~Aae 138 (576)
T PTZ00441 107 -------------------------------------------KEQALIIVKSLRKTYL--P---YGKTNMTDALLEVRK 138 (576)
T ss_pred -------------------------------------------HHHHHHHHHHHHhhcc--C---CCCccHHHHHHHHHH
Confidence 0111122333322111 1 124778999999888
Q ss_pred HhhccC--CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEec
Q 005340 281 LLGACV--PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACA 358 (701)
Q Consensus 281 ll~~~~--~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~ 358 (701)
.+.... ....+.||+++.|.++.+. . . .+.++++...||.|-++.++
T Consensus 139 ~L~sr~~R~nvpKVVILLTDG~sns~~-----------------------d-------v-leaAq~LR~~GVeI~vIGVG 187 (576)
T PTZ00441 139 HLNDRVNRENAIQLVILMTDGIPNSKY-----------------------R-------A-LEESRKLKDRNVKLAVIGIG 187 (576)
T ss_pred HHhhcccccCCceEEEEEecCCCCCcc-----------------------c-------H-HHHHHHHHHCCCEEEEEEeC
Confidence 876310 0123678999888643210 0 0 12355666778876666664
Q ss_pred CCccChhcchhhh----ccccceEEEeCCCCc
Q 005340 359 LDQVGVAELKVAV----EKTGGLVVLSDSFGH 386 (701)
Q Consensus 359 ~~~~~l~~l~~l~----~~TGG~v~~~~~f~~ 386 (701)
. ..+...+..++ ..++|.+|...+|+.
T Consensus 188 ~-g~n~e~LrlIAgC~p~~g~c~~Y~vadf~e 218 (576)
T PTZ00441 188 Q-GINHQFNRLLAGCRPREGKCKFYSDADWEE 218 (576)
T ss_pred C-CcCHHHHHHHhccCCCCCCCceEEeCCHHH
Confidence 3 45655555555 335567888778853
No 51
>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=97.03 E-value=0.033 Score=51.87 Aligned_cols=148 Identities=24% Similarity=0.315 Sum_probs=94.5
Q ss_pred EEEEEEECCCch--hhHHHHHHHHHHHhhcCCC---CcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHHHh
Q 005340 131 VFMFVVDTCIIE--EEMSFLKSALSQAIDLLPD---NSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (701)
Q Consensus 131 ~~vFvIDvs~~~--~~l~~~~~~l~~~l~~lp~---~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (701)
.++|+||+|.++ ..++.+++.+...+..++. ..++|++.|+...+.+- . .. .
T Consensus 2 ~v~~viD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~f~~~~~~~~-~-~~-~-------------------- 58 (161)
T cd00198 2 DIVFLLDVSGSMGGEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARVVL-P-LT-T-------------------- 58 (161)
T ss_pred cEEEEEeCCCCcCcchHHHHHHHHHHHHHhcccCCCCcEEEEEEecCccceee-c-cc-c--------------------
Confidence 478999999987 3388888888888888875 78999999997443321 1 00 0
Q ss_pred HhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhcc
Q 005340 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (701)
Q Consensus 206 ~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~ 285 (701)
. ...+.+...++.+.. .......+..|+..|...+...
T Consensus 59 ------------------------------~-----~~~~~~~~~~~~~~~-------~~~~~t~~~~al~~~~~~~~~~ 96 (161)
T cd00198 59 ------------------------------D-----TDKADLLEAIDALKK-------GLGGGTNIGAALRLALELLKSA 96 (161)
T ss_pred ------------------------------c-----CCHHHHHHHHHhccc-------CCCCCccHHHHHHHHHHHhccc
Confidence 0 011123344444432 1123457788999999988742
Q ss_pred C-CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCccCh
Q 005340 286 V-PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGV 364 (701)
Q Consensus 286 ~-~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l 364 (701)
. +.....+++|++|.++.++ . -..+..+.+.+.++.+.++.++. ..+-
T Consensus 97 ~~~~~~~~lvvitDg~~~~~~-----~-------------------------~~~~~~~~~~~~~v~v~~v~~g~-~~~~ 145 (161)
T cd00198 97 KRPNARRVIILLTDGEPNDGP-----E-------------------------LLAEAARELRKLGITVYTIGIGD-DANE 145 (161)
T ss_pred CCCCCceEEEEEeCCCCCCCc-----c-------------------------hhHHHHHHHHHcCCEEEEEEcCC-CCCH
Confidence 1 2346678888888765443 0 01234555666799998888775 3456
Q ss_pred hcchhhhccc
Q 005340 365 AELKVAVEKT 374 (701)
Q Consensus 365 ~~l~~l~~~T 374 (701)
..+..++..|
T Consensus 146 ~~l~~l~~~~ 155 (161)
T cd00198 146 DELKEIADKT 155 (161)
T ss_pred HHHHHHhccc
Confidence 6788888877
No 52
>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=97.00 E-value=0.029 Score=55.41 Aligned_cols=149 Identities=13% Similarity=0.071 Sum_probs=88.6
Q ss_pred EEEEEECCCchhh--HH-HHHHHHHHHhhcC---CCCcEEEEEEECCEEEEE-EcCCCCCCCCceeeecCCccCChHHHH
Q 005340 132 FMFVVDTCIIEEE--MS-FLKSALSQAIDLL---PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (701)
Q Consensus 132 ~vFvIDvs~~~~~--l~-~~~~~l~~~l~~l---p~~~~VgiItf~~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (701)
.+|+||.|.+..+ ++ .+++.++..++.+ ++++|||+|+|++..+++ .+. .. .
T Consensus 3 i~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~~~~~~~-~~-~------------------- 61 (192)
T cd01473 3 LTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNRDVVPFS-DE-E------------------- 61 (192)
T ss_pred EEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCceeEEecC-cc-c-------------------
Confidence 5899999998754 55 4677777777766 457899999999866543 222 10 0
Q ss_pred hHhhcccCCCCCCCccccCccCCCCcccccceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhhc
Q 005340 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (701)
Q Consensus 205 ~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~ 284 (701)
...+..+.+.++++... + . ....+.+|.||..|...+..
T Consensus 62 ------------------------------------~~~~~~l~~~i~~l~~~-~--~--~~g~T~~~~AL~~a~~~~~~ 100 (192)
T cd01473 62 ------------------------------------RYDKNELLKKINDLKNS-Y--R--SGGETYIVEALKYGLKNYTK 100 (192)
T ss_pred ------------------------------------ccCHHHHHHHHHHHHhc-c--C--CCCcCcHHHHHHHHHHHhcc
Confidence 00112334555666531 1 1 12356889999999887752
Q ss_pred cCCC--CCcE-EEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHHcCcEEEEEEecCCc
Q 005340 285 CVPG--SGAR-ILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (701)
Q Consensus 285 ~~~~--~gg~-Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~ 361 (701)
..+. ...| ++++|.|..+.+- ..--.+.++.+.+.||.+-.+..+.
T Consensus 101 ~~~~r~~~~kv~IllTDG~s~~~~-----------------------------~~~~~~~a~~lk~~gV~i~~vGiG~-- 149 (192)
T cd01473 101 HGNRRKDAPKVTMLFTDGNDTSAS-----------------------------KKELQDISLLYKEENVKLLVVGVGA-- 149 (192)
T ss_pred CCCCcccCCeEEEEEecCCCCCcc-----------------------------hhhHHHHHHHHHHCCCEEEEEEecc--
Confidence 1100 0123 6777877432210 0001345777888898887777764
Q ss_pred cChhcchhhhcc
Q 005340 362 VGVAELKVAVEK 373 (701)
Q Consensus 362 ~~l~~l~~l~~~ 373 (701)
.+-.++..++..
T Consensus 150 ~~~~el~~ia~~ 161 (192)
T cd01473 150 ASENKLKLLAGC 161 (192)
T ss_pred ccHHHHHHhcCC
Confidence 356677777754
No 53
>cd01458 vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.
Probab=96.37 E-value=0.23 Score=50.06 Aligned_cols=69 Identities=19% Similarity=0.190 Sum_probs=46.8
Q ss_pred CccchhHHHHHHHHHhhccCC-CCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHH
Q 005340 267 STRCTGTALSIAASLLGACVP-GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQL 345 (701)
Q Consensus 267 ~~~~~G~Al~~A~~ll~~~~~-~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~ 345 (701)
....++.||.+|..++..... ...-+|++||+|--..|.. .....-...++.++
T Consensus 104 ~~~~l~~aL~~a~~~~~~~~~~~~~k~IvL~TDg~~p~~~~-------------------------~~~~~~~~~~a~~l 158 (218)
T cd01458 104 GQVSLSDALWVCLDLFSKGKKKKSHKRIFLFTNNDDPHGGD-------------------------SIKDSQAAVKAEDL 158 (218)
T ss_pred CCccHHHHHHHHHHHHHhccccccccEEEEECCCCCCCCCC-------------------------HHHHHHHHHHHHHH
Confidence 467899999999999985211 2345799999975333210 01123355688888
Q ss_pred HHcCcEEEEEEecCC
Q 005340 346 VHQGHVLDLFACALD 360 (701)
Q Consensus 346 ~~~~isvDlf~~~~~ 360 (701)
.+.||.+.+|.....
T Consensus 159 ~~~gI~i~~i~i~~~ 173 (218)
T cd01458 159 KDKGIELELFPLSSP 173 (218)
T ss_pred HhCCcEEEEEecCCC
Confidence 888999999887543
No 54
>cd01454 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial denitrification has been established as NO3- ------ NO2- ------ NO ------- N2O --------- N2. This reaction generally occurs under oxygen limiting conditions. Genetic and biochemical studies have shown that the first srep of the biochemical pathway is catalyzed by periplasmic nitrate reductases. This family is widely present in proteobacteria and firmicutes. This version of the domain is also present in some archaeal members. The function of the vWA domain in this sub-group is not known. Members of this subgroup have a conserved MIDAS motif.
Probab=96.30 E-value=0.17 Score=48.92 Aligned_cols=43 Identities=14% Similarity=0.095 Sum_probs=34.8
Q ss_pred EEEEEEECCCchhh---HHHHHHHHHHHhhcCCC-CcEEEEEEECCE
Q 005340 131 VFMFVVDTCIIEEE---MSFLKSALSQAIDLLPD-NSLVGLITFGTL 173 (701)
Q Consensus 131 ~~vFvIDvs~~~~~---l~~~~~~l~~~l~~lp~-~~~VgiItf~~~ 173 (701)
.++|+||+|.++.. ++.+++++...++.+.+ +.++|+++|++.
T Consensus 2 ~v~~llD~SgSM~~~~kl~~ak~a~~~l~~~l~~~~d~~~l~~F~~~ 48 (174)
T cd01454 2 AVTLLLDLSGSMRSDRRIDVAKKAAVLLAEALEACGVPHAILGFTTD 48 (174)
T ss_pred EEEEEEECCCCCCCCcHHHHHHHHHHHHHHHHHHcCCcEEEEEecCC
Confidence 57899999998743 78888888877777764 789999999875
No 55
>cd01462 VWA_YIEM_type VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=95.82 E-value=0.3 Score=45.91 Aligned_cols=43 Identities=16% Similarity=0.098 Sum_probs=32.4
Q ss_pred EEEEEECCCchhh--HHHHHHHHHHHhhcCC-CCcEEEEEEECCEE
Q 005340 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP-DNSLVGLITFGTLV 174 (701)
Q Consensus 132 ~vFvIDvs~~~~~--l~~~~~~l~~~l~~lp-~~~~VgiItf~~~V 174 (701)
++|+||+|.++.. ++..+..+...+..+. ++.+|++|+|++..
T Consensus 3 v~illD~SgSM~~~k~~~a~~~~~~l~~~~~~~~~~v~li~F~~~~ 48 (152)
T cd01462 3 VILLVDQSGSMYGAPEEVAKAVALALLRIALAENRDTYLILFDSEF 48 (152)
T ss_pred EEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHcCCcEEEEEeCCCc
Confidence 6899999999864 5566666666666554 46799999999873
No 56
>KOG2884 consensus 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=95.58 E-value=0.55 Score=46.03 Aligned_cols=79 Identities=23% Similarity=0.242 Sum_probs=54.4
Q ss_pred ccchhHHHHHHHHHhhccCC-CCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHH
Q 005340 268 TRCTGTALSIAASLLGACVP-GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLV 346 (701)
Q Consensus 268 ~~~~G~Al~~A~~ll~~~~~-~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~ 346 (701)
+.-++.+|+.|...|++.-. ..--||++|.++|-.. ..+-.-++|+++.
T Consensus 84 ~~~~~~~i~iA~lalkhRqnk~~~~riVvFvGSpi~e------------------------------~ekeLv~~akrlk 133 (259)
T KOG2884|consen 84 KANFMTGIQIAQLALKHRQNKNQKQRIVVFVGSPIEE------------------------------SEKELVKLAKRLK 133 (259)
T ss_pred cccHHHHHHHHHHHHHhhcCCCcceEEEEEecCcchh------------------------------hHHHHHHHHHHHH
Confidence 35678999999999996421 1236999999985311 1223457899999
Q ss_pred HcCcEEEEEEecCCccChhcchhhhccccc
Q 005340 347 HQGHVLDLFACALDQVGVAELKVAVEKTGG 376 (701)
Q Consensus 347 ~~~isvDlf~~~~~~~~l~~l~~l~~~TGG 376 (701)
+.+|.||++.|+-..-+-.-+......++|
T Consensus 134 k~~Vaidii~FGE~~~~~e~l~~fida~N~ 163 (259)
T KOG2884|consen 134 KNKVAIDIINFGEAENNTEKLFEFIDALNG 163 (259)
T ss_pred hcCeeEEEEEeccccccHHHHHHHHHHhcC
Confidence 999999999998655553444444444444
No 57
>smart00262 GEL Gelsolin homology domain. Gelsolin/severin/villin homology domain. Calcium-binding and actin-binding. Both intra- and extracellular domains.
Probab=95.33 E-value=0.016 Score=49.60 Aligned_cols=32 Identities=9% Similarity=0.216 Sum_probs=28.9
Q ss_pred ccccccccccCCeEEEEeCCcEEEEEECCChh
Q 005340 643 PALLDVAAIAADRILLLDSYFTVVIFHGATIA 674 (701)
Q Consensus 643 ~~~ls~~~l~~d~iyLlD~~~~i~i~~G~~v~ 674 (701)
.++++.++|.++.+||||++..||+|+|+.+.
T Consensus 15 ~~~~~~~~L~s~d~fild~~~~iyvW~G~~as 46 (90)
T smart00262 15 EVPFSQGSLNSGDCYILDTGSEIYVWVGKKSS 46 (90)
T ss_pred EcCCCHHHCCCCCEEEEECCCEEEEEECCCCC
Confidence 35678889999999999999999999999884
No 58
>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=93.84 E-value=0.089 Score=51.00 Aligned_cols=45 Identities=20% Similarity=0.251 Sum_probs=36.3
Q ss_pred EEEEEECCCchhh--HHHHHHHHHHHhhcCCC------CcEEEEEEECCEEEE
Q 005340 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLPD------NSLVGLITFGTLVQV 176 (701)
Q Consensus 132 ~vFvIDvs~~~~~--l~~~~~~l~~~l~~lp~------~~~VgiItf~~~V~~ 176 (701)
++||||+|.++.. ++.++++++..++.+.+ +.+||+|+|++..+.
T Consensus 6 v~~llD~SgSM~~~~~~~~k~a~~~~~~~l~~~~~~~~~~~v~ii~F~~~a~~ 58 (176)
T cd01464 6 IYLLLDTSGSMAGEPIEALNQGLQMLQSELRQDPYALESVEISVITFDSAARV 58 (176)
T ss_pred EEEEEECCCCCCChHHHHHHHHHHHHHHHHhcChhhccccEEEEEEecCCceE
Confidence 5799999998753 78888888888877743 469999999987654
No 59
>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=93.79 E-value=1.5 Score=51.01 Aligned_cols=73 Identities=18% Similarity=0.199 Sum_probs=44.8
Q ss_pred cchhHHHHHHHHHhhccCCCCC-cEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHH
Q 005340 269 RCTGTALSIAASLLGACVPGSG-ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVH 347 (701)
Q Consensus 269 ~~~G~Al~~A~~ll~~~~~~~g-g~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~ 347 (701)
..+..||.+|..++..+.++.+ -||++||+.-.-.|. + .. ...-=...|..+..
T Consensus 117 ~~l~daL~~~~~~f~~~~~k~~~kRI~lfTd~D~P~~~--------------------~-~~----~~~~a~~~a~dl~~ 171 (584)
T TIGR00578 117 YSLSEVLWVCANLFSDVQFRMSHKRIMLFTNEDNPHGN--------------------D-SA----KASRARTKAGDLRD 171 (584)
T ss_pred CcHHHHHHHHHHHHHhcchhhcCcEEEEECCCCCCCCC--------------------c-hh----HHHHHHHHHHHHHh
Confidence 4789999999999985433444 469999974221110 0 00 00011224788889
Q ss_pred cCcEEEEEEec-CCccChhc
Q 005340 348 QGHVLDLFACA-LDQVGVAE 366 (701)
Q Consensus 348 ~~isvDlf~~~-~~~~~l~~ 366 (701)
.||.+++|..+ .+.+|...
T Consensus 172 ~gi~ielf~l~~~~~Fd~s~ 191 (584)
T TIGR00578 172 TGIFLDLMHLKKPGGFDISL 191 (584)
T ss_pred cCeEEEEEecCCCCCCChhh
Confidence 99999999654 23355553
No 60
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=93.14 E-value=0.15 Score=48.92 Aligned_cols=48 Identities=25% Similarity=0.367 Sum_probs=38.7
Q ss_pred CcEEEEEEECCCchhh--HHHHHHHHHHHhhcCCC------CcEEEEEEECCEEEEE
Q 005340 129 PPVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPD------NSLVGLITFGTLVQVH 177 (701)
Q Consensus 129 ~p~~vFvIDvs~~~~~--l~~~~~~l~~~l~~lp~------~~~VgiItf~~~V~~~ 177 (701)
-|+| |++|+|.++.- .+.+..+|+..++.|.. .+.++|||||+.+++|
T Consensus 4 lP~~-lllDtSgSM~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~~a~~~ 59 (207)
T COG4245 4 LPCY-LLLDTSGSMIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGPARVI 59 (207)
T ss_pred CCEE-EEEecCcccccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecCcceEE
Confidence 3555 89999999864 88888888888887743 4799999999977776
No 61
>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=92.15 E-value=11 Score=39.28 Aligned_cols=46 Identities=24% Similarity=0.302 Sum_probs=35.2
Q ss_pred CCcEEEEEEECCCchhh-------HHHHHHHHHHHhhcCCCCcEEEEEEECCEEE
Q 005340 128 VPPVFMFVVDTCIIEEE-------MSFLKSALSQAIDLLPDNSLVGLITFGTLVQ 175 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~~-------l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~ 175 (701)
...-++++||.|.++.+ ++ .+..|..++..++. .+||++.|+..+.
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 57789999999999865 45 44466777776766 5899999997653
No 62
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=90.11 E-value=9.9 Score=36.60 Aligned_cols=59 Identities=31% Similarity=0.342 Sum_probs=43.5
Q ss_pred cchhHHHHHHHHHhhccCCCCC--cEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHH
Q 005340 269 RCTGTALSIAASLLGACVPGSG--ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLV 346 (701)
Q Consensus 269 ~~~G~Al~~A~~ll~~~~~~~g--g~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~ 346 (701)
--+|.+|+.|..++++.- ..| .||++|.++|... +.+-.=.+|+++.
T Consensus 85 a~~~~~lqiaql~lkhR~-nk~q~qriVaFvgSpi~e------------------------------sedeLirlak~lk 133 (243)
T COG5148 85 ADIMRCLQIAQLILKHRD-NKGQRQRIVAFVGSPIQE------------------------------SEDELIRLAKQLK 133 (243)
T ss_pred chHHHHHHHHHHHHhccc-CCccceEEEEEecCcccc------------------------------cHHHHHHHHHHHH
Confidence 457899999999999642 233 6999999975311 1122346799999
Q ss_pred HcCcEEEEEEec
Q 005340 347 HQGHVLDLFACA 358 (701)
Q Consensus 347 ~~~isvDlf~~~ 358 (701)
++++.||++-++
T Consensus 134 knnVAidii~fG 145 (243)
T COG5148 134 KNNVAIDIIFFG 145 (243)
T ss_pred hcCeeEEEEehh
Confidence 999999999876
No 63
>KOG0443 consensus Actin regulatory proteins (gelsolin/villin family) [Cytoskeleton]
Probab=89.68 E-value=0.34 Score=56.00 Aligned_cols=54 Identities=22% Similarity=0.291 Sum_probs=39.2
Q ss_pred HHhhcccceecccC-CC---CcccccccccccCCeEEEEeCCcEEEEEECCCh-hHHHH
Q 005340 625 VVMIQPSLISYSFH-SG---PEPALLDVAAIAADRILLLDSYFTVVIFHGATI-AQWRK 678 (701)
Q Consensus 625 ~~~iyP~l~~~~~~-~~---p~~~~ls~~~l~~d~iyLlD~~~~i~i~~G~~v-~~~~~ 678 (701)
..-..|+||..+.. +- -+-...+-+.|.+|.|||||++..||||+|++| ..|..
T Consensus 615 ~~~~~PrLF~Cs~~~g~f~~~EI~~F~QdDL~tdDi~lLDt~~evfvWvG~~a~~~eK~ 673 (827)
T KOG0443|consen 615 KPERDPRLFSCSNKTGSFVVEEIYNFTQDDLMTDDIMLLDTWSEVFVWVGQEANEKEKE 673 (827)
T ss_pred cCCCCCcEEEEEecCCcEEEEEecCcchhhccccceEEEecCceEEEEecCCCChhHHH
Confidence 35567888887653 10 111255667899999999999999999999998 44553
No 64
>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=86.89 E-value=28 Score=36.46 Aligned_cols=86 Identities=19% Similarity=0.113 Sum_probs=57.2
Q ss_pred cchhHHHHHHHHHhhccC-------CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHH
Q 005340 269 RCTGTALSIAASLLGACV-------PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDAL 341 (701)
Q Consensus 269 ~~~G~Al~~A~~ll~~~~-------~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~l 341 (701)
..+..||..|+-.+.-.. ....+||+++.++-+.. .. +.-=+=+.
T Consensus 116 s~LagALS~ALCyINR~~~~~~~~~~~~~~RILv~~s~s~d~------------------------~~----QYi~~MN~ 167 (276)
T PF03850_consen 116 SLLAGALSMALCYINRISRESPSGGTSLKSRILVIVSGSPDS------------------------SS----QYIPLMNC 167 (276)
T ss_pred hhhHHHHHHHHHHHhhhhhcccCCCCCcCccEEEEEecCCCc------------------------cH----HHHHHHHH
Confidence 677888888887776321 13557999964431100 01 11112234
Q ss_pred HHHHHHcCcEEEEEEecCCccChhcchhhhccccceEEEeCCC
Q 005340 342 SKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSF 384 (701)
Q Consensus 342 a~~~~~~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f 384 (701)
.-.|.+.+|.||++..+. -+-.-|++.+..|||.-...+..
T Consensus 168 iFaAqk~~v~IDv~~L~~--~~s~fLqQa~d~T~G~y~~~~~~ 208 (276)
T PF03850_consen 168 IFAAQKQKVPIDVCKLGG--KDSTFLQQASDITGGIYLKVSKP 208 (276)
T ss_pred HHHHhcCCceeEEEEecC--CchHHHHHHHHHhCceeeccCcc
Confidence 667888999999999976 35566999999999988876663
No 65
>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=85.92 E-value=61 Score=35.83 Aligned_cols=279 Identities=14% Similarity=0.106 Sum_probs=146.6
Q ss_pred CcEEEEEEECCCchhh----HHHHHHHHHHHhhcCCCCcEEEEEEECC-EEEEEEcCCCCCCCCceeeecCCccCChHHH
Q 005340 129 PPVFMFVVDTCIIEEE----MSFLKSALSQAIDLLPDNSLVGLITFGT-LVQVHELGGFGQIIPKTYVFKGSKDVSKDQL 203 (701)
Q Consensus 129 ~p~~vFvIDvs~~~~~----l~~~~~~l~~~l~~lp~~~~VgiItf~~-~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l 203 (701)
|-=..|+.|+|.++.+ +..+...|...|..+..+.|+||=+|=+ .|.=|- . .. ++.+
T Consensus 99 PvDLYyLMDlS~SM~ddl~~lk~lg~~L~~~m~~it~n~rlGfGsFVDK~v~P~~---~--t~-------------p~~l 160 (423)
T smart00187 99 PVDLYYLMDLSYSMKDDLDNLKSLGDDLAREMKGLTSNFRLGFGSFVDKTVSPFV---S--TR-------------PEKL 160 (423)
T ss_pred ccceEEEEeCCccHHHHHHHHHHHHHHHHHHHHhcccCceeeEEEeecCccCCcc---c--CC-------------HHHh
Confidence 4457799999999876 6666677777778888999999988743 332221 0 01 1222
Q ss_pred HhHhhcccCCCCCCCccccCccCCCCccc-c-cceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHH
Q 005340 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDT-I-ARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (701)
Q Consensus 204 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~p-~-~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~l 281 (701)
+... . + ......| . -+-..++.+.-..+.+.+....- .. +...|+..+-+-+++|+--
T Consensus 161 ~~PC---~-----~--------~~~~c~p~f~f~~~L~LT~~~~~F~~~V~~~~i-Sg---N~D~PEgG~DAimQaaVC~ 220 (423)
T smart00187 161 ENPC---P-----N--------YNLTCEPPYGFKHVLSLTDDTDEFNEEVKKQRI-SG---NLDAPEGGFDAIMQAAVCT 220 (423)
T ss_pred cCCC---c-----C--------CCCCcCCCcceeeeccCCCCHHHHHHHHhhcee-ec---CCcCCcccHHHHHHHHhhc
Confidence 1110 0 0 0000112 1 12345677665566666666543 21 2345676777777877532
Q ss_pred hhccCCCCCcEEEEEecCCCC--CCCcccccCCCCCCcCCCCCCCCCCCccc---chhHHHHHHHHHHHHHcCcEEEEEE
Q 005340 282 LGACVPGSGARILAFVGGPST--EGPAAIVSKNLSEPIRSHKDLDKDSAPHY---HKAVKFYDALSKQLVHQGHVLDLFA 356 (701)
Q Consensus 282 l~~~~~~~gg~Ii~F~~g~pt--~GpG~l~~~~~~~~~~~~~d~~~~~~~~~---~~~~~fY~~la~~~~~~~isvDlf~ 356 (701)
=+...+...-|+++|++-.+- -|-|+|...-..+..+-|-+ .+ -.|. .....--..|++++.+++|-+ ||+
T Consensus 221 ~~IGWR~~a~rllv~~TDa~fH~AGDGkLaGIv~PNDg~CHL~--~~-g~Yt~s~~~DYPSi~ql~~kL~e~nI~~-IFA 296 (423)
T smart00187 221 EQIGWREDARRLLVFSTDAGFHFAGDGKLAGIVQPNDGQCHLD--NN-GEYTMSTTQDYPSIGQLNQKLAENNINP-IFA 296 (423)
T ss_pred cccccCCCceEEEEEEcCCCccccCCcceeeEecCCCCcceeC--CC-CCcCccCcCCCCCHHHHHHHHHhcCceE-EEE
Confidence 211123345689998877663 68888766544444444422 11 0111 111223467888888888864 777
Q ss_pred ecCCccChhcchhhhccccceEEEeCCCCchhhHHHHHHHhccCccCCcceeeEEEEEEe-cCCceEEEEEcCCcccCCC
Q 005340 357 CALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVFHSGDYDLGLSSNGIFEINC-SKDIKVQGIIGPCASLEKK 435 (701)
Q Consensus 357 ~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l~~~~~~~~~~~~~~l~vr~-S~gl~v~~~~G~~~~~~~~ 435 (701)
....+.+++ ..|+.+-.|...=- . +.+..++..++++. |......++|+... +.+++++-. ..|......
T Consensus 297 VT~~~~~~Y--~~Ls~lipgs~vg~--L--s~DSsNIv~LI~~a--Y~~i~S~V~l~~~~~p~~v~~~y~-s~C~~g~~~ 367 (423)
T smart00187 297 VTKKQVSLY--KELSALIPGSSVGV--L--SEDSSNVVELIKDA--YNKISSRVELEDNSLPEGVSVTYT-SSCPGGVVG 367 (423)
T ss_pred EcccchhHH--HHHHHhcCcceeee--c--ccCcchHHHHHHHH--HHhhceEEEEecCCCCCcEEEEEE-eeCCCCCcc
Confidence 777766653 45555555444310 1 11223444444322 23345566666664 667777533 333321100
Q ss_pred CCCcccccccCCCCCceEEecCCCCcEEEEEEEEec
Q 005340 436 GPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVK 471 (701)
Q Consensus 436 ~~~~sd~~~g~~~~~~~~~~~~~~~~s~~~~~~~~~ 471 (701)
...-...++.....+.|..++.-
T Consensus 368 -------------~~~~~C~~v~iG~~V~F~v~vta 390 (423)
T smart00187 368 -------------PGTRKCEGVKIGDTVSFEVTVTA 390 (423)
T ss_pred -------------cCCcccCCcccCCEEEEEEEEEe
Confidence 00113445666666667666664
No 66
>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]
Probab=85.34 E-value=0.71 Score=52.25 Aligned_cols=43 Identities=26% Similarity=0.312 Sum_probs=35.1
Q ss_pred cceecccCC---CCcccccccccccCCeEEEEeCCcEEEEEECCCh
Q 005340 631 SLISYSFHS---GPEPALLDVAAIAADRILLLDSYFTVVIFHGATI 673 (701)
Q Consensus 631 ~l~~~~~~~---~p~~~~ls~~~l~~d~iyLlD~~~~i~i~~G~~v 673 (701)
|||.++..+ .-+||+|+..||++.-++|||.|.+||||-|...
T Consensus 623 RlYrv~~~g~~i~lEPVpl~~tSLDPRf~FlLD~G~~IyiW~G~~s 668 (1255)
T KOG0444|consen 623 RLYRVGVNGTAIELEPVPLSVTSLDPRFCFLLDAGETIYIWSGYKS 668 (1255)
T ss_pred hhheeccccceeEeeccCccccccCcceEEEEeCCceEEEEeccch
Confidence 345555433 2579999999999999999999999999999853
No 67
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=84.38 E-value=20 Score=37.67 Aligned_cols=89 Identities=20% Similarity=0.200 Sum_probs=57.4
Q ss_pred ccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHH
Q 005340 268 TRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVH 347 (701)
Q Consensus 268 ~~~~G~Al~~A~~ll~~~~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~~~ 347 (701)
.-++-.||+.|...|+..-....-.|++..++..|.-||.+ |+. -+.+.+
T Consensus 142 ~fSLqNaLe~a~~~Lk~~p~H~sREVLii~sslsT~DPgdi-----------------------------~~t-I~~lk~ 191 (378)
T KOG2807|consen 142 DFSLQNALELAREVLKHMPGHVSREVLIIFSSLSTCDPGDI-----------------------------YET-IDKLKA 191 (378)
T ss_pred ChHHHHHHHHHHHHhcCCCcccceEEEEEEeeecccCcccH-----------------------------HHH-HHHHHh
Confidence 34677899999999984322222345666677777777655 222 344666
Q ss_pred cCcEEEEEEecCCccChhcchhhhccccceEEEeCCCCchhhHH
Q 005340 348 QGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKD 391 (701)
Q Consensus 348 ~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~ 391 (701)
..|-|.++..+. .+..-..||+.|||. |+=..++.++++
T Consensus 192 ~kIRvsvIgLsa---Ev~icK~l~kaT~G~--Y~V~lDe~Hlke 230 (378)
T KOG2807|consen 192 YKIRVSVIGLSA---EVFICKELCKATGGR--YSVALDEGHLKE 230 (378)
T ss_pred hCeEEEEEeech---hHHHHHHHHHhhCCe--EEEEeCHHHHHH
Confidence 788899887765 455568999999993 333445555443
No 68
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.86 E-value=18 Score=37.75 Aligned_cols=95 Identities=18% Similarity=0.073 Sum_probs=61.3
Q ss_pred CccchhHHHHHHHHHhhcc------CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHH
Q 005340 267 STRCTGTALSIAASLLGAC------VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDA 340 (701)
Q Consensus 267 ~~~~~G~Al~~A~~ll~~~------~~~~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~ 340 (701)
....+..||..|+..+.-. ..+..+||+++..++ +. ..+..=+-+
T Consensus 117 ~~s~lagals~ALcyinr~~~~~~~~~~~~~RIlii~~s~-----------~~------------------~~qYi~~mn 167 (279)
T TIGR00627 117 SRTVLAGALSDALGYINRSEQSETASEKLKSRILVISITP-----------DM------------------ALQYIPLMN 167 (279)
T ss_pred ccccchhHHHhhhhhhcccccccccCcCCcceEEEEECCC-----------Cc------------------hHHHHHHHH
Confidence 4556788888888887521 123468999998752 00 011111236
Q ss_pred HHHHHHHcCcEEEEEEecCCccChhcchhhhccccceEEEeCCCCchhhHHHH
Q 005340 341 LSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSV 393 (701)
Q Consensus 341 la~~~~~~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l 393 (701)
....|.+.+|.||++..+.+ -+..-+++++..|||.-.... ++..+.+-|
T Consensus 168 ~Ifaaqk~~I~Idv~~L~~e-~~~~~lqQa~~~TgG~Y~~~~--~~~~L~q~L 217 (279)
T TIGR00627 168 CIFSAQKQNIPIDVVSIGGD-FTSGFLQQAADITGGSYLHVK--KPQGLLQYL 217 (279)
T ss_pred HHHHHHHcCceEEEEEeCCc-cccHHHHHHHHHhCCEEeccC--CHhHHHHHH
Confidence 67788999999999988653 356779999999999544433 333444443
No 69
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=79.77 E-value=1.3 Score=34.08 Aligned_cols=33 Identities=27% Similarity=0.507 Sum_probs=24.8
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N 90 (701)
+.-|++|+.--.-+-+-+...-+|+|..|+..|
T Consensus 22 aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 22 ALICSKCFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred eEECcccchhhcccccccCCceEEEcCCCCCcC
Confidence 566999998754443555555699999999877
No 70
>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=78.76 E-value=2.1 Score=28.85 Aligned_cols=30 Identities=27% Similarity=0.483 Sum_probs=22.7
Q ss_pred cccCCCCceecCceEEEcCCceEEeCCCCCCCCC
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~ 92 (701)
+.|..|+..+-- -.+...++|..|...|.+
T Consensus 2 ~~C~~C~t~L~y----P~gA~~vrCs~C~~vt~v 31 (31)
T TIGR01053 2 VVCGGCRTLLMY----PRGASSVRCALCQTVNLV 31 (31)
T ss_pred cCcCCCCcEeec----CCCCCeEECCCCCeEecC
Confidence 579999987642 256789999999988753
No 71
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=77.25 E-value=1.8 Score=31.91 Aligned_cols=30 Identities=23% Similarity=0.484 Sum_probs=21.1
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~ 91 (701)
..+|.+|++-+. ++.....++|+.||+...
T Consensus 3 ~y~C~~CG~~~~----~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVE----LDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEE----ECCCCCceECCCCCCeEE
Confidence 368999999542 233333799999997654
No 72
>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=76.76 E-value=1.3e+02 Score=33.56 Aligned_cols=281 Identities=12% Similarity=0.115 Sum_probs=133.1
Q ss_pred CCcEEEEEEECCCchhh----HHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEEEcCCCCCCCCceeeecCCccCChHHH
Q 005340 128 VPPVFMFVVDTCIIEEE----MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQL 203 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~~----l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l 203 (701)
.|-=.-|++|+|.++.+ ++.+...|...|..+.++.|+||=+|=+..- .|- + ..+.+.+
T Consensus 101 yPvDLYyLmDlS~Sm~ddl~~l~~lg~~l~~~~~~it~~~~~GfGsfvdK~~----------~P~--~-----~~~p~~l 163 (426)
T PF00362_consen 101 YPVDLYYLMDLSYSMKDDLENLKSLGQDLAEEMRNITSNFRLGFGSFVDKPV----------MPF--V-----STTPEKL 163 (426)
T ss_dssp --EEEEEEEE-SGGGHHHHHHHCCCCHHHHHHHHTT-SSEEEEEEEESSSSS----------TTT--S-----T-SSHCH
T ss_pred cceeEEEEeechhhhhhhHHHHHHHHHHHHHHHHhcCccceEechhhccccc----------CCc--c-----cCChhhh
Confidence 34456799999999876 4555677888888999999999988753220 110 0 0001222
Q ss_pred HhHhhcccCCCCCCCccccCccCCCCccc-c-cceeEehhhhHHHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHH
Q 005340 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDT-I-ARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (701)
Q Consensus 204 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~p-~-~~~l~~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~l 281 (701)
+... .. . .....| . -+-..++.+......+.+.+..- .+ +-..|+..+=+-+++|+--
T Consensus 164 ~~pc--~~--~------------~~~c~~~~~f~~~l~Lt~~~~~F~~~v~~~~i-s~---n~D~PEgg~dal~Qa~vC~ 223 (426)
T PF00362_consen 164 KNPC--PS--K------------NPNCQPPFSFRHVLSLTDDITEFNEEVNKQKI-SG---NLDAPEGGLDALMQAAVCQ 223 (426)
T ss_dssp HSTS--CC--T------------TS--B---SEEEEEEEES-HHHHHHHHHTS---B-----SSSSBSHHHHHHHHHH-H
T ss_pred cCcc--cc--c------------CCCCCCCeeeEEeecccchHHHHHHhhhhccc-cC---CCCCCccccchheeeeecc
Confidence 2211 00 0 001112 1 12345777766666666665432 22 2345677777778877653
Q ss_pred hhccCCCCCcEEEEEecCCC--CCCCcccccCCCCCCcCCCCCCCCCCCccc---chhHHHHHHHHHHHHHcCcEEEEEE
Q 005340 282 LGACVPGSGARILAFVGGPS--TEGPAAIVSKNLSEPIRSHKDLDKDSAPHY---HKAVKFYDALSKQLVHQGHVLDLFA 356 (701)
Q Consensus 282 l~~~~~~~gg~Ii~F~~g~p--t~GpG~l~~~~~~~~~~~~~d~~~~~~~~~---~~~~~fY~~la~~~~~~~isvDlf~ 356 (701)
=...-+...-||++|++-.+ .-|-|++...-..+..+-|-+ .+ ..|. .....-...|.+.+.+++|.+ ||+
T Consensus 224 ~~igWr~~a~~llv~~TD~~fH~agDg~l~gi~~pnd~~Chl~--~~-~~y~~~~~~DYPSv~ql~~~l~e~~i~~-IFA 299 (426)
T PF00362_consen 224 EEIGWRNEARRLLVFSTDAGFHFAGDGKLAGIVKPNDGKCHLD--DN-GMYTASTEQDYPSVGQLVRKLSENNINP-IFA 299 (426)
T ss_dssp HHHT--STSEEEEEEEESS-B--TTGGGGGT--S---SS--BS--TT-SBBGGGGCS----HHHHHHHHHHTTEEE-EEE
T ss_pred cccCcccCceEEEEEEcCCccccccccccceeeecCCCceEEC--CC-CcccccccccCCCHHHHHHHHHHcCCEE-EEE
Confidence 22222345678988887666 589999887665555555533 21 1221 234556778888888887765 777
Q ss_pred ecCCccChhcchhhhccccceEE-EeCCCCchhhHHHHHHHhccCccCCcceeeEEEEEEe-cCCceEEEEEcCCcccCC
Q 005340 357 CALDQVGVAELKVAVEKTGGLVV-LSDSFGHAVFKDSVRRVFHSGDYDLGLSSNGIFEINC-SKDIKVQGIIGPCASLEK 434 (701)
Q Consensus 357 ~~~~~~~l~~l~~l~~~TGG~v~-~~~~f~~~~~~~~l~~~l~~~~~~~~~~~~~~l~vr~-S~gl~v~~~~G~~~~~~~ 434 (701)
......+++ ..|+..-+|... .... +. .++..++++. |......+.++... ++++++ .+..+|.....
T Consensus 300 Vt~~~~~~Y--~~L~~~i~~s~vg~L~~-dS----sNIv~LI~~a--Y~~i~s~V~L~~~~~p~~v~v-~y~s~C~~~~~ 369 (426)
T PF00362_consen 300 VTKDVYSIY--EELSNLIPGSSVGELSS-DS----SNIVQLIKEA--YNKISSKVELKHDNAPDGVKV-SYTSNCPNGST 369 (426)
T ss_dssp EEGGGHHHH--HHHHHHSTTEEEEEEST-TS----HTHHHHHHHH--HHHHCTEEEEEECS--TTEEE-EEEEEESSSEE
T ss_pred EchhhhhHH--HHHhhcCCCceeccccc-Cc----hhHHHHHHHH--HHHHhheEEEEecCCCCcEEE-EEEEEccCCcc
Confidence 776655543 444444444433 3322 11 2233333211 12234455555333 345666 44444432100
Q ss_pred CCCCcccccccCCCCCceEEecCCCCcEEEEEEEEecC
Q 005340 435 KGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKK 472 (701)
Q Consensus 435 ~~~~~sd~~~g~~~~~~~~~~~~~~~~s~~~~~~~~~~ 472 (701)
. ...-...++....++.|.+.+.-.
T Consensus 370 ----~---------~~~~~C~~V~iG~~V~F~VtVta~ 394 (426)
T PF00362_consen 370 ----V---------PGTNECSNVKIGDTVTFNVTVTAK 394 (426)
T ss_dssp ----E---------ECCEEECSE-TT-EEEEEEEEEES
T ss_pred ----c---------CcCccccCEecCCEEEEEEEEEEe
Confidence 0 011334456666666666666543
No 73
>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]
Probab=75.35 E-value=2.9 Score=47.55 Aligned_cols=69 Identities=19% Similarity=0.276 Sum_probs=46.4
Q ss_pred HHhhcccceecccC----CCCcccc-----cccccccCCeEEEEeCCcEEEEEECCChhHHH-------HcCCC---CCC
Q 005340 625 VVMIQPSLISYSFH----SGPEPAL-----LDVAAIAADRILLLDSYFTVVIFHGATIAQWR-------KAGYH---NQP 685 (701)
Q Consensus 625 ~~~iyP~l~~~~~~----~~p~~~~-----ls~~~l~~d~iyLlD~~~~i~i~~G~~v~~~~-------~~~~~---~~~ 685 (701)
..--+|+||.+... ..|+--. |--.-|.+.++|+||+...+|+|+|+...-.+ ...+| +.|
T Consensus 729 f~p~qpkLYkV~lGmGyLELPQvel~P~~~l~q~lL~sk~VyiLDc~sDiF~W~GkKs~RLvraAa~KL~~EL~~M~dRP 808 (1255)
T KOG0444|consen 729 FVPEQPKLYKVNLGMGYLELPQVELLPKGILKQDLLGSKGVYILDCNSDIFLWIGKKSNRLVRAAAQKLVVELHQMIDRP 808 (1255)
T ss_pred cCCCCcceEEEccccceeecchhhhchhhHHHHHhhcCCeEEEEecCCceEEEecccchHHHHHHHHHHHHHHHhhhcCc
Confidence 34568999998642 3454322 22345689999999999999999999764333 23333 468
Q ss_pred ccHHHHHH
Q 005340 686 EHQVVNFV 693 (701)
Q Consensus 686 e~~~~~~~ 693 (701)
+|+.+..-
T Consensus 809 dyA~V~R~ 816 (1255)
T KOG0444|consen 809 DYAQVYRE 816 (1255)
T ss_pred chhheeec
Confidence 88876543
No 74
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=74.82 E-value=7.4 Score=35.54 Aligned_cols=42 Identities=19% Similarity=0.195 Sum_probs=32.3
Q ss_pred EEEEECCCchhh--HHHHHHHHHHHhhcCCCCcEEEEEEECCEEEE
Q 005340 133 MFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQV 176 (701)
Q Consensus 133 vFvIDvs~~~~~--l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~ 176 (701)
+++||+|++..+ |..+...+...+... +.+|-+|.||..|+-
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 689999998754 777777777777766 456899999988854
No 75
>KOG0443 consensus Actin regulatory proteins (gelsolin/villin family) [Cytoskeleton]
Probab=71.99 E-value=3.3 Score=48.26 Aligned_cols=46 Identities=15% Similarity=0.164 Sum_probs=34.1
Q ss_pred cccceeccc--CCC--Cc--ccccccccccCCeEEEEeCC-cEEEEEECCChh
Q 005340 629 QPSLISYSF--HSG--PE--PALLDVAAIAADRILLLDSY-FTVVIFHGATIA 674 (701)
Q Consensus 629 yP~l~~~~~--~~~--p~--~~~ls~~~l~~d~iyLlD~~-~~i~i~~G~~v~ 674 (701)
.++||.++. .+. |. .-+|+-+-|.++.+||||+| ..||||+|+.+.
T Consensus 254 ~~kLYkVsd~~g~l~v~~va~~~l~qdlLd~~dCYILD~g~~~IfVW~Gr~as 306 (827)
T KOG0443|consen 254 AAKLYKVSDASGGLKVPVVADGPLTKDLLDTEDCYILDCGGGEIFVWKGRQAS 306 (827)
T ss_pred ccEEEEEeccCCCccccccccchhhHHhhccCCeEEEecCCceEEEEeCCCCC
Confidence 456888863 111 11 11277888999999999999 999999999873
No 76
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=66.05 E-value=4.1 Score=30.65 Aligned_cols=33 Identities=18% Similarity=0.413 Sum_probs=22.7
Q ss_pred ccCCCCceecCceEEEcCCceEEeCCCCCCCCCCc
Q 005340 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p~ 94 (701)
.|..|+..+-+- -..++..|+|+-|++.-.+.+
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCCeEECCC
Confidence 599999976332 222235899999998766543
No 77
>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=64.80 E-value=11 Score=37.98 Aligned_cols=42 Identities=21% Similarity=0.304 Sum_probs=25.4
Q ss_pred EEEEEEECCCchhh--------HHHHHHHHHHHhhcC---CCCcEEEEEEECC
Q 005340 131 VFMFVVDTCIIEEE--------MSFLKSALSQAIDLL---PDNSLVGLITFGT 172 (701)
Q Consensus 131 ~~vFvIDvs~~~~~--------l~~~~~~l~~~l~~l---p~~~~VgiItf~~ 172 (701)
+.+|+||++.++.+ |+.+.+++...+... .+...||+|.|++
T Consensus 1 ~~vflID~s~sM~~~~~~~~~~l~~al~~i~~~~~~ki~~~~kD~vgvvl~gt 53 (224)
T PF03731_consen 1 ATVFLIDVSPSMFEPSSESESPLEEALKAIEDLMQQKIISSPKDEVGVVLFGT 53 (224)
T ss_dssp EEEEEEE-SCGGGS-BTTCS-HHHHHHHHHHHHHHHHHHTT---EEEEEEES-
T ss_pred CEEEEEECCHHHCCCCCCcchhHHHHHHHHHHHHHHHHcCCCCCeEEEEEEcC
Confidence 46899999999863 555555555555431 2347899998764
No 78
>KOG2487 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription; Replication, recombination and repair]
Probab=59.10 E-value=2.2e+02 Score=29.40 Aligned_cols=43 Identities=19% Similarity=0.087 Sum_probs=34.2
Q ss_pred HHHHHHHHcCcEEEEEEecCCccChhcchhhhccccceEEEeCCCC
Q 005340 340 ALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFG 385 (701)
Q Consensus 340 ~la~~~~~~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f~ 385 (701)
+.--.|.+++|.||++....+ -..+.+.|..|||.....+.-.
T Consensus 187 NciFaAqKq~I~Idv~~l~~~---s~~LqQa~D~TGG~YL~v~~~~ 229 (314)
T KOG2487|consen 187 NCIFAAQKQNIPIDVVSLGGD---SGFLQQACDITGGDYLHVEKPD 229 (314)
T ss_pred HHHHHHHhcCceeEEEEecCC---chHHHHHHhhcCCeeEecCCcc
Confidence 445567889999999999876 3458999999999988877543
No 79
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=57.84 E-value=4.9 Score=29.05 Aligned_cols=30 Identities=20% Similarity=0.437 Sum_probs=25.1
Q ss_pred cccCCCCceecCceEEEcCCceEEeCCCCCC
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
-||..|+....-+..+.+ .....|+-|+..
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-DDPVPCPECGST 35 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-CCCCcCCCCCCC
Confidence 489999988888887777 678999999983
No 80
>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=56.87 E-value=13 Score=26.87 Aligned_cols=27 Identities=26% Similarity=0.502 Sum_probs=20.8
Q ss_pred ccCCCCceecCceEEEcCCceEEeCCCCCC
Q 005340 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
+|++|++-- ..+|.....++|.-||..
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 699999932 567777778999999975
No 81
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=55.79 E-value=7.4 Score=27.27 Aligned_cols=32 Identities=16% Similarity=0.361 Sum_probs=22.6
Q ss_pred cccCCCCceecCce-EEEcCCceEEeCCCCCCC
Q 005340 59 LRCRTCRSILNPFS-IVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 59 ~RC~~C~ayiNp~~-~~~~~g~~w~C~~C~~~N 90 (701)
++|.+|++-.+-=- ++..+|.+.+|.-|++.-
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 67888888655333 455667788898888753
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=55.66 E-value=7.9 Score=26.35 Aligned_cols=23 Identities=30% Similarity=0.836 Sum_probs=15.3
Q ss_pred ccCCCCceecCceEEEcCCceEEeCCCCC
Q 005340 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 88 (701)
+|..|+=...+-. .-|+|+.|+.
T Consensus 3 ~C~~CGy~y~~~~------~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGEE------APWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCCc------CCCcCcCCCC
Confidence 5777875444432 4688888886
No 83
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=55.06 E-value=4.7 Score=31.21 Aligned_cols=23 Identities=30% Similarity=0.703 Sum_probs=15.6
Q ss_pred CccccCCCCceecCceEEEcCCceEEeCCCCCC
Q 005340 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 57 ~p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
.|.||.+||- .|+.|+|+-||..
T Consensus 37 ~I~Rc~~CRk----------~g~~Y~Cp~CGF~ 59 (61)
T COG2888 37 EIYRCAKCRK----------LGNPYRCPKCGFE 59 (61)
T ss_pred eeehhhhHHH----------cCCceECCCcCcc
Confidence 3667777765 4567788888764
No 84
>PRK03954 ribonuclease P protein component 4; Validated
Probab=53.75 E-value=8.5 Score=34.80 Aligned_cols=34 Identities=24% Similarity=0.459 Sum_probs=24.8
Q ss_pred ccCCCCceecCc----eEEEcCC---ceEEeCCCCCCCCCC
Q 005340 60 RCRTCRSILNPF----SIVDFAA---KIWICPFCFQRNHFP 93 (701)
Q Consensus 60 RC~~C~ayiNp~----~~~~~~g---~~w~C~~C~~~N~~p 93 (701)
-|++|.+++=|- +.+..++ -.++|..||+....|
T Consensus 66 ~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~P 106 (121)
T PRK03954 66 YCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRYP 106 (121)
T ss_pred HhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEeec
Confidence 599999998764 2333332 245999999998887
No 85
>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=52.39 E-value=17 Score=35.84 Aligned_cols=44 Identities=7% Similarity=-0.004 Sum_probs=31.6
Q ss_pred cEEEEEEECCCchh---------hHHHHHHHHHHHhhcCC--CCcEEEEEEECCE
Q 005340 130 PVFMFVVDTCIIEE---------EMSFLKSALSQAIDLLP--DNSLVGLITFGTL 173 (701)
Q Consensus 130 p~~vFvIDvs~~~~---------~l~~~~~~l~~~l~~lp--~~~~VgiItf~~~ 173 (701)
.-++|+||.|.++. .++.+++++...+..+. +...+++++|++.
T Consensus 3 ~dvv~~ID~SgSM~~~~~~~~~~k~~~ak~~~~~l~~~~~~~D~d~i~l~~f~~~ 57 (199)
T cd01457 3 RDYTLLIDKSGSMAEADEAKERSRWEEAQESTRALARKCEEYDSDGITVYLFSGD 57 (199)
T ss_pred cCEEEEEECCCcCCCCCCCCCchHHHHHHHHHHHHHHHHHhcCCCCeEEEEecCC
Confidence 35789999999985 26788888777776543 2345888877654
No 86
>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=50.36 E-value=8.1 Score=29.16 Aligned_cols=30 Identities=30% Similarity=0.785 Sum_probs=19.5
Q ss_pred ccCCCCceecCc-----------eEEEcCCceEEeCCCCCC
Q 005340 60 RCRTCRSILNPF-----------SIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 60 RC~~C~ayiNp~-----------~~~~~~g~~w~C~~C~~~ 89 (701)
+|..|+=..+|- ..|.+-...|+|+.|+..
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 688888666654 234333457899999753
No 87
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=50.27 E-value=7.9 Score=35.02 Aligned_cols=32 Identities=19% Similarity=0.589 Sum_probs=22.5
Q ss_pred CccccCCCCceecCceEEEcCCceEEeCCCCCCCCC
Q 005340 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (701)
Q Consensus 57 ~p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~ 92 (701)
..-.|.||++-+.--+ +.-.|+||+|...-.+
T Consensus 88 q~r~CARCGGrv~lrs----NKv~wvcnlc~k~q~i 119 (169)
T KOG3799|consen 88 QTRFCARCGGRVSLRS----NKVMWVCNLCRKQQEI 119 (169)
T ss_pred hhhHHHhcCCeeeecc----CceEEeccCCcHHHHH
Confidence 4556899999765433 3458999999876543
No 88
>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=49.56 E-value=8.4 Score=29.03 Aligned_cols=31 Identities=19% Similarity=0.460 Sum_probs=22.4
Q ss_pred cccCCCCceecCceEEEcCCceEEeCCCCCCC
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N 90 (701)
.||..|+....-+..+.+ .....|+-|+..+
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~~ 36 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-DPLATCPECGGEK 36 (52)
T ss_pred EEeCCCCCEeEEEEecCC-CCCCCCCCCCCCc
Confidence 489999986666555444 3568899999854
No 89
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=49.38 E-value=7 Score=30.39 Aligned_cols=22 Identities=32% Similarity=0.801 Sum_probs=15.2
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
|.||.+||- .+..|+|+-||..
T Consensus 36 I~RC~~CRk----------~~~~Y~CP~CGF~ 57 (59)
T PRK14890 36 IYRCEKCRK----------QSNPYTCPKCGFE 57 (59)
T ss_pred EeechhHHh----------cCCceECCCCCCc
Confidence 667777765 3566788888864
No 90
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=49.31 E-value=4.4 Score=27.93 Aligned_cols=30 Identities=20% Similarity=0.270 Sum_probs=15.2
Q ss_pred ccCCCCceecCceEEEcCCceEEeCCCCCC
Q 005340 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
.|+.|++-+..-.--.++..+|+|.-|+..
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 488888875433332345578999999864
No 91
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=48.33 E-value=8.7 Score=23.93 Aligned_cols=21 Identities=24% Similarity=0.605 Sum_probs=12.2
Q ss_pred ccCCCCceecCceEEEcCCceEEeCCCCC
Q 005340 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 88 (701)
+|.+|++-+.+-.+| |+-||+
T Consensus 1 ~Cp~CG~~~~~~~~f--------C~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKF--------CPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcc--------hhhhCC
Confidence 477777755443333 666665
No 92
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=48.23 E-value=11 Score=33.83 Aligned_cols=27 Identities=19% Similarity=0.564 Sum_probs=19.4
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N 90 (701)
-.||..|+.... .....|.|+-||..+
T Consensus 70 ~~~C~~Cg~~~~------~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 70 QAWCWDCSQVVE------IHQHDAQCPHCHGER 96 (113)
T ss_pred EEEcccCCCEEe------cCCcCccCcCCCCCC
Confidence 579999995433 223567899999765
No 93
>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=47.57 E-value=9.5 Score=28.70 Aligned_cols=34 Identities=29% Similarity=0.511 Sum_probs=23.7
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p 93 (701)
-+||.+|+-.+----.+. .-.-+|+=|++.|.+-
T Consensus 4 eiRC~~CnklLa~~g~~~--~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVI--ELEIKCPRCKTINHVR 37 (51)
T ss_pred ceeccchhHHHhhhcCcc--EEEEECCCCCccceEe
Confidence 389999987664421122 1358999999999874
No 94
>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=47.23 E-value=12 Score=33.72 Aligned_cols=27 Identities=22% Similarity=0.634 Sum_probs=20.1
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N 90 (701)
-.||.+|+....+- ...|.|+-|+..+
T Consensus 70 ~~~C~~Cg~~~~~~------~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 70 ECECEDCSEEVSPE------IDLYRCPKCHGIM 96 (115)
T ss_pred EEEcccCCCEEecC------CcCccCcCCcCCC
Confidence 47999999654432 2368999999876
No 95
>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=46.70 E-value=9.6 Score=30.56 Aligned_cols=30 Identities=27% Similarity=0.461 Sum_probs=20.5
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p 93 (701)
+.|| .|+.|+ --+++.++-+| .||....+-
T Consensus 3 ifrC-~Cgr~l----ya~e~~kTkkC-~CG~~l~vk 32 (68)
T PF09082_consen 3 IFRC-DCGRYL----YAKEGAKTKKC-VCGKTLKVK 32 (68)
T ss_dssp EEEE-TTS--E----EEETT-SEEEE-TTTEEEE--
T ss_pred EEEe-cCCCEE----EecCCcceeEe-cCCCeeeee
Confidence 6899 799965 45667789999 999987765
No 96
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=45.75 E-value=14 Score=25.82 Aligned_cols=31 Identities=13% Similarity=0.284 Sum_probs=20.1
Q ss_pred cccCCCCceecCce-EEEcCCceEEeCCCCCC
Q 005340 59 LRCRTCRSILNPFS-IVDFAAKIWICPFCFQR 89 (701)
Q Consensus 59 ~RC~~C~ayiNp~~-~~~~~g~~w~C~~C~~~ 89 (701)
++|.+|++-.+-=- ++-..|.+.+|.-|++.
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 57888887544332 23445678888888764
No 97
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=45.35 E-value=12 Score=28.21 Aligned_cols=25 Identities=24% Similarity=0.530 Sum_probs=18.4
Q ss_pred cccCCCCc-eecCceEEEcCCceEEeCCCCCC
Q 005340 59 LRCRTCRS-ILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 59 ~RC~~C~a-yiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
..|.+|++ ++-+.. .+|.|.-|+..
T Consensus 21 ~fCP~Cg~~~m~~~~------~r~~C~~Cgyt 46 (50)
T PRK00432 21 KFCPRCGSGFMAEHL------DRWHCGKCGYT 46 (50)
T ss_pred CcCcCCCcchheccC------CcEECCCcCCE
Confidence 46999998 544432 58999999864
No 98
>PRK10997 yieM hypothetical protein; Provisional
Probab=45.07 E-value=31 Score=39.03 Aligned_cols=50 Identities=26% Similarity=0.167 Sum_probs=34.0
Q ss_pred EEEEEEECCCchh-hHHHHHHHHHHHhh--cCCCCcEEEEEEECCEEEEEEcC
Q 005340 131 VFMFVVDTCIIEE-EMSFLKSALSQAID--LLPDNSLVGLITFGTLVQVHELG 180 (701)
Q Consensus 131 ~~vFvIDvs~~~~-~l~~~~~~l~~~l~--~lp~~~~VgiItf~~~V~~~~l~ 180 (701)
-+++|||+|.++. .-+....++..+|- .+.++-++++|.|++.+.-|.+.
T Consensus 325 piII~VDtSGSM~G~ke~~AkalAaAL~~iAl~q~dr~~li~Fs~~i~~~~l~ 377 (487)
T PRK10997 325 PFIVCVDTSGSMGGFNEQCAKAFCLALMRIALAENRRCYIMLFSTEVVTYELT 377 (487)
T ss_pred cEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHhcCCCEEEEEecCCceeeccC
Confidence 5789999999886 21222234444443 34677889999999988777555
No 99
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=44.81 E-value=12 Score=28.09 Aligned_cols=28 Identities=25% Similarity=0.610 Sum_probs=18.8
Q ss_pred cccCCCCceecCceEEEcCCceEEeCCCCCCC
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N 90 (701)
-+|.+|++-+ ..+.....-.|+-||+.-
T Consensus 7 Y~C~~Cg~~~----~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 7 YKCARCGREV----ELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEhhhcCCee----ehhhccCceeCCCCCcEE
Confidence 4688888866 434445667888888753
No 100
>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=44.73 E-value=16 Score=25.47 Aligned_cols=27 Identities=22% Similarity=0.439 Sum_probs=20.5
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
..+|..|++. +...++ ..|.|.-|++.
T Consensus 8 ~~~C~~C~~~---~~~~~d--G~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSR---WFYSDD--GFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCe---EeEccC--CEEEhhhCceE
Confidence 3569999998 444444 48999999975
No 101
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=43.58 E-value=82 Score=37.61 Aligned_cols=108 Identities=17% Similarity=0.225 Sum_probs=61.9
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCCCCCccccCCCCCCCCccccCCCccEEEeCCC-C------CCCCCCCc
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPG-P------GEKSSVPP 130 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p~~y~~~~~~~~~pEL~~~~~tvey~~~~-~------~~~~~~~p 130 (701)
+.+|.+|-++ ..+-...+.-.|..||+.-.+|. .| |+. .+..+-|..+- + ....+..+
T Consensus 444 v~~Cp~Cd~~----lt~H~~~~~L~CH~Cg~~~~~p~--~C-------p~C--gs~~L~~~G~GterieeeL~~~FP~~r 508 (730)
T COG1198 444 IAECPNCDSP----LTLHKATGQLRCHYCGYQEPIPQ--SC-------PEC--GSEHLRAVGPGTERIEEELKRLFPGAR 508 (730)
T ss_pred cccCCCCCcc----eEEecCCCeeEeCCCCCCCCCCC--CC-------CCC--CCCeeEEecccHHHHHHHHHHHCCCCc
Confidence 5556666554 34555668999999999977773 22 344 22233333321 0 00011567
Q ss_pred EEEEEEECCCchhhHHHHHHHHHHHh-----------h--cCCCCcEEEEEEECCEEEEEEcC
Q 005340 131 VFMFVVDTCIIEEEMSFLKSALSQAI-----------D--LLPDNSLVGLITFGTLVQVHELG 180 (701)
Q Consensus 131 ~~vFvIDvs~~~~~l~~~~~~l~~~l-----------~--~lp~~~~VgiItf~~~V~~~~l~ 180 (701)
++.|--|++.....++.+.+.+..-= + ..|+=+.||++-=|..++.-++.
T Consensus 509 v~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfR 571 (730)
T COG1198 509 IIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFR 571 (730)
T ss_pred EEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcc
Confidence 77777777776665555444433211 1 12444899999877777666655
No 102
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=43.41 E-value=13 Score=35.99 Aligned_cols=25 Identities=32% Similarity=0.719 Sum_probs=20.4
Q ss_pred cccCCCCceecCceEEEcCCceEEeCCCCCC
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
.||++|++-+=+ .+..-+|+-|+..
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 599999996543 4679999999975
No 103
>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=42.69 E-value=12 Score=26.46 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=21.6
Q ss_pred cccCCCCceecCceEEEcCCceEEeCCCCC
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 88 (701)
.||..|+..+........ +....|+-|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 489999987766655544 46788999987
No 104
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=41.11 E-value=29 Score=23.70 Aligned_cols=29 Identities=24% Similarity=0.428 Sum_probs=19.7
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N 90 (701)
+.+|..|++-. .+.......+|.+|+...
T Consensus 3 ~~~C~~C~~~~----i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNG----IVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCe----EEEecCCeEEcccCCcEe
Confidence 56899998854 221233579999998754
No 105
>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=40.87 E-value=47 Score=33.41 Aligned_cols=44 Identities=18% Similarity=0.141 Sum_probs=26.6
Q ss_pred CCc-EEEEEEECCCchhhHHHHHHHHHHHh-hcCCCCcEEEEEEECCEE
Q 005340 128 VPP-VFMFVVDTCIIEEEMSFLKSALSQAI-DLLPDNSLVGLITFGTLV 174 (701)
Q Consensus 128 ~~p-~~vFvIDvs~~~~~l~~~~~~l~~~l-~~lp~~~~VgiItf~~~V 174 (701)
..| -+|+++|+|+++.....+.-.+..++ ...+ ++.++.|++.+
T Consensus 55 ~~~~~lvvl~DvSGSM~~~s~~~l~~~~~l~~~~~---~~~~f~F~~~l 100 (222)
T PF05762_consen 55 RKPRRLVVLCDVSGSMAGYSEFMLAFLYALQRQFR---RVRVFVFSTRL 100 (222)
T ss_pred CCCccEEEEEeCCCChHHHHHHHHHHHHHHHHhCC---CEEEEEEeeeh
Confidence 345 89999999999887432222222222 2233 57777777554
No 106
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=39.73 E-value=18 Score=32.46 Aligned_cols=28 Identities=21% Similarity=0.618 Sum_probs=18.8
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N 90 (701)
-.||..|+.+...- ....|.|+-||..+
T Consensus 70 ~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 70 ECWCETCQQYVTLL-----TQRVRRCPQCHGDM 97 (114)
T ss_pred EEEcccCCCeeecC-----CccCCcCcCcCCCC
Confidence 57999999633221 11238899999765
No 107
>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=39.54 E-value=2.7e+02 Score=27.43 Aligned_cols=97 Identities=12% Similarity=-0.017 Sum_probs=61.1
Q ss_pred HHHHHHHHHccCCCCCCCCCCCCccchhHHHHHHHHHhh-ccCCCCCc-EEEEEecCCCCCCCcccccCCCCCCcCCCCC
Q 005340 245 FTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG-ACVPGSGA-RILAFVGGPSTEGPAAIVSKNLSEPIRSHKD 322 (701)
Q Consensus 245 ~~i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~-~~~~~~gg-~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d 322 (701)
+.+..+|+.++- .+ + + ..|..||..|+.-++ .. .... -||+++.|--|.|- +
T Consensus 75 ~~l~~~l~~~q~-g~--a-g----~~TadAi~~av~rl~~~~--~a~~kvvILLTDG~n~~~~--i-------------- 128 (191)
T cd01455 75 ETLKMMHAHSQF-CW--S-G----DHTVEATEFAIKELAAKE--DFDEAIVIVLSDANLERYG--I-------------- 128 (191)
T ss_pred HHHHHHHHhccc-Cc--c-C----ccHHHHHHHHHHHHHhcC--cCCCcEEEEEeCCCcCCCC--C--------------
Confidence 467788887764 22 2 1 123389999998885 32 2234 45667776433221 1
Q ss_pred CCCCCCcccchhHHHHHHH-HHHHHHcCcEEEEEEecCCccChhcchhhhccccceEEEeCC
Q 005340 323 LDKDSAPHYHKAVKFYDAL-SKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDS 383 (701)
Q Consensus 323 ~~~~~~~~~~~~~~fY~~l-a~~~~~~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~ 383 (701)
.| .+. |+.+.+.||-|..+.++.. |-.++..+++.|||+-|...+
T Consensus 129 ---------~P-----~~aAa~lA~~~gV~iytIgiG~~--d~~~l~~iA~~tgG~~F~A~d 174 (191)
T cd01455 129 ---------QP-----KKLADALAREPNVNAFVIFIGSL--SDEADQLQRELPAGKAFVCMD 174 (191)
T ss_pred ---------Ch-----HHHHHHHHHhCCCEEEEEEecCC--CHHHHHHHHhCCCCcEEEeCC
Confidence 11 123 3556677888777776643 667799999999999998754
No 108
>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=39.17 E-value=22 Score=28.49 Aligned_cols=28 Identities=18% Similarity=0.459 Sum_probs=22.2
Q ss_pred cccCCCCceecCceEEEcCCceEEeCCCCCCC
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N 90 (701)
-.|..|+...-. ...++.|.|+-||..-
T Consensus 29 q~C~~CG~~~~~----~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 29 QTCPRCGHRNKK----RRSGRVFTCPNCGFEM 56 (69)
T ss_pred cCccCccccccc----ccccceEEcCCCCCEE
Confidence 569999987666 4556899999999863
No 109
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=37.91 E-value=23 Score=34.71 Aligned_cols=39 Identities=21% Similarity=0.479 Sum_probs=27.4
Q ss_pred CccccCCCCceecCceEEEcCCceEEeCCCCCCCCCCcc
Q 005340 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPH 95 (701)
Q Consensus 57 ~p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p~~ 95 (701)
...-|+.|.-=-+-+.--......|+|.+|++.|..|.+
T Consensus 191 ~alIC~~C~hhngl~~~~ek~~~efiC~~Cn~~n~~~~~ 229 (251)
T COG5415 191 KALICPQCHHHNGLYRLAEKPIIEFICPHCNHKNDEVKE 229 (251)
T ss_pred hhhccccccccccccccccccchheecccchhhcCcccc
Confidence 346788887655544444444457999999999987754
No 110
>PF12773 DZR: Double zinc ribbon
Probab=37.71 E-value=20 Score=26.70 Aligned_cols=32 Identities=25% Similarity=0.330 Sum_probs=24.5
Q ss_pred CccccCCCCceecCceEEEcCCceEEeCCCCCCCCCC
Q 005340 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (701)
Q Consensus 57 ~p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p 93 (701)
+-..|.+|++-+. ......++|.-|++.|.-.
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCcCC
Confidence 4577999999887 3445689999999987643
No 111
>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=37.33 E-value=16 Score=33.00 Aligned_cols=32 Identities=22% Similarity=0.498 Sum_probs=25.0
Q ss_pred ccccCCCCceecCceEEEc-CCceEEeCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDF-AAKIWICPFCFQR 89 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~-~g~~w~C~~C~~~ 89 (701)
...|..|+-.+-.-|.+.. +...|.|++|...
T Consensus 71 ~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k~ 103 (118)
T PF02318_consen 71 GRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQKQ 103 (118)
T ss_dssp CEEETTTTEEEETTSEEETSSSCCEEEHHHHHH
T ss_pred CCcCCcCCccccCccCCcCCCCCCEEChhhHHH
Confidence 4778888888888887764 5679999999753
No 112
>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=37.18 E-value=40 Score=24.73 Aligned_cols=27 Identities=19% Similarity=0.540 Sum_probs=18.9
Q ss_pred cccCCCCceecCceEEEcCCceEEeCCCCC
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 88 (701)
+.|.+|++- ..+ .+. +...|.|.-|++
T Consensus 19 ~~CP~Cg~~-~~~-~~~-~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-KHY-RLK-TRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-eeE-EeC-CCCeEECCCCCC
Confidence 569999987 222 222 247899999985
No 113
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=37.00 E-value=1.8e+02 Score=32.40 Aligned_cols=49 Identities=20% Similarity=0.139 Sum_probs=31.7
Q ss_pred EEEEEEECCCchhh-HHHHHHHHHHHhh--cCCCCcEEEEEEECCEEEEEEc
Q 005340 131 VFMFVVDTCIIEEE-MSFLKSALSQAID--LLPDNSLVGLITFGTLVQVHEL 179 (701)
Q Consensus 131 ~~vFvIDvs~~~~~-l~~~~~~l~~~l~--~lp~~~~VgiItf~~~V~~~~l 179 (701)
-++.+||.|+++.- -+....++..+|- .+-+|.++.++.||+.++=|.+
T Consensus 274 pvilllD~SGSM~G~~e~~AKAvalAl~~~alaenR~~~~~lF~s~~~~~el 325 (437)
T COG2425 274 PVILLLDKSGSMSGFKEQWAKAVALALMRIALAENRDCYVILFDSEVIEYEL 325 (437)
T ss_pred CEEEEEeCCCCcCCcHHHHHHHHHHHHHHHHHHhccceEEEEecccceeeee
Confidence 35589999999864 3333334444443 3568889999999994433333
No 114
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=36.74 E-value=25 Score=32.39 Aligned_cols=34 Identities=29% Similarity=0.539 Sum_probs=23.1
Q ss_pred cccCCCCceecCceEEEcCCceEEeCCCCCCCCCCc
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p~ 94 (701)
++|.-|+..- -.........|.|+-|+..|-+..
T Consensus 1 v~C~fC~~~s--~~~~~~~~~~w~C~~C~q~N~f~e 34 (131)
T PF09779_consen 1 VNCWFCGQNS--KVPYDNRNSNWTCPHCEQYNGFDE 34 (131)
T ss_pred CeeccCCCCC--CCCCCCCCCeeECCCCCCccCccc
Confidence 4688887742 233333344599999999998764
No 115
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=36.09 E-value=30 Score=25.34 Aligned_cols=26 Identities=19% Similarity=0.259 Sum_probs=16.3
Q ss_pred ccCCCCceecCceEEEcCCceEEeCCCCCCC
Q 005340 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N 90 (701)
+|.+|++-+..- .+..-+|+-||+.-
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~rI 29 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGYRI 29 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCceE
Confidence 577777754432 24567777777653
No 116
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=35.84 E-value=22 Score=26.97 Aligned_cols=32 Identities=16% Similarity=0.271 Sum_probs=26.4
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
+.+|.+|+.--.|...-...|..-.||-|+-.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~ 34 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLY 34 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHH
Confidence 57899999988888877777777999999864
No 117
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=35.79 E-value=29 Score=27.63 Aligned_cols=34 Identities=21% Similarity=0.457 Sum_probs=25.7
Q ss_pred CccccCCCCceecCceEEEcCCceEEeCCCCCCCCCC
Q 005340 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (701)
Q Consensus 57 ~p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p 93 (701)
--++|..|+ |--+.|.......+|..|+..=--|
T Consensus 18 l~VkCpdC~---N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 18 LRVKCPDCG---NEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EEEECCCCC---CEEEEeccCceEEEecccccEEEec
Confidence 358999998 4556666677889999999875544
No 118
>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=35.70 E-value=12 Score=27.91 Aligned_cols=30 Identities=23% Similarity=0.700 Sum_probs=15.1
Q ss_pred ccCCCCceecCce-----------EEEcCCceEEeCCCCCC
Q 005340 60 RCRTCRSILNPFS-----------IVDFAAKIWICPFCFQR 89 (701)
Q Consensus 60 RC~~C~ayiNp~~-----------~~~~~g~~w~C~~C~~~ 89 (701)
+|..|+-..+|-. .|++--..|+|+.|+..
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 5777775554433 23333346888888753
No 119
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=34.85 E-value=37 Score=21.69 Aligned_cols=24 Identities=29% Similarity=0.620 Sum_probs=12.8
Q ss_pred cCCCCceecCceEEEcCCceEEeCCCCC
Q 005340 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (701)
Q Consensus 61 C~~C~ayiNp~~~~~~~g~~w~C~~C~~ 88 (701)
|.+||..+. .-.|...++|..|++
T Consensus 1 C~~Cr~~L~----yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLM----YPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEE----cCCCCCCeECCccCc
Confidence 555655442 223455677776654
No 120
>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=34.53 E-value=20 Score=23.10 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=15.8
Q ss_pred ccCCCCceecCceEEEcCCceEEeCCCCCCC
Q 005340 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N 90 (701)
+|..|++-++- ..-.|+.||+.-
T Consensus 2 ~CP~C~~~V~~--------~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPE--------SAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchh--------hcCcCCCCCCCC
Confidence 58888887632 346788888753
No 121
>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=34.45 E-value=29 Score=21.94 Aligned_cols=24 Identities=29% Similarity=0.618 Sum_probs=15.7
Q ss_pred cCCCCceecCceEEEcCCceEEeCCCCC
Q 005340 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (701)
Q Consensus 61 C~~C~ayiNp~~~~~~~g~~w~C~~C~~ 88 (701)
|.+|+.-|-|--+ +..|.|+-||.
T Consensus 1 C~sC~~~i~~r~~----~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQ----AVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCccc----CceEeCCCCCC
Confidence 6677776665432 45788888873
No 122
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=34.17 E-value=23 Score=28.13 Aligned_cols=25 Identities=20% Similarity=0.549 Sum_probs=17.9
Q ss_pred cccCCCCceecCceEEEcCCceEEeCCCCCCCCCC
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p 93 (701)
.-|++|+...+ + . +|+.|+..+..+
T Consensus 6 ~AC~~C~~i~~-------~-~--~Cp~Cgs~~~S~ 30 (64)
T PRK06393 6 RACKKCKRLTP-------E-K--TCPVHGDEKTTT 30 (64)
T ss_pred hhHhhCCcccC-------C-C--cCCCCCCCcCCc
Confidence 34999998763 1 2 999999975433
No 123
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.95 E-value=17 Score=32.79 Aligned_cols=30 Identities=23% Similarity=0.655 Sum_probs=18.9
Q ss_pred CccccCCCCceecCceEEEcCCceEEeCCCCCCCC
Q 005340 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (701)
Q Consensus 57 ~p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~ 91 (701)
...||..|+.+..+- . ...+.|+-|+..+.
T Consensus 70 ~~~~C~~Cg~~~~~~----~-~~~~~CP~Cgs~~~ 99 (117)
T PRK00564 70 VELECKDCSHVFKPN----A-LDYGVCEKCHSKNV 99 (117)
T ss_pred CEEEhhhCCCccccC----C-ccCCcCcCCCCCce
Confidence 357999999543221 1 12345999998763
No 124
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.68 E-value=21 Score=30.25 Aligned_cols=36 Identities=25% Similarity=0.519 Sum_probs=24.8
Q ss_pred CccccCCCCceecCceEEEcCCceEEeCCCCCCCCCCccc
Q 005340 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHY 96 (701)
Q Consensus 57 ~p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p~~y 96 (701)
.|.||++|+--.++ -.+. .--+|+-|+..-.-++.|
T Consensus 57 ~Pa~CkkCGfef~~-~~ik---~pSRCP~CKSE~Ie~prF 92 (97)
T COG3357 57 RPARCKKCGFEFRD-DKIK---KPSRCPKCKSEWIEEPRF 92 (97)
T ss_pred cChhhcccCccccc-cccC---CcccCCcchhhcccCCce
Confidence 58999999976666 2222 356799999876555444
No 125
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=33.67 E-value=25 Score=24.52 Aligned_cols=31 Identities=13% Similarity=0.347 Sum_probs=15.2
Q ss_pred cccCCCCceecCce-EEEcCCceEEeCCCCCC
Q 005340 59 LRCRTCRSILNPFS-IVDFAAKIWICPFCFQR 89 (701)
Q Consensus 59 ~RC~~C~ayiNp~~-~~~~~g~~w~C~~C~~~ 89 (701)
++|.+|++-..--. .+...+....|+-|++.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 45777776321111 12223446677777653
No 126
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=33.61 E-value=34 Score=23.27 Aligned_cols=29 Identities=17% Similarity=0.466 Sum_probs=17.7
Q ss_pred ccCCCCceecCc-eEEEcCCce-----EEeCCCCC
Q 005340 60 RCRTCRSILNPF-SIVDFAAKI-----WICPFCFQ 88 (701)
Q Consensus 60 RC~~C~ayiNp~-~~~~~~g~~-----w~C~~C~~ 88 (701)
||.+|+..|-+- ..+...++. |.|..|+.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~ 35 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGK 35 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCC
Confidence 688888888774 333333333 46666664
No 127
>PHA00626 hypothetical protein
Probab=32.59 E-value=41 Score=25.85 Aligned_cols=14 Identities=14% Similarity=0.377 Sum_probs=11.6
Q ss_pred CceEEeCCCCCCCC
Q 005340 78 AKIWICPFCFQRNH 91 (701)
Q Consensus 78 g~~w~C~~C~~~N~ 91 (701)
.+.|+|+-||+.-.
T Consensus 21 snrYkCkdCGY~ft 34 (59)
T PHA00626 21 SDDYVCCDCGYNDS 34 (59)
T ss_pred CcceEcCCCCCeec
Confidence 57899999998654
No 128
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=32.08 E-value=25 Score=39.57 Aligned_cols=29 Identities=24% Similarity=0.512 Sum_probs=22.1
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCCCCCc
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p~ 94 (701)
.-+|++|+. ....-.|+|+-|+..|.+..
T Consensus 7 ~y~C~~Cg~--------~~~~~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 7 KFVCQHCGA--------DSPKWQGKCPACHAWNTITE 35 (454)
T ss_pred eEECCcCCC--------CCccccEECcCCCCccccch
Confidence 468999986 22234699999999999864
No 129
>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=31.28 E-value=40 Score=29.68 Aligned_cols=28 Identities=25% Similarity=0.583 Sum_probs=19.6
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N 90 (701)
.+.|.+|.+- |.- ++|..|+|+-|++.=
T Consensus 2 lp~CP~C~se---ytY--~dg~~~iCpeC~~EW 29 (109)
T TIGR00686 2 LPPCPKCNSE---YTY--HDGTQLICPSCLYEW 29 (109)
T ss_pred CCcCCcCCCc---ceE--ecCCeeECccccccc
Confidence 4679999862 222 235689999999864
No 130
>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=31.04 E-value=23 Score=23.70 Aligned_cols=27 Identities=22% Similarity=0.502 Sum_probs=13.8
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
.+.|..|++=-+- .+|..++|+-|++.
T Consensus 2 ~p~Cp~C~se~~y-----~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCPLCGSEYTY-----EDGELLVCPECGHE 28 (30)
T ss_dssp S---TTT-----E-----E-SSSEEETTTTEE
T ss_pred CCCCCCCCCccee-----ccCCEEeCCccccc
Confidence 3578889874333 34678999999863
No 131
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=30.80 E-value=49 Score=30.54 Aligned_cols=32 Identities=19% Similarity=0.430 Sum_probs=26.3
Q ss_pred ccccCCCCceecCceEEEcCCceE--EeCCCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIW--ICPFCFQRNHF 92 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w--~C~~C~~~N~~ 92 (701)
-+-|+.|+. |=..+...++.| +|.-||..-++
T Consensus 97 yVlC~~C~s---PdT~l~k~~r~~~l~C~ACGa~~~v 130 (133)
T TIGR00311 97 YVICRECNR---PDTRIIKEGRVSLLKCEACGAKAPL 130 (133)
T ss_pred eEECCCCCC---CCcEEEEeCCeEEEecccCCCCCcc
Confidence 488999997 778777767776 89999998766
No 132
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=30.78 E-value=43 Score=26.04 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=20.5
Q ss_pred CccccCCCCceecCceEEEcCCceEEeCCCCCCCC
Q 005340 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (701)
Q Consensus 57 ~p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~ 91 (701)
.+..|.+|+.+.=| .-.|..||+.+.
T Consensus 26 ~l~~C~~CG~~~~~---------H~vC~~CG~Y~g 51 (57)
T PRK12286 26 GLVECPNCGEPKLP---------HRVCPSCGYYKG 51 (57)
T ss_pred cceECCCCCCccCC---------eEECCCCCcCCC
Confidence 46789999997655 578999997654
No 133
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=30.63 E-value=33 Score=29.97 Aligned_cols=27 Identities=26% Similarity=0.725 Sum_probs=21.6
Q ss_pred ccCCCCceecCceEEEcCCceEEeCCCCCCCCC
Q 005340 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~ 92 (701)
.|.+|++.+.|- +..|.|.-|+.....
T Consensus 2 fC~~Cg~~l~~~------~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPK------NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccC------CCeEECcCCCCcccc
Confidence 599999999663 348999999987554
No 134
>PRK11823 DNA repair protein RadA; Provisional
Probab=30.39 E-value=27 Score=39.31 Aligned_cols=29 Identities=21% Similarity=0.442 Sum_probs=22.0
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCCCCCc
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p~ 94 (701)
.-+|++|+. ....-.|+|+-|+..|.+..
T Consensus 7 ~y~C~~Cg~--------~~~~~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 7 AYVCQECGA--------ESPKWLGRCPECGAWNTLVE 35 (446)
T ss_pred eEECCcCCC--------CCcccCeeCcCCCCccceee
Confidence 468999986 22234699999999999863
No 135
>KOG2353 consensus L-type voltage-dependent Ca2+ channel, alpha2/delta subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=30.36 E-value=65 Score=40.17 Aligned_cols=50 Identities=22% Similarity=0.387 Sum_probs=43.9
Q ss_pred CCcEEEEEEECCCchhh--HHHHHHHHHHHhhcCCCCcEEEEEEECCEEEEE
Q 005340 128 VPPVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVH 177 (701)
Q Consensus 128 ~~p~~vFvIDvs~~~~~--l~~~~~~l~~~l~~lp~~~~VgiItf~~~V~~~ 177 (701)
.|--.+|++|+|++... +...+..+.++|+.|.++..|-++||++.++.-
T Consensus 224 ~pKdiviLlD~SgSm~g~~~~lak~tv~~iLdtLs~~Dfvni~tf~~~~~~v 275 (1104)
T KOG2353|consen 224 SPKDIVILLDVSGSMSGLRLDLAKQTVNEILDTLSDNDFVNILTFNSEVNPV 275 (1104)
T ss_pred CccceEEEEeccccccchhhHHHHHHHHHHHHhcccCCeEEEEeeccccCcc
Confidence 56678999999998765 889999999999999999999999999887553
No 136
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.97 E-value=24 Score=32.12 Aligned_cols=33 Identities=21% Similarity=0.399 Sum_probs=19.9
Q ss_pred ccccCCCCceecCc-eEEEcCCceEEeCCCCCCCC
Q 005340 58 PLRCRTCRSILNPF-SIVDFAAKIWICPFCFQRNH 91 (701)
Q Consensus 58 p~RC~~C~ayiNp~-~~~~~~g~~w~C~~C~~~N~ 91 (701)
-.|| .|+.+..+- ...+.-...|.|+-||..+.
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~ 103 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRA 103 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCCCCCC
Confidence 5799 999775432 11111111378999997663
No 137
>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=29.71 E-value=29 Score=38.05 Aligned_cols=27 Identities=22% Similarity=0.445 Sum_probs=20.7
Q ss_pred ccCCCCceecCceEEEcCCceEEeCCCCCCCCCCc
Q 005340 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p~ 94 (701)
+|++|+.- ...-.|+|+-|+..|.+..
T Consensus 2 ~c~~cg~~--------~~~~~g~cp~c~~w~~~~e 28 (372)
T cd01121 2 VCSECGYV--------SPKWLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCC--------CCCccEECcCCCCceeeee
Confidence 69999862 2233699999999999863
No 138
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=29.63 E-value=31 Score=25.79 Aligned_cols=25 Identities=20% Similarity=0.525 Sum_probs=17.9
Q ss_pred cccCCCC--ceecCceEEEcCCceEEeCCCCCC
Q 005340 59 LRCRTCR--SILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 59 ~RC~~C~--ayiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
..|.||+ .++--+ +.+|.|.=|+..
T Consensus 20 ~~CPrCG~gvfmA~H------~dR~~CGkCgyT 46 (51)
T COG1998 20 RFCPRCGPGVFMADH------KDRWACGKCGYT 46 (51)
T ss_pred ccCCCCCCcchhhhc------CceeEeccccce
Confidence 5699999 444322 358999999974
No 139
>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=29.60 E-value=34 Score=32.12 Aligned_cols=33 Identities=30% Similarity=0.598 Sum_probs=22.6
Q ss_pred ccccCCCCceecCceEE-----------EcCCceEEeCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIV-----------DFAAKIWICPFCFQRN 90 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~-----------~~~g~~w~C~~C~~~N 90 (701)
..||..|.+-+-+-.+- .....-|.|+-|+..-
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 47999999965433221 1234699999999864
No 140
>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=28.87 E-value=19 Score=23.77 Aligned_cols=14 Identities=36% Similarity=0.688 Sum_probs=12.0
Q ss_pred ceEEeCCCCCCCCC
Q 005340 79 KIWICPFCFQRNHF 92 (701)
Q Consensus 79 ~~w~C~~C~~~N~~ 92 (701)
..|.|..|...|..
T Consensus 3 g~W~C~~C~~~N~~ 16 (30)
T PF00641_consen 3 GDWKCPSCTFMNPA 16 (30)
T ss_dssp SSEEETTTTEEEES
T ss_pred cCccCCCCcCCchH
Confidence 37999999999974
No 141
>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=28.75 E-value=1.1e+02 Score=29.18 Aligned_cols=76 Identities=17% Similarity=0.181 Sum_probs=45.3
Q ss_pred CccchhHHHHHHHHHhhccCCC-----C---CcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHH
Q 005340 267 STRCTGTALSIAASLLGACVPG-----S---GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFY 338 (701)
Q Consensus 267 ~~~~~G~Al~~A~~ll~~~~~~-----~---gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY 338 (701)
..+++|.||..|...+...... . -..|+++|+|.|+.++. ...+.+
T Consensus 77 GgT~l~~aL~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~~~~~~--------------------------~~~~~~ 130 (176)
T cd01464 77 GGTSMGAALELALDCIDRRVQRYRADQKGDWRPWVFLLTDGEPTDDLT--------------------------AAIERI 130 (176)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHhcccCcCCcCcEEEEEcCCCCCchHH--------------------------HHHHHH
Confidence 4689999999999998632100 0 12689999997653321 011122
Q ss_pred HHHHHHHHHcCcEEEEEEecCCccChhcchhhhcc
Q 005340 339 DALSKQLVHQGHVLDLFACALDQVGVAELKVAVEK 373 (701)
Q Consensus 339 ~~la~~~~~~~isvDlf~~~~~~~~l~~l~~l~~~ 373 (701)
..+...++.+..|.++. .++...|..++..
T Consensus 131 ----~~~~~~~~~i~~igiG~-~~~~~~L~~ia~~ 160 (176)
T cd01464 131 ----KEARDSKGRIVACAVGP-KADLDTLKQITEG 160 (176)
T ss_pred ----HhhcccCCcEEEEEecc-ccCHHHHHHHHCC
Confidence 22333466777776665 5777777777743
No 142
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=28.73 E-value=1.1e+02 Score=30.54 Aligned_cols=86 Identities=19% Similarity=0.167 Sum_probs=54.2
Q ss_pred ccchhHHHHHHHHHhhccCCC--CCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHH
Q 005340 268 TRCTGTALSIAASLLGACVPG--SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQL 345 (701)
Q Consensus 268 ~~~~G~Al~~A~~ll~~~~~~--~gg~Ii~F~~g~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~ 345 (701)
..-.|-|+..+..+....... .-+||++|+.+ | ++.+ ..+.| |-+---.|
T Consensus 128 r~~v~gams~glay~n~~~~e~slkSriliftls----G------~d~~--------------~qYip----~mnCiF~A 179 (296)
T COG5242 128 RYDVGGAMSLGLAYCNHRDEETSLKSRILIFTLS----G------RDRK--------------DQYIP----YMNCIFAA 179 (296)
T ss_pred eeehhhhhhhhHHHHhhhcccccccceEEEEEec----C------chhh--------------hhhch----hhhheeeh
Confidence 346688888888887643221 34899999983 2 2211 11111 11112335
Q ss_pred HHcCcEEEEEEecCCccChhcchhhhccccceEEEeCCC
Q 005340 346 VHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSF 384 (701)
Q Consensus 346 ~~~~isvDlf~~~~~~~~l~~l~~l~~~TGG~v~~~~~f 384 (701)
.+.||-+|+|-+... -..+.+.+..|||.-...++-
T Consensus 180 qk~~ipI~v~~i~g~---s~fl~Q~~daTgG~Yl~ve~~ 215 (296)
T COG5242 180 QKFGIPISVFSIFGN---SKFLLQCCDATGGDYLTVEDT 215 (296)
T ss_pred hhcCCceEEEEecCc---cHHHHHHhhccCCeeEeecCc
Confidence 567999999987654 346889999999988877653
No 143
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=28.58 E-value=36 Score=26.82 Aligned_cols=23 Identities=35% Similarity=0.792 Sum_probs=16.8
Q ss_pred ccCCCCceecCceEEEcCCceEEeCCCCCCCCC
Q 005340 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~ 92 (701)
-|++|+.... + . +|+.|+...-.
T Consensus 5 AC~~C~~i~~-------~-~--~CP~Cgs~~~T 27 (61)
T PRK08351 5 ACRHCHYITT-------E-D--RCPVCGSRDLS 27 (61)
T ss_pred hhhhCCcccC-------C-C--cCCCCcCCccc
Confidence 4999998773 1 1 69999997633
No 144
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.17 E-value=36 Score=31.53 Aligned_cols=34 Identities=26% Similarity=0.437 Sum_probs=20.6
Q ss_pred CccccCCCCceecCce---E----------EEc--CCceEEeCCCCCCC
Q 005340 57 APLRCRTCRSILNPFS---I----------VDF--AAKIWICPFCFQRN 90 (701)
Q Consensus 57 ~p~RC~~C~ayiNp~~---~----------~~~--~g~~w~C~~C~~~N 90 (701)
...+|..|+....+-- + +.+ ....|.|+-||..+
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 3579999996554430 0 000 03468899999765
No 145
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=27.28 E-value=74 Score=33.54 Aligned_cols=27 Identities=37% Similarity=0.572 Sum_probs=24.9
Q ss_pred hHHHHHHHHHHHhhcCCCCcEEEEEEE
Q 005340 144 EMSFLKSALSQAIDLLPDNSLVGLITF 170 (701)
Q Consensus 144 ~l~~~~~~l~~~l~~lp~~~~VgiItf 170 (701)
||+.+.++|.++++.|.++.|+++|||
T Consensus 219 EL~~L~~~L~~a~~~L~~gGRl~VIsF 245 (314)
T COG0275 219 ELEELEEALEAALDLLKPGGRLAVISF 245 (314)
T ss_pred HHHHHHHHHHHHHHhhCCCcEEEEEEe
Confidence 499999999999999999999999984
No 146
>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=27.05 E-value=17 Score=32.53 Aligned_cols=27 Identities=30% Similarity=0.627 Sum_probs=17.6
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N 90 (701)
-.||..|+.-..+- ...+.|+.|+..+
T Consensus 70 ~~~C~~Cg~~~~~~------~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 70 RARCRDCGHEFEPD------EFDFSCPRCGSPD 96 (113)
T ss_dssp EEEETTTS-EEECH------HCCHH-SSSSSS-
T ss_pred cEECCCCCCEEecC------CCCCCCcCCcCCC
Confidence 57999999865443 2347799999986
No 147
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=27.04 E-value=32 Score=36.36 Aligned_cols=36 Identities=19% Similarity=0.375 Sum_probs=25.7
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p 93 (701)
-.-|+.|+.==+-.-.-+..=-.|+|.+|++.|+-+
T Consensus 220 ALIC~~C~~HNGla~~ee~~yi~F~C~~Cn~LN~~~ 255 (328)
T KOG2846|consen 220 ALICSQCHHHNGLARKEEYEYITFRCPHCNALNPAK 255 (328)
T ss_pred hhcchhhccccCcCChhhcCceEEECccccccCCCc
Confidence 456999988655444433334689999999999854
No 148
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=27.03 E-value=34 Score=32.78 Aligned_cols=15 Identities=33% Similarity=1.094 Sum_probs=11.8
Q ss_pred CCceEEeCCCCCCCC
Q 005340 77 AAKIWICPFCFQRNH 91 (701)
Q Consensus 77 ~g~~w~C~~C~~~N~ 91 (701)
+|+.|+|+.||+.-.
T Consensus 131 ~~~~~vC~vCGy~~~ 145 (166)
T COG1592 131 EGKVWVCPVCGYTHE 145 (166)
T ss_pred cCCEEEcCCCCCccc
Confidence 356899999998654
No 149
>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=26.55 E-value=35 Score=20.29 Aligned_cols=11 Identities=27% Similarity=0.815 Sum_probs=6.5
Q ss_pred EEeCCCCCCCC
Q 005340 81 WICPFCFQRNH 91 (701)
Q Consensus 81 w~C~~C~~~N~ 91 (701)
|.|++|+....
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 78888887644
No 150
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=26.39 E-value=21 Score=24.79 Aligned_cols=28 Identities=18% Similarity=0.304 Sum_probs=19.3
Q ss_pred cCCCCceecCceEEEcCCceEEeCCCCC
Q 005340 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (701)
Q Consensus 61 C~~C~ayiNp~~~~~~~g~~w~C~~C~~ 88 (701)
|.+|++-=.|.-.-...|....||-|+.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~ 28 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGL 28 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHH
Confidence 7889998888888888888889998874
No 151
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=25.92 E-value=37 Score=23.32 Aligned_cols=11 Identities=36% Similarity=1.301 Sum_probs=9.5
Q ss_pred eEEeCCCCCCC
Q 005340 80 IWICPFCFQRN 90 (701)
Q Consensus 80 ~w~C~~C~~~N 90 (701)
.|+|..||..-
T Consensus 2 ~~~C~~CG~i~ 12 (34)
T cd00729 2 VWVCPVCGYIH 12 (34)
T ss_pred eEECCCCCCEe
Confidence 69999999873
No 152
>PRK12722 transcriptional activator FlhC; Provisional
Probab=25.65 E-value=32 Score=33.57 Aligned_cols=29 Identities=14% Similarity=0.453 Sum_probs=20.5
Q ss_pred CccccCCCCc-eecCceEEEcCCceEEeCCCCC
Q 005340 57 APLRCRTCRS-ILNPFSIVDFAAKIWICPFCFQ 88 (701)
Q Consensus 57 ~p~RC~~C~a-yiNp~~~~~~~g~~w~C~~C~~ 88 (701)
...+|..|++ |+- ...+....++|++|+-
T Consensus 133 ~l~~C~~Cgg~fv~---~~~e~~~~f~CplC~~ 162 (187)
T PRK12722 133 QLSSCNCCGGHFVT---HAHDPVGSFVCGLCQP 162 (187)
T ss_pred eeccCCCCCCCeec---cccccCCCCcCCCCCC
Confidence 4788999987 331 2223456899999987
No 153
>PRK10220 hypothetical protein; Provisional
Probab=25.08 E-value=68 Score=28.30 Aligned_cols=29 Identities=24% Similarity=0.599 Sum_probs=19.7
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~ 91 (701)
.+.|..|.+- |. . .+|..|+|+-|+++-.
T Consensus 3 lP~CP~C~se---yt-Y-~d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 3 LPHCPKCNSE---YT-Y-EDNGMYICPECAHEWN 31 (111)
T ss_pred CCcCCCCCCc---ce-E-cCCCeEECCcccCcCC
Confidence 3669999862 22 1 2457899999998643
No 154
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=24.64 E-value=39 Score=35.84 Aligned_cols=29 Identities=24% Similarity=0.642 Sum_probs=22.0
Q ss_pred CccccCCCCceecCceEEEcCCceEEeCCCCCCCCCC
Q 005340 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (701)
Q Consensus 57 ~p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~~p 93 (701)
..-||.+|+- ....-.|.|+-|+..-.+-
T Consensus 353 ~~YRC~~CGF--------~a~~l~W~CPsC~~W~Tik 381 (389)
T COG2956 353 PRYRCQNCGF--------TAHTLYWHCPSCRAWETIK 381 (389)
T ss_pred CCceecccCC--------cceeeeeeCCCcccccccC
Confidence 5689999983 2333589999999987664
No 155
>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=24.36 E-value=64 Score=22.74 Aligned_cols=27 Identities=26% Similarity=0.727 Sum_probs=17.8
Q ss_pred ccCCCCceecCceEEEc--CCceEEeCCCCC
Q 005340 60 RCRTCRSILNPFSIVDF--AAKIWICPFCFQ 88 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~--~g~~w~C~~C~~ 88 (701)
-|..|++ ---|- |++ +...|.|+-|+.
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 3888887 22333 444 446899999975
No 156
>PF14353 CpXC: CpXC protein
Probab=22.93 E-value=75 Score=28.84 Aligned_cols=35 Identities=14% Similarity=0.475 Sum_probs=23.1
Q ss_pred cccCCCCcee--cCceEEEcC-------------CceEEeCCCCCCCCCC
Q 005340 59 LRCRTCRSIL--NPFSIVDFA-------------AKIWICPFCFQRNHFP 93 (701)
Q Consensus 59 ~RC~~C~ayi--Np~~~~~~~-------------g~~w~C~~C~~~N~~p 93 (701)
++|.+|+.-. .-|..++.. =..++|+-||+...++
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 5799998863 223333321 1389999999988764
No 157
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=22.81 E-value=33 Score=33.27 Aligned_cols=29 Identities=28% Similarity=0.688 Sum_probs=10.4
Q ss_pred CccccCCCCceecCceEEE-cCCceEEeCCCCC
Q 005340 57 APLRCRTCRSILNPFSIVD-FAAKIWICPFCFQ 88 (701)
Q Consensus 57 ~p~RC~~C~ayiNp~~~~~-~~g~~w~C~~C~~ 88 (701)
...+|.+|++ .|..-. +....++|++|+-
T Consensus 133 ~l~~C~~C~~---~fv~~~~~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 133 QLAPCRRCGG---HFVTHAHDPRHSFVCPFCQP 162 (175)
T ss_dssp EEEE-TTT-----EEEEESS--SS----TT---
T ss_pred cccCCCCCCC---CeECcCCCCCcCcCCCCCCC
Confidence 4678999997 222221 2246899999993
No 158
>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=22.60 E-value=31 Score=25.95 Aligned_cols=13 Identities=31% Similarity=0.943 Sum_probs=5.3
Q ss_pred cCCceEEeCCCCC
Q 005340 76 FAAKIWICPFCFQ 88 (701)
Q Consensus 76 ~~g~~w~C~~C~~ 88 (701)
...+.|.|++|++
T Consensus 37 ~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 37 QRTPKWKCPICNK 49 (50)
T ss_dssp HHS---B-TTT--
T ss_pred hccCCeECcCCcC
Confidence 3456799999986
No 159
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=22.35 E-value=65 Score=23.47 Aligned_cols=23 Identities=13% Similarity=0.353 Sum_probs=15.5
Q ss_pred cccCCCCceecCceEEEcCCceEEeCCCCC
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 88 (701)
+.|..|+. .|.. |.+|+|..|..
T Consensus 1 I~CDgCg~--~PI~-----G~RykC~~C~d 23 (43)
T cd02342 1 IQCDGCGV--LPIT-----GPRYKSKVKED 23 (43)
T ss_pred CCCCCCCC--Cccc-----ccceEeCCCCC
Confidence 46777874 3332 68899998853
No 160
>PF06707 DUF1194: Protein of unknown function (DUF1194); InterPro: IPR010607 This family consists of several hypothetical Rhizobiales specific proteins of around 270 residues in length. The function of this family is unknown.
Probab=22.28 E-value=7.9e+02 Score=24.51 Aligned_cols=99 Identities=23% Similarity=0.302 Sum_probs=57.3
Q ss_pred ccchhHHHHHHHHHhhccCCCCCcEEEEEecC--CCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHH
Q 005340 268 TRCTGTALSIAASLLGACVPGSGARILAFVGG--PSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQL 345 (701)
Q Consensus 268 ~~~~G~Al~~A~~ll~~~~~~~gg~Ii~F~~g--~pt~GpG~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~fY~~la~~~ 345 (701)
.++.|.||..|..++... +..+.|-++=.+| +.|.|+.-+ +..-..+
T Consensus 94 ~Taig~Al~~a~~ll~~~-~~~~~RrVIDvSGDG~~N~G~~p~------------------------------~~ard~~ 142 (205)
T PF06707_consen 94 RTAIGSALDFAAALLAQN-PFECWRRVIDVSGDGPNNQGPRPV------------------------------TSARDAA 142 (205)
T ss_pred CchHHHHHHHHHHHHHhC-CCCCceEEEEECCCCCCCCCCCcc------------------------------HHHHHHH
Confidence 389999999999999853 2225555555553 444443111 1122345
Q ss_pred HHcCcEEEEEEecCCcc----ChhcchhhhccccceEEEeCCCCchhhHHHHHHHh
Q 005340 346 VHQGHVLDLFACALDQV----GVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF 397 (701)
Q Consensus 346 ~~~~isvDlf~~~~~~~----~l~~l~~l~~~TGG~v~~~~~f~~~~~~~~l~~~l 397 (701)
...||.|+=+.+....- +|...-.=+-..|---+..+.-+.+.|.+.++|-|
T Consensus 143 ~~~GitINgL~I~~~~~~~~~~L~~yy~~~VIgGpgAFV~~a~~~~df~~AirrKL 198 (205)
T PF06707_consen 143 VAAGITINGLAILDDDPFGGADLDAYYRRCVIGGPGAFVETARGFEDFAEAIRRKL 198 (205)
T ss_pred HHCCeEEeeeEecCCCCCccccHHHHHhhhcccCCCceEEEcCCHHHHHHHHHHHH
Confidence 56799999998887655 66666444444443333333333344666665543
No 161
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=22.15 E-value=48 Score=31.68 Aligned_cols=35 Identities=20% Similarity=0.633 Sum_probs=20.7
Q ss_pred ccccCCCCc------eecCceEEEcCC------ceEEeCCCCCCCCC
Q 005340 58 PLRCRTCRS------ILNPFSIVDFAA------KIWICPFCFQRNHF 92 (701)
Q Consensus 58 p~RC~~C~a------yiNp~~~~~~~g------~~w~C~~C~~~N~~ 92 (701)
-+.|.+|+- |+|++-+.+..| -.|+|.+|++.+.+
T Consensus 30 kvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~si 76 (161)
T PF05907_consen 30 KVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRESSI 76 (161)
T ss_dssp EEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEE
T ss_pred EEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCccEE
Confidence 478999995 578887776533 37999999998765
No 162
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=22.04 E-value=84 Score=21.04 Aligned_cols=26 Identities=19% Similarity=0.341 Sum_probs=14.4
Q ss_pred ccCCCCceecCceEEEcCCceEEeCCCCCC
Q 005340 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
.|.+|++= +....+|..-+|+-|+..
T Consensus 5 fC~~CG~~----t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAP----TKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--B----EEE-SSSS-EEESSSS-E
T ss_pred ccCcCCcc----ccCCCCcCEeECCCCcCE
Confidence 58888883 445566788899988863
No 163
>KOG0445 consensus Actin regulatory protein supervillin (gelsolin/villin family) [Cytoskeleton]
Probab=22.03 E-value=79 Score=36.63 Aligned_cols=29 Identities=17% Similarity=0.401 Sum_probs=25.7
Q ss_pred ccccccccCCeEEEEeCCcEEEEEECCCh
Q 005340 645 LLDVAAIAADRILLLDSYFTVVIFHGATI 673 (701)
Q Consensus 645 ~ls~~~l~~d~iyLlD~~~~i~i~~G~~v 673 (701)
.++.+-|++..+++.|-|-.||+|.|+.+
T Consensus 362 ipk~~~l~p~eVLvFDFGSEvYVW~Gk~~ 390 (919)
T KOG0445|consen 362 IPKCSLLQPKEVLVFDFGSEVYVWHGKEV 390 (919)
T ss_pred cccccccCcceEEEEecCceEEEEcCccC
Confidence 44566789999999999999999999987
No 164
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=21.62 E-value=40 Score=21.19 Aligned_cols=14 Identities=36% Similarity=0.733 Sum_probs=11.7
Q ss_pred eEEeCCCCCCCCCC
Q 005340 80 IWICPFCFQRNHFP 93 (701)
Q Consensus 80 ~w~C~~C~~~N~~p 93 (701)
.|.|..|...|...
T Consensus 2 ~W~C~~C~~~N~~~ 15 (26)
T smart00547 2 DWECPACTFLNFAS 15 (26)
T ss_pred cccCCCCCCcChhh
Confidence 59999999998643
No 165
>PF02905 EBV-NA1: Epstein Barr virus nuclear antigen-1, DNA-binding domain; InterPro: IPR004186 The Epstein-Barr virus (strain GD1) nuclear antigen 1 (EBNA1) binds to and activates DNA replication from the latent origin of replication. The crystal structure of the DNA-binding and dimerization domains were solved [], and it was found that EBNA1 appears to bind DNA via two independent regions, the core and the flanking DNA-binding domains. This DNA-binding domain has a ferredoxin-like fold.; GO: 0003677 DNA binding, 0003688 DNA replication origin binding, 0006260 DNA replication, 0006275 regulation of DNA replication, 0045893 positive regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1B3T_B 1VHI_B.
Probab=21.48 E-value=1e+02 Score=27.76 Aligned_cols=33 Identities=24% Similarity=0.209 Sum_probs=24.6
Q ss_pred hhHHHHHHHHHHHhhcCCC---CcEEEEEEECCEEE
Q 005340 143 EEMSFLKSALSQAIDLLPD---NSLVGLITFGTLVQ 175 (701)
Q Consensus 143 ~~l~~~~~~l~~~l~~lp~---~~~VgiItf~~~V~ 175 (701)
.--+.++++|+.-+..-|. +.+|.+++||+.|-
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 3356889999888877663 57999999998773
No 166
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=21.26 E-value=50 Score=27.45 Aligned_cols=30 Identities=23% Similarity=0.460 Sum_probs=16.8
Q ss_pred cccCCCCceecCce----EEE-----cCCceEEeCCCCC
Q 005340 59 LRCRTCRSILNPFS----IVD-----FAAKIWICPFCFQ 88 (701)
Q Consensus 59 ~RC~~C~ayiNp~~----~~~-----~~g~~w~C~~C~~ 88 (701)
.-|++|++++=|-. .+. .+.-.|+|..|++
T Consensus 47 ~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 47 TICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp TB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred ccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 46999999976653 344 2334899999984
No 167
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=21.24 E-value=37 Score=24.30 Aligned_cols=9 Identities=22% Similarity=1.176 Sum_probs=7.3
Q ss_pred cccCCCCce
Q 005340 59 LRCRTCRSI 67 (701)
Q Consensus 59 ~RC~~C~ay 67 (701)
+||.+|++|
T Consensus 2 ~kC~~CG~~ 10 (40)
T PF15288_consen 2 VKCKNCGAF 10 (40)
T ss_pred ccccccccc
Confidence 588999885
No 168
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=21.06 E-value=35 Score=28.55 Aligned_cols=15 Identities=33% Similarity=0.961 Sum_probs=6.7
Q ss_pred ceEEeCCCCCCCCCC
Q 005340 79 KIWICPFCFQRNHFP 93 (701)
Q Consensus 79 ~~w~C~~C~~~N~~p 93 (701)
+.|.|+||++.+.+.
T Consensus 21 ~~F~CPfC~~~~sV~ 35 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVS 35 (81)
T ss_dssp S----TTT--SS-EE
T ss_pred ceEcCCcCCCCCeEE
Confidence 689999999999875
No 169
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.99 E-value=53 Score=34.91 Aligned_cols=25 Identities=20% Similarity=0.644 Sum_probs=19.9
Q ss_pred ccccCCCCceecCceEEEcCCceEEeCCCCCCCC
Q 005340 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (701)
Q Consensus 58 p~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~N~ 91 (701)
-..|+.|+. ..++.|.|+-||...+
T Consensus 309 S~~C~~cg~---------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 309 SKTCPCCGH---------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred cccccccCC---------ccceeEECCCCCCeeh
Confidence 367999999 3357899999999754
No 170
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=20.92 E-value=35 Score=23.16 Aligned_cols=12 Identities=42% Similarity=1.088 Sum_probs=7.0
Q ss_pred CCCccccCCCCc
Q 005340 55 PYAPLRCRTCRS 66 (701)
Q Consensus 55 ~~~p~RC~~C~a 66 (701)
..+++||..|+.
T Consensus 14 ~~~~irC~~CG~ 25 (32)
T PF03604_consen 14 PGDPIRCPECGH 25 (32)
T ss_dssp TSSTSSBSSSS-
T ss_pred CCCcEECCcCCC
Confidence 345677777764
No 171
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=20.60 E-value=71 Score=29.30 Aligned_cols=25 Identities=28% Similarity=0.623 Sum_probs=19.1
Q ss_pred cccCCCCceecCceEEEcCCceEEeCCCCCC
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 89 (701)
.-|..|+. |.++ .+| .-.|+.|++.
T Consensus 29 ~hCp~Cg~---PLF~--KdG-~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGT---PLFR--KDG-EVFCPVCGYR 53 (131)
T ss_pred hhCcccCC---ccee--eCC-eEECCCCCce
Confidence 35999997 7776 444 7899999953
No 172
>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=20.56 E-value=67 Score=21.08 Aligned_cols=27 Identities=22% Similarity=0.754 Sum_probs=14.7
Q ss_pred ccCCCCceecCceEEEcCCceEEeCCCCC
Q 005340 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (701)
Q Consensus 60 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 88 (701)
.|.+|+.++-.... .+...+.|+-|..
T Consensus 3 ~C~rC~~~~~~~~~--~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGI--NGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEE--TTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEe--cCCCCeECcCCcC
Confidence 59999998544332 3345789998864
No 173
>PRK12860 transcriptional activator FlhC; Provisional
Probab=20.12 E-value=51 Score=32.25 Aligned_cols=28 Identities=18% Similarity=0.496 Sum_probs=20.1
Q ss_pred CccccCCCCc-eecCceEEEcCCceEEeCCCC
Q 005340 57 APLRCRTCRS-ILNPFSIVDFAAKIWICPFCF 87 (701)
Q Consensus 57 ~p~RC~~C~a-yiNp~~~~~~~g~~w~C~~C~ 87 (701)
...+|..|++ |+- ...+....++|++|.
T Consensus 133 ~l~~C~~Cgg~fv~---~~~e~~~~f~CplC~ 161 (189)
T PRK12860 133 QLARCCRCGGKFVT---HAHDLRHNFVCGLCQ 161 (189)
T ss_pred eeccCCCCCCCeec---cccccCCCCcCCCCC
Confidence 5789999987 331 222445789999999
No 174
>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=20.12 E-value=1.1e+02 Score=32.48 Aligned_cols=27 Identities=33% Similarity=0.468 Sum_probs=24.3
Q ss_pred hHHHHHHHHHHHhhcCCCCcEEEEEEE
Q 005340 144 EMSFLKSALSQAIDLLPDNSLVGLITF 170 (701)
Q Consensus 144 ~l~~~~~~l~~~l~~lp~~~~VgiItf 170 (701)
||+.+..+|..+.+.|.++.++++|||
T Consensus 215 EL~~L~~~L~~~~~~L~~gGrl~VISf 241 (305)
T TIGR00006 215 ELEELEEALQFAPNLLAPGGRLSIISF 241 (305)
T ss_pred hHHHHHHHHHHHHHHhcCCCEEEEEec
Confidence 388999999999999999999999985
No 175
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=20.04 E-value=51 Score=36.25 Aligned_cols=27 Identities=26% Similarity=0.741 Sum_probs=19.8
Q ss_pred cccCCCCceecCceEEEcCCceE--EeCCCCCCCCCCcc
Q 005340 59 LRCRTCRSILNPFSIVDFAAKIW--ICPFCFQRNHFPPH 95 (701)
Q Consensus 59 ~RC~~C~ayiNp~~~~~~~g~~w--~C~~C~~~N~~p~~ 95 (701)
..|+.|++- ..+| +|+-|+..|.+-..
T Consensus 8 f~C~~CG~~----------s~KW~GkCp~Cg~Wns~vE~ 36 (456)
T COG1066 8 FVCQECGYV----------SPKWLGKCPACGAWNTLVEE 36 (456)
T ss_pred EEcccCCCC----------CccccccCCCCCCccceEEe
Confidence 469999872 2345 79999999987543
Done!