Query 004199
Match_columns 769
No_of_seqs 191 out of 762
Neff 8.1
Searched_HMMs 46136
Date Thu Mar 28 19:15:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004199.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004199hhsearch_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-170 4E-175 1491.0 78.8 755 2-769 1-760 (761)
2 KOG1986 Vesicle coat complex C 100.0 3E-171 6E-176 1385.1 66.1 740 3-769 2-743 (745)
3 COG5047 SEC23 Vesicle coat com 100.0 1E-161 3E-166 1274.1 52.4 748 2-769 1-753 (755)
4 KOG1985 Vesicle coat complex C 100.0 4E-122 8E-127 1015.2 49.6 665 7-769 167-887 (887)
5 KOG1984 Vesicle coat complex C 100.0 3E-120 7E-125 1000.1 52.5 671 6-768 283-1003(1007)
6 PTZ00395 Sec24-related protein 100.0 4E-111 9E-116 966.1 55.3 669 6-768 648-1554(1560)
7 COG5028 Vesicle coat complex C 100.0 1E-108 3E-113 900.0 51.2 657 6-767 146-859 (861)
8 cd01478 Sec23-like Sec23-like: 100.0 2.5E-55 5.3E-60 457.0 27.2 266 128-395 2-267 (267)
9 cd01468 trunk_domain trunk dom 100.0 2.8E-44 6E-49 371.9 21.7 228 128-395 2-235 (239)
10 cd01479 Sec24-like Sec24-like: 100.0 2.9E-44 6.4E-49 371.2 21.6 223 128-394 2-233 (244)
11 PF04811 Sec23_trunk: Sec23/Se 100.0 3.5E-43 7.5E-48 365.2 20.4 232 128-397 2-239 (243)
12 PF08033 Sec23_BS: Sec23/Sec24 99.9 7.8E-22 1.7E-26 174.0 12.3 96 407-513 1-96 (96)
13 PF04815 Sec23_helical: Sec23/ 99.7 7.5E-18 1.6E-22 150.6 9.1 101 528-628 1-103 (103)
14 PF04810 zf-Sec23_Sec24: Sec23 99.6 1.7E-16 3.7E-21 114.7 2.2 40 57-96 1-40 (40)
15 cd01465 vWA_subgroup VWA subgr 98.5 3.4E-06 7.4E-11 82.4 16.7 158 132-384 3-163 (170)
16 cd01463 vWA_VGCC_like VWA Volt 98.5 6.1E-06 1.3E-10 82.5 17.2 167 128-384 12-189 (190)
17 cd01451 vWA_Magnesium_chelatas 98.4 1.2E-05 2.6E-10 79.5 18.1 163 132-389 3-172 (178)
18 cd01466 vWA_C3HC4_type VWA C3H 98.4 7.1E-06 1.5E-10 79.2 15.5 149 132-381 3-154 (155)
19 cd01456 vWA_ywmD_type VWA ywmD 98.4 5.7E-06 1.2E-10 83.9 15.3 168 128-378 19-196 (206)
20 PRK13685 hypothetical protein; 98.4 1.4E-05 3E-10 87.0 19.0 162 128-383 87-275 (326)
21 cd01453 vWA_transcription_fact 98.3 1.2E-05 2.5E-10 80.0 15.2 152 131-383 5-167 (183)
22 PF00626 Gelsolin: Gelsolin re 98.3 8.3E-07 1.8E-11 74.5 5.8 72 640-727 4-76 (76)
23 cd01472 vWA_collagen von Wille 98.2 0.0001 2.3E-09 71.6 18.1 152 132-384 3-164 (164)
24 TIGR00868 hCaCC calcium-activa 98.1 0.00018 3.8E-09 85.9 21.2 154 128-383 303-462 (863)
25 cd01470 vWA_complement_factors 98.1 8.7E-05 1.9E-09 74.7 15.9 168 132-385 3-191 (198)
26 cd01467 vWA_BatA_type VWA BatA 98.1 0.00028 6E-09 69.7 18.2 156 130-383 3-176 (180)
27 cd01452 VWA_26S_proteasome_sub 98.1 0.00014 3.1E-09 71.8 15.7 144 131-374 5-161 (187)
28 TIGR03436 acidobact_VWFA VWFA- 98.0 0.00032 6.9E-09 75.3 19.1 49 128-176 52-102 (296)
29 cd01461 vWA_interalpha_trypsin 97.9 0.00052 1.1E-08 66.9 17.5 160 129-385 2-163 (171)
30 cd01480 vWA_collagen_alpha_1-V 97.9 0.00034 7.5E-09 69.6 16.3 157 131-385 4-173 (186)
31 PF13768 VWA_3: von Willebrand 97.9 0.00027 5.8E-09 68.0 14.4 151 132-379 3-154 (155)
32 PF13519 VWA_2: von Willebrand 97.8 0.00034 7.5E-09 67.8 13.8 150 132-382 2-159 (172)
33 cd01475 vWA_Matrilin VWA_Matri 97.8 0.00073 1.6E-08 69.4 16.8 155 129-385 2-170 (224)
34 cd01482 vWA_collagen_alphaI-XI 97.8 0.0014 2.9E-08 63.9 17.7 45 132-176 3-52 (164)
35 cd01469 vWA_integrins_alpha_su 97.8 0.0014 3.1E-08 64.6 17.2 156 132-385 3-172 (177)
36 cd01474 vWA_ATR ATR (Anthrax T 97.7 0.00086 1.9E-08 66.7 14.8 85 267-385 78-168 (185)
37 TIGR03788 marine_srt_targ mari 97.6 0.005 1.1E-07 72.7 21.8 186 128-414 270-457 (596)
38 cd01481 vWA_collagen_alpha3-VI 97.6 0.0043 9.3E-08 60.5 17.0 149 132-384 3-165 (165)
39 cd01471 vWA_micronemal_protein 97.5 0.0025 5.4E-08 63.3 15.3 148 132-373 3-160 (186)
40 cd01450 vWFA_subfamily_ECM Von 97.5 0.004 8.6E-08 59.7 16.3 145 132-375 3-156 (161)
41 cd01477 vWA_F09G8-8_type VWA F 97.5 0.0043 9.3E-08 62.1 15.7 49 128-176 18-77 (193)
42 TIGR02031 BchD-ChlD magnesium 97.4 0.0052 1.1E-07 72.1 17.9 176 128-387 406-586 (589)
43 PF00092 VWA: von Willebrand f 97.4 0.0039 8.4E-08 60.9 14.4 156 132-386 2-170 (178)
44 PRK13406 bchD magnesium chelat 97.3 0.012 2.6E-07 68.6 19.5 172 128-390 400-576 (584)
45 smart00327 VWA von Willebrand 97.3 0.02 4.3E-07 55.6 18.1 154 130-380 2-164 (177)
46 cd01476 VWA_integrin_invertebr 97.2 0.015 3.3E-07 56.2 16.1 41 132-172 3-47 (163)
47 TIGR02442 Cob-chelat-sub cobal 97.2 0.0096 2.1E-07 70.6 16.9 161 128-381 464-632 (633)
48 smart00262 GEL Gelsolin homolo 97.0 0.0024 5.2E-08 55.4 7.7 70 643-728 15-85 (90)
49 cd00198 vWFA Von Willebrand fa 97.0 0.036 7.8E-07 52.3 16.0 147 131-374 2-155 (161)
50 cd01473 vWA_CTRP CTRP for CS 96.9 0.044 9.5E-07 54.8 16.5 146 132-373 3-161 (192)
51 PTZ00441 sporozoite surface pr 96.8 0.044 9.6E-07 62.5 17.5 164 128-385 41-217 (576)
52 COG1240 ChlD Mg-chelatase subu 96.8 0.051 1.1E-06 55.6 16.0 169 128-389 77-252 (261)
53 PF04056 Ssl1: Ssl1-like; Int 96.7 0.035 7.7E-07 55.0 13.5 95 267-396 78-172 (193)
54 cd01454 vWA_norD_type norD typ 96.1 0.17 3.7E-06 49.5 14.6 43 131-173 2-48 (174)
55 cd01458 vWA_ku Ku70/Ku80 N-ter 96.0 0.16 3.5E-06 51.8 14.2 155 131-359 3-172 (218)
56 cd01462 VWA_YIEM_type VWA YIEM 95.2 0.55 1.2E-05 44.7 14.2 43 132-174 3-48 (152)
57 KOG0443 Actin regulatory prote 94.4 0.065 1.4E-06 62.3 6.1 86 625-723 615-706 (827)
58 KOG2884 26S proteasome regulat 94.3 2 4.4E-05 42.7 15.0 86 268-383 84-175 (259)
59 TIGR00578 ku70 ATP-dependent D 93.4 0.99 2.1E-05 53.1 13.6 73 268-365 116-190 (584)
60 cd01464 vWA_subfamily VWA subf 93.0 0.13 2.7E-06 50.6 4.7 45 132-176 6-58 (176)
61 smart00187 INB Integrin beta s 92.8 19 0.00041 40.1 24.2 282 128-472 98-391 (423)
62 KOG0444 Cytoskeletal regulator 92.8 0.16 3.5E-06 57.7 5.4 90 631-736 623-717 (1255)
63 COG4245 TerY Uncharacterized p 92.2 0.21 4.5E-06 48.5 4.6 49 129-178 4-60 (207)
64 cd01460 vWA_midasin VWA_Midasi 90.8 12 0.00026 39.4 16.4 46 128-175 59-111 (266)
65 COG5148 RPN10 26S proteasome r 89.7 8.7 0.00019 37.4 12.9 74 245-358 70-145 (243)
66 KOG0443 Actin regulatory prote 88.0 0.8 1.7E-05 53.7 5.7 92 629-737 254-358 (827)
67 cd01457 vWA_ORF176_type VWA OR 87.0 8.7 0.00019 38.4 12.1 44 130-173 3-57 (199)
68 PF03850 Tfb4: Transcription f 82.6 70 0.0015 33.9 17.8 87 269-385 116-209 (276)
69 PF10058 DUF2296: Predicted in 82.3 0.89 1.9E-05 35.3 1.8 33 58-90 22-54 (54)
70 PRK00398 rpoP DNA-directed RNA 79.7 1.3 2.9E-05 33.0 2.0 30 58-91 3-32 (46)
71 TIGR01053 LSD1 zinc finger dom 79.2 2 4.3E-05 29.2 2.5 30 59-92 2-31 (31)
72 PF00362 Integrin_beta: Integr 79.1 1.2E+02 0.0026 34.3 21.0 283 128-473 101-395 (426)
73 TIGR00627 tfb4 transcription f 76.1 32 0.00069 36.4 11.7 86 267-382 117-208 (279)
74 KOG2807 RNA polymerase II tran 75.6 77 0.0017 33.8 13.9 76 268-376 142-217 (378)
75 PF09967 DUF2201: VWA-like dom 71.7 8.4 0.00018 35.6 5.5 42 133-176 2-45 (126)
76 smart00661 RPOL9 RNA polymeras 68.2 3.5 7.7E-05 31.4 1.8 32 60-93 2-33 (52)
77 KOG2487 RNA polymerase II tran 65.1 1.6E+02 0.0034 30.8 13.1 45 338-385 185-229 (314)
78 PF08271 TF_Zn_Ribbon: TFIIB z 63.2 8.3 0.00018 28.2 2.9 27 60-89 2-28 (43)
79 cd00350 rubredoxin_like Rubred 62.8 4.7 0.0001 27.8 1.4 24 60-89 3-26 (33)
80 KOG2353 L-type voltage-depende 61.1 60 0.0013 40.9 11.3 65 112-176 204-274 (1104)
81 PF09723 Zn-ribbon_8: Zinc rib 60.4 3.9 8.4E-05 29.9 0.7 30 59-89 6-35 (42)
82 cd00730 rubredoxin Rubredoxin; 60.1 4.3 9.4E-05 30.9 0.9 30 60-89 3-43 (50)
83 KOG0444 Cytoskeletal regulator 58.4 9.9 0.00021 44.0 3.7 55 621-675 725-788 (1255)
84 PRK03954 ribonuclease P protei 56.1 7.2 0.00016 35.7 1.8 36 59-94 65-107 (121)
85 PRK12380 hydrogenase nickel in 54.8 7 0.00015 35.4 1.5 27 58-90 70-96 (113)
86 PF10122 Mu-like_Com: Mu-like 54.7 4.5 9.8E-05 30.7 0.2 33 58-92 4-36 (51)
87 cd01455 vWA_F11C1-5a_type Von 53.7 2.4E+02 0.0052 28.1 12.6 98 245-383 75-174 (191)
88 PF13719 zinc_ribbon_5: zinc-r 53.5 8 0.00017 27.4 1.3 32 59-90 3-35 (37)
89 TIGR00100 hypA hydrogenase nic 53.2 7.9 0.00017 35.2 1.6 27 58-90 70-96 (115)
90 TIGR02605 CxxC_CxxC_SSSS putat 52.6 6.5 0.00014 30.0 0.9 31 59-90 6-36 (52)
91 COG2888 Predicted Zn-ribbon RN 51.7 6.1 0.00013 30.9 0.5 23 57-89 37-59 (61)
92 PF13240 zinc_ribbon_2: zinc-r 51.7 7.6 0.00017 24.4 0.9 21 60-88 1-21 (23)
93 PF03731 Ku_N: Ku70/Ku80 N-ter 51.5 20 0.00044 36.4 4.5 43 131-173 1-54 (224)
94 PF14803 Nudix_N_2: Nudix N-te 49.9 6 0.00013 27.5 0.2 30 60-89 2-31 (34)
95 COG1996 RPC10 DNA-directed RNA 48.5 9.1 0.0002 29.0 1.0 28 59-90 7-34 (49)
96 TIGR00416 sms DNA repair prote 48.0 9.9 0.00022 43.3 1.7 29 58-94 7-35 (454)
97 PRK03681 hypA hydrogenase nick 47.1 11 0.00024 34.2 1.6 28 58-90 70-97 (114)
98 PF00301 Rubredoxin: Rubredoxi 46.5 5.8 0.00013 29.8 -0.3 30 60-89 3-43 (47)
99 cd01121 Sms Sms (bacterial rad 46.3 11 0.00023 41.8 1.7 27 60-94 2-28 (372)
100 PRK14890 putative Zn-ribbon RN 46.0 8.9 0.00019 30.1 0.6 22 58-89 36-57 (59)
101 smart00834 CxxC_CXXC_SSSS Puta 45.7 9.4 0.0002 27.3 0.7 29 59-88 6-34 (41)
102 COG1198 PriA Primosomal protei 45.5 85 0.0018 37.9 8.9 105 58-180 444-571 (730)
103 PRK11823 DNA repair protein Ra 45.2 11 0.00024 42.9 1.5 29 58-94 7-35 (446)
104 PF08792 A2L_zn_ribbon: A2L zi 43.3 26 0.00056 24.2 2.5 29 58-90 3-31 (33)
105 PF13717 zinc_ribbon_4: zinc-r 43.3 15 0.00033 25.9 1.4 31 59-89 3-34 (36)
106 PF09082 DUF1922: Domain of un 43.0 11 0.00023 30.6 0.7 30 58-93 3-32 (68)
107 PF07754 DUF1610: Domain of un 42.4 24 0.00052 22.5 2.1 24 61-88 1-24 (24)
108 PF07282 OrfB_Zn_ribbon: Putat 41.7 19 0.00041 29.2 2.1 27 59-89 29-55 (69)
109 PF09779 Ima1_N: Ima1 N-termin 41.6 19 0.00041 33.6 2.2 35 59-95 1-35 (131)
110 COG2260 Predicted Zn-ribbon RN 41.1 23 0.00051 27.7 2.2 33 58-100 5-39 (59)
111 PRK00432 30S ribosomal protein 40.5 17 0.00036 27.7 1.4 25 59-89 21-46 (50)
112 smart00659 RPOLCX RNA polymera 39.3 24 0.00051 26.2 2.0 25 60-89 4-28 (44)
113 PF10571 UPF0547: Uncharacteri 39.0 16 0.00034 23.8 0.9 23 60-90 2-24 (26)
114 PRK00564 hypA hydrogenase nick 39.0 12 0.00026 34.1 0.5 28 58-90 71-98 (117)
115 COG1096 Predicted RNA-binding 38.7 18 0.00039 35.5 1.6 25 59-89 150-174 (188)
116 PF06943 zf-LSD1: LSD1 zinc fi 38.6 30 0.00065 22.3 2.1 24 61-88 1-24 (25)
117 PF11781 RRN7: RNA polymerase 38.4 30 0.00066 24.4 2.3 27 58-89 8-34 (36)
118 PF02318 FYVE_2: FYVE-type zin 38.3 14 0.00031 33.7 0.9 32 58-89 71-103 (118)
119 PRK06393 rpoE DNA-directed RNA 37.2 19 0.00042 28.9 1.3 24 59-92 6-29 (64)
120 PF01927 Mut7-C: Mut7-C RNAse 37.1 21 0.00046 33.9 1.9 33 58-90 91-134 (147)
121 PF12773 DZR: Double zinc ribb 37.0 21 0.00046 26.8 1.5 35 57-96 11-45 (50)
122 PF12760 Zn_Tnp_IS1595: Transp 36.6 42 0.0009 24.9 3.0 27 59-88 19-45 (46)
123 PRK10997 yieM hypothetical pro 35.4 43 0.00092 38.4 4.2 51 130-180 324-377 (487)
124 PRK00762 hypA hydrogenase nick 35.2 17 0.00036 33.6 0.8 33 58-91 70-103 (124)
125 PRK03824 hypA hydrogenase nick 34.4 24 0.00052 33.1 1.7 33 58-90 70-117 (135)
126 KOG3799 Rab3 effector RIM1 and 34.3 19 0.00042 32.9 1.0 31 57-91 88-118 (169)
127 PRK12286 rpmF 50S ribosomal pr 33.8 35 0.00076 26.8 2.3 26 57-91 26-51 (57)
128 PF00641 zf-RanBP: Zn-finger i 33.0 14 0.00031 24.6 0.0 16 79-94 3-18 (30)
129 smart00401 ZnF_GATA zinc finge 32.8 29 0.00063 26.7 1.6 32 58-89 3-34 (52)
130 COG2051 RPS27A Ribosomal prote 32.6 37 0.00079 27.4 2.2 34 57-93 18-51 (67)
131 COG5415 Predicted integral mem 32.2 40 0.00086 33.5 2.8 40 57-96 191-230 (251)
132 TIGR00686 phnA alkylphosphonat 32.2 38 0.00082 30.1 2.4 28 58-90 2-29 (109)
133 TIGR01384 TFS_arch transcripti 31.9 30 0.00066 30.6 1.9 27 60-92 2-28 (104)
134 PRK08351 DNA-directed RNA poly 31.8 30 0.00064 27.6 1.6 23 60-92 5-27 (61)
135 TIGR02098 MJ0042_CXXC MJ0042 f 31.7 27 0.00059 24.6 1.3 31 59-89 3-34 (38)
136 KOG2846 Predicted membrane pro 31.2 25 0.00053 37.6 1.4 36 58-93 220-255 (328)
137 COG3357 Predicted transcriptio 31.0 24 0.00053 30.1 1.0 35 57-95 57-91 (97)
138 PF05762 VWA_CoxE: VWA domain 30.3 97 0.0021 31.6 5.6 44 128-174 55-100 (222)
139 PF01155 HypA: Hydrogenase exp 30.3 12 0.00027 33.8 -0.9 27 58-90 70-96 (113)
140 PF02891 zf-MIZ: MIZ/SP-RING z 29.9 19 0.00041 27.4 0.2 19 70-88 31-49 (50)
141 PF13894 zf-C2H2_4: C2H2-type 29.4 26 0.00056 21.1 0.8 11 81-91 1-11 (24)
142 PHA00626 hypothetical protein 29.4 48 0.001 25.8 2.3 14 78-91 21-34 (59)
143 smart00132 LIM Zinc-binding do 29.1 43 0.00093 23.0 2.0 29 60-88 1-35 (39)
144 cd01464 vWA_subfamily VWA subf 29.0 1.1E+02 0.0025 29.5 5.7 76 267-373 77-160 (176)
145 TIGR01031 rpmF_bact ribosomal 28.9 34 0.00075 26.6 1.5 25 57-90 25-49 (55)
146 COG2425 Uncharacterized protei 28.7 2.2E+02 0.0047 32.2 8.2 45 129-174 273-320 (437)
147 COG0275 Predicted S-adenosylme 28.2 62 0.0013 34.5 3.7 28 143-170 218-245 (314)
148 smart00778 Prim_Zn_Ribbon Zinc 27.7 51 0.0011 23.5 2.0 27 60-88 5-33 (37)
149 COG1066 Sms Predicted ATP-depe 27.7 30 0.00064 38.4 1.3 27 59-95 8-36 (456)
150 COG1545 Predicted nucleic-acid 27.6 79 0.0017 29.8 4.0 65 59-140 30-94 (140)
151 PRK13130 H/ACA RNA-protein com 27.1 76 0.0016 24.9 3.1 34 57-100 4-39 (56)
152 PRK05580 primosome assembly pr 27.1 2.1E+02 0.0047 34.5 8.5 35 59-93 382-421 (679)
153 PF13248 zf-ribbon_3: zinc-rib 26.9 32 0.0007 22.2 0.9 22 59-88 3-24 (26)
154 PF08274 PhnA_Zn_Ribbon: PhnA 26.9 30 0.00065 23.4 0.7 26 59-89 3-28 (30)
155 TIGR00311 aIF-2beta translatio 26.8 61 0.0013 30.3 3.0 32 58-92 97-130 (133)
156 PF14353 CpXC: CpXC protein 26.5 57 0.0012 30.0 2.8 34 59-92 2-50 (128)
157 smart00547 ZnF_RBZ Zinc finger 26.1 29 0.00062 22.1 0.5 14 80-93 2-15 (26)
158 PRK12722 transcriptional activ 25.7 32 0.00069 34.0 1.0 29 57-88 133-162 (187)
159 PF12172 DUF35_N: Rubredoxin-l 25.5 38 0.00082 23.8 1.1 24 58-89 11-34 (37)
160 COG2956 Predicted N-acetylgluc 25.4 37 0.0008 36.4 1.4 28 57-92 353-380 (389)
161 PF06707 DUF1194: Protein of u 25.4 7.1E+02 0.015 25.1 11.0 97 268-397 94-198 (205)
162 COG2093 DNA-directed RNA polym 24.7 34 0.00075 27.2 0.8 25 60-92 6-30 (64)
163 PRK14810 formamidopyrimidine-D 24.7 56 0.0012 34.6 2.7 28 59-88 245-272 (272)
164 PF00320 GATA: GATA zinc finge 24.0 27 0.0006 24.5 0.1 28 61-88 1-28 (36)
165 COG4416 Com Mu-like prophage p 23.9 16 0.00034 28.0 -1.1 33 58-92 4-36 (60)
166 PF03604 DNA_RNApol_7kD: DNA d 23.4 28 0.0006 23.9 0.1 12 55-66 14-25 (32)
167 PF08273 Prim_Zn_Ribbon: Zinc- 22.9 60 0.0013 23.5 1.7 27 61-88 6-34 (40)
168 PRK10220 hypothetical protein; 22.8 70 0.0015 28.5 2.4 28 58-90 3-30 (111)
169 COG1645 Uncharacterized Zn-fin 22.4 55 0.0012 30.3 1.8 25 59-89 29-53 (131)
170 PF04032 Rpr2: RNAse P Rpr2/Rp 22.0 51 0.0011 27.8 1.5 30 59-88 47-85 (85)
171 PF02905 EBV-NA1: Epstein Barr 21.9 98 0.0021 28.2 3.2 31 145-175 112-145 (146)
172 PRK00420 hypothetical protein; 21.9 66 0.0014 29.1 2.1 29 59-92 24-52 (112)
173 PF05280 FlhC: Flagellar trans 21.3 37 0.00079 33.3 0.5 29 57-88 133-162 (175)
174 PF06827 zf-FPG_IleRS: Zinc fi 21.3 65 0.0014 21.4 1.5 27 60-88 3-29 (30)
175 PF13453 zf-TFIIB: Transcripti 21.3 72 0.0016 23.0 1.9 28 60-89 1-28 (41)
176 TIGR00354 polC DNA polymerase, 21.1 49 0.0011 40.4 1.5 26 57-92 624-649 (1095)
177 COG2023 RPR2 RNase P subunit R 21.0 57 0.0012 29.0 1.5 35 59-93 57-95 (105)
178 PF05907 DUF866: Eukaryotic pr 20.9 47 0.001 32.2 1.1 35 58-92 30-76 (161)
179 COG0675 Transposase and inacti 20.5 55 0.0012 35.3 1.7 24 59-91 310-333 (364)
180 COG0266 Nei Formamidopyrimidin 20.4 51 0.0011 34.7 1.3 27 60-88 247-273 (273)
181 TIGR00595 priA primosomal prot 20.3 3.2E+02 0.0069 31.7 7.9 18 76-93 236-253 (505)
182 TIGR00006 S-adenosyl-methyltra 20.3 96 0.0021 33.3 3.4 27 144-170 215-241 (305)
183 COG1592 Rubrerythrin [Energy p 20.3 55 0.0012 31.8 1.4 26 77-113 131-156 (166)
184 PF05129 Elf1: Transcription e 20.2 37 0.00081 28.7 0.2 15 79-93 21-35 (81)
185 COG1773 Rubredoxin [Energy pro 20.2 50 0.0011 25.7 0.9 15 74-88 30-44 (55)
186 PRK12366 replication factor A; 20.2 71 0.0015 38.2 2.6 26 58-89 532-557 (637)
187 TIGR00375 conserved hypothetic 20.0 33 0.00071 37.9 -0.2 30 56-89 238-267 (374)
No 1
>PLN00162 transport protein sec23; Provisional
Probab=100.00 E-value=1.7e-170 Score=1491.02 Aligned_cols=755 Identities=73% Similarity=1.207 Sum_probs=701.6
Q ss_pred CCcccccCCCeeeecCCCCCCCHHHhhcCCCceeEEEccCCCCCCCCCCCCCCCCCCccCCCCCceecCccEEEcCCceE
Q 004199 2 TEFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRTCRSILNPFSIVDFAAKIW 81 (769)
Q Consensus 2 ~~~~~~~~~~~vR~t~~~~P~t~~~~~~~~lPlg~~v~P~~~~~~~~~~vp~~~~~p~rC~~C~aylNp~~~~~~~~~~w 81 (769)
|||+|.|+.++||+|||+||+|+.++++++|||||+|+||++.+ ++|+++++|+||++|+|||||||+||.++++|
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 79999999999999999999999999999999999999999876 68999999999999999999999999999999
Q ss_pred EecCCCCCCCCCcCCCCCCCCCCCccccCCCccEEEecC---CCCCCCCCCcEEEEEEEcCcchhHHHHHHHHHHHhccc
Q 004199 82 ICPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPP---GPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDL 158 (769)
Q Consensus 82 ~C~~C~~~N~~p~~y~~~~~~~~~pEL~~~~~tvey~~~---~~~~~~~~~p~~vFvID~s~~~~~l~~~~~~l~~~l~~ 158 (769)
+||||++.|++|++|..++++++||||.|+++||||.+| .++| .||+|+||||+|..+++++.++++|+++|+.
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 999999999999999888888999999888999999999 6677 8999999999999999999999999999999
Q ss_pred CCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHHHhhcccCCCCCCCccccCcCCCCCcccc-ccce
Q 004199 159 LPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTI-ARFL 237 (769)
Q Consensus 159 lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~-~~~l 237 (769)
||++++|||||||++||||+|+ .. ++|+++||+|+++++.+|+++++++.+..+.++... ++......+.|. ++||
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-ECSKSYVFRGNKEVSKDQILEQLGLGGKKRRPAGGG-IAGARDGLSSSGVNRFL 230 (761)
T ss_pred CCCCCEEEEEEECCEEEEEEcC-CC-CCcceEEecCCccCCHHHHHHHhccccccccccccc-cccccccccCCCcccee
Confidence 9999999999999999999998 65 689999999999999999999998754111111000 000000012343 8999
Q ss_pred eechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCc
Q 004199 238 VPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPI 317 (769)
Q Consensus 238 ~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~ 317 (769)
+|++||++.|.++||+|+++.|++++++|+.||+|+||++|..+|+++.++.||||++|++||||.|||+|+.++.++++
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 99999999999999999999999999999999999999999999998888899999999999999999999999999999
Q ss_pred CCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccChhhhhhhhhccCceEEEeCCCCchhhHHHHHHHh
Q 004199 318 RSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF 397 (769)
Q Consensus 318 rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~v~~~~~f~~~~~~~~l~~~~ 397 (769)
|+|+|++++++++++++.+||++||.+|+++||+||+|+++.+|+|++||+.|++.|||.+++|++|+.+.|+++|+|+|
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 99999999989999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred -hcCccCccceeeeEEEEEecCCceEEeEEcCCcccCCCCCCccccccccCCCCceeEecCCCCceEEEEEEEecCCCCc
Q 004199 398 -HSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPD 476 (769)
Q Consensus 398 -~~~~~~~~~~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~vsd~~~g~~~~~~~~l~~~~~~~s~~~~~~~~~~~~~~ 476 (769)
++..+++.+||+|+||||||+|++|++++||++++.++++++||+++|.|+|+.|+++++++++|++|+|++++... .
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 ERDGEGSLGLSFNGTFEVNCSKDVKVQGAIGPCASLEKKGPSVSDTEIGEGGTTAWKLCGLDKKTSLAVFFEVANSGQ-S 469 (761)
T ss_pred cccccccccccceeEEEEEecCCeEEeeeEcCcccccccCCccccccccCCCCceeeecCcCcCCEEEEEEEEccccc-c
Confidence 56566678999999999999999999999999988888889999999999999999999999999999999998751 0
Q ss_pred ccccCCCCeEEEEEEEEeEecCCcEEEEEEecccccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCCchhHHHHHH
Q 004199 477 ATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKMEIEAEFDPIRWLD 556 (769)
Q Consensus 477 ~~~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~~~~t~~~~~~~~i~~~~D~ea~~~llar~a~~~~~~~~~~d~~~~l~ 556 (769)
.++ ..+..+||||+++||+.+|+|||||||++++++.. .++.+++++|||||++++|||+++.++++++..|+++|||
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 011 34567999999999999999999999999997642 1478999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcccccCCCCccccCccccchHHHHHHHhcccCcCCCCCChHHHHHHHHHHccCChhhhhhhccceeEeec
Q 004199 557 KALIHMCSRFGDYQKDSPSSFSLSPRFSIFPQFMFHLRRSQFVQVFNNSPDETAYFRMILNRENVTNSVVMIQPSLISYS 636 (769)
Q Consensus 557 ~~l~~~~~~~~~y~~~~~~~l~lp~~l~~lP~~~~~L~ks~~l~~~~~s~Der~~~~~~l~~~~~~~~~~~i~P~L~~~~ 636 (769)
++|+++|++|+.|+|+++++|+||++|++||+|||+|+||++|+++|+|||||+|+||+++++++++++.||||+|++||
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 CCCCCccccccccccccCeEEEEeCCcEEEEEECCCchHHHHccCCCCchhHHHHHhhhCcHHHHHHHHhcCCCCcEEEE
Q 004199 637 FHSGPEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYHNQPEHQAFAQLLQAPHDDAGVIMKERFPVPRLVI 716 (769)
Q Consensus 637 ~~~~p~~v~Ls~~~l~~d~i~llD~g~~i~i~~G~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~R~~~p~~~~ 716 (769)
.+++|+|++||+++|++|+|||||+|++|+||+|++++||++++||++|+|++|+++|++|+++|++|+++|||+||+++
T Consensus 628 ~~~~P~pv~Ld~~si~~d~ilLLD~~f~vvi~~G~~ia~w~~~~~~~~~~~~~~~~~l~~p~~~a~~~~~~Rfp~Pr~i~ 707 (761)
T PLN00162 628 FNGPPEPVLLDVASIAADRILLLDSYFSVVIFHGSTIAQWRKAGYHNQPEHEAFAQLLEAPQADAQAIIKERFPVPRLVV 707 (761)
T ss_pred CCCCCcceecchhhccCCceEEEeCCCEEEEEecCcccchhhcCCCCCcchhhHHHHHHhHHHHHHHHHhcCCCCCeEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCCChHHHHHhhhCCCCcCCCCCCCCCCceeecCCchHHHHHHHHHHHhhC
Q 004199 717 CDQHGSQARFLLAKLNPSATYNSDAQIPGGDIIFTDDVSFEVFLDHLQRLAVQ 769 (769)
Q Consensus 717 ~~~g~s~~r~l~s~L~p~~~~~~~~~~~~~~~~~tdd~S~~~f~~~l~~~~~~ 769 (769)
|+||+||||||++||||+.+|++.+-.++|++|+|||+||+.||+||+|+||+
T Consensus 708 ~~~~~SqaRfl~~klnPs~~~~~~~~~~~~~~~~tdd~sl~~f~~~l~~~~v~ 760 (761)
T PLN00162 708 CDQHGSQARFLLAKLNPSATYNSANAMGGSDIIFTDDVSLQVFMEHLQRLAVQ 760 (761)
T ss_pred eCCCCcHHHHHHHhcCCcccccCCCCCCCCCeeecCCcCHHHHHHHHHHHhcC
Confidence 99999999999999999999865321136779999999999999999999996
No 2
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.7e-171 Score=1385.08 Aligned_cols=740 Identities=59% Similarity=1.028 Sum_probs=704.6
Q ss_pred CcccccCCCeeeecCCCCCCCHHHhhcCCCceeEEEccCCCCCCCCCCCCCCCCCCccCCCCCceecCccEEEcCCceEE
Q 004199 3 EFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRTCRSILNPFSIVDFAAKIWI 82 (769)
Q Consensus 3 ~~~~~~~~~~vR~t~~~~P~t~~~~~~~~lPlg~~v~P~~~~~~~~~~vp~~~~~p~rC~~C~aylNp~~~~~~~~~~w~ 82 (769)
.++++|+.++||+|||+||+++.+..++++|++|+|+||++.+ .+|.+.|+|+||++|+||+||||.+|.+.+.|.
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 3667999999999999999999999999999999999999866 578999999999999999999999999999999
Q ss_pred ecCCCCCCCCCcCCCCCCCCCCCccccCCCccEEEecCCCCCCCCCCcEEEEEEEcCcchhHHHHHHHHHHHhcccCCCC
Q 004199 83 CPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPGPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLPDN 162 (769)
Q Consensus 83 C~~C~~~N~~p~~y~~~~~~~~~pEL~~~~~tvey~~~~~~~~~~~~p~~vFvID~s~~~~~l~~~~~~l~~~l~~lp~~ 162 (769)
|+||+++|.+|++|..++++|.|+||.|+++||||.+++... .||+|+||||+|+.+++|+.+|++|+.+|+.||++
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 999999999999999999999999999999999999996555 79999999999999999999999999999999999
Q ss_pred ceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHHHhhcccCCCCCCCccccCcCCCCCccccccceeechh
Q 004199 163 SLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFD 242 (769)
Q Consensus 163 ~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e 242 (769)
++||||||++.|++|+++ .. .+++++||+|+|+++.++++++++++. .... +.. ...+.++||.|+++
T Consensus 155 alvGlItfg~~v~v~el~-~~-~~sk~~VF~G~ke~s~~q~~~~L~~~~-~~~~------~~~---~~~~~~rFL~P~~~ 222 (745)
T KOG1986|consen 155 ALVGLITFGTMVQVHELG-FE-ECSKSYVFSGNKEYSAKQLLDLLGLSG-GAGK------GSE---NQSASNRFLLPAQE 222 (745)
T ss_pred ceEEEEEecceEEEEEcC-CC-cccceeEEeccccccHHHHHHHhcCCc-cccc------CCc---ccccchhhhccHHH
Confidence 999999999999999999 76 799999999999999999999998754 1111 100 01234799999999
Q ss_pred cHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCC
Q 004199 243 CEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKD 322 (769)
Q Consensus 243 ~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d 322 (769)
|+..+.++|++|++++|++++++|+.||||+||++|+.||++|++++|+||++|++||||.|||+|+++++++++|+|+|
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 CCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccChhhhhhhhhccCceEEEeCCCCchhhHHHHHHHh-hcCc
Q 004199 323 LDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF-HSGD 401 (769)
Q Consensus 323 ~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~v~~~~~f~~~~~~~~l~~~~-~~~~ 401 (769)
+++++++|++++.+||++||++++.+|++||+|+++.||+|++||++|++.|||.+.+.++|+.+.|+++++|+| ++..
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 7888
Q ss_pred cCccceeeeEEEEEecCCceEEeEEcCCcccCCCCCCccccccccCCCCceeEecCCCCceEEEEEEEecCCCCcccccC
Q 004199 402 YDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPDATLQS 481 (769)
Q Consensus 402 ~~~~~~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~vsd~~~g~~~~~~~~l~~~~~~~s~~~~~~~~~~~~~~~~~~~ 481 (769)
+++.+||+|+|+|+||++++|.+.+|++.++++|+++|||+++|.|+|..|+++.+++.+++++.|++...... +
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 89999999999999999999999999999999999999999999999999999999999999999999987532 3
Q ss_pred CCCeEEEEEEEEeEecCCcEEEEEEecccccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHH
Q 004199 482 TNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKMEIEAEFDPIRWLDKALIH 561 (769)
Q Consensus 482 ~~~~~~iQ~al~Yt~~~G~rriRV~T~~~~~t~~~~~~~~i~~~~D~ea~~~llar~a~~~~~~~~~~d~~~~l~~~l~~ 561 (769)
.+..+||||+++|.+++|++|+||+|+++++++. ...++..+|||||++++|||+++.++.+++..|+++|+|+.|++
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 4678999999999999999999999999999985 23789999999999999999999999999999999999999999
Q ss_pred HHHHhcccccCCCCccccCccccchHHHHHHHhcccCcCCCCCChHHHHHHHHHHccCChhhhhhhccceeEeecCCCCC
Q 004199 562 MCSRFGDYQKDSPSSFSLSPRFSIFPQFMFHLRRSQFVQVFNNSPDETAYFRMILNRENVTNSVVMIQPSLISYSFHSGP 641 (769)
Q Consensus 562 ~~~~~~~y~~~~~~~l~lp~~l~~lP~~~~~L~ks~~l~~~~~s~Der~~~~~~l~~~~~~~~~~~i~P~L~~~~~~~~p 641 (769)
+|++|+.|+|++|+++.|+++|++||+||||||||++|+++|.|||||+||+|+|+++++.+++.||+|+|++|++++.|
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 ccccccccccccCeEEEEeCCcEEEEEECCCchHHHHccCCCCchhHHHHHhhhCcHHHHHHHHhcCCCCcEEEEEcCCC
Q 004199 642 EPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYHNQPEHQAFAQLLQAPHDDAGVIMKERFPVPRLVICDQHG 721 (769)
Q Consensus 642 ~~v~Ls~~~l~~d~i~llD~g~~i~i~~G~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~R~~~p~~~~~~~g~ 721 (769)
+|++||..+|.+|.|+|||++|+|+||+|+.++||++++||++|+|++|+++|++|+++|++|..+|||+||+++|+||+
T Consensus 616 epvlLD~~Si~~D~iLLlDt~f~i~i~hG~tIaqWR~~gy~~~pe~~~f~~LL~ap~~dA~el~~~RFP~PR~v~~~q~G 695 (745)
T KOG1986|consen 616 EPVLLDVASILADRILLLDTYFTIVIFHGSTIAQWRKAGYHEQPEYENFKELLEAPREDAQELLLERFPMPRYVVTDQGG 695 (745)
T ss_pred ceeEecccccCCceEEEeecceEEEEECCchHHHHHhcccccChhhHHHHHHHHhHHHHHHHHHHhhCCCCeEEEecCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChHHHHHhhhCCCCcCCCC-CCCCCCceeecCCchHHHHHHHHHHHhhC
Q 004199 722 SQARFLLAKLNPSATYNSD-AQIPGGDIIFTDDVSFEVFLDHLQRLAVQ 769 (769)
Q Consensus 722 s~~r~l~s~L~p~~~~~~~-~~~~~~~~~~tdd~S~~~f~~~l~~~~~~ 769 (769)
||||||++||||+.+|++. .+++ ++.|+|||+||++||+||+|++|+
T Consensus 696 SQARFLlsklnPS~t~~~~~~~~~-s~~I~TDDvSlq~fm~hLkklav~ 743 (745)
T KOG1986|consen 696 SQARFLLSKLNPSETHNNLTAHGG-SSIILTDDVSLQVFMEHLKKLAVS 743 (745)
T ss_pred cHHHhhhhhcCcchhccchhhccC-CCeeeeccccHHHHHHHHHhhcCC
Confidence 9999999999999988773 2333 778999999999999999999985
No 3
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=100.00 E-value=1.5e-161 Score=1274.11 Aligned_cols=748 Identities=47% Similarity=0.867 Sum_probs=703.9
Q ss_pred CCcccccCCCeeeecCCCCCCCHHHhhcCCCceeEEEccCCCCCCCCCCCCCCCCCCccCCC-CCceecCccEEEcCCce
Q 004199 2 TEFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRT-CRSILNPFSIVDFAAKI 80 (769)
Q Consensus 2 ~~~~~~~~~~~vR~t~~~~P~t~~~~~~~~lPlg~~v~P~~~~~~~~~~vp~~~~~p~rC~~-C~aylNp~~~~~~~~~~ 80 (769)
|+|+.+|+.++||+|||+||.|+.++.++.+|++|+|+||++.+ .+++..|+|+.|.. |+||+||||.+|.+++.
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 89999999999999999999999999999999999999999865 67888999999999 99999999999999999
Q ss_pred EEecCCCCCCCCCcCCCCCCCCCCCccccCCCccEEEecCCCCCCCCCCcEEEEEEEcCcchhHHHHHHHHHHHhcccCC
Q 004199 81 WICPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPGPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLP 160 (769)
Q Consensus 81 w~C~~C~~~N~~p~~y~~~~~~~~~pEL~~~~~tvey~~~~~~~~~~~~p~~vFvID~s~~~~~l~~~~~~l~~~l~~lp 160 (769)
|+|+||+++|.+|++|..++..++|+||.||++||||+++++.. .||+|+||||++++.+++.++|++|+..|+.+|
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 99999999999999999999999999999999999999998776 899999999999999999999999999999999
Q ss_pred CCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHHHhhcccCCCCCCC--ccccCcCCCCCcccccccee
Q 004199 161 DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPST--GVIAGVRDGLSSDTIARFLV 238 (769)
Q Consensus 161 ~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~~~--~~~~~~~~~~~~~p~~~~l~ 238 (769)
++++||||||++.|++|+++ .. ..++.+||+|+++|+...|+++++++. -.+|+. ....+.. .+. ..+|+.
T Consensus 154 peaLvglItygt~i~v~el~-ae-~~~r~~VF~g~~eyt~~~L~~ll~~~~-~~~~~~~es~is~~~---~~~-~~rFl~ 226 (755)
T COG5047 154 PEALVGLITYGTSIQVHELN-AE-NHRRSYVFSGNKEYTKENLQELLALSK-PTKSGGFESKISGIG---QFA-SSRFLL 226 (755)
T ss_pred ccceeeEEEecceeEEEecc-cc-ccCcceeecchHHHHHHHHHHHhcccC-CCCcchhhhhccccc---ccc-hhhhhc
Confidence 99999999999999999999 66 789999999999999999999998762 112210 0001100 011 267999
Q ss_pred echhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcC
Q 004199 239 PAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIR 318 (769)
Q Consensus 239 ~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~r 318 (769)
|+.+|+..+.++||+|++++|+++.++||.||||+||++|+.||+.++++.|+||++|++||||.|||+|+++++++++|
T Consensus 227 p~q~ce~~L~n~le~L~pd~~~v~~~~Rp~RCTGsAl~ias~Ll~~~~p~~~~~i~lF~~GPcTvGpG~Vvs~elkEpmR 306 (755)
T COG5047 227 PTQQCEFKLLNILEQLQPDPWPVPAGKRPLRCTGSALNIASSLLEQCFPNAGCHIVLFAGGPCTVGPGTVVSTELKEPMR 306 (755)
T ss_pred cHHHHHHHHHHHHHHhCCCCccCCCCCCCccccchhHHHHHHHHHhhccCcceeEEEEcCCCccccCceeeehhhccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccChhhhhhhhhccCceEEEeCCCCchhhHHHHHHHh-
Q 004199 319 SHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF- 397 (769)
Q Consensus 319 s~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~v~~~~~f~~~~~~~~l~~~~- 397 (769)
+|++++++.+++.+++++||+.||++.+.+|+++|+|+++.||+|+.||++|+..|||.+.+.++|+.++|+++++|+|
T Consensus 307 shH~ie~d~aqh~kka~KFY~~laeR~a~~gh~~DifagcldqIGI~eM~~L~~sTgg~lvlsdsF~t~ifkqSfqrif~ 386 (755)
T COG5047 307 SHHDIESDSAQHSKKATKFYKGLAERVANQGHALDIFAGCLDQIGIMEMEPLTTSTGGALVLSDSFTTSIFKQSFQRIFN 386 (755)
T ss_pred ccccccccchhhccchHHHHHHHHHHHhccchhHHHHHHHHHhhhhhcchhhccCCcceEEEeccccHHHHHHHHHHHhC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCccCccceeeeEEEEEecCCceEEeEEcCCcccCCCCCCccccccccCCCCceeEecCCCCceEEEEEEEecCCCCcc
Q 004199 398 HSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPDA 477 (769)
Q Consensus 398 ~~~~~~~~~~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~vsd~~~g~~~~~~~~l~~~~~~~s~~~~~~~~~~~~~~~ 477 (769)
++..|++.+||||.|+|.|||++++++++|+..+.++++.+|||.+||.|.|+.|++++++|.+++++.||+.......
T Consensus 387 ~d~~g~l~~gfNa~m~V~TsKnl~~~g~ig~a~~~~k~~~ni~~~eigi~~t~swkm~slsPk~nyal~fei~~~~~~~- 465 (755)
T COG5047 387 RDSEGYLKMGFNANMEVKTSKNLKIKGLIGHAVSVKKKANNISDSEIGIGATNSWKMASLSPKSNYALYFEIALGAASG- 465 (755)
T ss_pred cCcccchhhhhccceeEeeccCceeeeeecceeeecccccccccccccccccccccccccCCCcceEEEEEeccccCCC-
Confidence 8888899999999999999999999999999999999999999999999999999999999999999999998765321
Q ss_pred cccCCCCeEEEEEEEEeEecCCcEEEEEEecccccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCCchhHHHHHHH
Q 004199 478 TLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKMEIEAEFDPIRWLDK 557 (769)
Q Consensus 478 ~~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~~~~t~~~~~~~~i~~~~D~ea~~~llar~a~~~~~~~~~~d~~~~l~~ 557 (769)
+. +....+||||+++|++++|.-||||+|++..+++. ....+.++|||||+++++||+++.|+..++..|+.+|+|+
T Consensus 466 ~~-~~~~~a~iQfiT~yQhss~t~riRVtTvar~f~~~--~~p~i~~SFdqEaaaV~~aR~a~~K~~~ed~~Dv~rw~dr 542 (755)
T COG5047 466 SA-QRPAEAYIQFITTYQHSSGTYRIRVTTVARMFTDG--GLPKINRSFDQEAAAVFMARIAAFKAETEDIIDVFRWIDR 542 (755)
T ss_pred cc-CCcccchhhhhhhhhccCCcEEEEEeehhhhhccC--CChhhhhcchhhHHHHHHHHHHHhhcccccchhHHHHHHH
Confidence 11 33468999999999999999999999999999975 5788999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcccccCCCCccccCccccchHHHHHHHhcccCcCCCCCChHHHHHHHHHHccCChhhhhhhccceeEeecC
Q 004199 558 ALIHMCSRFGDYQKDSPSSFSLSPRFSIFPQFMFHLRRSQFVQVFNNSPDETAYFRMILNRENVTNSVVMIQPSLISYSF 637 (769)
Q Consensus 558 ~l~~~~~~~~~y~~~~~~~l~lp~~l~~lP~~~~~L~ks~~l~~~~~s~Der~~~~~~l~~~~~~~~~~~i~P~L~~~~~ 637 (769)
.++++|+.|+.|+|+.|+++.|+++|.++|+|||+|+||++|+++|.|||||+||+|++.+.++++++.||+|+|.+|++
T Consensus 543 ~lirlcq~fa~y~k~dpssfrl~~~f~lypqf~y~lrRSpfL~vfNnSPDEt~fyrh~l~~~dv~~sLimiqPtL~Sys~ 622 (755)
T COG5047 543 NLIRLCQKFADYRKDDPSSFRLDPNFTLYPQFMYHLRRSPFLSVFNNSPDETAFYRHMLNNADVNDSLIMIQPTLQSYSF 622 (755)
T ss_pred HHHHHHHHHHhcCCCCchhhcCCcchhhhhHHHhhhhccceeeccCCCcchHHHHHHHHhcccccchhhhhcchheeeec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccccccccccccCeEEEEeCCcEEEEEECCCchHHHHccCCCCchhHHHHHhhhCcHHHHHHHHhcCCCCcEEEEE
Q 004199 638 HSGPEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYHNQPEHQAFAQLLQAPHDDAGVIMKERFPVPRLVIC 717 (769)
Q Consensus 638 ~~~p~~v~Ls~~~l~~d~i~llD~g~~i~i~~G~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~R~~~p~~~~~ 717 (769)
++.+.||.||+-++++|.|+|||++++|+||+|+.++||++++|+++++|++++++|++|+.+|.+++.+|||.|++++|
T Consensus 623 ~~~~~pVlLDs~svkpdviLLlDtff~Ili~hG~~iaqwr~agyq~qpey~~lK~Ll~~p~~ea~ell~dRfP~Prfi~t 702 (755)
T COG5047 623 EKGGVPVLLDSVSVKPDVILLLDTFFHILIFHGSYIAQWRNAGYQEQPEYLNLKELLEAPRLEAAELLQDRFPIPRFIVT 702 (755)
T ss_pred cCCCceEEEeccccCCCeEEEeeceeEEEEECChHHHHHHhhhhhcCchhhhHHHHhhchhhHHHHHHHhhCCCCeEEEe
Confidence 88889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCChHHHHHhhhCCCCcCCCC-CCCCCCceeecCCchHHHHHHHHHHHhhC
Q 004199 718 DQHGSQARFLLAKLNPSATYNSD-AQIPGGDIIFTDDVSFEVFLDHLQRLAVQ 769 (769)
Q Consensus 718 ~~g~s~~r~l~s~L~p~~~~~~~-~~~~~~~~~~tdd~S~~~f~~~l~~~~~~ 769 (769)
+||+||+|||++|+||+..++.. + +|++.+.|||++|++||.||++++|.
T Consensus 703 eqggSQaRfLlskinPsd~~~~~~~--~~s~tilTddv~lq~fm~hl~~lav~ 753 (755)
T COG5047 703 EQGGSQARFLLSKINPSDITNKMSG--GGSETILTDDVNLQKFMNHLRKLAVS 753 (755)
T ss_pred cCCccHHHHHHhhcCcccccccccc--CccceeeecccCHHHHHHHHHHHhcc
Confidence 99999999999999999877642 2 34567999999999999999999984
No 4
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.9e-122 Score=1015.21 Aligned_cols=665 Identities=20% Similarity=0.322 Sum_probs=584.3
Q ss_pred ccCCCeeeecCCCCCCCHHHhhcCCCceeEEEccCCCCCCCCCCCCCC-CCCCccCCCCCceecCccEEEcCCceEEecC
Q 004199 7 LEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPIL-PYAPLRCRTCRSILNPFSIVDFAAKIWICPF 85 (769)
Q Consensus 7 ~~~~~~vR~t~~~~P~t~~~~~~~~lPlg~~v~P~~~~~~~~~~vp~~-~~~p~rC~~C~aylNp~~~~~~~~~~w~C~~ 85 (769)
|++++|+|+|.++||.+.+++++++||||++|+||++.. +..++|++ +..|+||++||+||||||.|++.|++|+||+
T Consensus 167 nc~p~y~RsTl~~iP~t~sLl~kskLPlglvv~Pf~~~~-d~~~~p~~~~~~IvRCr~CRtYiNPFV~fid~gr~WrCNl 245 (887)
T KOG1985|consen 167 NCSPSYVRSTLSAIPQTQSLLKKSKLPLGLVVHPFAHLD-DIDPLPVITSTLIVRCRRCRTYINPFVEFIDQGRRWRCNL 245 (887)
T ss_pred CCCHHHHHHHHHhCCccHHHHHhcCCCceEEEeeccccc-ccCCCCcccCCceeeehhhhhhcCCeEEecCCCceeeech
Confidence 889999999999999999999999999999999999766 34466766 4589999999999999999999999999999
Q ss_pred CCCCCCCCcCCC-C-C----CCCCCCccccCCCccEEEecCC----CCCCCCCCcEEEEEEEcCcchhH---HHHHHHHH
Q 004199 86 CFQRNHFPPHYA-S-I----TDDNLPAELFPQYTTIEYEPPG----PGEKSSVPPVFMFVVDTCIIEEE---MSFLKSAL 152 (769)
Q Consensus 86 C~~~N~~p~~y~-~-~----~~~~~~pEL~~~~~tvey~~~~----~~~~~~~~p~~vFvID~s~~~~~---l~~~~~~l 152 (769)
|+..|++|.+|. . . .....|||+. +++|||++|. ++| +|++|+||||||.++++ ++.++++|
T Consensus 246 C~~~NdvP~~f~~~~~t~~~~~~~~RpEl~--~s~vE~iAP~eYmlR~P---~Pavy~FliDVS~~a~ksG~L~~~~~sl 320 (887)
T KOG1985|consen 246 CGRVNDVPDDFDWDPLTGAYGDPYSRPELT--SSVVEFIAPSEYMLRPP---QPAVYVFLIDVSISAIKSGYLETVARSL 320 (887)
T ss_pred hhhhcCCcHHhhcCccccccCCcccCcccc--ceeEEEecCcccccCCC---CCceEEEEEEeehHhhhhhHHHHHHHHH
Confidence 999999999983 2 2 2335789997 9999999997 567 89999999999999988 89999999
Q ss_pred HHhcccCC--CCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHHHhhcccCCCCCCCccccCcCCCCCc
Q 004199 153 SQAIDLLP--DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSS 230 (769)
Q Consensus 153 ~~~l~~lp--~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (769)
...|+.|| +.++|||||||++||||++. .++.+|+++++ .|++|.| .+
T Consensus 321 L~~LD~lpgd~Rt~igfi~fDs~ihfy~~~-~~~~qp~mm~v--------sdl~d~f---------------------lp 370 (887)
T KOG1985|consen 321 LENLDALPGDPRTRIGFITFDSTIHFYSVQ-GDLNQPQMMIV--------SDLDDPF---------------------LP 370 (887)
T ss_pred HHhhhcCCCCCcceEEEEEeeceeeEEecC-CCcCCCceeee--------ccccccc---------------------cC
Confidence 99999999 66999999999999999998 55578888875 5677655 13
Q ss_pred cccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCCccccc
Q 004199 231 DTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVS 310 (769)
Q Consensus 231 ~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~ggrI~~F~sg~pt~GpG~l~~ 310 (769)
+| ++||+|+++||+.|..+|++|++ +|..++..++|+|+||++|..+|+ ..||||++|.+++||.|.|+|+.
T Consensus 371 ~p-d~lLv~L~~ck~~i~~lL~~lp~---~F~~~~~t~~alGpALkaaf~li~----~~GGri~vf~s~lPnlG~G~L~~ 442 (887)
T KOG1985|consen 371 MP-DSLLVPLKECKDLIETLLKTLPE---MFQDTRSTGSALGPALKAAFNLIG----STGGRISVFQSTLPNLGAGKLKP 442 (887)
T ss_pred Cc-hhheeeHHHHHHHHHHHHHHHHH---HHhhccCcccccCHHHHHHHHHHh----hcCCeEEEEeccCCCCCcccccc
Confidence 55 89999999999999999999999 688888899999999999999999 69999999999999999999999
Q ss_pred CCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccChhhhhhhhhccCceEEEeCCCCch---
Q 004199 311 KNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHA--- 387 (769)
Q Consensus 311 ~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~v~~~~~f~~~--- 387 (769)
||..+.-+ .++..+++.+++.|||++|.+|++.||+||+|+++.+|.|+|+++.|++.|||.+|+|++|+..
T Consensus 443 rEdp~~~~-----s~~~~qlL~~~t~FYK~~a~~cs~~qI~VDlFl~s~qY~DlAsLs~LskySgG~~y~YP~f~~s~p~ 517 (887)
T KOG1985|consen 443 REDPNVRS-----SDEDSQLLSPATDFYKDLALECSKSQICVDLFLFSEQYTDLASLSCLSKYSGGQVYYYPSFDGSNPH 517 (887)
T ss_pred cccccccc-----chhhhhccCCCchHHHHHHHHhccCceEEEEEeecccccchhhhhccccccCceeEEccCCCCCCHH
Confidence 96544322 2333678999999999999999999999999999999999999999999999999999999987
Q ss_pred ---hhHHHHHHHhhcCccCccceeeeEEEEEecCCceEEeEEcCCcccCCCCCCccccccccCCCCceeEecCCCCceEE
Q 004199 388 ---VFKDSVRRVFHSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLC 464 (769)
Q Consensus 388 ---~~~~~l~~~~~~~~~~~~~~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~vsd~~~g~~~~~~~~l~~~~~~~s~~ 464 (769)
+|..+|.|.+. +++||+|+||||||+|++++.+|||++. ++++++.++++.+|++++
T Consensus 518 ~~~Kf~~el~r~Lt-----r~~~feaVmRiR~S~gl~~~~f~GnFF~---------------RStDLla~~~v~~D~sy~ 577 (887)
T KOG1985|consen 518 DVLKFARELARYLT-----RKIGFEAVMRIRCSTGLRMSSFFGNFFV---------------RSTDLLALPNVNPDQSYA 577 (887)
T ss_pred HHHHHHHHHHHHhh-----hhhhhheeEEeeccccccccceeccccc---------------CcHHHhcccCCCCCccce
Confidence 45556666662 4579999999999999999999999997 468999999999999999
Q ss_pred EEEEEecCCCCcccccCCCCeEEEEEEEEeEecCCcEEEEEEecccccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhh
Q 004199 465 LVFEIVKKEIPDATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVSFKME 544 (769)
Q Consensus 465 ~~~~~~~~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~~~~t~~~~~~~~i~~~~D~ea~~~llar~a~~~~~ 544 (769)
|++++++.+. ....+||.|++||.+.|||||||||+++|++++ +.++|+++|++|++.+++++|+.+++
T Consensus 578 ~qisiEesl~--------~~~~~fQvAlLyT~~~GERRIRV~T~~lpt~~s---l~evY~saD~~AI~~lla~~Av~ksl 646 (887)
T KOG1985|consen 578 FQISIEESLT--------TGFCVFQVALLYTLSKGERRIRVHTLCLPTVSS---LNEVYASADQEAIASLLAKKAVEKSL 646 (887)
T ss_pred EEEEeehhcC--------CceeEEEeeeeecccCCceeEEEEEeecccccc---HHHHHhhcCHHHHHHHHHHHHHHHHH
Confidence 9999999874 467889999999999999999999999999985 99999999999999999999999999
Q ss_pred cCCchhHHHHHHHHHHHHHHHhcccccCCCC------ccccCccccchHHHHHHHhcccCcCC-CCCChHHHHHHHHHHc
Q 004199 545 IEAEFDPIRWLDKALIHMCSRFGDYQKDSPS------SFSLSPRFSIFPQFMFHLRRSQFVQV-FNNSPDETAYFRMILN 617 (769)
Q Consensus 545 ~~~~~d~~~~l~~~l~~~~~~~~~y~~~~~~------~l~lp~~l~~lP~~~~~L~ks~~l~~-~~~s~Der~~~~~~l~ 617 (769)
+..+.|+|+.|.+.++++ ++.|++.... .+.+|.+|++||+|+++|+|++.|+. .++++|+|++++..+.
T Consensus 647 ~ssL~dardal~~~~~D~---l~aYk~~~~~~~~~~~~l~~p~~LrllPllvlALlK~~~fr~g~~~~lD~R~~a~~~~~ 723 (887)
T KOG1985|consen 647 SSSLSDARDALTNAVVDI---LNAYKKLVSNQNGQGITLSLPASLRLLPLLVLALLKHPAFRPGTGTRLDYRAYAMCLMS 723 (887)
T ss_pred HhhhhhHHHHHHHHHHHH---HHHHHHHhcccccCCcceecCcchhhhHHHHHHHhcCCcccCCCCCCchHHHHHHHHhh
Confidence 999999999999999988 6677775433 78999999999999999999999994 5899999999999999
Q ss_pred cCChhhhhhhccceeEeecC--C--------C---CCccccccccccccCeEEEEeCCcEEEEEECCCchH-HHHccCCC
Q 004199 618 RENVTNSVVMIQPSLISYSF--H--------S---GPEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQ-WRKAGYHN 683 (769)
Q Consensus 618 ~~~~~~~~~~i~P~L~~~~~--~--------~---~p~~v~Ls~~~l~~d~i~llD~g~~i~i~~G~~v~~-~~~~~~~~ 683 (769)
.+++..++++|||+||++|. + + .|++++|+++.+++.|+||||+|..+++|+|+++++ ...+.|+.
T Consensus 724 ~lpl~~L~k~IYP~Lysl~~l~~ea~~~~~d~~~~~p~~L~ltae~l~~~GlyL~D~g~~lfl~vg~~a~P~ll~~vfg~ 803 (887)
T KOG1985|consen 724 TLPLKYLMKYIYPTLYSLHDLDDEAGLPIHDQTVVLPPPLNLTAELLSRRGLYLMDTGTTLFLWVGSNADPSLLFDVFGV 803 (887)
T ss_pred cCCHHHHHhhhcccceeccccccccCcccccccccCCCccchHHHHhccCceEEEecCcEEEEEEcCCCCccccccccCc
Confidence 99999999999999999986 1 1 378999999999999999999999999999999995 55665553
Q ss_pred CchhHHHH-----------HhhhCcHHHHHHHHhcCCCCcEEEEEcCC-CChH-HHHHhhhCCCCcCCCCCCCCCCceee
Q 004199 684 QPEHQAFA-----------QLLQAPHDDAGVIMKERFPVPRLVICDQH-GSQA-RFLLAKLNPSATYNSDAQIPGGDIIF 750 (769)
Q Consensus 684 ~~~~~~~~-----------~~l~~~~~~~~~l~~~R~~~p~~~~~~~g-~s~~-r~l~s~L~p~~~~~~~~~~~~~~~~~ 750 (769)
+. ++.+. ...+....+++++|.+|...|.++++|++ .+.+ -+|+++|++|++++.
T Consensus 804 ~~-~adi~~~~~~lp~~~n~~s~r~~~fI~~lR~d~~~~p~~~ivr~~~~s~~k~~f~~~lvEDrs~~~----------- 871 (887)
T KOG1985|consen 804 ST-LADIPIGKYTLPELDNEESDRVRRFIKKLRDDRTYFPNLYIVRGDDNSPLKAWFFSRLVEDRSENS----------- 871 (887)
T ss_pred ch-HhhcccccccCcccccchhHHHHHHHHHhhcCCcccceEEEEecCCCchHHHHHHHHHHhhhhcCc-----------
Confidence 32 22110 01122346788999999999999999964 3344 466889999998753
Q ss_pred cCCchHHHHHHHHHHHhhC
Q 004199 751 TDDVSFEVFLDHLQRLAVQ 769 (769)
Q Consensus 751 tdd~S~~~f~~~l~~~~~~ 769 (769)
.||.||++|||++|-+
T Consensus 872 ---~SY~efLq~lk~qv~~ 887 (887)
T KOG1985|consen 872 ---PSYYEFLQHLKAQVSK 887 (887)
T ss_pred ---HHHHHHHHHHHHHhcC
Confidence 8999999999998853
No 5
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.3e-120 Score=1000.12 Aligned_cols=671 Identities=19% Similarity=0.277 Sum_probs=598.1
Q ss_pred cccCCCeeeecCCCCCCCHHHhhcCCCceeEEEccCCCCCCCCCCCCCCCC---CCccCCCCCceecCccEEEcCCceEE
Q 004199 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPY---APLRCRTCRSILNPFSIVDFAAKIWI 82 (769)
Q Consensus 6 ~~~~~~~vR~t~~~~P~t~~~~~~~~lPlg~~v~P~~~~~~~~~~vp~~~~---~p~rC~~C~aylNp~~~~~~~~~~w~ 82 (769)
-|++|+|||+|+|++|.|.++++.++||||++|+||+...++|+++|+++. +|+||++|+||+|||++|..++++|+
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 399999999999999999999999999999999999999999999999875 79999999999999999999999999
Q ss_pred ecCCCCCCCCCcCC-CCCCCC------CCCccccCCCccEEEecCC------CCCCCCCCcEEEEEEEcCcchhH---HH
Q 004199 83 CPFCFQRNHFPPHY-ASITDD------NLPAELFPQYTTIEYEPPG------PGEKSSVPPVFMFVVDTCIIEEE---MS 146 (769)
Q Consensus 83 C~~C~~~N~~p~~y-~~~~~~------~~~pEL~~~~~tvey~~~~------~~~~~~~~p~~vFvID~s~~~~~---l~ 146 (769)
||||+.+|++|.+| +++++. +.||||+ .|||||++++ +.| .||+|||+||||+++++ +.
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 CNFCGSKNQVPDDYFNHLGPTGRRVDVEERPELC--LGTVDFVATKDYCRKTKPP---KPPAFVFMIDVSYNAISNGAVK 437 (1007)
T ss_pred ecCCCccccCChhhcccCCCcccccccccCchhc--ccccceeeehhhhhcCCCC---CCceEEEEEEeehhhhhcchHH
Confidence 99999999999999 677653 5789999 9999999986 256 89999999999999988 89
Q ss_pred HHHHHHHHhcccCC---CCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHHHhhcccCCCCCCCccccC
Q 004199 147 FLKSALSQAIDLLP---DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAG 223 (769)
Q Consensus 147 ~~~~~l~~~l~~lp---~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 223 (769)
+++++|++.|+.+| ++.+|||||||++|||||++ +.++.|+|+|+ .|++|+|
T Consensus 438 a~ce~ik~~l~~lp~~~p~~~Vgivtfd~tvhFfnl~-s~L~qp~mliV--------sdv~dvf---------------- 492 (1007)
T KOG1984|consen 438 AACEAIKSVLEDLPREEPNIRVGIVTFDKTVHFFNLS-SNLAQPQMLIV--------SDVDDVF---------------- 492 (1007)
T ss_pred HHHHHHHHHHhhcCccCCceEEEEEEecceeEeeccC-ccccCceEEEe--------ecccccc----------------
Confidence 99999999999998 36999999999999999999 88899999997 5777765
Q ss_pred cCCCCCcccc-ccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCC
Q 004199 224 VRDGLSSDTI-ARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPST 302 (769)
Q Consensus 224 ~~~~~~~~p~-~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~ggrI~~F~sg~pt 302 (769)
.|+ +.++++..||+..|+.+|++|+. ++..++.++.|+|+||++|..+|++ ..|||+++|++..||
T Consensus 493 -------vPf~~g~~V~~~es~~~i~~lLd~Ip~---mf~~sk~pes~~g~alqaa~lalk~---~~gGKl~vF~s~Lpt 559 (1007)
T KOG1984|consen 493 -------VPFLDGLFVNPNESRKVIELLLDSIPT---MFQDSKIPESVFGSALQAAKLALKA---ADGGKLFVFHSVLPT 559 (1007)
T ss_pred -------cccccCeeccchHHHHHHHHHHHHhhh---hhccCCCCchhHHHHHHHHHHHHhc---cCCceEEEEeccccc
Confidence 675 88999999999999999999999 6889999999999999999999996 239999999999999
Q ss_pred CCCc-ccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccChhhhhhhhhccCceEEEe
Q 004199 303 EGPA-AIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLS 381 (769)
Q Consensus 303 ~GpG-~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~v~~~ 381 (769)
.|-| ++..++.... ...+||+ .++.++++.|++||++|++.|+|||||++...++|+|+++.+++.|||.+|.|
T Consensus 560 ~g~g~kl~~r~D~~l----~~t~kek-~l~~pq~~~y~~LA~e~v~~g~svDlF~t~~ayvDvAtlg~v~~~TgG~vy~Y 634 (1007)
T KOG1984|consen 560 AGAGGKLSNRDDRRL----IGTDKEK-NLLQPQDKTYTTLAKEFVESGCSVDLFLTPNAYVDVATLGVVPALTGGQVYKY 634 (1007)
T ss_pred ccCcccccccchhhh----hcccchh-hccCcchhHHHHHHHHHHHhCceEEEEEcccceeeeeeecccccccCceeEEe
Confidence 9988 8887765443 3456665 79999999999999999999999999999999999999999999999999999
Q ss_pred CCCCchhhHHHHHHHh-hcCccCccceeeeEEEEEecCCceEEeEEcCCcccCCCCCCccccccccCCCCceeEecCCCC
Q 004199 382 DSFGHAVFKDSVRRVF-HSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKA 460 (769)
Q Consensus 382 ~~f~~~~~~~~l~~~~-~~~~~~~~~~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~vsd~~~g~~~~~~~~l~~~~~~ 460 (769)
.+|....+...|...+ ++. ..+.||+|.||||||+||++.+++||+.. ++++..+++.+|+|
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 9999886555555444 332 35689999999999999999999999874 45788999999999
Q ss_pred ceEEEEEEEecCCCCcccccCCCCeEEEEEEEEeEecCCcEEEEEEecccccccCCCCHHHHHhccCHHHHHHHHHHHHH
Q 004199 461 TSLCLVFEIVKKEIPDATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLVS 540 (769)
Q Consensus 461 ~s~~~~~~~~~~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~~~~t~~~~~~~~i~~~~D~ea~~~llar~a~ 540 (769)
++++++|++|+++. .+..++||+|++||+.+|+||+||+|+++++|+. +.++|+++|.|+++++|+|.|+
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 KTLTVEFKHDDKLQ-------DGSDVHFQTALLYTTIDGQRRLRVLNLSLAVTSQ---LSELYRSADTDPLIAIMAKQAA 767 (1007)
T ss_pred ceeEEEEecccccc-------CCcceeEEEEEEEeccCCceeEEEEecchhhhhh---HHHHHHhcCccHHHHHHHHHHH
Confidence 99999999999984 4778999999999999999999999999999984 9999999999999999999999
Q ss_pred HHhhcCCchhHHHHHHHHHHHHHHHhcccccCCC-----CccccCccccchHHHHHHHhcccCcCCCCCChHHHHHHHHH
Q 004199 541 FKMEIEAEFDPIRWLDKALIHMCSRFGDYQKDSP-----SSFSLSPRFSIFPQFMFHLRRSQFVQVFNNSPDETAYFRMI 615 (769)
Q Consensus 541 ~~~~~~~~~d~~~~l~~~l~~~~~~~~~y~~~~~-----~~l~lp~~l~~lP~~~~~L~ks~~l~~~~~s~Der~~~~~~ 615 (769)
..+..+.+.++|+.|++.++++ |+.|||.|+ +||+|||+||+||+||++|+||.+|+...++.|+|+|++.+
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 9999999999999999999888 788888864 69999999999999999999999999989999999999999
Q ss_pred HccCChhhhhhhccceeEeecC----C----CCCccccccccccccCeEEEEeCCcEEEEEECCCchHHHHccCCCCchh
Q 004199 616 LNRENVTNSVVMIQPSLISYSF----H----SGPEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYHNQPEH 687 (769)
Q Consensus 616 l~~~~~~~~~~~i~P~L~~~~~----~----~~p~~v~Ls~~~l~~d~i~llD~g~~i~i~~G~~v~~~~~~~~~~~~~~ 687 (769)
+.++++++++.++||+|+++|. + ..|.+|++|.+.|..+||||||+|..+|||+|+++++.+.+.++..++.
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 9999999999999999999996 1 3589999999999999999999999999999999997444444444444
Q ss_pred HHHHHh-hhCc----------HHHHHHHHhcCCCCcEEEEEcCCCChH-HHHHhhhCCCCcCCCCCCCCCCceeecCCch
Q 004199 688 QAFAQL-LQAP----------HDDAGVIMKERFPVPRLVICDQHGSQA-RFLLAKLNPSATYNSDAQIPGGDIIFTDDVS 755 (769)
Q Consensus 688 ~~~~~~-l~~~----------~~~~~~l~~~R~~~p~~~~~~~g~s~~-r~l~s~L~p~~~~~~~~~~~~~~~~~tdd~S 755 (769)
+++... ..+| ++.++.+++.|....+++++++|..+. -++.+.|++++.-+ ..|
T Consensus 925 ~~i~s~~~~Lpe~dn~lS~k~r~~i~~i~~~r~~~l~v~~~k~g~~~~~~~~~~~lved~~~~--------------~~s 990 (1007)
T KOG1984|consen 925 EQIDSQSGVLPELDNPLSRKVRNVISLIRRQRSSELPVVLVKQGLDGSEVEFSEYLVEDRGRN--------------ISS 990 (1007)
T ss_pred cccccccccccccCcHHHHHHHHHHHHHHhccccccccEEEecCCCchhhhhhhhhhcccccC--------------ccc
Confidence 433221 2222 345677778898999999999997776 67788899987421 389
Q ss_pred HHHHHHHHHHHhh
Q 004199 756 FEVFLDHLQRLAV 768 (769)
Q Consensus 756 ~~~f~~~l~~~~~ 768 (769)
|.+|++.||+.+-
T Consensus 991 Y~dyL~~~H~ki~ 1003 (1007)
T KOG1984|consen 991 YVDYLCELHKKIQ 1003 (1007)
T ss_pred cchHHHHHHHHHH
Confidence 9999999998763
No 6
>PTZ00395 Sec24-related protein; Provisional
Probab=100.00 E-value=4.3e-111 Score=966.07 Aligned_cols=669 Identities=15% Similarity=0.196 Sum_probs=552.0
Q ss_pred cccCCCeeeecCCCCCCCHHHhhcCCCceeEEEccCCCCCCCCCCCCCCC-----------CCCccCCCCCceecCccEE
Q 004199 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILP-----------YAPLRCRTCRSILNPFSIV 74 (769)
Q Consensus 6 ~~~~~~~vR~t~~~~P~t~~~~~~~~lPlg~~v~P~~~~~~~~~~vp~~~-----------~~p~rC~~C~aylNp~~~~ 74 (769)
.+++|++||+|++.||.+.++++.+.||||++++||+...++| +||.++ .+|+||.+|++|+|+++.+
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 4899999999999999999999999999999999999987655 466643 3789999999999999999
Q ss_pred EcCCceEEecCCCCCCCCCcC-------CC-CCC-----CC----CCCccccCCCccEEEecCCC---------------
Q 004199 75 DFAAKIWICPFCFQRNHFPPH-------YA-SIT-----DD----NLPAELFPQYTTIEYEPPGP--------------- 122 (769)
Q Consensus 75 ~~~~~~w~C~~C~~~N~~p~~-------y~-~~~-----~~----~~~pEL~~~~~tvey~~~~~--------------- 122 (769)
+-. +++.|+||++.+.+... |. .+. .+ ...|-| .|+||+.+|..
T Consensus 727 ~~~-~~~~c~~c~~~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~ 802 (1560)
T PTZ00395 727 DIS-SSVQCVFCDTDFLINENVLFDIFQYNEKIGHKESDHNEHGNSLSPLL---KGSVDIIIPPIYYHNVNKFKLTYTYL 802 (1560)
T ss_pred ccc-ceEEEEecCCcchhhHHHHHHHHHHhhhhccccccccccccccchhh---cCceeEEccchhhccCCccceeeehh
Confidence 964 99999999999876321 10 111 00 011222 34444443310
Q ss_pred --------------------------------------------------------------------------------
Q 004199 123 -------------------------------------------------------------------------------- 122 (769)
Q Consensus 123 -------------------------------------------------------------------------------- 122 (769)
T Consensus 803 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 882 (1560)
T PTZ00395 803 NKNINQTAFMITNKIMSFTKHISNSLVANDSKGGNKATSASAFGDSGDANFLAGGGYTNYGGAGGYNTYDNQSGYNNHDV 882 (1560)
T ss_pred hcchhhhhhhhhhhhhhhhhhhcchheecccccccccchhhhcccccccccccccccccccccccccccccccccccccc
Confidence
Q ss_pred --------------------------------------------------------------CC-CCCCCcEEEEEEEcC
Q 004199 123 --------------------------------------------------------------GE-KSSVPPVFMFVVDTC 139 (769)
Q Consensus 123 --------------------------------------------------------------~~-~~~~~p~~vFvID~s 139 (769)
+. ...+||+|+||||||
T Consensus 883 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~PP~YvFLIDVS 962 (1560)
T PTZ00395 883 VNNRGGSGAGNHLYGKDHDVQNFDNVMDNANFTIHDMKNLICEKNGEPDSAKIRRNSFLAKYPQVKNMLPPYFVFVVECS 962 (1560)
T ss_pred cccccccCcCcccccCcccccchhhhccCCceeeecchhhhhcccCCchhhhhhccchhhccccccCCCCCEEEEEEECC
Confidence 00 013789999999999
Q ss_pred cchhH---HHHHHHHHHHhcccCC-CCceEEEEEECCeEEEEEccCCC-------------CCCCeeEEecCCccCCHHH
Q 004199 140 IIEEE---MSFLKSALSQAIDLLP-DNSLVGLITFGTLVQVHELGGFG-------------QIIPKTYVFKGSKDVSKDQ 202 (769)
Q Consensus 140 ~~~~~---l~~~~~~l~~~l~~lp-~~~~VglITfd~~V~~~~l~~~~-------------~~~~~~~v~~g~~~~~~~~ 202 (769)
..+++ +++++++|+++|+.|+ +.++|||||||+.||||+|+ ++ ++.|+|+|+ .|
T Consensus 963 ~~AVkSGLl~tacesIK~sLDsL~dpRTRVGIITFDSsLHFYNLk-s~l~~~~~~~~~~~~l~qPQMLVV--------SD 1033 (1560)
T PTZ00395 963 YNAIYNNITYTILEGIRYAVQNVKCPQTKIAIITFNSSIYFYHCK-GGKGVSGEEGDGGGGSGNHQVIVM--------SD 1033 (1560)
T ss_pred HHHHhhChHHHHHHHHHHHHhcCCCCCcEEEEEEecCcEEEEecC-cccccccccccccccCCCceEEee--------cC
Confidence 99998 8999999999999997 56999999999999999997 43 467899986 57
Q ss_pred HHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHh
Q 004199 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (769)
Q Consensus 203 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll 282 (769)
|+|+| .+.|.+++|+++.|+++.|..+|+.|+. ++.....+..|+|+||++|..+|
T Consensus 1034 LDDPF---------------------LPlP~ddLLVnL~ESRevIe~LLDkLPe---mFt~t~~~esCLGSALqAA~~aL 1089 (1560)
T PTZ00395 1034 VDDPF---------------------LPLPLEDLFFGCVEEIDKINTLIDTIKS---VSTTMQSYGSCGNSALKIAMDML 1089 (1560)
T ss_pred CccCc---------------------CCCCccCeeechHHHHHHHHHHHHHHHH---HhhccCCCcccHHHHHHHHHHHH
Confidence 87766 1233478999999999999999999987 56677778999999999999999
Q ss_pred hccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCcc
Q 004199 283 GACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (769)
Q Consensus 283 ~~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~ 362 (769)
+. .+.||||++|++++|++|||+|+.++. ..++ ..++.++.+||++||.+|++.+|+||+|+++..++
T Consensus 1090 k~--~GGGGKIiVF~SSLPniGpGaLK~Re~---------~~KE-k~Ll~pqd~FYK~LA~ECsk~qISVDLFLfSsqYv 1157 (1560)
T PTZ00395 1090 KE--RNGLGSICMFYTTTPNCGIGAIKELKK---------DLQE-NFLEVKQKIFYDSLLLDLYAFNISVDIFIISSNNV 1157 (1560)
T ss_pred Hh--cCCCceEEEEEcCCCCCCCCccccccc---------cccc-ccccccchHHHHHHHHHHHhcCCceEEEEccCccc
Confidence 94 123599999999999999999986541 1233 25678899999999999999999999999998887
Q ss_pred C--hhhhhhhhhccCceEEEeCCCCchhhHHHHHHHh-hcCccCccceeeeEEEEEecCCceEEeEEcC--CcccCCCCC
Q 004199 363 G--VAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF-HSGDYDLGLSSNGIFEINCSKDIKVQGIIGP--CASLEKKGP 437 (769)
Q Consensus 363 ~--l~~m~~l~~~TGG~v~~~~~f~~~~~~~~l~~~~-~~~~~~~~~~~~~~l~vr~S~gl~v~~~~G~--~~~~~~~~~ 437 (769)
| +++|+.|++.|||.+++|+.|+..++...|...| +.++ ...+||+|+||||||+||+|+++||+ ++..
T Consensus 1158 DVDVATLg~Lsr~TGGqlyyYPnFna~rD~~KL~~DL~r~LT-re~iGyEAVMRVRCS~GLrVs~fyG~GnnF~s----- 1231 (1560)
T PTZ00395 1158 RVCVPSLQYVAQNTGGKILFVENFLWQKDYKEIYMNIMDTLT-SEDIAYCCELKLRYSHHMSVKKLFCCNNNFNS----- 1231 (1560)
T ss_pred ccccccccchhcccceeEEEeCCCcccccHHHHHHHHHHHhh-ccceeeEEEEEEECCCCeEEEEEeccCCcccc-----
Confidence 6 7999999999999999999999876554444333 2211 01369999999999999999999954 3310
Q ss_pred CccccccccCCCCceeEecCCCCceEEEEEEEecCCCCcccccCCCCeEEEEEEEEeEecCCcEEEEEEecccccccCCC
Q 004199 438 LCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPDATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPG 517 (769)
Q Consensus 438 ~vsd~~~g~~~~~~~~l~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~~~~t~~~~ 517 (769)
..+++++.++.+++|++|+|+|++++.+. ....+|||+|++||+.+|+|||||||+++|||++
T Consensus 1232 --------~rStDLLaLP~Id~DqSfaVeLk~DEkL~-------~~~~AYFQaALLYTSssGERRIRVHTLALPVTSs-- 1294 (1560)
T PTZ00395 1232 --------IISVDTIKIPKIRHDQTFAFLLNYSDISE-------SKKQIYFQCACIYTNLWGDRFVRLHTTHMNLTSS-- 1294 (1560)
T ss_pred --------ccccccccccccCCCceEEEEEEeccccC-------CCCcEEEEEEEeeccCCCcEEEEEEeeeecccCC--
Confidence 12467899999999999999999999874 3678999999999999999999999999999985
Q ss_pred CHHHHHhccCHHHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHHHHhcccccCC-----CCccccCccccchHHHHHH
Q 004199 518 SVQDLIAGFDQEAAAVVMARLVSFKMEIEAEFDPIRWLDKALIHMCSRFGDYQKDS-----PSSFSLSPRFSIFPQFMFH 592 (769)
Q Consensus 518 ~~~~i~~~~D~ea~~~llar~a~~~~~~~~~~d~~~~l~~~l~~~~~~~~~y~~~~-----~~~l~lp~~l~~lP~~~~~ 592 (769)
+.+||+++|++|++.+|+|+++.++++++ ++|+.|.+.++++ |..||+.| ++||+||++||+||+|+++
T Consensus 1295 -LseVFrsADqdAIvslLAK~AV~~aLsss--dARe~L~dklVdI---LtaYRK~CAsssssgQLILPESLKLLPLYILS 1368 (1560)
T PTZ00395 1295 -LSTVFRYTDAEALMNILIKQLCTNILHND--NYSKIIIDNLAAI---LFSYRINCASSAHSGQLILPDTLKLLPLFTSS 1368 (1560)
T ss_pred -HHHHHHhhcHHHHHHHHHHHHHHHhcccH--HHHHHHHHHHHHH---HHHHHHHhhccCCCccccchhHHHHHHHHHHH
Confidence 99999999999999999999999999874 8999999998888 67788765 4689999999999999999
Q ss_pred HhcccCcCCCCCChHHHHHHHHHHccCChhhhhhhccceeEeecC---C---------C---CCccccccccccccCeEE
Q 004199 593 LRRSQFVQVFNNSPDETAYFRMILNRENVTNSVVMIQPSLISYSF---H---------S---GPEPALLDVAAIAADRIL 657 (769)
Q Consensus 593 L~ks~~l~~~~~s~Der~~~~~~l~~~~~~~~~~~i~P~L~~~~~---~---------~---~p~~v~Ls~~~l~~d~i~ 657 (769)
|+||.+|+ ..+++|+|++.+++++++++..++.++||+||++|. + + +|.+++||.+.|.++|+|
T Consensus 1369 LLKS~AfR-t~I~sDeRVyaL~rL~SmPI~~Li~yLYPRLYpLHdL~~e~e~d~~d~d~~ivLPp~LrLS~ErLesdGIY 1447 (1560)
T PTZ00395 1369 LLKHNVTK-KEILHDLKVYSLIKLLSMPIISSLLYVYPVMYVIHIKGKTNEIDSMDVDDDLFIPKTIPSSAEKIYSNGIY 1447 (1560)
T ss_pred Hhcccccc-CCCCccHHHHHHHHHhCCCHHHHHhhhcCceEEcccccccccCCccCCCCccccCCcccchHHHhcCCcEE
Confidence 99999998 478999999999999999999999999999999985 0 1 488999999999999999
Q ss_pred EEeCCcEEEEEECCCch-HHHHccCCCCchhHHHHHh--hh-----CcHHHHHHHHhcC--CCCcEEEEEcCCCChHHHH
Q 004199 658 LLDSYFTVVIFHGATIA-QWRKAGYHNQPEHQAFAQL--LQ-----APHDDAGVIMKER--FPVPRLVICDQHGSQARFL 727 (769)
Q Consensus 658 llD~g~~i~i~~G~~v~-~~~~~~~~~~~~~~~~~~~--l~-----~~~~~~~~l~~~R--~~~p~~~~~~~g~s~~r~l 727 (769)
|||+|..+|||+|++++ +|+.+.|+..+.......+ ++ ..+..++.|++.| .+++++++++++++.+.+|
T Consensus 1448 LLDNGe~IyLWVG~~V~PqLLqDLFGv~~~~~~~~eLPelDT~iS~RVrnII~~LR~~r~~~~Y~pL~IVRqgDp~E~~F 1527 (1560)
T PTZ00395 1448 LLDACTHFYLYFGFHSDANFAKEIVGDIPTEKNAHELNLTDTPNAQKVQRIIKNLSRIHHFNKYVPLVMVAPKSNEEEHL 1527 (1560)
T ss_pred EEECCCEEEEEECCCCCHHHHHHHcCCCccccccccccCCCCHHHHHHHHHHHHHHHhccCCCcceEEEEeCCCchHHHH
Confidence 99999999999999999 6899999864321110011 11 1235567777776 4788889999999899999
Q ss_pred HhhhCCCCcCCCCCCCCCCceeecCCchHHHHHHHHHHHhh
Q 004199 728 LAKLNPSATYNSDAQIPGGDIIFTDDVSFEVFLDHLQRLAV 768 (769)
Q Consensus 728 ~s~L~p~~~~~~~~~~~~~~~~~tdd~S~~~f~~~l~~~~~ 768 (769)
++.|+||+... .+||.+||++|||.|-
T Consensus 1528 ~s~LVEDRs~g--------------~~SYvDFLc~LHKqIq 1554 (1560)
T PTZ00395 1528 ISLCVEDKADK--------------EYSYVNFLCFIHKLVH 1554 (1560)
T ss_pred HHhCeecCCCC--------------CCCHHHHHHHHHHHHH
Confidence 99999998531 3899999999999874
No 7
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=100.00 E-value=1.5e-108 Score=900.04 Aligned_cols=657 Identities=19% Similarity=0.324 Sum_probs=570.6
Q ss_pred cccCCCeeeecCCCCCCCHHHhhcCCCceeEEEccCCCCCCCCCCCCCCC-CCCccCCCCCceecCccEEEcCCceEEec
Q 004199 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILP-YAPLRCRTCRSILNPFSIVDFAAKIWICP 84 (769)
Q Consensus 6 ~~~~~~~vR~t~~~~P~t~~~~~~~~lPlg~~v~P~~~~~~~~~~vp~~~-~~p~rC~~C~aylNp~~~~~~~~~~w~C~ 84 (769)
.|++|+|||+|++++|.+.++.++++||||++++||.+..+++.++|+.. ..|+||++||+|+|||++|.++|.+|+||
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 38999999999999999999999999999999999999887777788764 46899999999999999999999999999
Q ss_pred CCCCCCCCCcCCC-CCC------CCCCCccccCCCccEEEecCC----CCCCCCCCcEEEEEEEcCcchhH---HHHHHH
Q 004199 85 FCFQRNHFPPHYA-SIT------DDNLPAELFPQYTTIEYEPPG----PGEKSSVPPVFMFVVDTCIIEEE---MSFLKS 150 (769)
Q Consensus 85 ~C~~~N~~p~~y~-~~~------~~~~~pEL~~~~~tvey~~~~----~~~~~~~~p~~vFvID~s~~~~~---l~~~~~ 150 (769)
+|+..|++|..+. +.. ..+.|+||. +++|||.+|. +.| .||+|||+||+|.++.+ +.++.+
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 ICRSKNDVPEGFDNPSGPNDPRSDRYSRPELK--SGVVDFLAPKEYSLRQP---PPPVYVFLIDVSFEAIKNGLVKAAIR 300 (861)
T ss_pred eccccccCcccccCcCCCCCccccccccchhh--ceeeEEecccceeeccC---CCCEEEEEEEeehHhhhcchHHHHHH
Confidence 9999999998874 221 235789998 9999999997 346 79999999999999987 889999
Q ss_pred HHHHhcccCC---CCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHHHhhcccCCCCCCCccccCcCCC
Q 004199 151 ALSQAIDLLP---DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDG 227 (769)
Q Consensus 151 ~l~~~l~~lp---~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 227 (769)
+|+..|+.+| ++++||||.||++||+++++ .+++- ++++ +.++++.|
T Consensus 301 ~Il~~l~~~~~~dpr~kIaii~fD~sl~ffk~s-~d~~~-~~~~--------vsdld~pF-------------------- 350 (861)
T COG5028 301 AILENLDQIPNFDPRTKIAIICFDSSLHFFKLS-PDLDE-QMLI--------VSDLDEPF-------------------- 350 (861)
T ss_pred HHHhhccCCCCCCCcceEEEEEEcceeeEEecC-CCCcc-ceee--------eccccccc--------------------
Confidence 9999999886 57999999999999999998 65211 3333 24555544
Q ss_pred CCcccc--ccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCC
Q 004199 228 LSSDTI--ARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGP 305 (769)
Q Consensus 228 ~~~~p~--~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~ggrI~~F~sg~pt~Gp 305 (769)
.|. +.|+.|+.+|+..+..||+.++. .+..++.++.|+|.||++|..+++ .+||||++|.+..||.|.
T Consensus 351 ---lPf~s~~fv~pl~~~k~~~etLl~~~~~---If~d~~~pk~~~G~aLk~a~~l~g----~~GGkii~~~stlPn~G~ 420 (861)
T COG5028 351 ---LPFPSGLFVLPLKSCKQIIETLLDRVPR---IFQDNKSPKNALGPALKAAKSLIG----GTGGKIIVFLSTLPNMGI 420 (861)
T ss_pred ---ccCCcchhcccHHHHHHHHHHHHHHhhh---hhcccCCCccccCHHHHHHHHHhh----ccCceEEEEeecCCCccc
Confidence 343 58999999999888899999988 577889999999999999999999 699999999999999999
Q ss_pred cccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccChhhhhhhhhccCceEEEeCCCC
Q 004199 306 AAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFG 385 (769)
Q Consensus 306 G~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~v~~~~~f~ 385 (769)
|+|.-|+. ++. .+++....||+++|.+|.+.||+||+|+++.+++|+++++.|++.|||.+++|++|+
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-----------KES-SLLSCKDSFYKEFAIECSKVGISVDLFLTSEDYIDVATLSHLCRYTGGQTYFYPNFS 488 (861)
T ss_pred cccccccc-----------chh-hhccccchHHHHHHHHHHHhcceEEEEeccccccchhhhcchhhccCcceEEcCCcc
Confidence 99998864 222 478899999999999999999999999999999999999999999999999999999
Q ss_pred chh------hHHHHHHHhhcCccCccceeeeEEEEEecCCceEEeEEcCCcccCCCCCCccccccccCCCCceeEecCCC
Q 004199 386 HAV------FKDSVRRVFHSGDYDLGLSSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDK 459 (769)
Q Consensus 386 ~~~------~~~~l~~~~~~~~~~~~~~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~vsd~~~g~~~~~~~~l~~~~~ 459 (769)
..+ |.++|.+.+ .+..||++.||||||+|++++++|||++. ++.+...++.++.
T Consensus 489 ~~~~~d~~kl~~dL~~~l-----s~~~gy~~~~rvR~S~glr~s~fyGnf~~---------------rs~dl~~F~tm~r 548 (861)
T COG5028 489 ATRPNDATKLANDLVSHL-----SMEIGYEAVMRVRCSTGLRVSSFYGNFFN---------------RSSDLCAFSTMPR 548 (861)
T ss_pred cCCchhHHHHHHHHHHhh-----hhhhhhheeeEeeccCceehhhhhccccc---------------cCcccccccccCC
Confidence 987 555555555 24579999999999999999999999986 3467899999999
Q ss_pred CceEEEEEEEecCCCCcccccCCCCeEEEEEEEEeEecCCcEEEEEEecccccccCCCCHHHHHhccCHHHHHHHHHHHH
Q 004199 460 ATSLCLVFEIVKKEIPDATLQSTNNQFYFQFLTYYQHNCGQMRLRVTTLSRRWVAGPGSVQDLIAGFDQEAAAVVMARLV 539 (769)
Q Consensus 460 ~~s~~~~~~~~~~~~~~~~~~~~~~~~~iQ~al~Yt~~~G~rriRV~T~~~~~t~~~~~~~~i~~~~D~ea~~~llar~a 539 (769)
|+|+.|+|++++++. ...+|||.|++||..+|+|||||.|++++++++ +.++|+++||+|++.+|+|+|
T Consensus 549 d~Sl~~~~sid~~l~--------~~~v~fQvAlL~T~~~GeRRiRVvn~s~~~ss~---~~evyasadq~aIa~~lak~a 617 (861)
T COG5028 549 DTSLLVEFSIDEKLM--------TSDVYFQVALLYTLNDGERRIRVVNLSLPTSSS---IREVYASADQLAIACILAKKA 617 (861)
T ss_pred CceEEEEEEeccccc--------CCceEEEEEEEeeccCCceEEEEEEeccccchh---HHHHHHhccHHHHHHHHHHHH
Confidence 999999999999974 489999999999999999999999999999985 999999999999999999999
Q ss_pred HHHhhcCCchhHHHHHHHHHHHHHHHhcccccC-----CCCccccCccccchHHHHHHHhcccCcCCCCCChHHHHHHHH
Q 004199 540 SFKMEIEAEFDPIRWLDKALIHMCSRFGDYQKD-----SPSSFSLSPRFSIFPQFMFHLRRSQFVQVFNNSPDETAYFRM 614 (769)
Q Consensus 540 ~~~~~~~~~~d~~~~l~~~l~~~~~~~~~y~~~-----~~~~l~lp~~l~~lP~~~~~L~ks~~l~~~~~s~Der~~~~~ 614 (769)
+.++......++|+.|++.++++ +..|||. .++++.||++|++||++|++|.||.+|+...++.|.|+++..
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 99999999999999999999999 6667763 467899999999999999999999999988888999999999
Q ss_pred HHccCChhhhhhhccceeEeecC----CC--------CCccccccccccccCeEEEEeCCcEEEEEECCCchHHHHccCC
Q 004199 615 ILNRENVTNSVVMIQPSLISYSF----HS--------GPEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYH 682 (769)
Q Consensus 615 ~l~~~~~~~~~~~i~P~L~~~~~----~~--------~p~~v~Ls~~~l~~d~i~llD~g~~i~i~~G~~v~~~~~~~~~ 682 (769)
.+-++++.+.+..|||+||++|. .+ .|+++.++.+.+.+.|+||+|+|..+|+|+|+++.+-+.+.++
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 99999999999999999999994 11 4789999999999999999999999999999999965444444
Q ss_pred CCchhHHH---HH--------hhhCcHHHHHHHHh-cCCCCcEEEEEcCCCChH--HHHHhhhCCCCcCCCCCCCCCCce
Q 004199 683 NQPEHQAF---AQ--------LLQAPHDDAGVIMK-ERFPVPRLVICDQHGSQA--RFLLAKLNPSATYNSDAQIPGGDI 748 (769)
Q Consensus 683 ~~~~~~~~---~~--------~l~~~~~~~~~l~~-~R~~~p~~~~~~~g~s~~--r~l~s~L~p~~~~~~~~~~~~~~~ 748 (769)
+.++...+ +. +-+...+.+.+++. .+..++.++++|+|+.+. -++++.|+||++++.
T Consensus 775 ~~~~~~~I~~~k~~~p~~~n~~n~~v~~iI~~lrs~~~~~tl~lvlVR~~~d~s~~~~~~s~lVEDk~~n~--------- 845 (861)
T COG5028 775 GVDSLSDIPSGKFTLPPTGNEFNERVRNIIGELRSVNDDSTLPLVLVRGGGDPSLRLWFFSTLVEDKTLNI--------- 845 (861)
T ss_pred CcchhhhccccccccCCcCCHHHHHHHHHHHHHHhhCCCCccceEEEecCCCcchhhheehheecccccCC---------
Confidence 44332222 11 11112345567776 677788899999986665 577899999998642
Q ss_pred eecCCchHHHHHHHHHHHh
Q 004199 749 IFTDDVSFEVFLDHLQRLA 767 (769)
Q Consensus 749 ~~tdd~S~~~f~~~l~~~~ 767 (769)
.||.+|++-||+-+
T Consensus 846 -----~SY~~yL~~lh~ki 859 (861)
T COG5028 846 -----PSYLDYLQILHEKI 859 (861)
T ss_pred -----ccHHHHHHHHHHHh
Confidence 89999999999865
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=2.5e-55 Score=456.95 Aligned_cols=266 Identities=56% Similarity=0.939 Sum_probs=237.4
Q ss_pred CCcEEEEEEEcCcchhHHHHHHHHHHHhcccCCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHHHh
Q 004199 128 VPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQL 207 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~~l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~ 207 (769)
.||+|+||||+|.+++++++++++|+++|+.||++++|||||||++||||+|+ .. ++++++||+|+++|+.+++++++
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 78999999999999999999999999999999999999999999999999998 66 79999999999999999999998
Q ss_pred hcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccCC
Q 004199 208 NFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVP 287 (769)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~ 287 (769)
+++.................+.+.+.++||+|++||++.|+++|++|+++.|++++++++.||+|+||++|..+|+++++
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~p~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~r~~r~~G~Al~~A~~ll~~~~~ 159 (267)
T cd01478 80 GLGGPAMRPSASQHPGAGNPLPSAAASRFLLPVSQCEFTLTDLLEQLQPDPWPVPAGHRPLRCTGVALSIAVGLLEACFP 159 (267)
T ss_pred ccccccccccccCcCCccccccccccccEEEEHHHHHHHHHHHHHhCcccccccCCCCCCCCchHHHHHHHHHHHHhhcC
Confidence 77431000000000000000111223799999999999999999999999999999999999999999999999998888
Q ss_pred CCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccChhhh
Q 004199 288 GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAEL 367 (769)
Q Consensus 288 ~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~m 367 (769)
+.||||++|++||||.|||+|+.++.++++|+|.|++++++++++++.+||++||.+|+++||+||+|+++.+|+|++||
T Consensus 160 ~~gGki~~F~sg~pT~GpG~l~~r~~~~~~r~~~d~~~~~~~~~~~a~~fY~~la~~~~~~~vsvDlF~~s~d~vglaem 239 (267)
T cd01478 160 NTGARIMLFAGGPCTVGPGAVVSTELKDPIRSHHDIDKDNAKYYKKAVKFYDSLAKRLAANGHAVDIFAGCLDQVGLLEM 239 (267)
T ss_pred CCCcEEEEEECCCCCCCCceeeccccccccccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEEeccccccCHHHH
Confidence 89999999999999999999999999999999999999988999999999999999999999999999999999999999
Q ss_pred hhhhhccCceEEEeCCCCchhhHHHHHH
Q 004199 368 KVAVEKTGGLVVLSDSFGHAVFKDSVRR 395 (769)
Q Consensus 368 ~~l~~~TGG~v~~~~~f~~~~~~~~l~~ 395 (769)
+.|++.|||.+++|++|+.+.|+++++|
T Consensus 240 ~~l~~~TGG~v~~~~~f~~~~f~~s~~~ 267 (267)
T cd01478 240 KVLVNSTGGHVVLSDSFTTSIFKQSFQR 267 (267)
T ss_pred HHHHHhcCcEEEEeCCcchHHHHHHhcC
Confidence 9999999999999999999999998864
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=2.8e-44 Score=371.90 Aligned_cols=228 Identities=40% Similarity=0.628 Sum_probs=197.7
Q ss_pred CCcEEEEEEEcCcch---hHHHHHHHHHHHhcccCC--CCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHH
Q 004199 128 VPPVFMFVVDTCIIE---EEMSFLKSALSQAIDLLP--DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQ 202 (769)
Q Consensus 128 ~~p~~vFvID~s~~~---~~l~~~~~~l~~~l~~lp--~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~ 202 (769)
+||+|+||||+|.++ .++++++++|+++|+.|| ++++|||||||++||||+++ .....++++|++ |
T Consensus 2 ~pp~~vFvID~s~~ai~~~~l~~~~~sl~~~l~~lp~~~~~~igiITf~~~V~~~~~~-~~~~~~~~~v~~--------d 72 (239)
T cd01468 2 QPPVFVFVIDVSYEAIKEGLLQALKESLLASLDLLPGDPRARVGLITYDSTVHFYNLS-SDLAQPKMYVVS--------D 72 (239)
T ss_pred CCCEEEEEEEcchHhccccHHHHHHHHHHHHHHhCCCCCCcEEEEEEeCCeEEEEECC-CCCCCCeEEEeC--------C
Confidence 799999999999995 449999999999999999 99999999999999999998 653457888874 4
Q ss_pred HHHHhhcccCCCCCCCccccCcCCCCCcccc-ccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHH
Q 004199 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTI-ARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (769)
Q Consensus 203 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~-~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~l 281 (769)
++|.+ .|. +++++|++|+++.|.++|++|++..+.. +++++.||+|+||++|..+
T Consensus 73 l~d~f-----------------------~p~~~~~l~~~~e~~~~i~~~l~~l~~~~~~~-~~~~~~~~~G~Al~~A~~l 128 (239)
T cd01468 73 LKDVF-----------------------LPLPDRFLVPLSECKKVIHDLLEQLPPMFWPV-PTHRPERCLGPALQAAFLL 128 (239)
T ss_pred CccCc-----------------------CCCcCceeeeHHHHHHHHHHHHHhhhhhcccc-CCCCCcccHHHHHHHHHHH
Confidence 44433 232 6799999999999999999999964322 3788999999999999999
Q ss_pred hhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCc
Q 004199 282 LGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (769)
Q Consensus 282 l~~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~ 361 (769)
|+.. ..||||++|++|+||.|||+|+.++.++.+|+| + ++++++++.+||++||.+|++++|+||+|+++.++
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 9941 139999999999999999999999988888876 2 35899999999999999999999999999999999
Q ss_pred cChhhhhhhhhccCceEEEeCCCCchhhHHHHHH
Q 004199 362 VGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRR 395 (769)
Q Consensus 362 ~~l~~m~~l~~~TGG~v~~~~~f~~~~~~~~l~~ 395 (769)
+|+++|++|++.|||.+++|++|+..+..+.|.+
T Consensus 202 ~dl~~l~~l~~~TGG~v~~y~~f~~~~~~~~~~~ 235 (239)
T cd01468 202 VDVATLKQLAKSTGGQVYLYDSFQAPNDGSKFKQ 235 (239)
T ss_pred cCHHHhhhhhhcCCceEEEeCCCCCcccHHHHHH
Confidence 9999999999999999999999955544444433
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=2.9e-44 Score=371.24 Aligned_cols=223 Identities=23% Similarity=0.333 Sum_probs=195.6
Q ss_pred CCcEEEEEEEcCcchhH---HHHHHHHHHHhcccCCCC---ceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHH
Q 004199 128 VPPVFMFVVDTCIIEEE---MSFLKSALSQAIDLLPDN---SLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~~---l~~~~~~l~~~l~~lp~~---~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~ 201 (769)
+||+|+||||+|..+++ +++++++|+++|+.+|++ ++|||||||+.||||+++ .+...++++|+ .
T Consensus 2 ~pp~~~FvIDvs~~a~~~g~~~~~~~si~~~L~~lp~~~~~~~VgiITfd~~v~~y~l~-~~~~~~q~~vv--------~ 72 (244)
T cd01479 2 QPAVYVFLIDVSYNAIKSGLLATACEALLSNLDNLPGDDPRTRVGFITFDSTLHFFNLK-SSLEQPQMMVV--------S 72 (244)
T ss_pred CCCEEEEEEEccHHHHhhChHHHHHHHHHHHHHhcCCCCCCeEEEEEEECCeEEEEECC-CCCCCCeEEEe--------e
Confidence 79999999999999986 999999999999999977 999999999999999998 66567888875 4
Q ss_pred HHHHHhhcccCCCCCCCccccCcCCCCCcccc-ccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHH
Q 004199 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTI-ARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAAS 280 (769)
Q Consensus 202 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~-~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ 280 (769)
|++|.+ .|+ ++||+|++||++.|.++|++|+. .+.+++++.||+|+||++|..
T Consensus 73 dl~d~f-----------------------~P~~~~~lv~l~e~~~~i~~lL~~L~~---~~~~~~~~~~c~G~Al~~A~~ 126 (244)
T cd01479 73 DLDDPF-----------------------LPLPDGLLVNLKESRQVIEDLLDQIPE---MFQDTKETESALGPALQAAFL 126 (244)
T ss_pred Cccccc-----------------------CCCCcceeecHHHHHHHHHHHHHHHHH---HHhcCCCCcccHHHHHHHHHH
Confidence 555543 344 78999999999999999999975 567788999999999999999
Q ss_pred HhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCC
Q 004199 281 LLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (769)
Q Consensus 281 ll~~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~ 360 (769)
+|+ +.||||++|++|+||.|||+|+.++.++ ++.|. ++ .++++++.+||+++|.+|+++||+||+|+++.+
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 7999999999999999999999987554 44432 33 378999999999999999999999999999999
Q ss_pred ccChhhhhhhhhccCceEEEeC--CCCchhhHHHHH
Q 004199 361 QVGVAELKVAVEKTGGLVVLSD--SFGHAVFKDSVR 394 (769)
Q Consensus 361 ~~~l~~m~~l~~~TGG~v~~~~--~f~~~~~~~~l~ 394 (769)
++|+++|+.|++.|||.+++|+ .|+..++.+.|.
T Consensus 198 ~~dla~l~~l~~~TGG~v~~y~~~~~~~~~d~~kl~ 233 (244)
T cd01479 198 YVDVATLGCLSRLTGGQVYYYPSFNFSAPNDVEKLV 233 (244)
T ss_pred ccChhhhhhhhhhcCceEEEECCccCCchhhHHHHH
Confidence 9999999999999999999999 666554443333
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=3.5e-43 Score=365.23 Aligned_cols=232 Identities=32% Similarity=0.506 Sum_probs=182.6
Q ss_pred CCcEEEEEEEcCcchhH---HHHHHHHHHHhcccCC--CCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHH
Q 004199 128 VPPVFMFVVDTCIIEEE---MSFLKSALSQAIDLLP--DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQ 202 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~~---l~~~~~~l~~~l~~lp--~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~ 202 (769)
+||+|+||||+|.++++ ++.++++|+++|+.+| ++++|||||||++||||+++ .+...++++|. .|
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-SSLSQPQMIVV--------SD 72 (243)
T ss_dssp S--EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTSSTSTT-EEEEEEESSSEEEEETT-TTSSSTEEEEE--------HH
T ss_pred CCCEEEEEEECchhhhhccHHHHHHHHHHHHHHhccCCCCcEEEEEEeCCEEEEEECC-CCcCCCcccch--------HH
Confidence 79999999999999665 9999999999999999 89999999999999999998 65466777775 78
Q ss_pred HHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHh
Q 004199 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (769)
Q Consensus 203 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll 282 (769)
++|++ . +.| ++|++++.|+++.|.++|++|++ .++...++++.||+|+||++|..+|
T Consensus 73 l~~~~-------~--------------p~~-~~llv~~~e~~~~i~~ll~~L~~-~~~~~~~~~~~~c~G~Al~~A~~ll 129 (243)
T PF04811_consen 73 LDDPF-------I--------------PLP-DGLLVPLSECRDAIEELLESLPS-IFPETAGKRPERCLGSALSAALSLL 129 (243)
T ss_dssp TTSHH-------S--------------STS-SSSSEETTTCHHHHHHHHHHHHH-HSTT-TTB-----HHHHHHHHHHHH
T ss_pred Hhhcc-------c--------------CCc-ccEEEEhHHhHHHHHHHHHHhhh-hcccccccCccccHHHHHHHHHHHH
Confidence 88876 0 134 88999999999999999999988 3333334889999999999999999
Q ss_pred hccCCCCCcEEEEEecCCCCCCC-cccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCc
Q 004199 283 GACVPGSGARILAFVGGPSTEGP-AAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (769)
Q Consensus 283 ~~~~~~~ggrI~~F~sg~pt~Gp-G~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~ 361 (769)
+. .+.||||++|++|+||.|| |++..++.. .+.++++++..+++++.+||++||.+|+++||+||+|+++.++
T Consensus 130 ~~--~~~gGkI~~F~s~~pt~G~Gg~l~~~~~~----~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~ 203 (243)
T PF04811_consen 130 SS--RNTGGKILVFTSGPPTYGPGGSLKKREDS----SHYDTEKEKALLLPPANEFYKKLAEECSKQGISVDLFVFSSDY 203 (243)
T ss_dssp HH--HTS-EEEEEEESS---SSSTTSS-SBTTS----CCCCHCTTHHCHSHSSSHHHHHHHHHHHHCTEEEEEEEECSS-
T ss_pred hc--cccCCEEEEEeccCCCCCCCceecccccc----cccccccchhhhccccchHHHHHHHHHHhcCCEEEEEeecCCC
Confidence 94 2489999999999999999 566665432 5667777777888999999999999999999999999999999
Q ss_pred cChhhhhhhhhccCceEEEeCCCCchhhHHHHHHHh
Q 004199 362 VGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF 397 (769)
Q Consensus 362 ~~l~~m~~l~~~TGG~v~~~~~f~~~~~~~~l~~~~ 397 (769)
+|+++|+.|++.|||.+++|++|+.+++.+.|++.|
T Consensus 204 ~~l~tl~~l~~~TGG~l~~y~~f~~~~~~~~l~~dl 239 (243)
T PF04811_consen 204 VDLATLGPLARYTGGSLYYYPNFNAERDGEKLRQDL 239 (243)
T ss_dssp -SHHHHTHHHHCTT-EEEEETTTTCHHHHHHHHHHH
T ss_pred CCcHhHHHHHHhCceeEEEeCCCCCchhHHHHHHHH
Confidence 999999999999999999999999555444444333
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=7.8e-22 Score=174.05 Aligned_cols=96 Identities=40% Similarity=0.683 Sum_probs=86.9
Q ss_pred eeeeEEEEEecCCceEEeEEcCCcccCCCCCCccccccccCCCCceeEecCCCCceEEEEEEEecCCCCcccccCCCCeE
Q 004199 407 SSNGIFEINCSKDIKVQGIIGPCASLEKKGPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKEIPDATLQSTNNQF 486 (769)
Q Consensus 407 ~~~~~l~vr~S~gl~v~~~~G~~~~~~~~~~~vsd~~~g~~~~~~~~l~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~ 486 (769)
||+|+||||||+|++|++++||+... .++||.++|.++++.|++++++++++++|+|++++++ ...+.+
T Consensus 1 g~~~~l~vr~S~gl~v~~~~G~~~~~----~~~s~~~~g~~~~~~~~~~~l~~~~s~~~~~~~~~~~-------~~~~~~ 69 (96)
T PF08033_consen 1 GFNAVLRVRCSKGLKVSGVIGPCFNR----SSVSDNEIGEGDTTRWKLPSLDPDTSFAFEFEIDEDL-------PNGSQA 69 (96)
T ss_dssp EEEEEEEEEE-TTEEEEEEESSSEES----STBESSECSBSSCSEEEEEEEETT--EEEEEEESSBT-------BTTSEE
T ss_pred CceEEEEEEECCCeEEEEEEcCcccc----ccccceeeccCCccEEEecccCCCCEEEEEEEECCCC-------CCCCeE
Confidence 79999999999999999999999974 4689999999999999999999999999999998876 346899
Q ss_pred EEEEEEEeEecCCcEEEEEEecccccc
Q 004199 487 YFQFLTYYQHNCGQMRLRVTTLSRRWV 513 (769)
Q Consensus 487 ~iQ~al~Yt~~~G~rriRV~T~~~~~t 513 (769)
|||++++||+.+|+|||||+|+++|+|
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=99.73 E-value=7.5e-18 Score=150.64 Aligned_cols=101 Identities=24% Similarity=0.291 Sum_probs=89.4
Q ss_pred HHHHHHHHHHHHHHHhhcCCchhHHHHHHHHHHHHHHHhcccccCCC--CccccCccccchHHHHHHHhcccCcCCCCCC
Q 004199 528 QEAAAVVMARLVSFKMEIEAEFDPIRWLDKALIHMCSRFGDYQKDSP--SSFSLSPRFSIFPQFMFHLRRSQFVQVFNNS 605 (769)
Q Consensus 528 ~ea~~~llar~a~~~~~~~~~~d~~~~l~~~l~~~~~~~~~y~~~~~--~~l~lp~~l~~lP~~~~~L~ks~~l~~~~~s 605 (769)
|||++++++|+++.++.+++..++|+++++++++++..|+.+....+ ++++|||+||+||+|+++|+||++|++.+++
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 79999999999999999999999999999999999666655555433 5799999999999999999999999999999
Q ss_pred hHHHHHHHHHHccCChhhhhhhc
Q 004199 606 PDETAYFRMILNRENVTNSVVMI 628 (769)
Q Consensus 606 ~Der~~~~~~l~~~~~~~~~~~i 628 (769)
+|||+|+++++++++++.++.||
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 99999999999999999998875
No 14
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=99.61 E-value=1.7e-16 Score=114.74 Aligned_cols=40 Identities=55% Similarity=1.250 Sum_probs=29.2
Q ss_pred CCccCCCCCceecCccEEEcCCceEEecCCCCCCCCCcCC
Q 004199 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHY 96 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p~~y 96 (769)
+|+||++|+||||||++++.++++|+|+||++.|++|++|
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=98.53 E-value=3.4e-06 Score=82.42 Aligned_cols=158 Identities=16% Similarity=0.205 Sum_probs=109.4
Q ss_pred EEEEEEcCcchhH--HHHHHHHHHHhcccCCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHHHhhc
Q 004199 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNF 209 (769)
Q Consensus 132 ~vFvID~s~~~~~--l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~ 209 (769)
++||+|+|.+... ++.+++++...+..++++.+||+++|++..+..--. .
T Consensus 3 ~~~vlD~S~SM~~~~~~~~k~a~~~~~~~l~~~~~v~li~f~~~~~~~~~~--~-------------------------- 54 (170)
T cd01465 3 LVFVIDRSGSMDGPKLPLVKSALKLLVDQLRPDDRLAIVTYDGAAETVLPA--T-------------------------- 54 (170)
T ss_pred EEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEecCCccEEecC--c--------------------------
Confidence 6899999998644 788899999999999888999999999765432100 0
Q ss_pred ccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccCC-C
Q 004199 210 FIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVP-G 288 (769)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~-~ 288 (769)
+ .. ....+...|+++.. ...+.++.||..|...+..... .
T Consensus 55 ----------------------~-------~~-~~~~l~~~l~~~~~---------~g~T~~~~al~~a~~~~~~~~~~~ 95 (170)
T cd01465 55 ----------------------P-------VR-DKAAILAAIDRLTA---------GGSTAGGAGIQLGYQEAQKHFVPG 95 (170)
T ss_pred ----------------------c-------cc-hHHHHHHHHHcCCC---------CCCCCHHHHHHHHHHHHHhhcCCC
Confidence 0 00 01233444545433 2245688999999888864211 1
Q ss_pred CCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccChhhhh
Q 004199 289 SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELK 368 (769)
Q Consensus 289 ~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~m~ 368 (769)
.-.+|++|+.|.++.|+.. .+-+.+....+...++.|+.+.++ +..+...|+
T Consensus 96 ~~~~ivl~TDG~~~~~~~~---------------------------~~~~~~~~~~~~~~~v~i~~i~~g-~~~~~~~l~ 147 (170)
T cd01465 96 GVNRILLATDGDFNVGETD---------------------------PDELARLVAQKRESGITLSTLGFG-DNYNEDLME 147 (170)
T ss_pred CeeEEEEEeCCCCCCCCCC---------------------------HHHHHHHHHHhhcCCeEEEEEEeC-CCcCHHHHH
Confidence 1267999999988776411 011234455566789999999987 678899999
Q ss_pred hhhhccCceEEEeCCC
Q 004199 369 VAVEKTGGLVVLSDSF 384 (769)
Q Consensus 369 ~l~~~TGG~v~~~~~f 384 (769)
.++..++|..++.++.
T Consensus 148 ~ia~~~~g~~~~~~~~ 163 (170)
T cd01465 148 AIADAGNGNTAYIDNL 163 (170)
T ss_pred HHHhcCCceEEEeCCH
Confidence 9999999998887654
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=98.48 E-value=6.1e-06 Score=82.52 Aligned_cols=167 Identities=16% Similarity=0.131 Sum_probs=106.8
Q ss_pred CCcEEEEEEEcCcchh--HHHHHHHHHHHhcccCCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHH
Q 004199 128 VPPVFMFVVDTCIIEE--EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~--~l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (769)
.|--.+||||+|.++. .++.+++++...++.++++.+||||+|++.++..---...
T Consensus 12 ~p~~vv~llD~SgSM~~~~l~~ak~~~~~ll~~l~~~d~v~lv~F~~~~~~~~~~~~~---------------------- 69 (190)
T cd01463 12 SPKDIVILLDVSGSMTGQRLHLAKQTVSSILDTLSDNDFFNIITFSNEVNPVVPCFND---------------------- 69 (190)
T ss_pred CCceEEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCCCEEEEEEeCCCeeEEeeeccc----------------------
Confidence 5678899999999864 3889999999999999999999999999987653210000
Q ss_pred HhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhcc
Q 004199 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (769)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~ 285 (769)
.++....+....+...|+.|+.. ..+.++.||..|...+...
T Consensus 70 -----------------------------~~~~~~~~~~~~~~~~l~~l~~~---------G~T~~~~al~~a~~~l~~~ 111 (190)
T cd01463 70 -----------------------------TLVQATTSNKKVLKEALDMLEAK---------GIANYTKALEFAFSLLLKN 111 (190)
T ss_pred -----------------------------ceEecCHHHHHHHHHHHhhCCCC---------CcchHHHHHHHHHHHHHHh
Confidence 00000111233445555555541 2467899999999888741
Q ss_pred ----C----CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHH-HHHhcCcEEEEEE
Q 004199 286 ----V----PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSK-QLVHQGHVLDLFA 356 (769)
Q Consensus 286 ----~----~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~-~~~~~~isvDlf~ 356 (769)
. +.....|++++.|.++.+.-. ...+.. .....++.|..|.
T Consensus 112 ~~~~~~~~~~~~~~~iillTDG~~~~~~~~------------------------------~~~~~~~~~~~~~v~i~tig 161 (190)
T cd01463 112 LQSNHSGSRSQCNQAIMLITDGVPENYKEI------------------------------FDKYNWDKNSEIPVRVFTYL 161 (190)
T ss_pred hhcccccccCCceeEEEEEeCCCCCcHhHH------------------------------HHHhcccccCCCcEEEEEEe
Confidence 0 112347899999976532100 011100 0011245555555
Q ss_pred ecCCccChhhhhhhhhccCceEEEeCCC
Q 004199 357 CALDQVGVAELKVAVEKTGGLVVLSDSF 384 (769)
Q Consensus 357 ~~~~~~~l~~m~~l~~~TGG~v~~~~~f 384 (769)
++.+..+...|..||..+||..++.++.
T Consensus 162 iG~~~~d~~~L~~lA~~~~G~~~~i~~~ 189 (190)
T cd01463 162 IGREVTDRREIQWMACENKGYYSHIQSL 189 (190)
T ss_pred cCCccccchHHHHHHhhcCCeEEEcccC
Confidence 5555568899999999999999987653
No 17
>cd01451 vWA_Magnesium_chelatase Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto). In chlorophyll biosynthesis, insertion of Mg2+ into protoporphyrin IX is catalysed by magnesium chelatase in an ATP-dependent reaction. Magnesium chelatase is a three sub-unit (BchI, BchD and BchH) enzyme with a novel arrangement of domains: the C-terminal helical domain is located behind the nucleotide binding site. The BchD domain contains a AAA domain at its N-terminus and a VWA domain at its C-terminus. The VWA domain has been speculated to be involved in mediating protein-protein interactions.
Probab=98.45 E-value=1.2e-05 Score=79.48 Aligned_cols=163 Identities=18% Similarity=0.119 Sum_probs=109.1
Q ss_pred EEEEEEcCcchh---HHHHHHHHHHHhccc-CCCCceEEEEEECCe-EEEEEccCCCCCCCeeEEecCCccCCHHHHHHH
Q 004199 132 FMFVVDTCIIEE---EMSFLKSALSQAIDL-LPDNSLVGLITFGTL-VQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQ 206 (769)
Q Consensus 132 ~vFvID~s~~~~---~l~~~~~~l~~~l~~-lp~~~~VglITfd~~-V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~ 206 (769)
++||||+|.++. .++.+++++...+.. ++++.+||+|+|++. .++. +. .+
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 679999999865 478888888887754 567889999999864 2221 11 00
Q ss_pred hhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccC
Q 004199 207 LNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACV 286 (769)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~ 286 (769)
.....+...|+.++. ...+.++.||..|...++...
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 001123344555543 235689999999999882111
Q ss_pred CCC--CcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccCh
Q 004199 287 PGS--GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGV 364 (769)
Q Consensus 287 ~~~--ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l 364 (769)
+.. ...|++++.|.++.|.... ..+ -.+++.++...||.+..+....+..+-
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 112 2589999999888763100 000 145677788889988777666566677
Q ss_pred hhhhhhhhccCceEEEeCCCCchhh
Q 004199 365 AELKVAVEKTGGLVVLSDSFGHAVF 389 (769)
Q Consensus 365 ~~m~~l~~~TGG~v~~~~~f~~~~~ 389 (769)
..|..|++.|||..++.++.+...|
T Consensus 148 ~~l~~iA~~tgG~~~~~~d~~~~~~ 172 (178)
T cd01451 148 GLAKDLARALGGQYVRLPDLSADAI 172 (178)
T ss_pred cHHHHHHHHcCCeEEEcCcCCHHHH
Confidence 8899999999999999988876544
No 18
>cd01466 vWA_C3HC4_type VWA C3HC4-type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most,
Probab=98.42 E-value=7.1e-06 Score=79.21 Aligned_cols=149 Identities=20% Similarity=0.206 Sum_probs=103.0
Q ss_pred EEEEEEcCcchhH--HHHHHHHHHHhcccCCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHHHhhc
Q 004199 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNF 209 (769)
Q Consensus 132 ~vFvID~s~~~~~--l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~ 209 (769)
.+||||+|.+... ++.+++++...++.|+++.+||||+|++..+.. . . +
T Consensus 3 v~~vlD~S~SM~~~rl~~ak~a~~~l~~~l~~~~~~~li~F~~~~~~~--~-~------------------------~-- 53 (155)
T cd01466 3 LVAVLDVSGSMAGDKLQLVKHALRFVISSLGDADRLSIVTFSTSAKRL--S-P------------------------L-- 53 (155)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcceEEEEEecCCcccc--C-C------------------------C--
Confidence 4799999998754 888999999999999998999999999865432 1 0 0
Q ss_pred ccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccC-CC
Q 004199 210 FIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACV-PG 288 (769)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~-~~ 288 (769)
.+.. ...+..+.++++.+.+ ...++++.||..|..++.... .+
T Consensus 54 ---------------------~~~~------~~~~~~~~~~i~~~~~---------~g~T~~~~al~~a~~~~~~~~~~~ 97 (155)
T cd01466 54 ---------------------RRMT------AKGKRSAKRVVDGLQA---------GGGTNVVGGLKKALKVLGDRRQKN 97 (155)
T ss_pred ---------------------cccC------HHHHHHHHHHHHhccC---------CCCccHHHHHHHHHHHHhhcccCC
Confidence 0000 0113345566666544 235789999999999987311 12
Q ss_pred CCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccChhhhh
Q 004199 289 SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELK 368 (769)
Q Consensus 289 ~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~m~ 368 (769)
....|+++++|.++.|+.. . ++.+.++.|..+..+. ..+..+|+
T Consensus 98 ~~~~iillTDG~~~~~~~~---------~--------------------------~~~~~~v~v~~igig~-~~~~~~l~ 141 (155)
T cd01466 98 PVASIMLLSDGQDNHGAVV---------L--------------------------RADNAPIPIHTFGLGA-SHDPALLA 141 (155)
T ss_pred CceEEEEEcCCCCCcchhh---------h--------------------------cccCCCceEEEEecCC-CCCHHHHH
Confidence 3468999999987765100 0 0112577777777653 56888999
Q ss_pred hhhhccCceEEEe
Q 004199 369 VAVEKTGGLVVLS 381 (769)
Q Consensus 369 ~l~~~TGG~v~~~ 381 (769)
.||..|||..++.
T Consensus 142 ~iA~~t~G~~~~~ 154 (155)
T cd01466 142 FIAEITGGTFSYV 154 (155)
T ss_pred HHHhccCceEEEe
Confidence 9999999998874
No 19
>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=98.41 E-value=5.7e-06 Score=83.87 Aligned_cols=168 Identities=23% Similarity=0.278 Sum_probs=109.1
Q ss_pred CCcEEEEEEEcCcchh--------HHHHHHHHHHHhcccCCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCC
Q 004199 128 VPPVFMFVVDTCIIEE--------EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVS 199 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~--------~l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~ 199 (769)
.+..++||||+|.++. .++.+++++...++.++++.+|||++|++.++- . .. . + .++
T Consensus 19 ~~~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~l~~~~~v~lv~F~~~~~~---~-~~--~-~-~~~------- 83 (206)
T cd01456 19 LPPNVAIVLDNSGSMREVDGGGETRLDNAKAALDETANALPDGTRLGLWTFSGDGDN---P-LD--V-R-VLV------- 83 (206)
T ss_pred CCCcEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHhCCCCceEEEEEecCCCCC---C-cc--c-c-ccc-------
Confidence 6788999999999875 389999999999999999999999999985521 0 00 0 0 000
Q ss_pred HHHHHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcC-CCCCCCCCCCCCccchhHHHHHH
Q 004199 200 KDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQ-KDPWPVPPDQRSTRCTGTALSIA 278 (769)
Q Consensus 200 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~-~~~~~~~~~~~~~~~~G~Al~~A 278 (769)
+ ...+. .++..+. ...+..+...|+.+. . ...+.++.||..|
T Consensus 84 -p-~~~~~-----------------------~~~~~~~---~~~~~~l~~~i~~i~~~---------~G~T~l~~aL~~a 126 (206)
T cd01456 84 -P-KGCLT-----------------------APVNGFP---SAQRSALDAALNSLQTP---------TGWTPLAAALAEA 126 (206)
T ss_pred -c-ccccc-----------------------cccCCCC---cccHHHHHHHHHhhcCC---------CCcChHHHHHHHH
Confidence 0 00000 0000010 012456777777776 2 2356899999999
Q ss_pred HHHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHH-HHhcCcEEEEEEe
Q 004199 279 ASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQ-LVHQGHVLDLFAC 357 (769)
Q Consensus 279 ~~ll~~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~-~~~~~isvDlf~~ 357 (769)
..++. +.....|+++++|.++.|+.. .+..++++.. ....+|.|+.+.+
T Consensus 127 ~~~l~---~~~~~~iillTDG~~~~~~~~---------------------------~~~~~~~~~~~~~~~~i~i~~igi 176 (206)
T cd01456 127 AAYVD---PGRVNVVVLITDGEDTCGPDP---------------------------CEVARELAKRRTPAPPIKVNVIDF 176 (206)
T ss_pred HHHhC---CCCcceEEEEcCCCccCCCCH---------------------------HHHHHHHHHhcCCCCCceEEEEEe
Confidence 99985 133378999999977655300 0011122211 0225899999988
Q ss_pred cCCccChhhhhhhhhccCceE
Q 004199 358 ALDQVGVAELKVAVEKTGGLV 378 (769)
Q Consensus 358 ~~~~~~l~~m~~l~~~TGG~v 378 (769)
+.+ .+...|..+++.|||..
T Consensus 177 G~~-~~~~~l~~iA~~tgG~~ 196 (206)
T cd01456 177 GGD-ADRAELEAIAEATGGTY 196 (206)
T ss_pred cCc-ccHHHHHHHHHhcCCeE
Confidence 754 67889999999999988
No 20
>PRK13685 hypothetical protein; Provisional
Probab=98.41 E-value=1.4e-05 Score=86.95 Aligned_cols=162 Identities=20% Similarity=0.180 Sum_probs=113.5
Q ss_pred CCcEEEEEEEcCcchh-------HHHHHHHHHHHhcccCCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCH
Q 004199 128 VPPVFMFVVDTCIIEE-------EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSK 200 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~-------~l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~ 200 (769)
.+...+||||+|.++. .++.++++++..++.++++.+||+|+|++..++. .
T Consensus 87 ~~~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l~~~d~vglv~Fa~~a~~~--~-------------------- 144 (326)
T PRK13685 87 NRAVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELTPGINLGLIAFAGTATVL--V-------------------- 144 (326)
T ss_pred CCceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhCCCCCeEEEEEEcCceeec--C--------------------
Confidence 3446899999999864 3899999999999999888999999999765431 0
Q ss_pred HHHHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHH
Q 004199 201 DQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAAS 280 (769)
Q Consensus 201 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ 280 (769)
| ....+..+...|+.+... ..++.|.|+..|..
T Consensus 145 -------------------------------p-------~t~d~~~l~~~l~~l~~~---------~~T~~g~al~~A~~ 177 (326)
T PRK13685 145 -------------------------------S-------PTTNREATKNAIDKLQLA---------DRTATGEAIFTALQ 177 (326)
T ss_pred -------------------------------C-------CCCCHHHHHHHHHhCCCC---------CCcchHHHHHHHHH
Confidence 1 011234566777777652 24567899999988
Q ss_pred Hhhcc-------CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEE
Q 004199 281 LLGAC-------VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLD 353 (769)
Q Consensus 281 ll~~~-------~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvD 353 (769)
.+... .....++|+++++|-.+.|..... . ... .+.+..+.+.||.|.
T Consensus 178 ~l~~~~~~~~~~~~~~~~~IILlTDG~~~~~~~~~~-------------~--------~~~----~~aa~~a~~~gi~i~ 232 (326)
T PRK13685 178 AIATVGAVIGGGDTPPPARIVLMSDGKETVPTNPDN-------------P--------RGA----YTAARTAKDQGVPIS 232 (326)
T ss_pred HHHhhhcccccccCCCCCEEEEEcCCCCCCCCCCCC-------------c--------ccH----HHHHHHHHHcCCeEE
Confidence 87621 012347899999997776531100 0 000 134666778899999
Q ss_pred EEEecCCc-------------cChhhhhhhhhccCceEEEeCC
Q 004199 354 LFACALDQ-------------VGVAELKVAVEKTGGLVVLSDS 383 (769)
Q Consensus 354 lf~~~~~~-------------~~l~~m~~l~~~TGG~v~~~~~ 383 (769)
.+..+.+. .|-..|+.+++.|||..+..++
T Consensus 233 ~Ig~G~~~g~~~~~g~~~~~~~d~~~L~~iA~~tgG~~~~~~~ 275 (326)
T PRK13685 233 TISFGTPYGSVEINGQRQPVPVDDESLKKIAQLSGGEFYTAAS 275 (326)
T ss_pred EEEECCCCCCcCcCCceeeecCCHHHHHHHHHhcCCEEEEcCC
Confidence 99887642 5778999999999998888754
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=98.34 E-value=1.2e-05 Score=79.95 Aligned_cols=152 Identities=13% Similarity=0.089 Sum_probs=99.5
Q ss_pred EEEEEEEcCcchh-------HHHHHHHHHHHhcccC---CCCceEEEEEE-CCeEEEEEccCCCCCCCeeEEecCCccCC
Q 004199 131 VFMFVVDTCIIEE-------EMSFLKSALSQAIDLL---PDNSLVGLITF-GTLVQVHELGGFGQIIPKTYVFKGSKDVS 199 (769)
Q Consensus 131 ~~vFvID~s~~~~-------~l~~~~~~l~~~l~~l---p~~~~VglITf-d~~V~~~~l~~~~~~~~~~~v~~g~~~~~ 199 (769)
-.+++||+|.++. .++.+++.+...++.+ .++.+||||+| ++.-++-
T Consensus 5 ~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~a~~~---------------------- 62 (183)
T cd01453 5 HLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKL---------------------- 62 (183)
T ss_pred EEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCccEEE----------------------
Confidence 4689999999865 3899999998888754 34579999999 4433321
Q ss_pred HHHHHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHH
Q 004199 200 KDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAA 279 (769)
Q Consensus 200 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~ 279 (769)
.|+ ......+...|+.+.. . ...+.++.||..|.
T Consensus 63 -------------------------------~Pl-------T~D~~~~~~~L~~~~~-----~---~G~t~l~~aL~~A~ 96 (183)
T cd01453 63 -------------------------------TDL-------TGNPRKHIQALKTARE-----C---SGEPSLQNGLEMAL 96 (183)
T ss_pred -------------------------------ECC-------CCCHHHHHHHhhcccC-----C---CCchhHHHHHHHHH
Confidence 111 1111122333333311 1 22478999999999
Q ss_pred HHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecC
Q 004199 280 SLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACAL 359 (769)
Q Consensus 280 ~ll~~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~ 359 (769)
..++..-....++|++++++.-+.+|+ -+.++++.+.+.+|.|++...+.
T Consensus 97 ~~l~~~~~~~~~~iiil~sd~~~~~~~------------------------------~~~~~~~~l~~~~I~v~~IgiG~ 146 (183)
T cd01453 97 ESLKHMPSHGSREVLIIFSSLSTCDPG------------------------------NIYETIDKLKKENIRVSVIGLSA 146 (183)
T ss_pred HHHhcCCccCceEEEEEEcCCCcCChh------------------------------hHHHHHHHHHHcCcEEEEEEech
Confidence 999742112346788887762211110 02457888889999999999864
Q ss_pred CccChhhhhhhhhccCceEEEeCC
Q 004199 360 DQVGVAELKVAVEKTGGLVVLSDS 383 (769)
Q Consensus 360 ~~~~l~~m~~l~~~TGG~v~~~~~ 383 (769)
+...|+.+|+.|||..|...+
T Consensus 147 ---~~~~L~~ia~~tgG~~~~~~~ 167 (183)
T cd01453 147 ---EMHICKEICKATNGTYKVILD 167 (183)
T ss_pred ---HHHHHHHHHHHhCCeeEeeCC
Confidence 467899999999999998654
No 22
>PF00626 Gelsolin: Gelsolin repeat; InterPro: IPR007123 Gelsolin is a cytoplasmic, calcium-regulated, actin-modulating protein that binds to the barbed ends of actin filaments, preventing monomer exchange (end-blocking or capping) []. It can promote nucleation (the assembly of monomers into filaments), as well as sever existing filaments. In addition, this protein binds with high affinity to fibronectin. Plasma gelsolin and cytoplasmic gelsolin are derived from a single gene by alternate initiation sites and differential splicing. Sequence comparisons indicate an evolutionary relationship between gelsolin, villin, fragmin and severin []. Six large repeating segments occur in gelsolin and villin, and 3 similar segments in severin and fragmin. While the multiple repeats have yet to be related to any known function of the actin-severing proteins, the superfamily appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues [].; PDB: 3FG6_F 1RGI_G 2FGH_A 1D0N_B 3EGD_B 2NUP_B 2NUT_B 3EGX_B 1JHW_A 1J72_A ....
Probab=98.34 E-value=8.3e-07 Score=74.52 Aligned_cols=72 Identities=21% Similarity=0.416 Sum_probs=58.2
Q ss_pred CCccccccccccccCeEEEEeCCcEEEEEECCCchHHHHccCCCCchhHHHHHhhhCcHHHHHHHH-hcCCCCcEEEEEc
Q 004199 640 GPEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYHNQPEHQAFAQLLQAPHDDAGVIM-KERFPVPRLVICD 718 (769)
Q Consensus 640 ~p~~v~Ls~~~l~~d~i~llD~g~~i~i~~G~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~-~~R~~~p~~~~~~ 718 (769)
.|++++++.++|.++++||||+|..||+|+|++++. . + . ......|+++. .+|.+.|+++.+.
T Consensus 4 ~~~~~~~s~~~L~s~~~yIld~~~~i~vW~G~~~~~-~----------e---~--~~a~~~a~~~~~~~~~~~~~~~~~~ 67 (76)
T PF00626_consen 4 RPEQVPLSQSSLNSDDCYILDCGYEIFVWVGKKSSP-E----------E---K--AFAAQLAQELLSEERPPLPEVIRVE 67 (76)
T ss_dssp EEEEESSSGGGEETTSEEEEEESSEEEEEEHTTSHH-H----------H---H--HHHHHHHHHHHHHHTTTTSEEEEEE
T ss_pred cCCcCCCCHHHcCCCCEEEEEeCCCcEEEEeccCCH-H----------H---H--HHHHHHHHHhhhhcCCCCCEEEEec
Confidence 367889999999999999999999999999998431 1 0 0 11234667777 8899999999999
Q ss_pred CCCChHHHH
Q 004199 719 QHGSQARFL 727 (769)
Q Consensus 719 ~g~s~~r~l 727 (769)
+|...++|+
T Consensus 68 eg~E~~~F~ 76 (76)
T PF00626_consen 68 EGKEPAEFL 76 (76)
T ss_dssp TTHHHHHHH
T ss_pred CCCCChHHC
Confidence 999888886
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=98.20 E-value=0.0001 Score=71.65 Aligned_cols=152 Identities=16% Similarity=0.151 Sum_probs=96.1
Q ss_pred EEEEEEcCcchhH--HHHHHHHHHHhcccCC---CCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHHH
Q 004199 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQ 206 (769)
Q Consensus 132 ~vFvID~s~~~~~--l~~~~~~l~~~l~~lp---~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~ 206 (769)
.+|+||+|.+... ++.++++++..+..+. ++.+||||+|++..+..- . ..
T Consensus 3 vv~vlD~SgSm~~~~~~~~k~~~~~~~~~l~~~~~~~~~giv~Fs~~~~~~~-~-~~----------------------- 57 (164)
T cd01472 3 IVFLVDGSESIGLSNFNLVKDFVKRVVERLDIGPDGVRVGVVQYSDDPRTEF-Y-LN----------------------- 57 (164)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHhhcccCCCCeEEEEEEEcCceeEEE-e-cC-----------------------
Confidence 4799999997644 7888888888887764 468999999998765421 1 00
Q ss_pred hhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhcc-
Q 004199 207 LNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC- 285 (769)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~- 285 (769)
. .. .+..+...|+.++.. ...+.+|.||..|...+...
T Consensus 58 ----------------------------~----~~-~~~~~~~~l~~l~~~--------~g~T~~~~al~~a~~~l~~~~ 96 (164)
T cd01472 58 ----------------------------T----YR-SKDDVLEAVKNLRYI--------GGGTNTGKALKYVRENLFTEA 96 (164)
T ss_pred ----------------------------C----CC-CHHHHHHHHHhCcCC--------CCCchHHHHHHHHHHHhCCcc
Confidence 0 00 122444556666541 23468999999999988741
Q ss_pred ---CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCcc
Q 004199 286 ---VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (769)
Q Consensus 286 ---~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~ 362 (769)
.++....|++++.|-++.+. ...+..+.+.||.+-.+..+ ..
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 12334567888887332110 11223445567765555444 34
Q ss_pred ChhhhhhhhhccCc-eEEEeCCC
Q 004199 363 GVAELKVAVEKTGG-LVVLSDSF 384 (769)
Q Consensus 363 ~l~~m~~l~~~TGG-~v~~~~~f 384 (769)
+...|..++..++| +++.+.+|
T Consensus 142 ~~~~L~~ia~~~~~~~~~~~~~~ 164 (164)
T cd01472 142 DEEELKQIASDPKELYVFNVADF 164 (164)
T ss_pred CHHHHHHHHCCCchheEEeccCC
Confidence 99999999999987 66665543
No 24
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=98.13 E-value=0.00018 Score=85.92 Aligned_cols=154 Identities=16% Similarity=0.230 Sum_probs=103.4
Q ss_pred CCcEEEEEEEcCcchh---HHHHHHHHHHHhc-ccCCCCceEEEEEECCeEEEEE-ccCCCCCCCeeEEecCCccCCHHH
Q 004199 128 VPPVFMFVVDTCIIEE---EMSFLKSALSQAI-DLLPDNSLVGLITFGTLVQVHE-LGGFGQIIPKTYVFKGSKDVSKDQ 202 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~---~l~~~~~~l~~~l-~~lp~~~~VglITfd~~V~~~~-l~~~~~~~~~~~v~~g~~~~~~~~ 202 (769)
.+...++|||+|.++. .++.++++++..+ +.++++.+||||+|++..++.. +.
T Consensus 303 ~~r~VVLVLDvSGSM~g~dRL~~lkqAA~~fL~~~l~~~DrVGLVtFsssA~vl~pLt---------------------- 360 (863)
T TIGR00868 303 RQRIVCLVLDKSGSMTVEDRLKRMNQAAKLFLLQTVEKGSWVGMVTFDSAAYIKNELI---------------------- 360 (863)
T ss_pred CCceEEEEEECCccccccCHHHHHHHHHHHHHHHhCCCCCEEEEEEECCceeEeeccc----------------------
Confidence 4567999999999974 3788888877665 4578889999999999876421 11
Q ss_pred HHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHh
Q 004199 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (769)
Q Consensus 203 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll 282 (769)
++.. .. .+..+.. .|+. . ....+++|.||..|..+|
T Consensus 361 -----------------------------~Its----~~-dr~aL~~---~L~~----~---A~GGT~I~~GL~~Alq~L 396 (863)
T TIGR00868 361 -----------------------------QITS----SA-ERDALTA---NLPT----A---ASGGTSICSGLKAAFQVI 396 (863)
T ss_pred -----------------------------cCCc----HH-HHHHHHH---hhcc----c---cCCCCcHHHHHHHHHHHH
Confidence 0000 00 0122222 2221 1 124689999999999999
Q ss_pred hccC-CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCc
Q 004199 283 GACV-PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (769)
Q Consensus 283 ~~~~-~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~ 361 (769)
.... +..++.|++++.|-.+.+ ..+...+.+.|+.|..+.++.+.
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 8532 235678999988843211 12344556689999999887653
Q ss_pred cChhhhhhhhhccCceEEEeCC
Q 004199 362 VGVAELKVAVEKTGGLVVLSDS 383 (769)
Q Consensus 362 ~~l~~m~~l~~~TGG~v~~~~~ 383 (769)
-..|..||+.|||..++.++
T Consensus 443 --d~~L~~IA~~TGG~~f~asd 462 (863)
T TIGR00868 443 --AKELEELSDMTGGLRFYASD 462 (863)
T ss_pred --HHHHHHHHHhcCCEEEEeCC
Confidence 35699999999999999864
No 25
>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=98.11 E-value=8.7e-05 Score=74.69 Aligned_cols=168 Identities=15% Similarity=0.107 Sum_probs=100.1
Q ss_pred EEEEEEcCcchhH--HHHHHHHHHHhcccCC---CCceEEEEEECCeEEEE-EccCCCCCCCeeEEecCCccCCHHHHHH
Q 004199 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (769)
Q Consensus 132 ~vFvID~s~~~~~--l~~~~~~l~~~l~~lp---~~~~VglITfd~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (769)
++||||+|.+... ++.+++++...++.|+ .+.+||+|+|++.++.. .+. ..
T Consensus 3 i~~vlD~SgSM~~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~~~~~~~~-~~---------------------- 59 (198)
T cd01470 3 IYIALDASDSIGEEDFDEAKNAIKTLIEKISSYEVSPRYEIISYASDPKEIVSIR-DF---------------------- 59 (198)
T ss_pred EEEEEECCCCccHHHHHHHHHHHHHHHHHccccCCCceEEEEEecCCceEEEecc-cC----------------------
Confidence 6899999998753 8899999999998875 36899999999876542 222 10
Q ss_pred HhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhcc
Q 004199 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (769)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~ 285 (769)
. ...+..+...|+.++.... +....+.++.||..|...+...
T Consensus 60 -------------------------~---------~~~~~~~~~~l~~~~~~~~----~~~ggT~~~~Al~~~~~~l~~~ 101 (198)
T cd01470 60 -------------------------N---------SNDADDVIKRLEDFNYDDH----GDKTGTNTAAALKKVYERMALE 101 (198)
T ss_pred -------------------------C---------CCCHHHHHHHHHhCCcccc----cCccchhHHHHHHHHHHHHHHH
Confidence 0 0012234445555543211 1123567888888887766310
Q ss_pred C-C------CCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHH------HHHhcCcEE
Q 004199 286 V-P------GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSK------QLVHQGHVL 352 (769)
Q Consensus 286 ~-~------~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~------~~~~~~isv 352 (769)
. + ...-.|++++.|-++.|... ..+.+.++++.. .+...++.|
T Consensus 102 ~~~~~~~~~~~~~~iillTDG~~~~g~~~------------------------~~~~~~~~~~~~~~~~~~~~~~~~v~i 157 (198)
T cd01470 102 KVRNKEAFNETRHVIILFTDGKSNMGGSP------------------------LPTVDKIKNLVYKNNKSDNPREDYLDV 157 (198)
T ss_pred HhcCccchhhcceEEEEEcCCCcCCCCCh------------------------hHHHHHHHHHHhcccccccchhcceeE
Confidence 0 0 01134789999988876210 011111222211 123345555
Q ss_pred EEEEecCCccChhhhhhhhhccCc--eEEEeCCCC
Q 004199 353 DLFACALDQVGVAELKVAVEKTGG--LVVLSDSFG 385 (769)
Q Consensus 353 Dlf~~~~~~~~l~~m~~l~~~TGG--~v~~~~~f~ 385 (769)
..+..+ +.++-.+|..|+..||| ++|...+|.
T Consensus 158 ~~iGvG-~~~~~~~L~~iA~~~~g~~~~f~~~~~~ 191 (198)
T cd01470 158 YVFGVG-DDVNKEELNDLASKKDNERHFFKLKDYE 191 (198)
T ss_pred EEEecC-cccCHHHHHHHhcCCCCCceEEEeCCHH
Confidence 555443 45789999999999999 577766663
No 26
>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=98.06 E-value=0.00028 Score=69.68 Aligned_cols=156 Identities=17% Similarity=0.199 Sum_probs=101.5
Q ss_pred cEEEEEEEcCcchh--------HHHHHHHHHHHhcccCCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHH
Q 004199 130 PVFMFVVDTCIIEE--------EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (769)
Q Consensus 130 p~~vFvID~s~~~~--------~l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~ 201 (769)
.-++||||+|.+.. .++.++..+...+... ++.+||+|+|++.++..- .
T Consensus 3 ~~vv~vlD~S~SM~~~~~~~~~r~~~a~~~~~~~~~~~-~~~~v~lv~f~~~~~~~~-~--------------------- 59 (180)
T cd01467 3 RDIMIALDVSGSMLAQDFVKPSRLEAAKEVLSDFIDRR-ENDRIGLVVFAGAAFTQA-P--------------------- 59 (180)
T ss_pred ceEEEEEECCcccccccCCCCCHHHHHHHHHHHHHHhC-CCCeEEEEEEcCCeeecc-C---------------------
Confidence 34789999998753 2567777777766655 467999999987664310 0
Q ss_pred HHHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHH
Q 004199 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (769)
Q Consensus 202 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~l 281 (769)
+ ...+..+..+++.|... . ....+.++.||..|..+
T Consensus 60 -------------------------------~-------~~~~~~~~~~l~~l~~~---~---~~g~T~l~~al~~a~~~ 95 (180)
T cd01467 60 -------------------------------L-------TLDRESLKELLEDIKIG---L---AGQGTAIGDAIGLAIKR 95 (180)
T ss_pred -------------------------------C-------CccHHHHHHHHHHhhhc---c---cCCCCcHHHHHHHHHHH
Confidence 0 00012334455555421 1 12346789999999998
Q ss_pred hhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCC-
Q 004199 282 LGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD- 360 (769)
Q Consensus 282 l~~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~- 360 (769)
+... ......|++++.|.++.|+- . ..+.+..+.+.||.|+.+.++..
T Consensus 96 l~~~-~~~~~~iiliTDG~~~~g~~-------------------------~-----~~~~~~~~~~~gi~i~~i~ig~~~ 144 (180)
T cd01467 96 LKNS-EAKERVIVLLTDGENNAGEI-------------------------D-----PATAAELAKNKGVRIYTIGVGKSG 144 (180)
T ss_pred HHhc-CCCCCEEEEEeCCCCCCCCC-------------------------C-----HHHHHHHHHHCCCEEEEEEecCCC
Confidence 8631 12346799999997765420 0 01223445568999998888752
Q ss_pred ---------ccChhhhhhhhhccCceEEEeCC
Q 004199 361 ---------QVGVAELKVAVEKTGGLVVLSDS 383 (769)
Q Consensus 361 ---------~~~l~~m~~l~~~TGG~v~~~~~ 383 (769)
..+...|..|++.|||..++..+
T Consensus 145 ~~~~~~~~~~~~~~~l~~la~~tgG~~~~~~~ 176 (180)
T cd01467 145 SGPKPDGSTILDEDSLVEIADKTGGRIFRALD 176 (180)
T ss_pred CCcCCCCcccCCHHHHHHHHHhcCCEEEEecC
Confidence 46778899999999999998753
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=0.00014 Score=71.84 Aligned_cols=144 Identities=22% Similarity=0.215 Sum_probs=95.4
Q ss_pred EEEEEEEcCcchhH-------HHHHHHHHHHhc----ccCCCCceEEEEEECC-eEEEEEccCCCCCCCeeEEecCCccC
Q 004199 131 VFMFVVDTCIIEEE-------MSFLKSALSQAI----DLLPDNSLVGLITFGT-LVQVHELGGFGQIIPKTYVFKGSKDV 198 (769)
Q Consensus 131 ~~vFvID~s~~~~~-------l~~~~~~l~~~l----~~lp~~~~VglITfd~-~V~~~~l~~~~~~~~~~~v~~g~~~~ 198 (769)
+.+++||+|..+.+ +++.++.+...+ +..|++ +||||+|.+ .-++.
T Consensus 5 a~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np~~-~vGlv~fag~~a~v~--------------------- 62 (187)
T cd01452 5 ATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPEN-NVGLMTMAGNSPEVL--------------------- 62 (187)
T ss_pred EEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCCCc-cEEEEEecCCceEEE---------------------
Confidence 56899999998643 888888887664 666654 999999875 32221
Q ss_pred CHHHHHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHH
Q 004199 199 SKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIA 278 (769)
Q Consensus 199 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A 278 (769)
+|+......+...|+.+... ....+|.||+.|
T Consensus 63 ---------------------------------------~plT~D~~~~~~~L~~i~~~---------g~~~l~~AL~~A 94 (187)
T cd01452 63 ---------------------------------------VTLTNDQGKILSKLHDVQPK---------GKANFITGIQIA 94 (187)
T ss_pred ---------------------------------------ECCCCCHHHHHHHHHhCCCC---------CcchHHHHHHHH
Confidence 11111234556666665541 345799999999
Q ss_pred HHHhhccCCC-CCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEe
Q 004199 279 ASLLGACVPG-SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFAC 357 (769)
Q Consensus 279 ~~ll~~~~~~-~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~ 357 (769)
...|+..-.. ...||++|.+++.+.-|| + ..++++++.++||.||++.+
T Consensus 95 ~~~L~~~~~~~~~~rivi~v~S~~~~d~~-----------------------------~-i~~~~~~lkk~~I~v~vI~~ 144 (187)
T cd01452 95 QLALKHRQNKNQKQRIVAFVGSPIEEDEK-----------------------------D-LVKLAKRLKKNNVSVDIINF 144 (187)
T ss_pred HHHHhcCCCcCCcceEEEEEecCCcCCHH-----------------------------H-HHHHHHHHHHcCCeEEEEEe
Confidence 9999853222 235999999875332111 1 23678999999999999999
Q ss_pred cCCccChhhhhhhhhcc
Q 004199 358 ALDQVGVAELKVAVEKT 374 (769)
Q Consensus 358 ~~~~~~l~~m~~l~~~T 374 (769)
+...-+..-+..+.+..
T Consensus 145 G~~~~~~~~l~~~~~~~ 161 (187)
T cd01452 145 GEIDDNTEKLTAFIDAV 161 (187)
T ss_pred CCCCCCHHHHHHHHHHh
Confidence 86655555555555544
No 28
>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=98.02 E-value=0.00032 Score=75.33 Aligned_cols=49 Identities=22% Similarity=0.265 Sum_probs=42.0
Q ss_pred CCcEEEEEEEcCcchhH-HHHHHHHHHHhccc-CCCCceEEEEEECCeEEE
Q 004199 128 VPPVFMFVVDTCIIEEE-MSFLKSALSQAIDL-LPDNSLVGLITFGTLVQV 176 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~~-l~~~~~~l~~~l~~-lp~~~~VglITfd~~V~~ 176 (769)
.|...+||||+|.+... +..+++++...++. ++++.+||||+|++.+++
T Consensus 52 ~p~~vvlvlD~SgSM~~~~~~a~~a~~~~l~~~l~~~d~v~lv~f~~~~~~ 102 (296)
T TIGR03436 52 LPLTVGLVIDTSGSMRNDLDRARAAAIRFLKTVLRPNDRVFVVTFNTRLRL 102 (296)
T ss_pred CCceEEEEEECCCCchHHHHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeE
Confidence 57899999999998765 77888888888876 788899999999987765
No 29
>cd01461 vWA_interalpha_trypsin_inhibitor vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to the extracellular matrix by binding to hyaluronic acid. The heavy chains carry the VWA domain with a conserved MIDAS motif. Although the exact role of the VWA domains remains unknown, it has been speculated to be involved in mediating protein-protein interactions with the components of the extracellular matrix.
Probab=97.95 E-value=0.00052 Score=66.92 Aligned_cols=160 Identities=20% Similarity=0.190 Sum_probs=102.8
Q ss_pred CcEEEEEEEcCcchhH--HHHHHHHHHHhcccCCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHHH
Q 004199 129 PPVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQ 206 (769)
Q Consensus 129 ~p~~vFvID~s~~~~~--l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~ 206 (769)
|.-++||+|+|.+... ++.+++++...+..++++.+|++++|++.++.+ . .. .
T Consensus 2 ~~~v~~vlD~S~SM~~~~~~~~~~al~~~l~~l~~~~~~~l~~Fs~~~~~~--~-~~-~--------------------- 56 (171)
T cd01461 2 PKEVVFVIDTSGSMSGTKIEQTKEALLTALKDLPPGDYFNIIGFSDTVEEF--S-PS-S--------------------- 56 (171)
T ss_pred CceEEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEeCCCceee--c-Cc-c---------------------
Confidence 5568999999998743 888999999999999988899999999876543 1 10 0
Q ss_pred hhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccC
Q 004199 207 LNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACV 286 (769)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~ 286 (769)
.+.+ .+....+.+.++.+.+ ...+.++.||..|...+.. .
T Consensus 57 ------------------------~~~~------~~~~~~~~~~l~~~~~---------~g~T~l~~al~~a~~~l~~-~ 96 (171)
T cd01461 57 ------------------------VSAT------AENVAAAIEYVNRLQA---------LGGTNMNDALEAALELLNS-S 96 (171)
T ss_pred ------------------------eeCC------HHHHHHHHHHHHhcCC---------CCCcCHHHHHHHHHHhhcc-C
Confidence 0000 0001122334444433 2245688999999888863 1
Q ss_pred CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccChhh
Q 004199 287 PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAE 366 (769)
Q Consensus 287 ~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~ 366 (769)
+.....|++|+.|.++. ..+.+ +...++.+.++.|..+.++ ...+-..
T Consensus 97 ~~~~~~iillTDG~~~~------------------------------~~~~~-~~~~~~~~~~i~i~~i~~g-~~~~~~~ 144 (171)
T cd01461 97 PGSVPQIILLTDGEVTN------------------------------ESQIL-KNVREALSGRIRLFTFGIG-SDVNTYL 144 (171)
T ss_pred CCCccEEEEEeCCCCCC------------------------------HHHHH-HHHHHhcCCCceEEEEEeC-CccCHHH
Confidence 23456788888884210 01222 3334444457777766665 3456788
Q ss_pred hhhhhhccCceEEEeCCCC
Q 004199 367 LKVAVEKTGGLVVLSDSFG 385 (769)
Q Consensus 367 m~~l~~~TGG~v~~~~~f~ 385 (769)
|..+++.|||..++..+-.
T Consensus 145 l~~ia~~~gG~~~~~~~~~ 163 (171)
T cd01461 145 LERLAREGRGIARRIYETD 163 (171)
T ss_pred HHHHHHcCCCeEEEecChH
Confidence 9999999999999986543
No 30
>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=97.94 E-value=0.00034 Score=69.62 Aligned_cols=157 Identities=15% Similarity=0.124 Sum_probs=99.6
Q ss_pred EEEEEEEcCcchh--HHHHHHHHHHHhcccC---------CCCceEEEEEECCeEEEE-EccCCCCCCCeeEEecCCccC
Q 004199 131 VFMFVVDTCIIEE--EMSFLKSALSQAIDLL---------PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDV 198 (769)
Q Consensus 131 ~~vFvID~s~~~~--~l~~~~~~l~~~l~~l---------p~~~~VglITfd~~V~~~-~l~~~~~~~~~~~v~~g~~~~ 198 (769)
-.+||||.|.+.. .++.+++.++..++.+ +++.+||+|+|++..++. .+. .
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 4689999999865 3777777777777766 456899999999765431 111 0
Q ss_pred CHHHHHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHH
Q 004199 199 SKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIA 278 (769)
Q Consensus 199 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A 278 (769)
. ...+..+.+.|++++.. ...+.+|.||..|
T Consensus 67 -------------------------------------~----~~~~~~l~~~i~~l~~~--------gg~T~~~~AL~~a 97 (186)
T cd01480 67 -------------------------------------D----IRNYTSLKEAVDNLEYI--------GGGTFTDCALKYA 97 (186)
T ss_pred -------------------------------------c----cCCHHHHHHHHHhCccC--------CCCccHHHHHHHH
Confidence 0 00134556666666531 2357899999999
Q ss_pred HHHhhcc-CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEe
Q 004199 279 ASLLGAC-VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFAC 357 (769)
Q Consensus 279 ~~ll~~~-~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~ 357 (769)
...+... .+.....|++++.|.++.++. .-..+.+..+...||.|-.+..
T Consensus 98 ~~~l~~~~~~~~~~~iillTDG~~~~~~~-----------------------------~~~~~~~~~~~~~gi~i~~vgi 148 (186)
T cd01480 98 TEQLLEGSHQKENKFLLVITDGHSDGSPD-----------------------------GGIEKAVNEADHLGIKIFFVAV 148 (186)
T ss_pred HHHHhccCCCCCceEEEEEeCCCcCCCcc-----------------------------hhHHHHHHHHHHCCCEEEEEec
Confidence 9988741 123446777888886532110 0013445667777887655555
Q ss_pred cCCccChhhhhhhhhccCceEEEeCCCC
Q 004199 358 ALDQVGVAELKVAVEKTGGLVVLSDSFG 385 (769)
Q Consensus 358 ~~~~~~l~~m~~l~~~TGG~v~~~~~f~ 385 (769)
+. .+...|..++...+|. ++.++|.
T Consensus 149 g~--~~~~~L~~IA~~~~~~-~~~~~~~ 173 (186)
T cd01480 149 GS--QNEEPLSRIACDGKSA-LYRENFA 173 (186)
T ss_pred Cc--cchHHHHHHHcCCcch-hhhcchh
Confidence 43 7888899999887775 4445554
No 31
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=97.91 E-value=0.00027 Score=68.03 Aligned_cols=151 Identities=21% Similarity=0.234 Sum_probs=99.9
Q ss_pred EEEEEEcCcchhH-HHHHHHHHHHhcccCCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHHHhhcc
Q 004199 132 FMFVVDTCIIEEE-MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFF 210 (769)
Q Consensus 132 ~vFvID~s~~~~~-l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~~~~~~ 210 (769)
.+||||+|.++.. .+.++++|+..++.|+++.++.||+|++.+..+. . . ....
T Consensus 3 vvilvD~S~Sm~g~~~~~k~al~~~l~~L~~~d~fnii~f~~~~~~~~-~--~-------------------~~~~---- 56 (155)
T PF13768_consen 3 VVILVDTSGSMSGEKELVKDALRAILRSLPPGDRFNIIAFGSSVRPLF-P--G-------------------LVPA---- 56 (155)
T ss_pred EEEEEeCCCCCCCcHHHHHHHHHHHHHhCCCCCEEEEEEeCCEeeEcc-h--h-------------------HHHH----
Confidence 5899999998654 4889999999999999999999999999776442 1 1 0000
Q ss_pred cCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCC
Q 004199 211 IKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSG 290 (769)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~g 290 (769)
. .+........|+++..+ ...+.++.||..|...+.. ++..
T Consensus 57 --------------------~---------~~~~~~a~~~I~~~~~~--------~G~t~l~~aL~~a~~~~~~--~~~~ 97 (155)
T PF13768_consen 57 --------------------T---------EENRQEALQWIKSLEAN--------SGGTDLLAALRAALALLQR--PGCV 97 (155)
T ss_pred --------------------h---------HHHHHHHHHHHHHhccc--------CCCccHHHHHHHHHHhccc--CCCc
Confidence 0 01122334455555441 3456889999999998621 2566
Q ss_pred cEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccChhhhhhh
Q 004199 291 ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVA 370 (769)
Q Consensus 291 grI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l~~m~~l 370 (769)
-.|++++.|.++.++ ....+.+ ..+. ..+.+..|.++. ..+-..|..|
T Consensus 98 ~~IilltDG~~~~~~-----------------------------~~i~~~v-~~~~-~~~~i~~~~~g~-~~~~~~L~~L 145 (155)
T PF13768_consen 98 RAIILLTDGQPVSGE-----------------------------EEILDLV-RRAR-GHIRIFTFGIGS-DADADFLREL 145 (155)
T ss_pred cEEEEEEeccCCCCH-----------------------------HHHHHHH-HhcC-CCceEEEEEECC-hhHHHHHHHH
Confidence 789999998663332 1111111 1111 456677776654 4567889999
Q ss_pred hhccCceEE
Q 004199 371 VEKTGGLVV 379 (769)
Q Consensus 371 ~~~TGG~v~ 379 (769)
++.|||..+
T Consensus 146 A~~~~G~~~ 154 (155)
T PF13768_consen 146 ARATGGSFH 154 (155)
T ss_pred HHcCCCEEE
Confidence 999999865
No 32
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=97.82 E-value=0.00034 Score=67.83 Aligned_cols=150 Identities=23% Similarity=0.233 Sum_probs=96.2
Q ss_pred EEEEEEcCcchhH-------HHHHHHHHHHhcccCCCCceEEEEEECCeEEEE-EccCCCCCCCeeEEecCCccCCHHHH
Q 004199 132 FMFVVDTCIIEEE-------MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQL 203 (769)
Q Consensus 132 ~vFvID~s~~~~~-------l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l 203 (769)
++||||+|.+... ++.+++++...++.+|.+ +|||++|++..++. .+.
T Consensus 2 vv~v~D~SgSM~~~~~~~~~~~~~~~~~~~~~~~~~~~-~v~l~~f~~~~~~~~~~t----------------------- 57 (172)
T PF13519_consen 2 VVFVLDNSGSMNGYDGNRTRIDQAKDALNELLANLPGD-RVGLVSFSDSSRTLSPLT----------------------- 57 (172)
T ss_dssp EEEEEE-SGGGGTTTSSS-HHHHHHHHHHHHHHHHTTS-EEEEEEESTSCEEEEEEE-----------------------
T ss_pred EEEEEECCcccCCCCCCCcHHHHHHHHHHHHHHHCCCC-EEEEEEeccccccccccc-----------------------
Confidence 5899999998642 788899999998888844 99999999754221 111
Q ss_pred HHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhh
Q 004199 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG 283 (769)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~ 283 (769)
..+..+.+.++++.... ......+++.|+..|..++.
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 01223333344433210 01234688999999999998
Q ss_pred ccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccC
Q 004199 284 ACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVG 363 (769)
Q Consensus 284 ~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~ 363 (769)
.. +.....|++|+.|.++ . . ..+.+..+...+|.+.++.++.+...
T Consensus 95 ~~-~~~~~~iv~iTDG~~~-------~------------------~--------~~~~~~~~~~~~i~i~~v~~~~~~~~ 140 (172)
T PF13519_consen 95 SS-DNRRRAIVLITDGEDN-------S------------------S--------DIEAAKALKQQGITIYTVGIGSDSDA 140 (172)
T ss_dssp C--SSEEEEEEEEES-TTH-------C------------------H--------HHHHHHHHHCTTEEEEEEEES-TT-E
T ss_pred hC-CCCceEEEEecCCCCC-------c------------------c--------hhHHHHHHHHcCCeEEEEEECCCccH
Confidence 51 1234567777776333 0 0 01256677889999999998887766
Q ss_pred hhhhhhhhhccCceEEEeC
Q 004199 364 VAELKVAVEKTGGLVVLSD 382 (769)
Q Consensus 364 l~~m~~l~~~TGG~v~~~~ 382 (769)
-..|..+++.|||..+...
T Consensus 141 ~~~l~~la~~tgG~~~~~~ 159 (172)
T PF13519_consen 141 NEFLQRLAEATGGRYFHVD 159 (172)
T ss_dssp HHHHHHHHHHTEEEEEEE-
T ss_pred HHHHHHHHHhcCCEEEEec
Confidence 6789999999999988873
No 33
>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
Probab=97.82 E-value=0.00073 Score=69.41 Aligned_cols=155 Identities=22% Similarity=0.332 Sum_probs=97.2
Q ss_pred CcEEEEEEEcCcchh--HHHHHHHHHHHhcccC---CCCceEEEEEECCeEEEEE-ccCCCCCCCeeEEecCCccCCHHH
Q 004199 129 PPVFMFVVDTCIIEE--EMSFLKSALSQAIDLL---PDNSLVGLITFGTLVQVHE-LGGFGQIIPKTYVFKGSKDVSKDQ 202 (769)
Q Consensus 129 ~p~~vFvID~s~~~~--~l~~~~~~l~~~l~~l---p~~~~VglITfd~~V~~~~-l~~~~~~~~~~~v~~g~~~~~~~~ 202 (769)
|.-.+|+||.|.+.. +++.+++.++..++.+ |+.++||+|+|++.+++.- +. .
T Consensus 2 ~~DlvfllD~S~Sm~~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~~~~~~l~-~-------------------- 60 (224)
T cd01475 2 PTDLVFLIDSSRSVRPENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTVKQEFPLG-R-------------------- 60 (224)
T ss_pred CccEEEEEeCCCCCCHHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCceeEEeccc-c--------------------
Confidence 345799999999854 4889999999888776 4568999999998775421 11 0
Q ss_pred HHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHh
Q 004199 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (769)
Q Consensus 203 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll 282 (769)
+ . .+..+.+.|+.++.. ...+.+|.||..|...+
T Consensus 61 ---------------------------------~----~-~~~~l~~~i~~i~~~--------~~~t~tg~AL~~a~~~~ 94 (224)
T cd01475 61 ---------------------------------F----K-SKADLKRAVRRMEYL--------ETGTMTGLAIQYAMNNA 94 (224)
T ss_pred ---------------------------------c----C-CHHHHHHHHHhCcCC--------CCCChHHHHHHHHHHHh
Confidence 0 0 122344555555431 12457899999888653
Q ss_pred -hcc--CC-CC---CcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEE
Q 004199 283 -GAC--VP-GS---GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLF 355 (769)
Q Consensus 283 -~~~--~~-~~---ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf 355 (769)
... .+ .. ...|++++.|.++. + ..+.+.++...||.| |
T Consensus 95 ~~~~~g~r~~~~~~~kvvillTDG~s~~------------------~---------------~~~~a~~lk~~gv~i--~ 139 (224)
T cd01475 95 FSEAEGARPGSERVPRVGIVVTDGRPQD------------------D---------------VSEVAAKARALGIEM--F 139 (224)
T ss_pred CChhcCCCCCCCCCCeEEEEEcCCCCcc------------------c---------------HHHHHHHHHHCCcEE--E
Confidence 210 01 11 22457888874310 0 234567777778655 5
Q ss_pred EecCCccChhhhhhhhhccC-ceEEEeCCCC
Q 004199 356 ACALDQVGVAELKVAVEKTG-GLVVLSDSFG 385 (769)
Q Consensus 356 ~~~~~~~~l~~m~~l~~~TG-G~v~~~~~f~ 385 (769)
+.+....+..+|..++..++ +.++..++|+
T Consensus 140 ~VgvG~~~~~~L~~ias~~~~~~~f~~~~~~ 170 (224)
T cd01475 140 AVGVGRADEEELREIASEPLADHVFYVEDFS 170 (224)
T ss_pred EEeCCcCCHHHHHHHhCCCcHhcEEEeCCHH
Confidence 54444578899999998765 4677777765
No 34
>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=97.81 E-value=0.0014 Score=63.87 Aligned_cols=45 Identities=24% Similarity=0.462 Sum_probs=36.1
Q ss_pred EEEEEEcCcchhH--HHHHHHHHHHhcccC---CCCceEEEEEECCeEEE
Q 004199 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLL---PDNSLVGLITFGTLVQV 176 (769)
Q Consensus 132 ~vFvID~s~~~~~--l~~~~~~l~~~l~~l---p~~~~VglITfd~~V~~ 176 (769)
.+|++|.|.+..+ ++.+++.++..++.+ +++.+||+|+|++..++
T Consensus 3 v~~vlD~S~Sm~~~~~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~~~ 52 (164)
T cd01482 3 IVFLVDGSWSIGRSNFNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDPRT 52 (164)
T ss_pred EEEEEeCCCCcChhhHHHHHHHHHHHHhheeeCCCceEEEEEEECCCeeE
Confidence 6899999998653 888888888777665 46799999999986543
No 35
>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=97.76 E-value=0.0014 Score=64.59 Aligned_cols=156 Identities=16% Similarity=0.161 Sum_probs=98.3
Q ss_pred EEEEEEcCcchh--HHHHHHHHHHHhcccCC---CCceEEEEEECCeEEEE-EccCCCCCCCeeEEecCCccCCHHHHHH
Q 004199 132 FMFVVDTCIIEE--EMSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (769)
Q Consensus 132 ~vFvID~s~~~~--~l~~~~~~l~~~l~~lp---~~~~VglITfd~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (769)
.+|+||.|.+.. +++.+++.++..++.+. ++++||+|+|++..++. .+. .
T Consensus 3 i~fvlD~S~S~~~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~~~~~~l~-~----------------------- 58 (177)
T cd01469 3 IVFVLDGSGSIYPDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESFRTEFTLN-E----------------------- 58 (177)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCceeEEEecC-c-----------------------
Confidence 589999999854 48888888888887764 46899999999876542 121 0
Q ss_pred HhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhc-
Q 004199 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA- 284 (769)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~- 284 (769)
+ . +...+.+.++.++.. ...+.+|.||..|...+-.
T Consensus 59 ------------------------------~----~-~~~~~~~~i~~~~~~--------~g~T~~~~AL~~a~~~l~~~ 95 (177)
T cd01469 59 ------------------------------Y----R-TKEEPLSLVKHISQL--------LGLTNTATAIQYVVTELFSE 95 (177)
T ss_pred ------------------------------c----C-CHHHHHHHHHhCccC--------CCCccHHHHHHHHHHHhcCc
Confidence 0 0 011233444454431 1237899999999887621
Q ss_pred --c-CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCC-
Q 004199 285 --C-VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD- 360 (769)
Q Consensus 285 --~-~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~- 360 (769)
. .++...-+++++.|..+.|+ . .++.+..+...|+.|-.+..+.+
T Consensus 96 ~~g~R~~~~kv~illTDG~~~~~~-----------------------~--------~~~~~~~~k~~gv~v~~Vgvg~~~ 144 (177)
T cd01469 96 SNGARKDATKVLVVITDGESHDDP-----------------------L--------LKDVIPQAEREGIIRYAIGVGGHF 144 (177)
T ss_pred ccCCCCCCCeEEEEEeCCCCCCcc-----------------------c--------cHHHHHHHHHCCcEEEEEEecccc
Confidence 0 11223357888888654332 0 02345556667887766666543
Q ss_pred --ccChhhhhhhhhccCc-eEEEeCCCC
Q 004199 361 --QVGVAELKVAVEKTGG-LVVLSDSFG 385 (769)
Q Consensus 361 --~~~l~~m~~l~~~TGG-~v~~~~~f~ 385 (769)
..+..+|..++..+++ ++|..++|+
T Consensus 145 ~~~~~~~~L~~ias~p~~~h~f~~~~~~ 172 (177)
T cd01469 145 QRENSREELKTIASKPPEEHFFNVTDFA 172 (177)
T ss_pred cccccHHHHHHHhcCCcHHhEEEecCHH
Confidence 2347889999998874 677777764
No 36
>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=97.71 E-value=0.00086 Score=66.66 Aligned_cols=85 Identities=13% Similarity=0.098 Sum_probs=51.7
Q ss_pred CccchhHHHHHHHHHhhccCCCCC-----cEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHH
Q 004199 267 STRCTGTALSIAASLLGACVPGSG-----ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDAL 341 (769)
Q Consensus 267 ~~~~~G~Al~~A~~ll~~~~~~~g-----grI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~l 341 (769)
..+++|.||..|...+... ..| ..|++++.|.++...+. .+ ...
T Consensus 78 g~T~~~~aL~~a~~~l~~~--~~~~r~~~~~villTDG~~~~~~~~------------------------~~-----~~~ 126 (185)
T cd01474 78 GQTYIHEGLENANEQIFNR--NGGGRETVSVIIALTDGQLLLNGHK------------------------YP-----EHE 126 (185)
T ss_pred CCCcHHHHHHHHHHHHHhh--ccCCCCCCeEEEEEcCCCcCCCCCc------------------------ch-----HHH
Confidence 4678999999999877310 122 34888888865311000 00 122
Q ss_pred HHHHHhcCcEEEEEEecCCccChhhhhhhhhccCceEE-EeCCCC
Q 004199 342 SKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVV-LSDSFG 385 (769)
Q Consensus 342 a~~~~~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~v~-~~~~f~ 385 (769)
+..+.+.|+.|-.+.. ...+..+|..++..++ .+| ...+|.
T Consensus 127 a~~l~~~gv~i~~vgv--~~~~~~~L~~iA~~~~-~~f~~~~~~~ 168 (185)
T cd01474 127 AKLSRKLGAIVYCVGV--TDFLKSQLINIADSKE-YVFPVTSGFQ 168 (185)
T ss_pred HHHHHHcCCEEEEEee--chhhHHHHHHHhCCCC-eeEecCccHH
Confidence 4456667876555444 6678899999998875 455 344554
No 37
>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein. Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092).
Probab=97.61 E-value=0.005 Score=72.69 Aligned_cols=186 Identities=16% Similarity=0.111 Sum_probs=113.2
Q ss_pred CCcEEEEEEEcCcchh--HHHHHHHHHHHhcccCCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHHH
Q 004199 128 VPPVFMFVVDTCIIEE--EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~--~l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (769)
.|.-++||||+|.++. .++.+++++..+|..|+++.+++||+|++.++.+.-. . .
T Consensus 270 ~p~~vvfvlD~SgSM~g~~i~~ak~al~~~l~~L~~~d~~~ii~F~~~~~~~~~~--~--~------------------- 326 (596)
T TIGR03788 270 LPRELVFVIDTSGSMAGESIEQAKSALLLALDQLRPGDRFNIIQFDSDVTLLFPV--P--V------------------- 326 (596)
T ss_pred CCceEEEEEECCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEECCcceEeccc--c--c-------------------
Confidence 5667999999999874 3888999999999999999999999999988654211 0 0
Q ss_pred HhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhcc
Q 004199 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (769)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~ 285 (769)
+.+ .+....+...|+.|..+ ..+.+..||..|.......
T Consensus 327 --------------------------~~~------~~~~~~a~~~i~~l~a~---------GgT~l~~aL~~a~~~~~~~ 365 (596)
T TIGR03788 327 --------------------------PAT------AHNLARARQFVAGLQAD---------GGTEMAGALSAALRDDGPE 365 (596)
T ss_pred --------------------------cCC------HHHHHHHHHHHhhCCCC---------CCccHHHHHHHHHHhhccc
Confidence 000 00112334455555442 3467889999988765321
Q ss_pred CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccChh
Q 004199 286 VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVA 365 (769)
Q Consensus 286 ~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~l~ 365 (769)
....-.+|+++++|..+- .....+.+. ....++.+..|.++. ..+-.
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 112234799999984200 001122221 122356666666654 46778
Q ss_pred hhhhhhhccCceEEEeCCCCchhhHHHHHHHhhcCccCccceeeeEEEE
Q 004199 366 ELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVFHSGDYDLGLSSNGIFEI 414 (769)
Q Consensus 366 ~m~~l~~~TGG~v~~~~~f~~~~~~~~l~~~~~~~~~~~~~~~~~~l~v 414 (769)
.|..||+.+||..++..+ .+...+.+.+++.... .+...+..+++
T Consensus 413 lL~~lA~~g~G~~~~i~~--~~~~~~~~~~~l~~~~--~p~l~~v~v~~ 457 (596)
T TIGR03788 413 FMRKAAQFGRGSFTFIGS--TDEVQRKMSQLFAKLE--QPALTDIALTF 457 (596)
T ss_pred HHHHHHHcCCCEEEECCC--HHHHHHHHHHHHHhhc--CeEEEEEEEEE
Confidence 899999999998777643 3344455556663321 22345555544
No 38
>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=97.56 E-value=0.0043 Score=60.48 Aligned_cols=149 Identities=19% Similarity=0.245 Sum_probs=92.8
Q ss_pred EEEEEEcCcchh--HHHHHHHHHHHhcccCC---CCceEEEEEECCeEEEE-EccCCCCCCCeeEEecCCccCCHHHHHH
Q 004199 132 FMFVVDTCIIEE--EMSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (769)
Q Consensus 132 ~vFvID~s~~~~--~l~~~~~~l~~~l~~lp---~~~~VglITfd~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (769)
.+|+||.|.+-. +++.+++.++..++.++ +.++||+|+|++..+.. ++. .
T Consensus 3 ivfllD~S~Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~~~~~l~-~----------------------- 58 (165)
T cd01481 3 IVFLIDGSDNVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPRPEFYLN-T----------------------- 58 (165)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCeeEEEecc-c-----------------------
Confidence 589999999744 58889988888888774 56999999998765431 111 0
Q ss_pred HhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhcc
Q 004199 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (769)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~ 285 (769)
+- .+..+.+.+++++. ..+ ..+.+|.||..|...+-.
T Consensus 59 ------------------------------~~-----~~~~l~~~i~~i~~-----~~g--~~t~t~~AL~~~~~~~f~- 95 (165)
T cd01481 59 ------------------------------HS-----TKADVLGAVRRLRL-----RGG--SQLNTGSALDYVVKNLFT- 95 (165)
T ss_pred ------------------------------cC-----CHHHHHHHHHhccc-----CCC--CcccHHHHHHHHHHhhcC-
Confidence 00 12234445555533 111 235689999987664321
Q ss_pred CCCCCc-------E-EEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEe
Q 004199 286 VPGSGA-------R-ILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFAC 357 (769)
Q Consensus 286 ~~~~gg-------r-I~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~ 357 (769)
...|+ | ++++++|..+ .+ ..+-|..+...|| .+|+.
T Consensus 96 -~~~g~R~~~~~~kv~vviTdG~s~------------------d~---------------~~~~a~~lr~~gv--~i~~v 139 (165)
T cd01481 96 -KSAGSRIEEGVPQFLVLITGGKSQ------------------DD---------------VERPAVALKRAGI--VPFAI 139 (165)
T ss_pred -ccccCCccCCCCeEEEEEeCCCCc------------------ch---------------HHHHHHHHHHCCc--EEEEE
Confidence 12222 2 5677777321 00 2344667777775 56777
Q ss_pred cCCccChhhhhhhhhccCceEEEeCCC
Q 004199 358 ALDQVGVAELKVAVEKTGGLVVLSDSF 384 (769)
Q Consensus 358 ~~~~~~l~~m~~l~~~TGG~v~~~~~f 384 (769)
+....+..+|..++... -.++..++|
T Consensus 140 G~~~~~~~eL~~ias~p-~~vf~v~~f 165 (165)
T cd01481 140 GARNADLAELQQIAFDP-SFVFQVSDF 165 (165)
T ss_pred eCCcCCHHHHHHHhCCC-ccEEEecCC
Confidence 66668888998888766 466665554
No 39
>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell. In association with invasion, T. gondii sequentially discharges three sets of secretory organelles beginning with the micronemes, which contain adhesive proteins involved in parasite attachment to a host cell. Deployed as protein complexes, several micronemal proteins possess vertebrate-derived adhesive sequences that function in binding receptors. The VWA domain likely mediates the protein-protein interactions of these with their interacting partners.
Probab=97.54 E-value=0.0025 Score=63.31 Aligned_cols=148 Identities=14% Similarity=0.078 Sum_probs=90.6
Q ss_pred EEEEEEcCcchh--H-HHHHHHHHHHhcccCC---CCceEEEEEECCeEEE-EEccCCCCCCCeeEEecCCccCCHHHHH
Q 004199 132 FMFVVDTCIIEE--E-MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQV-HELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (769)
Q Consensus 132 ~vFvID~s~~~~--~-l~~~~~~l~~~l~~lp---~~~~VglITfd~~V~~-~~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (769)
++||||.|.+.. + ++.+++.+...++.++ ++.+||+|+|++..+. +.+. ..
T Consensus 3 v~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~~~~~l~-~~--------------------- 60 (186)
T cd01471 3 LYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAKELIRLS-SP--------------------- 60 (186)
T ss_pred EEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCceEEEECC-Cc---------------------
Confidence 689999999854 3 7788888888888764 6789999999987653 3332 10
Q ss_pred HHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhc
Q 004199 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (769)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~ 284 (769)
. ...+..+.++++.+.... . ....+.++.||..|...+..
T Consensus 61 --~---------------------------------~~~~~~~~~~i~~l~~~~--~---~~G~T~l~~aL~~a~~~l~~ 100 (186)
T cd01471 61 --N---------------------------------STNKDLALNAIRALLSLY--Y---PNGSTNTTSALLVVEKHLFD 100 (186)
T ss_pred --c---------------------------------ccchHHHHHHHHHHHhCc--C---CCCCccHHHHHHHHHHHhhc
Confidence 0 000112233344433311 1 12357899999999998864
Q ss_pred c---CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCc
Q 004199 285 C---VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (769)
Q Consensus 285 ~---~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~ 361 (769)
. .++....|+++++|.++.++. . .+.++++.+.|+.+-++..+ ..
T Consensus 101 ~~~~r~~~~~~villTDG~~~~~~~---------------------------~----~~~a~~l~~~gv~v~~igiG-~~ 148 (186)
T cd01471 101 TRGNRENAPQLVIIMTDGIPDSKFR---------------------------T----LKEARKLRERGVIIAVLGVG-QG 148 (186)
T ss_pred cCCCcccCceEEEEEccCCCCCCcc---------------------------h----hHHHHHHHHCCCEEEEEEee-hh
Confidence 1 112234688888887543210 0 02355666778776666554 45
Q ss_pred cChhhhhhhhhc
Q 004199 362 VGVAELKVAVEK 373 (769)
Q Consensus 362 ~~l~~m~~l~~~ 373 (769)
.+..+|..|+..
T Consensus 149 ~d~~~l~~ia~~ 160 (186)
T cd01471 149 VNHEENRSLVGC 160 (186)
T ss_pred hCHHHHHHhcCC
Confidence 777778777764
No 40
>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=97.54 E-value=0.004 Score=59.68 Aligned_cols=145 Identities=19% Similarity=0.193 Sum_probs=96.5
Q ss_pred EEEEEEcCcchhH--HHHHHHHHHHhcccCC---CCceEEEEEECCeEEEE-EccCCCCCCCeeEEecCCccCCHHHHHH
Q 004199 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (769)
Q Consensus 132 ~vFvID~s~~~~~--l~~~~~~l~~~l~~lp---~~~~VglITfd~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (769)
++|++|+|.+... ++.+++.+...+..+. ++.++||++|++..... ++. ..
T Consensus 3 i~~llD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~~~~~~~-~~---------------------- 59 (161)
T cd01450 3 IVFLLDGSESVGPENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVRVEFSLN-DY---------------------- 59 (161)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCceEEEECC-CC----------------------
Confidence 4799999998654 7778888887777664 47899999999754321 111 00
Q ss_pred HhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhcc
Q 004199 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (769)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~ 285 (769)
. ....+...++.+... .+ +.+.++.||..|...+...
T Consensus 60 ------------------------------~------~~~~~~~~i~~~~~~-----~~--~~t~~~~al~~a~~~~~~~ 96 (161)
T cd01450 60 ------------------------------K------SKDDLLKAVKNLKYL-----GG--GGTNTGKALQYALEQLFSE 96 (161)
T ss_pred ------------------------------C------CHHHHHHHHHhcccC-----CC--CCccHHHHHHHHHHHhccc
Confidence 0 122444455554431 11 3578899999999988842
Q ss_pred C---CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCcc
Q 004199 286 V---PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (769)
Q Consensus 286 ~---~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~ 362 (769)
. ......|++|++|.++.++ + ..++.+.+.+.++.|..+..+. .
T Consensus 97 ~~~~~~~~~~iiliTDG~~~~~~------~-------------------------~~~~~~~~~~~~v~v~~i~~g~--~ 143 (161)
T cd01450 97 SNARENVPKVIIVLTDGRSDDGG------D-------------------------PKEAAAKLKDEGIKVFVVGVGP--A 143 (161)
T ss_pred ccccCCCCeEEEEECCCCCCCCc------c-------------------------hHHHHHHHHHCCCEEEEEeccc--c
Confidence 2 2344579999999776553 0 1344566667788888887765 7
Q ss_pred ChhhhhhhhhccC
Q 004199 363 GVAELKVAVEKTG 375 (769)
Q Consensus 363 ~l~~m~~l~~~TG 375 (769)
+...|..|+..||
T Consensus 144 ~~~~l~~la~~~~ 156 (161)
T cd01450 144 DEEELREIASCPS 156 (161)
T ss_pred CHHHHHHHhCCCC
Confidence 8888999999883
No 41
>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=97.46 E-value=0.0043 Score=62.09 Aligned_cols=49 Identities=22% Similarity=0.290 Sum_probs=37.9
Q ss_pred CCcEEEEEEEcCcchh--HHHHHHHHHHHhcccC---------CCCceEEEEEECCeEEE
Q 004199 128 VPPVFMFVVDTCIIEE--EMSFLKSALSQAIDLL---------PDNSLVGLITFGTLVQV 176 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~--~l~~~~~~l~~~l~~l---------p~~~~VglITfd~~V~~ 176 (769)
.+-=.+||||.|.+.. +++.+++.++..+..+ |..+|||+|+|++..++
T Consensus 18 ~~~DivfvlD~S~Sm~~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a~~ 77 (193)
T cd01477 18 LWLDIVFVVDNSKGMTQGGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNATV 77 (193)
T ss_pred ceeeEEEEEeCCCCcchhhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCceEE
Confidence 4556899999999853 4888888887766543 44589999999987755
No 42
>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=97.40 E-value=0.0052 Score=72.05 Aligned_cols=176 Identities=18% Similarity=0.080 Sum_probs=115.5
Q ss_pred CCcEEEEEEEcCcchhH--HHHHHHHHHHhccc-CCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHH
Q 004199 128 VPPVFMFVVDTCIIEEE--MSFLKSALSQAIDL-LPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~~--l~~~~~~l~~~l~~-lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (769)
..-.++||||+|.++.. ++.+|.++...+.. +.+.-+||||+|++...-+-+. .+
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 45568899999998753 88999998888875 4456699999997543111111 00
Q ss_pred HHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhc
Q 004199 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (769)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~ 284 (769)
.....+...|+.|+. ...+.++.||..|...+..
T Consensus 464 -------------------------------------~~~~~~~~~L~~l~~---------gGgTpL~~gL~~A~~~~~~ 497 (589)
T TIGR02031 464 -------------------------------------RSVEQAKRRLDVLPG---------GGGTPLAAGLAAAFQTALQ 497 (589)
T ss_pred -------------------------------------CCHHHHHHHHhcCCC---------CCCCcHHHHHHHHHHHHHH
Confidence 011122344555543 2346789999999999874
Q ss_pred cCCCCC--cEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCcc
Q 004199 285 CVPGSG--ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (769)
Q Consensus 285 ~~~~~g--grI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~ 362 (769)
... .+ -.|++++.|-+|.|-+.....+ + .-..+..+-...++..+...||.+=++-+...+.
T Consensus 498 ~~~-~~~~~~ivllTDG~~nv~~~~~~~~~------------~---~~~~~~~~~~~~~a~~~~~~gi~~~vid~~~~~~ 561 (589)
T TIGR02031 498 ARS-SGGTPTIVLITDGRGNIPLDGDPESI------------K---ADREQAAEEALALARKIREAGMPALVIDTAMRFV 561 (589)
T ss_pred hcc-cCCceEEEEECCCCCCCCCCcccccc------------c---ccchhHHHHHHHHHHHHHhcCCeEEEEeCCCCCc
Confidence 222 23 3799999999998753110000 0 0012233444567888888998877777776666
Q ss_pred ChhhhhhhhhccCceEEEeCCCCch
Q 004199 363 GVAELKVAVEKTGGLVVLSDSFGHA 387 (769)
Q Consensus 363 ~l~~m~~l~~~TGG~v~~~~~f~~~ 387 (769)
....+..||+..||..|+.++.+.+
T Consensus 562 ~~~~~~~lA~~~~g~y~~l~~~~a~ 586 (589)
T TIGR02031 562 STGFAQKLARKMGAHYIYLPNATAA 586 (589)
T ss_pred cchHHHHHHHhcCCcEEeCCCCChh
Confidence 6667889999999999999887654
No 43
>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=97.39 E-value=0.0039 Score=60.92 Aligned_cols=156 Identities=21% Similarity=0.250 Sum_probs=95.2
Q ss_pred EEEEEEcCcchhH--HHHHHHHHHHhcccC---CCCceEEEEEECCeEEEE-EccCCCCCCCeeEEecCCccCCHHHHHH
Q 004199 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLL---PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (769)
Q Consensus 132 ~vFvID~s~~~~~--l~~~~~~l~~~l~~l---p~~~~VglITfd~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l~~ 205 (769)
.+|+||.|..... ++.+++.+...++.+ ++.++||+|+|++..+.+ .+. .. .+
T Consensus 2 ivflvD~S~sm~~~~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~~~~~~~-~~-----------------~~--- 60 (178)
T PF00092_consen 2 IVFLVDTSGSMSGDNFEKAKQFVKSIISRLSISNNGTRVGIVTFSDSARVLFSLT-DY-----------------QS--- 60 (178)
T ss_dssp EEEEEE-STTSCHHHHHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEEEEEETT-SH-----------------SS---
T ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHHhhhccccccccceeeeecccccccccc-cc-----------------cc---
Confidence 5899999998654 888888888888754 567999999999877532 222 10 00
Q ss_pred HhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHH-HHcCCCCCCCCCCCCCccchhHHHHHHHHHhhc
Q 004199 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVL-EELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (769)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll-~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~ 284 (769)
...+...+ ..++. ....+.+|.||..|...+..
T Consensus 61 --------------------------------------~~~~~~~i~~~~~~--------~~g~t~~~~aL~~a~~~l~~ 94 (178)
T PF00092_consen 61 --------------------------------------KNDLLNAINDSIPS--------SGGGTNLGAALKFAREQLFS 94 (178)
T ss_dssp --------------------------------------HHHHHHHHHTTGGC--------CBSSB-HHHHHHHHHHHTTS
T ss_pred --------------------------------------cccccccccccccc--------cchhhhHHHHHhhhhhcccc
Confidence 11112222 22222 23456799999999999874
Q ss_pred c----CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCC
Q 004199 285 C----VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (769)
Q Consensus 285 ~----~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~ 360 (769)
. .++...-|++++.|.++.++- ... .+..+... ..|.+|+.+.+
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 122334578888886654420 001 11111111 56677777667
Q ss_pred ccChhhhhhhhhc--cCceEEEeCCCCc
Q 004199 361 QVGVAELKVAVEK--TGGLVVLSDSFGH 386 (769)
Q Consensus 361 ~~~l~~m~~l~~~--TGG~v~~~~~f~~ 386 (769)
..+..++..|+.. .+|.+++..++..
T Consensus 143 ~~~~~~l~~la~~~~~~~~~~~~~~~~~ 170 (178)
T PF00092_consen 143 NADNEELRELASCPTSEGHVFYLADFSD 170 (178)
T ss_dssp CCHHHHHHHHSHSSTCHHHEEEESSHHH
T ss_pred cCCHHHHHHHhCCCCCCCcEEEcCCHHH
Confidence 7888999999965 3477888777754
No 44
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=97.33 E-value=0.012 Score=68.61 Aligned_cols=172 Identities=14% Similarity=0.089 Sum_probs=111.8
Q ss_pred CCcEEEEEEEcCcchh--HHHHHHHHHHHhccc-CCCCceEEEEEECCe-EEEEEccCCCCCCCeeEEecCCccCCHHHH
Q 004199 128 VPPVFMFVVDTCIIEE--EMSFLKSALSQAIDL-LPDNSLVGLITFGTL-VQVHELGGFGQIIPKTYVFKGSKDVSKDQL 203 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~--~l~~~~~~l~~~l~~-lp~~~~VglITfd~~-V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l 203 (769)
.+-.++||||+|.++. .+..+|.++...|.. +.+.-+||+|+|++. ..+ -+. .+
T Consensus 400 ~~~~vvfvvD~SGSM~~~rl~~aK~a~~~ll~~ay~~rD~v~lI~F~g~~a~~-~lp-pT-------------------- 457 (584)
T PRK13406 400 SETTTIFVVDASGSAALHRLAEAKGAVELLLAEAYVRRDQVALVAFRGRGAEL-LLP-PT-------------------- 457 (584)
T ss_pred CCccEEEEEECCCCCcHhHHHHHHHHHHHHHHhhcCCCCEEEEEEECCCceeE-EcC-CC--------------------
Confidence 4678999999999874 388999998888854 456679999999754 322 111 00
Q ss_pred HHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhh
Q 004199 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG 283 (769)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~ 283 (769)
.+...+...|+.|+. ...+.++.||..|..++.
T Consensus 458 --------------------------------------~~~~~~~~~L~~l~~---------gGgTpL~~gL~~A~~~l~ 490 (584)
T PRK13406 458 --------------------------------------RSLVRAKRSLAGLPG---------GGGTPLAAGLDAAAALAL 490 (584)
T ss_pred --------------------------------------cCHHHHHHHHhcCCC---------CCCChHHHHHHHHHHHHH
Confidence 011233344455543 235788999999998886
Q ss_pred ccC-CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCcc
Q 004199 284 ACV-PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (769)
Q Consensus 284 ~~~-~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~ 362 (769)
... ++.--.|+++|.|-+|.|.+.-..+. .....+ ..++..+...+|.+=++-+....
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 421 12236899999999988753211110 000111 34577777888876666555443
Q ss_pred ChhhhhhhhhccCceEEEeCCCCchhhH
Q 004199 363 GVAELKVAVEKTGGLVVLSDSFGHAVFK 390 (769)
Q Consensus 363 ~l~~m~~l~~~TGG~v~~~~~f~~~~~~ 390 (769)
...+..||+.+||..|..+..+.....
T Consensus 550 -~~~~~~LA~~~gg~y~~l~~~~a~~~~ 576 (584)
T PRK13406 550 -QPQARALAEAMGARYLPLPRADAGRLS 576 (584)
T ss_pred -cHHHHHHHHhcCCeEEECCCCCHHHHH
Confidence 345889999999999999988876543
No 45
>smart00327 VWA von Willebrand factor (vWF) type A domain. VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.
Probab=97.29 E-value=0.02 Score=55.60 Aligned_cols=154 Identities=21% Similarity=0.158 Sum_probs=100.4
Q ss_pred cEEEEEEEcCcch-hH-HHHHHHHHHHhcccCCC---CceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHHH
Q 004199 130 PVFMFVVDTCIIE-EE-MSFLKSALSQAIDLLPD---NSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (769)
Q Consensus 130 p~~vFvID~s~~~-~~-l~~~~~~l~~~l~~lp~---~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (769)
.-++||||+|.+. .. ++.+++.+...+..+.. +.+||+++|++..+.+.-- .
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 3478999999987 33 78888888888877765 8999999999844332100 0
Q ss_pred HHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhc
Q 004199 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (769)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~ 284 (769)
.......+...++.+... .....-++.|+..|...+..
T Consensus 59 -----------------------------------~~~~~~~~~~~i~~~~~~-------~~~~~~~~~al~~~~~~~~~ 96 (177)
T smart00327 59 -----------------------------------DSRSKDALLEALASLSYK-------LGGGTNLGAALQYALENLFS 96 (177)
T ss_pred -----------------------------------ccCCHHHHHHHHHhcCCC-------CCCCchHHHHHHHHHHHhcC
Confidence 000122444555555431 12345688888888888752
Q ss_pred cCCC----CCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCC
Q 004199 285 CVPG----SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (769)
Q Consensus 285 ~~~~----~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~ 360 (769)
.... ..-.|++|++|.++.+ ..+.+...++.+.+|.+..+..+.+
T Consensus 97 ~~~~~~~~~~~~iviitDg~~~~~-------------------------------~~~~~~~~~~~~~~i~i~~i~~~~~ 145 (177)
T smart00327 97 KSAGSRRGAPKVLILITDGESNDG-------------------------------GDLLKAAKELKRSGVKVFVVGVGND 145 (177)
T ss_pred cCCCCCCCCCeEEEEEcCCCCCCC-------------------------------ccHHHHHHHHHHCCCEEEEEEccCc
Confidence 1111 1346888888865533 1234567777788888888877654
Q ss_pred ccChhhhhhhhhccCceEEE
Q 004199 361 QVGVAELKVAVEKTGGLVVL 380 (769)
Q Consensus 361 ~~~l~~m~~l~~~TGG~v~~ 380 (769)
. +-..+..++..++|...+
T Consensus 146 ~-~~~~l~~~~~~~~~~~~~ 164 (177)
T smart00327 146 V-DEEELKKLASAPGGVYVF 164 (177)
T ss_pred c-CHHHHHHHhCCCcceEEe
Confidence 3 788899999999987655
No 46
>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=97.21 E-value=0.015 Score=56.22 Aligned_cols=41 Identities=22% Similarity=0.332 Sum_probs=32.7
Q ss_pred EEEEEEcCcchhH-HHHHHHHHHHhcccCC---CCceEEEEEECC
Q 004199 132 FMFVVDTCIIEEE-MSFLKSALSQAIDLLP---DNSLVGLITFGT 172 (769)
Q Consensus 132 ~vFvID~s~~~~~-l~~~~~~l~~~l~~lp---~~~~VglITfd~ 172 (769)
++|++|+|.+... ++..++.++..+..+. +..+||+|+|++
T Consensus 3 v~~llD~S~Sm~~~~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~~ 47 (163)
T cd01476 3 LLFVLDSSGSVRGKFEKYKKYIERIVEGLEIGPTATRVALITYSG 47 (163)
T ss_pred EEEEEeCCcchhhhHHHHHHHHHHHHHhcCCCCCCcEEEEEEEcC
Confidence 5899999998655 6667777777777664 478999999987
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=97.17 E-value=0.0096 Score=70.63 Aligned_cols=161 Identities=19% Similarity=0.145 Sum_probs=104.5
Q ss_pred CCcEEEEEEEcCcchh---HHHHHHHHHHHhccc-CCCCceEEEEEECCe-EEEEEccCCCCCCCeeEEecCCccCCHHH
Q 004199 128 VPPVFMFVVDTCIIEE---EMSFLKSALSQAIDL-LPDNSLVGLITFGTL-VQVHELGGFGQIIPKTYVFKGSKDVSKDQ 202 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~---~l~~~~~~l~~~l~~-lp~~~~VglITfd~~-V~~~~l~~~~~~~~~~~v~~g~~~~~~~~ 202 (769)
....++||||+|.++. .++.++.++...+.. .....+||+|+|++. ..+. +. .
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 4557889999999874 377788887776653 456789999999743 2210 00 0
Q ss_pred HHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHh
Q 004199 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (769)
Q Consensus 203 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll 282 (769)
......+...|+.|+. ...+.++.||..|..++
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 0112233345555543 23467899999999988
Q ss_pred hcc---CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecC
Q 004199 283 GAC---VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACAL 359 (769)
Q Consensus 283 ~~~---~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~ 359 (769)
... .+...+.|++++.|-+|.|.+. . + . ..+ -..++..+...||.+.++-+..
T Consensus 555 ~~~~~~~~~~~~~vvliTDG~~n~~~~~--~-~---~-----------------~~~-~~~~a~~l~~~~i~~~vIdt~~ 610 (633)
T TIGR02442 555 SNELLRDDDGRPLLVVITDGRANVADGG--E-P---P-----------------TDD-ARTIAAKLAARGILFVVIDTES 610 (633)
T ss_pred HHhhccCCCCceEEEEECCCCCCCCCCC--C-C---h-----------------HHH-HHHHHHHHHhcCCeEEEEeCCC
Confidence 721 1234577999999998876211 0 0 0 001 1456777777788777666666
Q ss_pred CccChhhhhhhhhccCceEEEe
Q 004199 360 DQVGVAELKVAVEKTGGLVVLS 381 (769)
Q Consensus 360 ~~~~l~~m~~l~~~TGG~v~~~ 381 (769)
..++...+..||+.+||..+..
T Consensus 611 ~~~~~~~~~~lA~~~gg~y~~l 632 (633)
T TIGR02442 611 GFVRLGLAEDLARALGGEYVRL 632 (633)
T ss_pred CCcchhHHHHHHHhhCCeEEec
Confidence 6677788999999999998864
No 48
>smart00262 GEL Gelsolin homology domain. Gelsolin/severin/villin homology domain. Calcium-binding and actin-binding. Both intra- and extracellular domains.
Probab=97.04 E-value=0.0024 Score=55.40 Aligned_cols=70 Identities=11% Similarity=0.095 Sum_probs=49.8
Q ss_pred cccccccccccCeEEEEeCCcEEEEEECCCchHHHHccCCCCchhHHHHHhhhCcHHHHHHHHh-cCCCCcEEEEEcCCC
Q 004199 643 PALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYHNQPEHQAFAQLLQAPHDDAGVIMK-ERFPVPRLVICDQHG 721 (769)
Q Consensus 643 ~v~Ls~~~l~~d~i~llD~g~~i~i~~G~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~-~R~~~p~~~~~~~g~ 721 (769)
.++++.++|.++.+||||+|..||+|+|+.++.- +. ..+...++.+.+ .|.+..++.++++|.
T Consensus 15 ~~~~~~~~L~s~d~fild~~~~iyvW~G~~as~~---------ek-------~~A~~~a~~~~~~~~~~~~~i~~v~eg~ 78 (90)
T smart00262 15 EVPFSQGSLNSGDCYILDTGSEIYVWVGKKSSQD---------EK-------KKAAELAVELDDTLGPGPVQVRVVDEGK 78 (90)
T ss_pred EcCCCHHHCCCCCEEEEECCCEEEEEECCCCCHH---------HH-------HHHHHHHHHHHHhcCCCCceEEEEeCCC
Confidence 4567888999999999999999999999987621 11 112234455543 445677888898998
Q ss_pred ChHHHHH
Q 004199 722 SQARFLL 728 (769)
Q Consensus 722 s~~r~l~ 728 (769)
....|+.
T Consensus 79 E~~~F~~ 85 (90)
T smart00262 79 EPPEFWS 85 (90)
T ss_pred CCHHHHH
Confidence 7766653
No 49
>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=96.97 E-value=0.036 Score=52.33 Aligned_cols=147 Identities=24% Similarity=0.322 Sum_probs=94.7
Q ss_pred EEEEEEEcCcch--hHHHHHHHHHHHhcccCCC---CceEEEEEECCeEEEEE-ccCCCCCCCeeEEecCCccCCHHHHH
Q 004199 131 VFMFVVDTCIIE--EEMSFLKSALSQAIDLLPD---NSLVGLITFGTLVQVHE-LGGFGQIIPKTYVFKGSKDVSKDQLL 204 (769)
Q Consensus 131 ~~vFvID~s~~~--~~l~~~~~~l~~~l~~lp~---~~~VglITfd~~V~~~~-l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (769)
.++|+||+|.++ ..++.+++.+...+..++. ..+||++.|+...+.+- +. .
T Consensus 2 ~v~~viD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~f~~~~~~~~~~~-~---------------------- 58 (161)
T cd00198 2 DIVFLLDVSGSMGGEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARVVLPLT-T---------------------- 58 (161)
T ss_pred cEEEEEeCCCCcCcchHHHHHHHHHHHHHhcccCCCCcEEEEEEecCccceeeccc-c----------------------
Confidence 378999999986 3388888888888888875 78999999997433221 11 0
Q ss_pred HHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhc
Q 004199 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (769)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~ 284 (769)
. .....+...++.+.. .......+..|+..|...+..
T Consensus 59 -------------------------------~-----~~~~~~~~~~~~~~~-------~~~~~t~~~~al~~~~~~~~~ 95 (161)
T cd00198 59 -------------------------------D-----TDKADLLEAIDALKK-------GLGGGTNIGAALRLALELLKS 95 (161)
T ss_pred -------------------------------c-----CCHHHHHHHHHhccc-------CCCCCccHHHHHHHHHHHhcc
Confidence 0 011233344444432 112345678889999888874
Q ss_pred cC-CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCCccC
Q 004199 285 CV-PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVG 363 (769)
Q Consensus 285 ~~-~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~~~~ 363 (769)
.. +.....+++|++|.++.++ . -..+....+...++.+.++.++. ..+
T Consensus 96 ~~~~~~~~~lvvitDg~~~~~~-----~-------------------------~~~~~~~~~~~~~v~v~~v~~g~-~~~ 144 (161)
T cd00198 96 AKRPNARRVIILLTDGEPNDGP-----E-------------------------LLAEAARELRKLGITVYTIGIGD-DAN 144 (161)
T ss_pred cCCCCCceEEEEEeCCCCCCCc-----c-------------------------hhHHHHHHHHHcCCEEEEEEcCC-CCC
Confidence 21 2356778888888655443 0 01234556667799998888775 455
Q ss_pred hhhhhhhhhcc
Q 004199 364 VAELKVAVEKT 374 (769)
Q Consensus 364 l~~m~~l~~~T 374 (769)
-..++.|+..|
T Consensus 145 ~~~l~~l~~~~ 155 (161)
T cd00198 145 EDELKEIADKT 155 (161)
T ss_pred HHHHHHHhccc
Confidence 66788888877
No 50
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=96.91 E-value=0.044 Score=54.84 Aligned_cols=146 Identities=13% Similarity=0.070 Sum_probs=88.9
Q ss_pred EEEEEEcCcchhH--HH-HHHHHHHHhcccC---CCCceEEEEEECCeEEEE-EccCCCCCCCeeEEecCCccCCHHHHH
Q 004199 132 FMFVVDTCIIEEE--MS-FLKSALSQAIDLL---PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (769)
Q Consensus 132 ~vFvID~s~~~~~--l~-~~~~~l~~~l~~l---p~~~~VglITfd~~V~~~-~l~~~~~~~~~~~v~~g~~~~~~~~l~ 204 (769)
.+|+||.|.+..+ ++ .+++.++..++.+ +++++||+|+|++..+++ .+. ..
T Consensus 3 i~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~~~~~~~-~~--------------------- 60 (192)
T cd01473 3 LTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNRDVVPFS-DE--------------------- 60 (192)
T ss_pred EEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCceeEEecC-cc---------------------
Confidence 5899999998644 55 4677777777765 467999999999876542 222 00
Q ss_pred HHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhc
Q 004199 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (769)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~ 284 (769)
....+..+...++++... +.. ...+.+|.||..|...+..
T Consensus 61 -----------------------------------~~~~~~~l~~~i~~l~~~---~~~--~g~T~~~~AL~~a~~~~~~ 100 (192)
T cd01473 61 -----------------------------------ERYDKNELLKKINDLKNS---YRS--GGETYIVEALKYGLKNYTK 100 (192)
T ss_pred -----------------------------------cccCHHHHHHHHHHHHhc---cCC--CCcCcHHHHHHHHHHHhcc
Confidence 000123445555566541 111 2356799999999887753
Q ss_pred cCCCCCc------EEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEec
Q 004199 285 CVPGSGA------RILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACA 358 (769)
Q Consensus 285 ~~~~~gg------rI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~ 358 (769)
..|+ -++++|.|..+.+- + .=-.+.+..+.+.||.+-.+..+
T Consensus 101 ---~~~~r~~~~kv~IllTDG~s~~~~------------------~-----------~~~~~~a~~lk~~gV~i~~vGiG 148 (192)
T cd01473 101 ---HGNRRKDAPKVTMLFTDGNDTSAS------------------K-----------KELQDISLLYKEENVKLLVVGVG 148 (192)
T ss_pred ---CCCCcccCCeEEEEEecCCCCCcc------------------h-----------hhHHHHHHHHHHCCCEEEEEEec
Confidence 2222 27777777432110 0 00124577788888888777665
Q ss_pred CCccChhhhhhhhhc
Q 004199 359 LDQVGVAELKVAVEK 373 (769)
Q Consensus 359 ~~~~~l~~m~~l~~~ 373 (769)
. .+-.++..++..
T Consensus 149 ~--~~~~el~~ia~~ 161 (192)
T cd01473 149 A--ASENKLKLLAGC 161 (192)
T ss_pred c--ccHHHHHHhcCC
Confidence 4 456778887764
No 51
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=96.84 E-value=0.044 Score=62.55 Aligned_cols=164 Identities=12% Similarity=0.051 Sum_probs=95.1
Q ss_pred CCcEEEEEEEcCcchhH---HHHHHHHHHHhcccC---CCCceEEEEEECCeEE-EEEccCCCCCCCeeEEecCCccCCH
Q 004199 128 VPPVFMFVVDTCIIEEE---MSFLKSALSQAIDLL---PDNSLVGLITFGTLVQ-VHELGGFGQIIPKTYVFKGSKDVSK 200 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~~---l~~~~~~l~~~l~~l---p~~~~VglITfd~~V~-~~~l~~~~~~~~~~~v~~g~~~~~~ 200 (769)
..--.+||||.|.+... ++.++..+...+..+ ++..+||+++|++..+ ++.+. .. . .+
T Consensus 41 ~~lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~r~vfpL~-s~--~----------s~-- 105 (576)
T PTZ00441 41 EEVDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNTTELIRLG-SG--A----------SK-- 105 (576)
T ss_pred CCceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCceEEEecC-CC--c----------cc--
Confidence 45668999999998643 466777777777666 3568999999998654 33333 11 0 00
Q ss_pred HHHHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHH
Q 004199 201 DQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAAS 280 (769)
Q Consensus 201 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ 280 (769)
+ +..+...|.+|.... .+ ...+.+|.||..|..
T Consensus 106 -D-----------------------------------------k~~aL~~I~sL~~~~--~p---gGgTnig~AL~~Aae 138 (576)
T PTZ00441 106 -D-----------------------------------------KEQALIIVKSLRKTY--LP---YGKTNMTDALLEVRK 138 (576)
T ss_pred -c-----------------------------------------HHHHHHHHHHHHhhc--cC---CCCccHHHHHHHHHH
Confidence 0 112222333332210 11 124678999999888
Q ss_pred Hhhcc--CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEec
Q 004199 281 LLGAC--VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACA 358 (769)
Q Consensus 281 ll~~~--~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~ 358 (769)
.+... ..+..+.||+|+.|.++.+. . -.+.+.++...||.|-++..+
T Consensus 139 ~L~sr~~R~nvpKVVILLTDG~sns~~-----------------------d--------vleaAq~LR~~GVeI~vIGVG 187 (576)
T PTZ00441 139 HLNDRVNRENAIQLVILMTDGIPNSKY-----------------------R--------ALEESRKLKDRNVKLAVIGIG 187 (576)
T ss_pred HHhhcccccCCceEEEEEecCCCCCcc-----------------------c--------HHHHHHHHHHCCCEEEEEEeC
Confidence 87631 01233678889888643110 0 012355666778866666554
Q ss_pred CCccChhhhhhhh----hccCceEEEeCCCC
Q 004199 359 LDQVGVAELKVAV----EKTGGLVVLSDSFG 385 (769)
Q Consensus 359 ~~~~~l~~m~~l~----~~TGG~v~~~~~f~ 385 (769)
+..+...+..++ ..++|.+|...+|.
T Consensus 188 -~g~n~e~LrlIAgC~p~~g~c~~Y~vadf~ 217 (576)
T PTZ00441 188 -QGINHQFNRLLAGCRPREGKCKFYSDADWE 217 (576)
T ss_pred -CCcCHHHHHHHhccCCCCCCCceEEeCCHH
Confidence 346666666666 33556777777885
No 52
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=96.83 E-value=0.051 Score=55.56 Aligned_cols=169 Identities=17% Similarity=0.110 Sum_probs=112.4
Q ss_pred CCcEEEEEEEcCcchhH---HHHHHHHHHHhcccCC-CCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHH
Q 004199 128 VPPVFMFVVDTCIIEEE---MSFLKSALSQAIDLLP-DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQL 203 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~~---l~~~~~~l~~~l~~lp-~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l 203 (769)
..--+|||||.|.++.- .+++|-++.+.|..-. ..-+|++|+|.. .. .
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 34568999999998654 7888888777775433 356999999752 11 0
Q ss_pred HHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhh
Q 004199 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG 283 (769)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~ 283 (769)
.+++|...+-+.+...|+.|+.- + .+=+..||..|..++.
T Consensus 129 -------------------------------~lll~pT~sv~~~~~~L~~l~~G------G---~TPL~~aL~~a~ev~~ 168 (261)
T COG1240 129 -------------------------------ELLLPPTSSVELAERALERLPTG------G---KTPLADALRQAYEVLA 168 (261)
T ss_pred -------------------------------eEEeCCcccHHHHHHHHHhCCCC------C---CCchHHHHHHHHHHHH
Confidence 01122222234556667777651 2 3457999999999998
Q ss_pred ccCC---CCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEecCC
Q 004199 284 ACVP---GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (769)
Q Consensus 284 ~~~~---~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~~~ 360 (769)
.+.+ ..--.+++.+.|.||.+++.=+ .+.- .+.+.++...|+-+=+.-+-..
T Consensus 169 r~~r~~p~~~~~~vviTDGr~n~~~~~~~-----------------------~~e~--~~~a~~~~~~g~~~lvid~e~~ 223 (261)
T COG1240 169 REKRRGPDRRPVMVVITDGRANVPIPLGP-----------------------KAET--LEAASKLRLRGIQLLVIDTEGS 223 (261)
T ss_pred HhhccCCCcceEEEEEeCCccCCCCCCch-----------------------HHHH--HHHHHHHhhcCCcEEEEecCCc
Confidence 5432 2446789999999887752210 0011 1345566667776666666777
Q ss_pred ccChhhhhhhhhccCceEEEeCCCCchhh
Q 004199 361 QVGVAELKVAVEKTGGLVVLSDSFGHAVF 389 (769)
Q Consensus 361 ~~~l~~m~~l~~~TGG~v~~~~~f~~~~~ 389 (769)
++.+.-...||...||.+++.+..+....
T Consensus 224 ~~~~g~~~~iA~~~Gg~~~~L~~l~~~~i 252 (261)
T COG1240 224 EVRLGLAEEIARASGGEYYHLDDLSDDSI 252 (261)
T ss_pred cccccHHHHHHHHhCCeEEecccccchHH
Confidence 77888888999999999999998887543
No 53
>PF04056 Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like proteins are 40 kDa subunits of the transcription factor II H complex. This domain is often found associated with the C2H2 type Zn-finger (IPR007087 from INTERPRO).; GO: 0008270 zinc ion binding, 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent
Probab=96.68 E-value=0.035 Score=55.01 Aligned_cols=95 Identities=20% Similarity=0.201 Sum_probs=65.7
Q ss_pred CccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHH
Q 004199 267 STRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLV 346 (769)
Q Consensus 267 ~~~~~G~Al~~A~~ll~~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~ 346 (769)
....+-.||+.|...|+..-.+..=.|+++.++.-|.-||.+ .+..+.+.
T Consensus 78 G~~SLqN~Le~A~~~L~~~p~~~srEIlvi~gSl~t~Dp~di------------------------------~~ti~~l~ 127 (193)
T PF04056_consen 78 GEPSLQNGLEMARSSLKHMPSHGSREILVIFGSLTTCDPGDI------------------------------HETIESLK 127 (193)
T ss_pred CChhHHHHHHHHHHHHhhCccccceEEEEEEeecccCCchhH------------------------------HHHHHHHH
Confidence 456788999999999985322222356666777666666532 24567888
Q ss_pred hcCcEEEEEEecCCccChhhhhhhhhccCceEEEeCCCCchhhHHHHHHH
Q 004199 347 HQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRV 396 (769)
Q Consensus 347 ~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~v~~~~~f~~~~~~~~l~~~ 396 (769)
+.+|-|++...+. .+.-.+.+|+.|||..... .++..|++.|...
T Consensus 128 ~~~IrvsvI~laa---Ev~I~k~i~~~T~G~y~V~--lde~H~~~lL~~~ 172 (193)
T PF04056_consen 128 KENIRVSVISLAA---EVYICKKICKETGGTYGVI--LDEDHFKELLMEH 172 (193)
T ss_pred HcCCEEEEEEEhH---HHHHHHHHHHhhCCEEEEe--cCHHHHHHHHHhh
Confidence 8999999999876 5777899999999954433 3445566544433
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=96.07 E-value=0.17 Score=49.54 Aligned_cols=43 Identities=14% Similarity=0.097 Sum_probs=34.6
Q ss_pred EEEEEEEcCcchh---HHHHHHHHHHHhcccCCC-CceEEEEEECCe
Q 004199 131 VFMFVVDTCIIEE---EMSFLKSALSQAIDLLPD-NSLVGLITFGTL 173 (769)
Q Consensus 131 ~~vFvID~s~~~~---~l~~~~~~l~~~l~~lp~-~~~VglITfd~~ 173 (769)
.++|+||+|.++. .++.+++++...++.+.+ +.++|+++|++.
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 5789999999864 378888888777777764 789999999875
No 55
>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=95.96 E-value=0.16 Score=51.85 Aligned_cols=155 Identities=17% Similarity=0.156 Sum_probs=87.5
Q ss_pred EEEEEEEcCcchh---------HHHHHHHHHHHhcccC---CCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccC
Q 004199 131 VFMFVVDTCIIEE---------EMSFLKSALSQAIDLL---PDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDV 198 (769)
Q Consensus 131 ~~vFvID~s~~~~---------~l~~~~~~l~~~l~~l---p~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~ 198 (769)
..+|+||+|.++. .++.+++.+...+... -++.+||+|.|++.-+-. .. .....+|+.
T Consensus 3 ~ivf~iDvS~SM~~~~~~~~~s~l~~a~~~i~~~~~~ki~~~~~D~vGlilf~t~~~~~----~~-~~~~i~v~~----- 72 (218)
T cd01458 3 SVVFLVDVSPSMFESKDGEYESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTEESKN----PV-GYENIYVLL----- 72 (218)
T ss_pred EEEEEEeCCHHHcCCCCCCCCChHHHHHHHHHHHHHhceeCCCCCeEEEEEEcccCCCC----cC-CCCceEEee-----
Confidence 4799999998652 2788888888888762 456799999998643210 00 111222210
Q ss_pred CHHHHHHHhhcccCCCCCCCccccCcCCCCCccccccceeechhcHHHHHHHHHHcCCCCCC--CCCCCCCccchhHHHH
Q 004199 199 SKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWP--VPPDQRSTRCTGTALS 276 (769)
Q Consensus 199 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~e~~~~i~~ll~~l~~~~~~--~~~~~~~~~~~G~Al~ 276 (769)
|+ ..| ....+..+++.+...... ...+......++.||.
T Consensus 73 ---------------------------------~l---~~~---~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~l~~aL~ 113 (218)
T cd01458 73 ---------------------------------DL---DTP---GAERVEDLKELIEPGGLSFAGQVGDSGQVSLSDALW 113 (218)
T ss_pred ---------------------------------cC---CCC---CHHHHHHHHHHhhcchhhhcccCCCCCCccHHHHHH
Confidence 00 000 012333333332221000 0011234678999999
Q ss_pred HHHHHhhccCC-CCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHhcCcEEEEE
Q 004199 277 IAASLLGACVP-GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLF 355 (769)
Q Consensus 277 ~A~~ll~~~~~-~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf 355 (769)
+|..++..+.+ ...-+|++||.|--..|.. .....-...++.++.+.||.+.+|
T Consensus 114 ~a~~~~~~~~~~~~~k~IvL~TDg~~p~~~~-------------------------~~~~~~~~~~a~~l~~~gI~i~~i 168 (218)
T cd01458 114 VCLDLFSKGKKKKSHKRIFLFTNNDDPHGGD-------------------------SIKDSQAAVKAEDLKDKGIELELF 168 (218)
T ss_pred HHHHHHHhccccccccEEEEECCCCCCCCCC-------------------------HHHHHHHHHHHHHHHhCCcEEEEE
Confidence 99999985212 2346799999984333210 001222456788888889999998
Q ss_pred EecC
Q 004199 356 ACAL 359 (769)
Q Consensus 356 ~~~~ 359 (769)
..+.
T Consensus 169 ~i~~ 172 (218)
T cd01458 169 PLSS 172 (218)
T ss_pred ecCC
Confidence 7654
No 56
>cd01462 VWA_YIEM_type VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=95.23 E-value=0.55 Score=44.69 Aligned_cols=43 Identities=16% Similarity=0.098 Sum_probs=32.1
Q ss_pred EEEEEEcCcchhH--HHHHHHHHHHhcccCC-CCceEEEEEECCeE
Q 004199 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP-DNSLVGLITFGTLV 174 (769)
Q Consensus 132 ~vFvID~s~~~~~--l~~~~~~l~~~l~~lp-~~~~VglITfd~~V 174 (769)
++|+||+|.+... ++..+..+...+..+. ++.+|++|+|++..
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 6899999998764 5566666666666554 47799999999873
No 57
>KOG0443 consensus Actin regulatory proteins (gelsolin/villin family) [Cytoskeleton]
Probab=94.44 E-value=0.065 Score=62.32 Aligned_cols=86 Identities=19% Similarity=0.222 Sum_probs=54.1
Q ss_pred hhhccceeEeecCC-CC---CccccccccccccCeEEEEeCCcEEEEEECCCchH-HHHccCCCCchhHHHHHhhhCcHH
Q 004199 625 VVMIQPSLISYSFH-SG---PEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQ-WRKAGYHNQPEHQAFAQLLQAPHD 699 (769)
Q Consensus 625 ~~~i~P~L~~~~~~-~~---p~~v~Ls~~~l~~d~i~llD~g~~i~i~~G~~v~~-~~~~~~~~~~~~~~~~~~l~~~~~ 699 (769)
..-..|+||..+.. +. -+-...+-+.|..|.|||||++..||||+|++++. +.. ..|+....
T Consensus 615 ~~~~~PrLF~Cs~~~g~f~~~EI~~F~QdDL~tdDi~lLDt~~evfvWvG~~a~~~eK~-------------~Al~~~~~ 681 (827)
T KOG0443|consen 615 KPERDPRLFSCSNKTGSFVVEEIYNFTQDDLMTDDIMLLDTWSEVFVWVGQEANEKEKE-------------EALTIGQK 681 (827)
T ss_pred cCCCCCcEEEEEecCCcEEEEEecCcchhhccccceEEEecCceEEEEecCCCChhHHH-------------HHHHHHHH
Confidence 45677999988863 21 12225666788999999999999999999998862 221 11111111
Q ss_pred HHHH-HHhcCCCCcEEEEEcCCCCh
Q 004199 700 DAGV-IMKERFPVPRLVICDQHGSQ 723 (769)
Q Consensus 700 ~~~~-l~~~R~~~p~~~~~~~g~s~ 723 (769)
..+. +...|-|.-.+++++||+-.
T Consensus 682 yl~~~~p~gr~~~TPI~vV~qG~EP 706 (827)
T KOG0443|consen 682 YLETDLPEGRDPRTPIYVVKQGHEP 706 (827)
T ss_pred HHhccCcccCCCCCceEEecCCCCC
Confidence 1111 24578886666677777543
No 58
>KOG2884 consensus 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=94.25 E-value=2 Score=42.65 Aligned_cols=86 Identities=22% Similarity=0.222 Sum_probs=57.4
Q ss_pred ccchhHHHHHHHHHhhccC-CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHH
Q 004199 268 TRCTGTALSIAASLLGACV-PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLV 346 (769)
Q Consensus 268 ~~~~G~Al~~A~~ll~~~~-~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~ 346 (769)
+.-++.+|++|...|++-. ++.--||++|.++|-.. ..+-.-++|+++.
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 4468899999999999521 12337999999986311 1112457899999
Q ss_pred hcCcEEEEEEecCCccChhhhhhhhhccCce-----EEEeCC
Q 004199 347 HQGHVLDLFACALDQVGVAELKVAVEKTGGL-----VVLSDS 383 (769)
Q Consensus 347 ~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~-----v~~~~~ 383 (769)
+++++|||.-++-..-+-.-+......++|. +...++
T Consensus 134 k~~Vaidii~FGE~~~~~e~l~~fida~N~~~~gshlv~Vpp 175 (259)
T KOG2884|consen 134 KNKVAIDIINFGEAENNTEKLFEFIDALNGKGDGSHLVSVPP 175 (259)
T ss_pred hcCeeEEEEEeccccccHHHHHHHHHHhcCCCCCceEEEeCC
Confidence 9999999999986555533444444444443 555554
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=93.42 E-value=0.99 Score=53.07 Aligned_cols=73 Identities=18% Similarity=0.207 Sum_probs=44.1
Q ss_pred ccchhHHHHHHHHHhhccCCCCC-cEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHH
Q 004199 268 TRCTGTALSIAASLLGACVPGSG-ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLV 346 (769)
Q Consensus 268 ~~~~G~Al~~A~~ll~~~~~~~g-grI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~ 346 (769)
...+..||.+|..++..+.++.+ -||++||+--.-.|. + + . ...-=...|..+.
T Consensus 116 ~~~l~daL~~~~~~f~~~~~k~~~kRI~lfTd~D~P~~~----------------~--~---~----~~~~a~~~a~dl~ 170 (584)
T TIGR00578 116 DYSLSEVLWVCANLFSDVQFRMSHKRIMLFTNEDNPHGN----------------D--S---A----KASRARTKAGDLR 170 (584)
T ss_pred CCcHHHHHHHHHHHHHhcchhhcCcEEEEECCCCCCCCC----------------c--h---h----HHHHHHHHHHHHH
Confidence 34789999999999985444555 469999965221110 0 0 0 0000122477888
Q ss_pred hcCcEEEEEEec-CCccChh
Q 004199 347 HQGHVLDLFACA-LDQVGVA 365 (769)
Q Consensus 347 ~~~isvDlf~~~-~~~~~l~ 365 (769)
..||.+++|..+ .+.+|..
T Consensus 171 ~~gi~ielf~l~~~~~Fd~s 190 (584)
T TIGR00578 171 DTGIFLDLMHLKKPGGFDIS 190 (584)
T ss_pred hcCeEEEEEecCCCCCCChh
Confidence 899999999654 2334444
No 60
>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=93.00 E-value=0.13 Score=50.63 Aligned_cols=45 Identities=20% Similarity=0.266 Sum_probs=35.7
Q ss_pred EEEEEEcCcchh--HHHHHHHHHHHhcccCC------CCceEEEEEECCeEEE
Q 004199 132 FMFVVDTCIIEE--EMSFLKSALSQAIDLLP------DNSLVGLITFGTLVQV 176 (769)
Q Consensus 132 ~vFvID~s~~~~--~l~~~~~~l~~~l~~lp------~~~~VglITfd~~V~~ 176 (769)
++||||+|.+.. .++.++++++..++.+. ++.+||+|+|++..++
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 579999999864 37888888888887774 3469999999987654
No 61
>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region). Portion of beta integrins that lies N-terminal to their EGF-like repeats. Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Beta integrins are proposed to have a von Willebrand factor type-A "insert" or "I" -like domain (although this remains to be confirmed).
Probab=92.83 E-value=19 Score=40.14 Aligned_cols=282 Identities=13% Similarity=0.081 Sum_probs=147.6
Q ss_pred CCcEEEEEEEcCcchhH----HHHHHHHHHHhcccCCCCceEEEEEEC-CeEEEEEccCCCCCCCeeEEecCCccCCHHH
Q 004199 128 VPPVFMFVVDTCIIEEE----MSFLKSALSQAIDLLPDNSLVGLITFG-TLVQVHELGGFGQIIPKTYVFKGSKDVSKDQ 202 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~~----l~~~~~~l~~~l~~lp~~~~VglITfd-~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~ 202 (769)
.|-=..|+.|+|.++.+ ++.+...|...|..+..+.++||=+|= +.|.=|-.. . .++
T Consensus 98 yPvDLYyLMDlS~SM~ddl~~lk~lg~~L~~~m~~it~n~rlGfGsFVDK~v~P~~~t-----~-------------p~~ 159 (423)
T smart00187 98 YPVDLYYLMDLSYSMKDDLDNLKSLGDDLAREMKGLTSNFRLGFGSFVDKTVSPFVST-----R-------------PEK 159 (423)
T ss_pred CccceEEEEeCCccHHHHHHHHHHHHHHHHHHHHhcccCceeeEEEeecCccCCcccC-----C-------------HHH
Confidence 56667899999999765 667777778888888899999999884 334221110 0 112
Q ss_pred HHHHhhcccCCCCCCCccccCcCCCCCcccc-ccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHH
Q 004199 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTI-ARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (769)
Q Consensus 203 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~-~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~l 281 (769)
+..+- ......+ ..|. =+-..++.+.-....+.+.+..-. .+.-.|+..+-+-+++|+--
T Consensus 160 l~~PC----------~~~~~~c-----~p~f~f~~~L~LT~~~~~F~~~V~~~~iS----gN~D~PEgG~DAimQaaVC~ 220 (423)
T smart00187 160 LENPC----------PNYNLTC-----EPPYGFKHVLSLTDDTDEFNEEVKKQRIS----GNLDAPEGGFDAIMQAAVCT 220 (423)
T ss_pred hcCCC----------cCCCCCc-----CCCcceeeeccCCCCHHHHHHHHhhceee----cCCcCCcccHHHHHHHHhhc
Confidence 22110 0000001 0122 122456666555556666554331 12234666666666776422
Q ss_pred hhccCCCCCcEEEEEecCCCC--CCCcccccCCCCCCcCCCCCCCCCCCcccc---hhHHHHHHHHHHHHhcCcEEEEEE
Q 004199 282 LGACVPGSGARILAFVGGPST--EGPAAIVSKNLSEPIRSHKDLDKDSAPHYH---KAVKFYDALSKQLVHQGHVLDLFA 356 (769)
Q Consensus 282 l~~~~~~~ggrI~~F~sg~pt--~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~---~a~~fY~~la~~~~~~~isvDlf~ 356 (769)
=+-..+...-|+++|++-.+- -|-|+|...-..+..+-|-+-.. .|.. ....--.+|++++.+++|-+ ||+
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 EQIGWREDARRLLVFSTDAGFHFAGDGKLAGIVQPNDGQCHLDNNG---EYTMSTTQDYPSIGQLNQKLAENNINP-IFA 296 (423)
T ss_pred cccccCCCceEEEEEEcCCCccccCCcceeeEecCCCCcceeCCCC---CcCccCcCCCCCHHHHHHHHHhcCceE-EEE
Confidence 111123445689999866544 68888776644444455533210 1111 11112457788888888865 888
Q ss_pred ecCCccChhhhhhhhhccCceEEEeCCCCchhhHHHHHHHhhcCccCccceeeeEEEEEe-cCCceEEeEEcCCcccCCC
Q 004199 357 CALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVFHSGDYDLGLSSNGIFEINC-SKDIKVQGIIGPCASLEKK 435 (769)
Q Consensus 357 ~~~~~~~l~~m~~l~~~TGG~v~~~~~f~~~~~~~~l~~~~~~~~~~~~~~~~~~l~vr~-S~gl~v~~~~G~~~~~~~~ 435 (769)
.+..+.++++ .|+..-.|...=-=+-+. ..+..++++. |.......+|+... +.+++++-.- .|-....
T Consensus 297 VT~~~~~~Y~--~Ls~lipgs~vg~Ls~DS----sNIv~LI~~a--Y~~i~S~V~l~~~~~p~~v~~~y~s-~C~~g~~- 366 (423)
T smart00187 297 VTKKQVSLYK--ELSALIPGSSVGVLSEDS----SNVVELIKDA--YNKISSRVELEDNSLPEGVSVTYTS-SCPGGVV- 366 (423)
T ss_pred EcccchhHHH--HHHHhcCcceeeecccCc----chHHHHHHHH--HHhhceEEEEecCCCCCcEEEEEEe-eCCCCCc-
Confidence 8888777763 455444444432111122 2233333221 12234555665553 5677775332 3321100
Q ss_pred CCCccccccccCCCCceeEecCCCCceEEEEEEEecC
Q 004199 436 GPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKK 472 (769)
Q Consensus 436 ~~~vsd~~~g~~~~~~~~l~~~~~~~s~~~~~~~~~~ 472 (769)
....-+..++.....+.|..++.-.
T Consensus 367 ------------~~~~~~C~~v~iG~~V~F~v~vta~ 391 (423)
T smart00187 367 ------------GPGTRKCEGVKIGDTVSFEVTVTAT 391 (423)
T ss_pred ------------ccCCcccCCcccCCEEEEEEEEEeC
Confidence 0111245567777888888877754
No 62
>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]
Probab=92.78 E-value=0.16 Score=57.75 Aligned_cols=90 Identities=23% Similarity=0.244 Sum_probs=65.1
Q ss_pred eeEeecCCC---CCccccccccccccCeEEEEeCCcEEEEEECCCchHHHHccCCCCchhHHHHHhhhCcHHHHHHHH-h
Q 004199 631 SLISYSFHS---GPEPALLDVAAIAADRILLLDSYFTVVIFHGATIAQWRKAGYHNQPEHQAFAQLLQAPHDDAGVIM-K 706 (769)
Q Consensus 631 ~L~~~~~~~---~p~~v~Ls~~~l~~d~i~llD~g~~i~i~~G~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~-~ 706 (769)
+||.++..| .-+||+|+..+|.+.-++|||.|.+||||-|....- . +-..++-+|..|- .
T Consensus 623 RlYrv~~~g~~i~lEPVpl~~tSLDPRf~FlLD~G~~IyiW~G~~s~~----------t------~~~KARLfAEkinK~ 686 (1255)
T KOG0444|consen 623 RLYRVGVNGTAIELEPVPLSVTSLDPRFCFLLDAGETIYIWSGYKSRI----------T------VSNKARLFAEKINKR 686 (1255)
T ss_pred hhheeccccceeEeeccCccccccCcceEEEEeCCceEEEEeccchhc----------c------cchHHHHHHHHhhhh
Confidence 455555443 358999999999999999999999999999976420 0 0011233555554 4
Q ss_pred cCCCCcEEEEEcCCCChHHHHHhh-hCCCCc
Q 004199 707 ERFPVPRLVICDQHGSQARFLLAK-LNPSAT 736 (769)
Q Consensus 707 ~R~~~p~~~~~~~g~s~~r~l~s~-L~p~~~ 736 (769)
+|-..--+-.++||.-...||.+- .+|++.
T Consensus 687 eRKgK~EI~l~rQg~e~pEFWqaLgg~p~e~ 717 (1255)
T KOG0444|consen 687 ERKGKSEIELCRQGREPPEFWQALGGNPDEP 717 (1255)
T ss_pred hccCceeeehhhhcCCCHHHHHHhCCCCccc
Confidence 677788888999999999999773 456663
No 63
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=92.16 E-value=0.21 Score=48.52 Aligned_cols=49 Identities=24% Similarity=0.371 Sum_probs=38.3
Q ss_pred CcEEEEEEEcCcchhH--HHHHHHHHHHhcccCCC------CceEEEEEECCeEEEEE
Q 004199 129 PPVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPD------NSLVGLITFGTLVQVHE 178 (769)
Q Consensus 129 ~p~~vFvID~s~~~~~--l~~~~~~l~~~l~~lp~------~~~VglITfd~~V~~~~ 178 (769)
-|+| |++|+|.+..- .+++..+|+..++.|.. .+.++|||||+.+++|.
T Consensus 4 lP~~-lllDtSgSM~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~~a~~~~ 60 (207)
T COG4245 4 LPCY-LLLDTSGSMIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGPARVIQ 60 (207)
T ss_pred CCEE-EEEecCcccccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecCcceEEe
Confidence 3554 89999998754 88888888888887743 47999999999777653
No 64
>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=90.77 E-value=12 Score=39.38 Aligned_cols=46 Identities=24% Similarity=0.302 Sum_probs=35.5
Q ss_pred CCcEEEEEEEcCcchhH-------HHHHHHHHHHhcccCCCCceEEEEEECCeEE
Q 004199 128 VPPVFMFVVDTCIIEEE-------MSFLKSALSQAIDLLPDNSLVGLITFGTLVQ 175 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~~-------l~~~~~~l~~~l~~lp~~~~VglITfd~~V~ 175 (769)
...-++++||.|.++.+ ++ .+..|..+++.++. .+||++.|++.+.
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 67889999999998754 45 45567777777764 5999999998753
No 65
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=89.73 E-value=8.7 Score=37.36 Aligned_cols=74 Identities=26% Similarity=0.305 Sum_probs=49.9
Q ss_pred HHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhhccCCCCC--cEEEEEecCCCCCCCcccccCCCCCCcCCCCC
Q 004199 245 FTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSG--ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKD 322 (769)
Q Consensus 245 ~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~~~~g--grI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d 322 (769)
.+|...|..++- +..--.+.+|+.|...++.- .+.| -||++|.++|...-
T Consensus 70 gkilt~lhd~~~---------~g~a~~~~~lqiaql~lkhR-~nk~q~qriVaFvgSpi~es------------------ 121 (243)
T COG5148 70 GKILTFLHDIRL---------HGGADIMRCLQIAQLILKHR-DNKGQRQRIVAFVGSPIQES------------------ 121 (243)
T ss_pred hHHHHHhccccc---------cCcchHHHHHHHHHHHHhcc-cCCccceEEEEEecCccccc------------------
Confidence 356666655544 12334788999999999851 1233 69999999863110
Q ss_pred CCCCCCcccchhHHHHHHHHHHHHhcCcEEEEEEec
Q 004199 323 LDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACA 358 (769)
Q Consensus 323 ~~~~~~~~~~~a~~fY~~la~~~~~~~isvDlf~~~ 358 (769)
.+-.-.+|+++.+++++||+.-++
T Consensus 122 ------------edeLirlak~lkknnVAidii~fG 145 (243)
T COG5148 122 ------------EDELIRLAKQLKKNNVAIDIIFFG 145 (243)
T ss_pred ------------HHHHHHHHHHHHhcCeeEEEEehh
Confidence 112336899999999999999875
No 66
>KOG0443 consensus Actin regulatory proteins (gelsolin/villin family) [Cytoskeleton]
Probab=87.99 E-value=0.8 Score=53.66 Aligned_cols=92 Identities=17% Similarity=0.139 Sum_probs=60.1
Q ss_pred cceeEeecC--CCC--C--ccccccccccccCeEEEEeCC-cEEEEEECCCchH-HHHccCCCCchhHHHHHhhhCcHHH
Q 004199 629 QPSLISYSF--HSG--P--EPALLDVAAIAADRILLLDSY-FTVVIFHGATIAQ-WRKAGYHNQPEHQAFAQLLQAPHDD 700 (769)
Q Consensus 629 ~P~L~~~~~--~~~--p--~~v~Ls~~~l~~d~i~llD~g-~~i~i~~G~~v~~-~~~~~~~~~~~~~~~~~~l~~~~~~ 700 (769)
.++||.++. .+. + ..-+|+-+-|..+.+||||+| ..||||+|..+.+ -++ ++...
T Consensus 254 ~~kLYkVsd~~g~l~v~~va~~~l~qdlLd~~dCYILD~g~~~IfVW~Gr~as~~ERk-----------------aAm~~ 316 (827)
T KOG0443|consen 254 AAKLYKVSDASGGLKVPVVADGPLTKDLLDTEDCYILDCGGGEIFVWKGRQASLDERK-----------------AAMSS 316 (827)
T ss_pred ccEEEEEeccCCCccccccccchhhHHhhccCCeEEEecCCceEEEEeCCCCCHHHHH-----------------HHHHH
Confidence 478999985 221 1 111277788899999999999 9999999998762 121 12234
Q ss_pred HHHHH--hcCCCCcEEEEEcCCCChHH---HHHhhhCCCCcC
Q 004199 701 AGVIM--KERFPVPRLVICDQHGSQAR---FLLAKLNPSATY 737 (769)
Q Consensus 701 ~~~l~--~~R~~~p~~~~~~~g~s~~r---~l~s~L~p~~~~ 737 (769)
|++.+ +.|.+.-.+..+.+|.-.+. +|.+=..++.++
T Consensus 317 AeeFlk~k~yP~~TqV~rv~EG~Esa~FKq~F~~W~~~~~t~ 358 (827)
T KOG0443|consen 317 AEEFLKKKKYPPNTQVVRVLEGAESAPFKQLFDSWPDKDQTN 358 (827)
T ss_pred HHHHHHhccCCCCceEEEecCCCcchhHHHHHhhCccccccc
Confidence 44444 35667788888888866554 444445555553
No 67
>cd01457 vWA_ORF176_type VWA ORF176 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most
Probab=87.01 E-value=8.7 Score=38.40 Aligned_cols=44 Identities=7% Similarity=-0.004 Sum_probs=30.4
Q ss_pred cEEEEEEEcCcchh---------HHHHHHHHHHHhcccCC--CCceEEEEEECCe
Q 004199 130 PVFMFVVDTCIIEE---------EMSFLKSALSQAIDLLP--DNSLVGLITFGTL 173 (769)
Q Consensus 130 p~~vFvID~s~~~~---------~l~~~~~~l~~~l~~lp--~~~~VglITfd~~ 173 (769)
.-++|+||.|.++. .++.+++++...+..++ +...+++++|++.
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 34789999999874 25777777777666543 2345887877543
No 68
>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=82.58 E-value=70 Score=33.87 Aligned_cols=87 Identities=18% Similarity=0.102 Sum_probs=58.9
Q ss_pred cchhHHHHHHHHHhhccC-------CCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHH
Q 004199 269 RCTGTALSIAASLLGACV-------PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDAL 341 (769)
Q Consensus 269 ~~~G~Al~~A~~ll~~~~-------~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~l 341 (769)
..+..||..|+-.+.-.. ....+||+++.++-+ +. ..+.-=+-+.
T Consensus 116 s~LagALS~ALCyINR~~~~~~~~~~~~~~RILv~~s~s~----------d~------------------~~QYi~~MN~ 167 (276)
T PF03850_consen 116 SLLAGALSMALCYINRISRESPSGGTSLKSRILVIVSGSP----------DS------------------SSQYIPLMNC 167 (276)
T ss_pred hhhHHHHHHHHHHHhhhhhcccCCCCCcCccEEEEEecCC----------Cc------------------cHHHHHHHHH
Confidence 678888888888776321 235679999644311 00 1111123455
Q ss_pred HHHHHhcCcEEEEEEecCCccChhhhhhhhhccCceEEEeCCCC
Q 004199 342 SKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFG 385 (769)
Q Consensus 342 a~~~~~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~v~~~~~f~ 385 (769)
.-.|.+.+|.||++..+. -+-.-|+..+..|||.-...+...
T Consensus 168 iFaAqk~~v~IDv~~L~~--~~s~fLqQa~d~T~G~y~~~~~~~ 209 (276)
T PF03850_consen 168 IFAAQKQKVPIDVCKLGG--KDSTFLQQASDITGGIYLKVSKPE 209 (276)
T ss_pred HHHHhcCCceeEEEEecC--CchHHHHHHHHHhCceeeccCccc
Confidence 677888999999999876 466678899999999888877643
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=82.30 E-value=0.89 Score=35.26 Aligned_cols=33 Identities=27% Similarity=0.507 Sum_probs=25.5
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
++-|++|+.--.-+-+.+...-+|+|+.|+..|
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 566999998744443666667799999999887
No 70
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.75 E-value=1.3 Score=33.02 Aligned_cols=30 Identities=23% Similarity=0.484 Sum_probs=21.3
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~ 91 (769)
..+|.+|++-+- ++.....++|+.||....
T Consensus 3 ~y~C~~CG~~~~----~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVE----LDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEE----ECCCCCceECCCCCCeEE
Confidence 368999999543 233334799999997654
No 71
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=79.24 E-value=2 Score=29.22 Aligned_cols=30 Identities=27% Similarity=0.483 Sum_probs=23.4
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~ 92 (769)
+.|..|+..|-- -.+..+++|..|...|.+
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 579999987643 257889999999988753
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=79.11 E-value=1.2e+02 Score=34.33 Aligned_cols=283 Identities=12% Similarity=0.114 Sum_probs=134.4
Q ss_pred CCcEEEEEEEcCcchhH----HHHHHHHHHHhcccCCCCceEEEEEECCeEEEEEccCCCCCCCeeEEecCCccCCHHHH
Q 004199 128 VPPVFMFVVDTCIIEEE----MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQL 203 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~~----l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~~~l~~~~~~~~~~~v~~g~~~~~~~~l 203 (769)
.|-=..|++|+|.++.+ ++.+-..|...|..+..+.++||=+|=+..- .|-... ....+
T Consensus 101 yPvDLYyLmDlS~Sm~ddl~~l~~lg~~l~~~~~~it~~~~~GfGsfvdK~~----------~P~~~~-------~p~~l 163 (426)
T PF00362_consen 101 YPVDLYYLMDLSYSMKDDLENLKSLGQDLAEEMRNITSNFRLGFGSFVDKPV----------MPFVST-------TPEKL 163 (426)
T ss_dssp --EEEEEEEE-SGGGHHHHHHHCCCCHHHHHHHHTT-SSEEEEEEEESSSSS----------TTTST--------SSHCH
T ss_pred cceeEEEEeechhhhhhhHHHHHHHHHHHHHHHHhcCccceEechhhccccc----------CCcccC-------Chhhh
Confidence 56667899999998765 5666678888888999999999999843321 010000 01223
Q ss_pred HHHhhcccCCCCCCCccccCcCCCCCcccc-ccceeechhcHHHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHh
Q 004199 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDTI-ARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (769)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~-~~~l~~~~e~~~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll 282 (769)
..+..- ....+ ..|. =+-..++.+........+.+..- . .+--.|+..+=+-+++|+--=
T Consensus 164 ~~pc~~----------~~~~c-----~~~~~f~~~l~Lt~~~~~F~~~v~~~~i-s---~n~D~PEgg~dal~Qa~vC~~ 224 (426)
T PF00362_consen 164 KNPCPS----------KNPNC-----QPPFSFRHVLSLTDDITEFNEEVNKQKI-S---GNLDAPEGGLDALMQAAVCQE 224 (426)
T ss_dssp HSTSCC----------TTS-------B---SEEEEEEEES-HHHHHHHHHTS---B-----SSSSBSHHHHHHHHHH-HH
T ss_pred cCcccc----------cCCCC-----CCCeeeEEeecccchHHHHHHhhhhccc-c---CCCCCCccccchheeeeeccc
Confidence 322100 00011 0122 12345666655556666655322 1 122356667777777765422
Q ss_pred hccCCCCCcEEEEEecCC--CCCCCcccccCCCCCCcCCCCCCCCCCCcccc---hhHHHHHHHHHHHHhcCcEEEEEEe
Q 004199 283 GACVPGSGARILAFVGGP--STEGPAAIVSKNLSEPIRSHKDLDKDSAPHYH---KAVKFYDALSKQLVHQGHVLDLFAC 357 (769)
Q Consensus 283 ~~~~~~~ggrI~~F~sg~--pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~---~a~~fY~~la~~~~~~~isvDlf~~ 357 (769)
.-..++..-|+++|++-. -.-|-|++...-..+..+-|-+-. ..|.. ....-..+|...+.+++|.+ ||+.
T Consensus 225 ~igWr~~a~~llv~~TD~~fH~agDg~l~gi~~pnd~~Chl~~~---~~y~~~~~~DYPSv~ql~~~l~e~~i~~-IFAV 300 (426)
T PF00362_consen 225 EIGWRNEARRLLVFSTDAGFHFAGDGKLAGIVKPNDGKCHLDDN---GMYTASTEQDYPSVGQLVRKLSENNINP-IFAV 300 (426)
T ss_dssp HHT--STSEEEEEEEESS-B--TTGGGGGT--S---SS--BSTT---SBBGGGGCS----HHHHHHHHHHTTEEE-EEEE
T ss_pred ccCcccCceEEEEEEcCCccccccccccceeeecCCCceEECCC---CcccccccccCCCHHHHHHHHHHcCCEE-EEEE
Confidence 212245567899988654 447889888775555555564321 12221 23344667788888877764 7887
Q ss_pred cCCccChhhhhhhhhcc-CceEEEeCCCCchhhHHHHHHHhhcCccCccceeeeEEEEEe-cCCceEEeEEcCCcccCCC
Q 004199 358 ALDQVGVAELKVAVEKT-GGLVVLSDSFGHAVFKDSVRRVFHSGDYDLGLSSNGIFEINC-SKDIKVQGIIGPCASLEKK 435 (769)
Q Consensus 358 ~~~~~~l~~m~~l~~~T-GG~v~~~~~f~~~~~~~~l~~~~~~~~~~~~~~~~~~l~vr~-S~gl~v~~~~G~~~~~~~~ 435 (769)
.....++++ .|+..- |+.+-.... +.+...+-+...+. .......++... ++++++ .+..+|.....
T Consensus 301 t~~~~~~Y~--~L~~~i~~s~vg~L~~-dSsNIv~LI~~aY~------~i~s~V~L~~~~~p~~v~v-~y~s~C~~~~~- 369 (426)
T PF00362_consen 301 TKDVYSIYE--ELSNLIPGSSVGELSS-DSSNIVQLIKEAYN------KISSKVELKHDNAPDGVKV-SYTSNCPNGST- 369 (426)
T ss_dssp EGGGHHHHH--HHHHHSTTEEEEEEST-TSHTHHHHHHHHHH------HHCTEEEEEECS--TTEEE-EEEEEESSSEE-
T ss_pred chhhhhHHH--HHhhcCCCceeccccc-CchhHHHHHHHHHH------HHhheEEEEecCCCCcEEE-EEEEEccCCcc-
Confidence 777766553 444433 444434433 22222222222221 123444554333 445666 34444432100
Q ss_pred CCCccccccccCCCCceeEecCCCCceEEEEEEEecCC
Q 004199 436 GPLCSDAVVGQGNTSAWKMCGLDKATSLCLVFEIVKKE 473 (769)
Q Consensus 436 ~~~vsd~~~g~~~~~~~~l~~~~~~~s~~~~~~~~~~~ 473 (769)
....-...++....++.|.+.+.-..
T Consensus 370 ------------~~~~~~C~~V~iG~~V~F~VtVta~~ 395 (426)
T PF00362_consen 370 ------------VPGTNECSNVKIGDTVTFNVTVTAKE 395 (426)
T ss_dssp ------------EECCEEECSE-TT-EEEEEEEEEESS
T ss_pred ------------cCcCccccCEecCCEEEEEEEEEEec
Confidence 01124455577777777777776543
No 73
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.06 E-value=32 Score=36.42 Aligned_cols=86 Identities=20% Similarity=0.100 Sum_probs=58.0
Q ss_pred CccchhHHHHHHHHHhhcc------CCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHH
Q 004199 267 STRCTGTALSIAASLLGAC------VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDA 340 (769)
Q Consensus 267 ~~~~~G~Al~~A~~ll~~~------~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~ 340 (769)
....+..||..|+-.+.-. ..+..+||+++..++ +. ..+..=+-+
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 3556788888888887521 123468999998752 10 011112346
Q ss_pred HHHHHHhcCcEEEEEEecCCccChhhhhhhhhccCceEEEeC
Q 004199 341 LSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSD 382 (769)
Q Consensus 341 la~~~~~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~v~~~~ 382 (769)
....|.+.+|.||++..+.+ -+..-++.+++.|||.-....
T Consensus 168 ~Ifaaqk~~I~Idv~~L~~e-~~~~~lqQa~~~TgG~Y~~~~ 208 (279)
T TIGR00627 168 CIFSAQKQNIPIDVVSIGGD-FTSGFLQQAADITGGSYLHVK 208 (279)
T ss_pred HHHHHHHcCceEEEEEeCCc-cccHHHHHHHHHhCCEEeccC
Confidence 67889999999999988643 357789999999999544443
No 74
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=75.65 E-value=77 Score=33.78 Aligned_cols=76 Identities=20% Similarity=0.145 Sum_probs=51.7
Q ss_pred ccchhHHHHHHHHHhhccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHHHh
Q 004199 268 TRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVH 347 (769)
Q Consensus 268 ~~~~G~Al~~A~~ll~~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~~~ 347 (769)
.-.+=.||+.|...|+..-.+..-.|++..++..|.-||.+-. .-..+..
T Consensus 142 ~fSLqNaLe~a~~~Lk~~p~H~sREVLii~sslsT~DPgdi~~------------------------------tI~~lk~ 191 (378)
T KOG2807|consen 142 DFSLQNALELAREVLKHMPGHVSREVLIIFSSLSTCDPGDIYE------------------------------TIDKLKA 191 (378)
T ss_pred ChHHHHHHHHHHHHhcCCCcccceEEEEEEeeecccCcccHHH------------------------------HHHHHHh
Confidence 3467789999999998421122235677778788887765443 2345566
Q ss_pred cCcEEEEEEecCCccChhhhhhhhhccCc
Q 004199 348 QGHVLDLFACALDQVGVAELKVAVEKTGG 376 (769)
Q Consensus 348 ~~isvDlf~~~~~~~~l~~m~~l~~~TGG 376 (769)
..|-|.+...+. .+.--+.|++.|||
T Consensus 192 ~kIRvsvIgLsa---Ev~icK~l~kaT~G 217 (378)
T KOG2807|consen 192 YKIRVSVIGLSA---EVFICKELCKATGG 217 (378)
T ss_pred hCeEEEEEeech---hHHHHHHHHHhhCC
Confidence 788888887654 45556789999999
No 75
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=71.66 E-value=8.4 Score=35.61 Aligned_cols=42 Identities=21% Similarity=0.202 Sum_probs=33.0
Q ss_pred EEEEEcCcchh--HHHHHHHHHHHhcccCCCCceEEEEEECCeEEE
Q 004199 133 MFVVDTCIIEE--EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQV 176 (769)
Q Consensus 133 vFvID~s~~~~--~l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~ 176 (769)
+++||+|.+.. +++.+...+...+... +.+|-+|.||..|+-
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 68999999854 4777777778777777 556899999988864
No 76
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=68.21 E-value=3.5 Score=31.37 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=22.5
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCCCCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p 93 (769)
.|..|+..+-+- -+.++..|.|+-|+..-.+.
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCCeEECC
Confidence 599999977332 22223589999999876654
No 77
>KOG2487 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription; Replication, recombination and repair]
Probab=65.08 E-value=1.6e+02 Score=30.81 Aligned_cols=45 Identities=20% Similarity=0.118 Sum_probs=35.7
Q ss_pred HHHHHHHHHhcCcEEEEEEecCCccChhhhhhhhhccCceEEEeCCCC
Q 004199 338 YDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFG 385 (769)
Q Consensus 338 Y~~la~~~~~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~v~~~~~f~ 385 (769)
|-+.--.|.+++|.||++....+ -..+...|..|||.....+.-.
T Consensus 185 ~MNciFaAqKq~I~Idv~~l~~~---s~~LqQa~D~TGG~YL~v~~~~ 229 (314)
T KOG2487|consen 185 YMNCIFAAQKQNIPIDVVSLGGD---SGFLQQACDITGGDYLHVEKPD 229 (314)
T ss_pred HHHHHHHHHhcCceeEEEEecCC---chHHHHHHhhcCCeeEecCCcc
Confidence 44556678889999999998776 3458899999999988887543
No 78
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=63.21 E-value=8.3 Score=28.25 Aligned_cols=27 Identities=26% Similarity=0.502 Sum_probs=21.7
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
+|+.|++-- ..+|...+.++|.-||..
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 678888899999999975
No 79
>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=62.81 E-value=4.7 Score=27.76 Aligned_cols=24 Identities=29% Similarity=0.786 Sum_probs=16.6
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
+|..|+=...+- ..-|.|+.|+..
T Consensus 3 ~C~~CGy~y~~~------~~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGE------EAPWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCC------cCCCcCcCCCCc
Confidence 588888555543 256899999864
No 80
>KOG2353 consensus L-type voltage-dependent Ca2+ channel, alpha2/delta subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=61.13 E-value=60 Score=40.92 Aligned_cols=65 Identities=18% Similarity=0.310 Sum_probs=50.4
Q ss_pred CccEEEecCCCC----CCCCCCcEEEEEEEcCcchhH--HHHHHHHHHHhcccCCCCceEEEEEECCeEEE
Q 004199 112 YTTIEYEPPGPG----EKSSVPPVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQV 176 (769)
Q Consensus 112 ~~tvey~~~~~~----~~~~~~p~~vFvID~s~~~~~--l~~~~~~l~~~l~~lp~~~~VglITfd~~V~~ 176 (769)
..++++--.+.- .....|--.+|++|+|++... +...+..+.++|+.|.++..|-++||++.++.
T Consensus 204 ~~~idl~D~R~r~Wyi~aAt~pKdiviLlD~SgSm~g~~~~lak~tv~~iLdtLs~~Dfvni~tf~~~~~~ 274 (1104)
T KOG2353|consen 204 DNSIDLYDCRNRSWYIQAATSPKDIVILLDVSGSMSGLRLDLAKQTVNEILDTLSDNDFVNILTFNSEVNP 274 (1104)
T ss_pred CCcceeeecccccccccccCCccceEEEEeccccccchhhHHHHHHHHHHHHhcccCCeEEEEeeccccCc
Confidence 556666655421 111267788999999998654 89999999999999999999999999988865
No 81
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=60.39 E-value=3.9 Score=29.89 Aligned_cols=30 Identities=20% Similarity=0.437 Sum_probs=25.3
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
.||..|+....-...+.. .....|+-|+..
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 479999988888877776 778999999983
No 82
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=60.14 E-value=4.3 Score=30.94 Aligned_cols=30 Identities=30% Similarity=0.785 Sum_probs=20.5
Q ss_pred cCCCCCceecCc-----------cEEEcCCceEEecCCCCC
Q 004199 60 RCRTCRSILNPF-----------SIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 60 rC~~C~aylNp~-----------~~~~~~~~~w~C~~C~~~ 89 (769)
+|..|+=+.+|- ..|+.-...|+|+.|+..
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 688888777764 234444567999999854
No 83
>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]
Probab=58.43 E-value=9.9 Score=43.96 Aligned_cols=55 Identities=20% Similarity=0.327 Sum_probs=38.5
Q ss_pred hhhhhhhccceeEeecCC----CCCcccc-----ccccccccCeEEEEeCCcEEEEEECCCchH
Q 004199 621 VTNSVVMIQPSLISYSFH----SGPEPAL-----LDVAAIAADRILLLDSYFTVVIFHGATIAQ 675 (769)
Q Consensus 621 ~~~~~~~i~P~L~~~~~~----~~p~~v~-----Ls~~~l~~d~i~llD~g~~i~i~~G~~v~~ 675 (769)
+.+-..-.+|+||.+.-. ..|+--. |--.-|.+.++|+||+...|+||+|+....
T Consensus 725 VPEdf~p~qpkLYkV~lGmGyLELPQvel~P~~~l~q~lL~sk~VyiLDc~sDiF~W~GkKs~R 788 (1255)
T KOG0444|consen 725 VPEDFVPEQPKLYKVNLGMGYLELPQVELLPKGILKQDLLGSKGVYILDCNSDIFLWIGKKSNR 788 (1255)
T ss_pred CCcccCCCCcceEEEccccceeecchhhhchhhHHHHHhhcCCeEEEEecCCceEEEecccchH
Confidence 334455678999999752 1332211 223456889999999999999999998764
No 84
>PRK03954 ribonuclease P protein component 4; Validated
Probab=56.06 E-value=7.2 Score=35.67 Aligned_cols=36 Identities=22% Similarity=0.384 Sum_probs=25.4
Q ss_pred ccCCCCCceecCc----cEEEcCC---ceEEecCCCCCCCCCc
Q 004199 59 LRCRTCRSILNPF----SIVDFAA---KIWICPFCFQRNHFPP 94 (769)
Q Consensus 59 ~rC~~C~aylNp~----~~~~~~~---~~w~C~~C~~~N~~p~ 94 (769)
--|++|.++|=|- +.+..+. -.++|..||+..-+|-
T Consensus 65 ~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~P~ 107 (121)
T PRK03954 65 RYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRYPY 107 (121)
T ss_pred HHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEeecc
Confidence 4599999998663 3344322 3459999999988763
No 85
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=54.76 E-value=7 Score=35.40 Aligned_cols=27 Identities=19% Similarity=0.519 Sum_probs=19.9
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
-.||..|+....+ ....|.||-||..+
T Consensus 70 ~~~C~~Cg~~~~~------~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 70 QAWCWDCSQVVEI------HQHDAQCPHCHGER 96 (113)
T ss_pred EEEcccCCCEEec------CCcCccCcCCCCCC
Confidence 4899999954333 34567899999775
No 86
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=54.66 E-value=4.5 Score=30.66 Aligned_cols=33 Identities=30% Similarity=0.535 Sum_probs=23.7
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~ 92 (769)
-+||.+|+-.|----.+. .-.-+|+=|++.|.+
T Consensus 4 eiRC~~CnklLa~~g~~~--~leIKCpRC~tiN~~ 36 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVI--ELEIKCPRCKTINHV 36 (51)
T ss_pred ceeccchhHHHhhhcCcc--EEEEECCCCCccceE
Confidence 389999987765421122 235899999999987
No 87
>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=53.74 E-value=2.4e+02 Score=28.12 Aligned_cols=98 Identities=12% Similarity=-0.048 Sum_probs=61.3
Q ss_pred HHHHHHHHHcCCCCCCCCCCCCCccchhHHHHHHHHHhh-ccCCCCCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCC
Q 004199 245 FTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG-ACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDL 323 (769)
Q Consensus 245 ~~i~~ll~~l~~~~~~~~~~~~~~~~~G~Al~~A~~ll~-~~~~~~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~ 323 (769)
..+..+|+..+.- .. + +. |..||..|+.-|+ . .+...--||+++.|--|.|- +
T Consensus 75 ~~l~~~l~~~q~g---~a-g--~~--TadAi~~av~rl~~~-~~a~~kvvILLTDG~n~~~~--i--------------- 128 (191)
T cd01455 75 ETLKMMHAHSQFC---WS-G--DH--TVEATEFAIKELAAK-EDFDEAIVIVLSDANLERYG--I--------------- 128 (191)
T ss_pred HHHHHHHHhcccC---cc-C--cc--HHHHHHHHHHHHHhc-CcCCCcEEEEEeCCCcCCCC--C---------------
Confidence 4777888877651 21 1 22 3389999998886 3 12233456677777433221 1
Q ss_pred CCCCCcccchhHHHHHHH-HHHHHhcCcEEEEEEecCCccChhhhhhhhhccCceEEEeCC
Q 004199 324 DKDSAPHYHKAVKFYDAL-SKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDS 383 (769)
Q Consensus 324 ~~~~~~~~~~a~~fY~~l-a~~~~~~~isvDlf~~~~~~~~l~~m~~l~~~TGG~v~~~~~ 383 (769)
.| .+. +..+.+.||-|..+..+. .|-..+..+++.|||.-|...+
T Consensus 129 --------~P-----~~aAa~lA~~~gV~iytIgiG~--~d~~~l~~iA~~tgG~~F~A~d 174 (191)
T cd01455 129 --------QP-----KKLADALAREPNVNAFVIFIGS--LSDEADQLQRELPAGKAFVCMD 174 (191)
T ss_pred --------Ch-----HHHHHHHHHhCCCEEEEEEecC--CCHHHHHHHHhCCCCcEEEeCC
Confidence 11 133 355667888877776654 3667799999999999998854
No 88
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=53.48 E-value=8 Score=27.39 Aligned_cols=32 Identities=16% Similarity=0.361 Sum_probs=23.2
Q ss_pred ccCCCCCceecCc-cEEEcCCceEEecCCCCCC
Q 004199 59 LRCRTCRSILNPF-SIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 59 ~rC~~C~aylNp~-~~~~~~~~~w~C~~C~~~N 90 (769)
++|.+|++..+-= .++...+++.+|+-|++.-
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 6788898876543 3455678888999998753
No 89
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=53.20 E-value=7.9 Score=35.19 Aligned_cols=27 Identities=22% Similarity=0.682 Sum_probs=20.4
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
-.+|.+|+....+ ....|.||-||..+
T Consensus 70 ~~~C~~Cg~~~~~------~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 70 ECECEDCSEEVSP------EIDLYRCPKCHGIM 96 (115)
T ss_pred EEEcccCCCEEec------CCcCccCcCCcCCC
Confidence 4899999965444 23468999999876
No 90
>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=52.63 E-value=6.5 Score=29.98 Aligned_cols=31 Identities=19% Similarity=0.460 Sum_probs=22.4
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
.||.+|+....-...+.. .....|+-|+..+
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~~ 36 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-DPLATCPECGGEK 36 (52)
T ss_pred EEeCCCCCEeEEEEecCC-CCCCCCCCCCCCc
Confidence 479999986665554443 4668899999854
No 91
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=51.73 E-value=6.1 Score=30.91 Aligned_cols=23 Identities=30% Similarity=0.703 Sum_probs=14.2
Q ss_pred CCccCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
.|.||.+||- .|+.++|+-||..
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 3566666665 3455677777754
No 92
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=51.71 E-value=7.6 Score=24.43 Aligned_cols=21 Identities=24% Similarity=0.605 Sum_probs=12.6
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 88 (769)
+|.+|++-+.+-.+| |+-||+
T Consensus 1 ~Cp~CG~~~~~~~~f--------C~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKF--------CPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcc--------hhhhCC
Confidence 477777766543332 777765
No 93
>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=51.51 E-value=20 Score=36.42 Aligned_cols=43 Identities=21% Similarity=0.266 Sum_probs=25.8
Q ss_pred EEEEEEEcCcchhH--------HHHHHHHHHHhcccC---CCCceEEEEEECCe
Q 004199 131 VFMFVVDTCIIEEE--------MSFLKSALSQAIDLL---PDNSLVGLITFGTL 173 (769)
Q Consensus 131 ~~vFvID~s~~~~~--------l~~~~~~l~~~l~~l---p~~~~VglITfd~~ 173 (769)
+.+|+||++.+..+ |+.+.+++...+... .+...||+|.|++.
T Consensus 1 ~~vflID~s~sM~~~~~~~~~~l~~al~~i~~~~~~ki~~~~kD~vgvvl~gt~ 54 (224)
T PF03731_consen 1 ATVFLIDVSPSMFEPSSESESPLEEALKAIEDLMQQKIISSPKDEVGVVLFGTD 54 (224)
T ss_dssp EEEEEEE-SCGGGS-BTTCS-HHHHHHHHHHHHHHHHHHTT---EEEEEEES-S
T ss_pred CEEEEEECCHHHCCCCCCcchhHHHHHHHHHHHHHHHHcCCCCCeEEEEEEcCC
Confidence 46899999998652 555555555555432 23478999988753
No 94
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=49.85 E-value=6 Score=27.52 Aligned_cols=30 Identities=20% Similarity=0.270 Sum_probs=15.9
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
.|..|++-+..-.--.++..+|+|+-|+..
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 488898876544443356788999999864
No 95
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=48.53 E-value=9.1 Score=28.96 Aligned_cols=28 Identities=25% Similarity=0.610 Sum_probs=19.5
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
-+|.+|++-+ ..+.....-.|+-||++-
T Consensus 7 Y~C~~Cg~~~----~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 7 YKCARCGREV----ELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEhhhcCCee----ehhhccCceeCCCCCcEE
Confidence 4688888876 444456678888888763
No 96
>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=47.96 E-value=9.9 Score=43.34 Aligned_cols=29 Identities=24% Similarity=0.512 Sum_probs=22.8
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCCCCCc
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p~ 94 (769)
.-+|++|+. ......|+||-|+..|.+-.
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 367999985 34457899999999999853
No 97
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=47.06 E-value=11 Score=34.17 Aligned_cols=28 Identities=21% Similarity=0.618 Sum_probs=19.1
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
-.+|.+|+.+...- ....|.||-||..+
T Consensus 70 ~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 70 ECWCETCQQYVTLL-----TQRVRRCPQCHGDM 97 (114)
T ss_pred EEEcccCCCeeecC-----CccCCcCcCcCCCC
Confidence 48999999643221 12238899999875
No 98
>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=46.49 E-value=5.8 Score=29.81 Aligned_cols=30 Identities=23% Similarity=0.700 Sum_probs=15.8
Q ss_pred cCCCCCceecCcc-----------EEEcCCceEEecCCCCC
Q 004199 60 RCRTCRSILNPFS-----------IVDFAAKIWICPFCFQR 89 (769)
Q Consensus 60 rC~~C~aylNp~~-----------~~~~~~~~w~C~~C~~~ 89 (769)
+|..|+-+.+|-- .|+.-...|+|+.|+..
T Consensus 3 ~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 3 QCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred CCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 5777776555443 23333456888888754
No 99
>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=46.33 E-value=11 Score=41.83 Aligned_cols=27 Identities=22% Similarity=0.372 Sum_probs=21.6
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCCCCCCCc
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p~ 94 (769)
+|++|+. ......|+|+-|+..|.+..
T Consensus 2 ~c~~cg~--------~~~~~~g~cp~c~~w~~~~e 28 (372)
T cd01121 2 VCSECGY--------VSPKWLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCC--------CCCCccEECcCCCCceeeee
Confidence 6999986 33456799999999999853
No 100
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=46.00 E-value=8.9 Score=30.13 Aligned_cols=22 Identities=32% Similarity=0.801 Sum_probs=13.9
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
+.||.+||- .+..++|+-||..
T Consensus 36 I~RC~~CRk----------~~~~Y~CP~CGF~ 57 (59)
T PRK14890 36 IYRCEKCRK----------QSNPYTCPKCGFE 57 (59)
T ss_pred EeechhHHh----------cCCceECCCCCCc
Confidence 566666665 3455677777764
No 101
>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=45.71 E-value=9.4 Score=27.31 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=21.7
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 88 (769)
.+|..|+........+.. +....|+-||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 379999997766655543 57788999997
No 102
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=45.52 E-value=85 Score=37.92 Aligned_cols=105 Identities=18% Similarity=0.224 Sum_probs=65.2
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCCCCCcCCCCCCCCCCCccccCCCccEEEecCC----------CCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPG----------PGEKSS 127 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p~~y~~~~~~~~~pEL~~~~~tvey~~~~----------~~~~~~ 127 (769)
+.+|.+|..++ .+-...+.-.|..||+.-.+|..= |+.- +..+-|.-+- --|
T Consensus 444 v~~Cp~Cd~~l----t~H~~~~~L~CH~Cg~~~~~p~~C---------p~Cg--s~~L~~~G~GterieeeL~~~FP--- 505 (730)
T COG1198 444 IAECPNCDSPL----TLHKATGQLRCHYCGYQEPIPQSC---------PECG--SEHLRAVGPGTERIEEELKRLFP--- 505 (730)
T ss_pred cccCCCCCcce----EEecCCCeeEeCCCCCCCCCCCCC---------CCCC--CCeeEEecccHHHHHHHHHHHCC---
Confidence 56666666653 334556899999999997776321 1331 2223333221 125
Q ss_pred CCcEEEEEEEcCcchhHHHHHHHHHHHhc-------------ccCCCCceEEEEEECCeEEEEEcc
Q 004199 128 VPPVFMFVVDTCIIEEEMSFLKSALSQAI-------------DLLPDNSLVGLITFGTLVQVHELG 180 (769)
Q Consensus 128 ~~p~~vFvID~s~~~~~l~~~~~~l~~~l-------------~~lp~~~~VglITfd~~V~~~~l~ 180 (769)
..+++.|--|++.....++.+.+.+..-= ...|.-++||++-=|..+..-|+.
T Consensus 506 ~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfR 571 (730)
T COG1198 506 GARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFR 571 (730)
T ss_pred CCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcc
Confidence 67888888888887777666555554311 123555899999888888776665
No 103
>PRK11823 DNA repair protein RadA; Provisional
Probab=45.24 E-value=11 Score=42.93 Aligned_cols=29 Identities=21% Similarity=0.442 Sum_probs=22.8
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCCCCCc
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p~ 94 (769)
.-+|++|+. ......|+||-|+..|.+..
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 367999986 34457799999999998853
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=43.32 E-value=26 Score=24.21 Aligned_cols=29 Identities=24% Similarity=0.428 Sum_probs=20.5
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
+.+|..|++-. -+........|.+|+...
T Consensus 3 ~~~C~~C~~~~----i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNG----IVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCe----EEEecCCeEEcccCCcEe
Confidence 57899998854 222345679999999764
No 105
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=43.29 E-value=15 Score=25.86 Aligned_cols=31 Identities=13% Similarity=0.281 Sum_probs=20.6
Q ss_pred ccCCCCCceecCc-cEEEcCCceEEecCCCCC
Q 004199 59 LRCRTCRSILNPF-SIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 59 ~rC~~C~aylNp~-~~~~~~~~~w~C~~C~~~ 89 (769)
++|.+|++-.+-= -++-..|.+.+|.-|++.
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 5788888765433 224456778888888764
No 106
>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=42.97 E-value=11 Score=30.58 Aligned_cols=30 Identities=27% Similarity=0.461 Sum_probs=20.7
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p 93 (769)
+.|| .|+.++ -.+++.++-+| .||....+-
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 45677899999 999987663
No 107
>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=42.44 E-value=24 Score=22.52 Aligned_cols=24 Identities=29% Similarity=0.642 Sum_probs=16.8
Q ss_pred CCCCCceecCccEEEcCCceEEecCCCC
Q 004199 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (769)
Q Consensus 61 C~~C~aylNp~~~~~~~~~~w~C~~C~~ 88 (769)
|.+|+.-|-|-- .+..+.|+-||.
T Consensus 1 C~sC~~~i~~r~----~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPRE----QAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcc----cCceEeCCCCCC
Confidence 777877777642 256788888874
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=41.73 E-value=19 Score=29.17 Aligned_cols=27 Identities=19% Similarity=0.503 Sum_probs=22.2
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
-.|..|+...-. ...++.|+|+-||..
T Consensus 29 q~C~~CG~~~~~----~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 29 QTCPRCGHRNKK----RRSGRVFTCPNCGFE 55 (69)
T ss_pred cCccCccccccc----ccccceEEcCCCCCE
Confidence 569999987766 556789999999986
No 109
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=41.57 E-value=19 Score=33.57 Aligned_cols=35 Identities=29% Similarity=0.551 Sum_probs=24.0
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCCCCCCcC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPH 95 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p~~ 95 (769)
++|--|+.. .-+..+.....|.|+-|+..|.+..+
T Consensus 1 v~C~fC~~~--s~~~~~~~~~~w~C~~C~q~N~f~e~ 35 (131)
T PF09779_consen 1 VNCWFCGQN--SKVPYDNRNSNWTCPHCEQYNGFDED 35 (131)
T ss_pred CeeccCCCC--CCCCCCCCCCeeECCCCCCccCcccc
Confidence 467788764 23333444556999999999988643
No 110
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=41.11 E-value=23 Score=27.68 Aligned_cols=33 Identities=21% Similarity=0.518 Sum_probs=22.8
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCCC--CCcCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH--FPPHYASIT 100 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~--~p~~y~~~~ 100 (769)
+-+|.+|+.|- -+=+|+.||.... .|+.|++-+
T Consensus 5 ~rkC~~cg~YT----------Lke~Cp~CG~~t~~~~PprFSPeD 39 (59)
T COG2260 5 IRKCPKCGRYT----------LKEKCPVCGGDTKVPHPPRFSPED 39 (59)
T ss_pred hhcCcCCCcee----------ecccCCCCCCccccCCCCCCCccc
Confidence 45799999872 1258999997654 566676543
No 111
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=40.45 E-value=17 Score=27.75 Aligned_cols=25 Identities=24% Similarity=0.542 Sum_probs=18.7
Q ss_pred ccCCCCCc-eecCccEEEcCCceEEecCCCCC
Q 004199 59 LRCRTCRS-ILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 59 ~rC~~C~a-ylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
..|.+|++ ++-+. ...|.|.-|+..
T Consensus 21 ~fCP~Cg~~~m~~~------~~r~~C~~Cgyt 46 (50)
T PRK00432 21 KFCPRCGSGFMAEH------LDRWHCGKCGYT 46 (50)
T ss_pred CcCcCCCcchhecc------CCcEECCCcCCE
Confidence 46999998 55443 368999999864
No 112
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=39.34 E-value=24 Score=26.17 Aligned_cols=25 Identities=20% Similarity=0.307 Sum_probs=16.7
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
+|.+|++-+..- .+..-+|+-||++
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCce
Confidence 578888755432 3466788888865
No 113
>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=39.03 E-value=16 Score=23.81 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=16.5
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
+|..|++.++- ..-.|+.||+..
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 58888887732 456788998753
No 114
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=38.96 E-value=12 Score=34.12 Aligned_cols=28 Identities=29% Similarity=0.779 Sum_probs=18.4
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
..||..|+.+..+- ....+.||-||..+
T Consensus 71 ~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 71 ELECKDCSHVFKPN-----ALDYGVCEKCHSKN 98 (117)
T ss_pred EEEhhhCCCccccC-----CccCCcCcCCCCCc
Confidence 48999999543321 11234599999876
No 115
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=38.73 E-value=18 Score=35.49 Aligned_cols=25 Identities=32% Similarity=0.719 Sum_probs=21.0
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
.+|++|++-|=+ .+++-+|+-|+..
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 799999996644 5789999999975
No 116
>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=38.57 E-value=30 Score=22.32 Aligned_cols=24 Identities=29% Similarity=0.620 Sum_probs=14.5
Q ss_pred CCCCCceecCccEEEcCCceEEecCCCC
Q 004199 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (769)
Q Consensus 61 C~~C~aylNp~~~~~~~~~~w~C~~C~~ 88 (769)
|.+|+..|. .-.+...++|..|++
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 566666543 124566777777764
No 117
>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=38.39 E-value=30 Score=24.39 Aligned_cols=27 Identities=22% Similarity=0.491 Sum_probs=20.4
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
..+|..|++. +...+ .+.|.|.=||+.
T Consensus 8 ~~~C~~C~~~---~~~~~--dG~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSR---WFYSD--DGFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCe---EeEcc--CCEEEhhhCceE
Confidence 3569999998 33334 478999999975
No 118
>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=38.35 E-value=14 Score=33.67 Aligned_cols=32 Identities=22% Similarity=0.498 Sum_probs=25.4
Q ss_pred CccCCCCCceecCccEEEc-CCceEEecCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDF-AAKIWICPFCFQR 89 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~-~~~~w~C~~C~~~ 89 (769)
...|..|+-.+-.-|.+.. +...|.|++|...
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 3778888888888888874 5789999999754
No 119
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=37.19 E-value=19 Score=28.87 Aligned_cols=24 Identities=21% Similarity=0.563 Sum_probs=17.8
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~ 92 (769)
.-|++|+...+. . +|+.||..+.-
T Consensus 6 ~AC~~C~~i~~~--------~--~Cp~Cgs~~~S 29 (64)
T PRK06393 6 RACKKCKRLTPE--------K--TCPVHGDEKTT 29 (64)
T ss_pred hhHhhCCcccCC--------C--cCCCCCCCcCC
Confidence 359999987731 1 99999998543
No 120
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=37.06 E-value=21 Score=33.88 Aligned_cols=33 Identities=30% Similarity=0.598 Sum_probs=22.9
Q ss_pred CccCCCCCceecCccEE-----------EcCCceEEecCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIV-----------DFAAKIWICPFCFQRN 90 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~-----------~~~~~~w~C~~C~~~N 90 (769)
.-||..|.+-+-+-.+- ......|.|+-|++.-
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 48999999965433221 1235699999999864
No 121
>PF12773 DZR: Double zinc ribbon
Probab=37.01 E-value=21 Score=26.81 Aligned_cols=35 Identities=23% Similarity=0.358 Sum_probs=26.5
Q ss_pred CCccCCCCCceecCccEEEcCCceEEecCCCCCCCCCcCC
Q 004199 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHY 96 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p~~y 96 (769)
+-..|.+|++-+. ......++|+-|++.|.-...|
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~~~~~f 45 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENPPNAKF 45 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCcCCcCc
Confidence 4577999999888 3456789999999987654444
No 122
>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=36.61 E-value=42 Score=24.94 Aligned_cols=27 Identities=19% Similarity=0.540 Sum_probs=19.3
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 88 (769)
+.|.+|++- ..| .+. +.+.|.|.-|++
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 669999987 332 222 258999999985
No 123
>PRK10997 yieM hypothetical protein; Provisional
Probab=35.42 E-value=43 Score=38.38 Aligned_cols=51 Identities=25% Similarity=0.153 Sum_probs=33.7
Q ss_pred cEEEEEEEcCcchh-HHHHHHHHHHHhcc--cCCCCceEEEEEECCeEEEEEcc
Q 004199 130 PVFMFVVDTCIIEE-EMSFLKSALSQAID--LLPDNSLVGLITFGTLVQVHELG 180 (769)
Q Consensus 130 p~~vFvID~s~~~~-~l~~~~~~l~~~l~--~lp~~~~VglITfd~~V~~~~l~ 180 (769)
--+++|||+|.+.. .-+....++..+|- .+.++-++++|.|++.+.-|.+.
T Consensus 324 GpiII~VDtSGSM~G~ke~~AkalAaAL~~iAl~q~dr~~li~Fs~~i~~~~l~ 377 (487)
T PRK10997 324 GPFIVCVDTSGSMGGFNEQCAKAFCLALMRIALAENRRCYIMLFSTEVVTYELT 377 (487)
T ss_pred CcEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHhcCCCEEEEEecCCceeeccC
Confidence 34789999999875 21222224444443 34577899999999988766554
No 124
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=35.19 E-value=17 Score=33.59 Aligned_cols=33 Identities=21% Similarity=0.399 Sum_probs=19.9
Q ss_pred CccCCCCCceecCc-cEEEcCCceEEecCCCCCCC
Q 004199 58 PLRCRTCRSILNPF-SIVDFAAKIWICPFCFQRNH 91 (769)
Q Consensus 58 p~rC~~C~aylNp~-~~~~~~~~~w~C~~C~~~N~ 91 (769)
-.|| .|+.+..+- ...+.-...|.||-||..+.
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~ 103 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRA 103 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCCCCCC
Confidence 4899 999765432 11111111378999997763
No 125
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.44 E-value=24 Score=33.07 Aligned_cols=33 Identities=24% Similarity=0.426 Sum_probs=20.4
Q ss_pred CccCCCCCceecCcc---E----------EEc--CCceEEecCCCCCC
Q 004199 58 PLRCRTCRSILNPFS---I----------VDF--AAKIWICPFCFQRN 90 (769)
Q Consensus 58 p~rC~~C~aylNp~~---~----------~~~--~~~~w~C~~C~~~N 90 (769)
..+|..|+....+-- + +.+ ....|.||-||..+
T Consensus 70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 488999996554420 0 000 03568899999775
No 126
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.31 E-value=19 Score=32.95 Aligned_cols=31 Identities=16% Similarity=0.575 Sum_probs=22.1
Q ss_pred CCccCCCCCceecCccEEEcCCceEEecCCCCCCC
Q 004199 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~ 91 (769)
..-.|.+|++-+.- ..+.-+|.||+|...-.
T Consensus 88 q~r~CARCGGrv~l----rsNKv~wvcnlc~k~q~ 118 (169)
T KOG3799|consen 88 QTRFCARCGGRVSL----RSNKVMWVCNLCRKQQE 118 (169)
T ss_pred hhhHHHhcCCeeee----ccCceEEeccCCcHHHH
Confidence 45668899986543 33456899999987654
No 127
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=33.85 E-value=35 Score=26.82 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=20.8
Q ss_pred CCccCCCCCceecCccEEEcCCceEEecCCCCCCC
Q 004199 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~ 91 (769)
.+..|.+|+.+.=| .-.|+.||+.+.
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 46789999998766 578999997653
No 128
>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=33.04 E-value=14 Score=24.60 Aligned_cols=16 Identities=31% Similarity=0.592 Sum_probs=13.1
Q ss_pred ceEEecCCCCCCCCCc
Q 004199 79 KIWICPFCFQRNHFPP 94 (769)
Q Consensus 79 ~~w~C~~C~~~N~~p~ 94 (769)
+.|.|+.|...|..-.
T Consensus 3 g~W~C~~C~~~N~~~~ 18 (30)
T PF00641_consen 3 GDWKCPSCTFMNPASR 18 (30)
T ss_dssp SSEEETTTTEEEESSS
T ss_pred cCccCCCCcCCchHHh
Confidence 4799999999997533
No 129
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=32.81 E-value=29 Score=26.66 Aligned_cols=32 Identities=16% Similarity=0.271 Sum_probs=26.9
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
+.+|.+|++--.|..+-...+..-.||-|+..
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~ 34 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLY 34 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHH
Confidence 57899999988888877777777999999954
No 130
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=32.57 E-value=37 Score=27.39 Aligned_cols=34 Identities=21% Similarity=0.457 Sum_probs=25.6
Q ss_pred CCccCCCCCceecCccEEEcCCceEEecCCCCCCCCC
Q 004199 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p 93 (769)
--++|..|+ |--+-|......-+|+.||..=--|
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 348999998 4566677778899999999874433
No 131
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=32.24 E-value=40 Score=33.48 Aligned_cols=40 Identities=20% Similarity=0.453 Sum_probs=27.9
Q ss_pred CCccCCCCCceecCccEEEcCCceEEecCCCCCCCCCcCC
Q 004199 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHY 96 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p~~y 96 (769)
.-+-|++|.-=-+-+.--......++|++|+..|..|..-
T Consensus 191 ~alIC~~C~hhngl~~~~ek~~~efiC~~Cn~~n~~~~~~ 230 (251)
T COG5415 191 KALICPQCHHHNGLYRLAEKPIIEFICPHCNHKNDEVKER 230 (251)
T ss_pred hhhccccccccccccccccccchheecccchhhcCccccc
Confidence 3467888876555444444445579999999999877543
No 132
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=32.19 E-value=38 Score=30.12 Aligned_cols=28 Identities=25% Similarity=0.586 Sum_probs=19.9
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
.+.|.+|.+ -|.-- ++..|+|+-|++.-
T Consensus 2 lp~CP~C~s---eytY~--dg~~~iCpeC~~EW 29 (109)
T TIGR00686 2 LPPCPKCNS---EYTYH--DGTQLICPSCLYEW 29 (109)
T ss_pred CCcCCcCCC---cceEe--cCCeeECccccccc
Confidence 367889986 23333 36789999999873
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=31.89 E-value=30 Score=30.58 Aligned_cols=27 Identities=26% Similarity=0.725 Sum_probs=21.8
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCCCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~ 92 (769)
.|.+|++.|.|- +..|.|+-|+.....
T Consensus 2 fC~~Cg~~l~~~------~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPK------NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccC------CCeEECcCCCCcccc
Confidence 599999999762 358999999987553
No 134
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=31.84 E-value=30 Score=27.59 Aligned_cols=23 Identities=35% Similarity=0.785 Sum_probs=17.1
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCCCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~ 92 (769)
-|++|+..... . +|+.|+...-.
T Consensus 5 AC~~C~~i~~~--------~--~CP~Cgs~~~T 27 (61)
T PRK08351 5 ACRHCHYITTE--------D--RCPVCGSRDLS 27 (61)
T ss_pred hhhhCCcccCC--------C--cCCCCcCCccc
Confidence 49999987731 1 59999997633
No 135
>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=31.66 E-value=27 Score=24.56 Aligned_cols=31 Identities=16% Similarity=0.366 Sum_probs=15.5
Q ss_pred ccCCCCCceecCc-cEEEcCCceEEecCCCCC
Q 004199 59 LRCRTCRSILNPF-SIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 59 ~rC~~C~aylNp~-~~~~~~~~~w~C~~C~~~ 89 (769)
+.|.+|++-..-- -.+...+....|+-|++.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 4577777642111 112223446677777654
No 136
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=31.22 E-value=25 Score=37.59 Aligned_cols=36 Identities=19% Similarity=0.375 Sum_probs=26.7
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p 93 (769)
-+-|++|+.==+-+-.-+..--.|+|++|+..|+-+
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 367999998655554444455789999999999754
No 137
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=31.01 E-value=24 Score=30.14 Aligned_cols=35 Identities=26% Similarity=0.477 Sum_probs=24.3
Q ss_pred CCccCCCCCceecCccEEEcCCceEEecCCCCCCCCCcC
Q 004199 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPH 95 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p~~ 95 (769)
.|.+|++|+=-.++ -++ ..--+|+-|+..-.-|+.
T Consensus 57 ~Pa~CkkCGfef~~-~~i---k~pSRCP~CKSE~Ie~pr 91 (97)
T COG3357 57 RPARCKKCGFEFRD-DKI---KKPSRCPKCKSEWIEEPR 91 (97)
T ss_pred cChhhcccCccccc-ccc---CCcccCCcchhhcccCCc
Confidence 68999999987766 222 245679999987544443
No 138
>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=30.27 E-value=97 Score=31.58 Aligned_cols=44 Identities=18% Similarity=0.141 Sum_probs=26.3
Q ss_pred CCc-EEEEEEEcCcchhHHHHHHHHHHHhc-ccCCCCceEEEEEECCeE
Q 004199 128 VPP-VFMFVVDTCIIEEEMSFLKSALSQAI-DLLPDNSLVGLITFGTLV 174 (769)
Q Consensus 128 ~~p-~~vFvID~s~~~~~l~~~~~~l~~~l-~~lp~~~~VglITfd~~V 174 (769)
..| -+|+++|+|.+......+.-.+..++ ...+ ++.++.|++.+
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 89999999999877433222233222 2333 66777776544
No 139
>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=30.26 E-value=12 Score=33.80 Aligned_cols=27 Identities=30% Similarity=0.627 Sum_probs=18.0
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
-.||..|+.-..+- ...+.||.|+..+
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 48999999866552 3347799999986
No 140
>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=29.94 E-value=19 Score=27.44 Aligned_cols=19 Identities=26% Similarity=0.712 Sum_probs=7.9
Q ss_pred CccEEEcCCceEEecCCCC
Q 004199 70 PFSIVDFAAKIWICPFCFQ 88 (769)
Q Consensus 70 p~~~~~~~~~~w~C~~C~~ 88 (769)
-|.......+.|.|++|++
T Consensus 31 ~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 31 SFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp HHHHHHHHS---B-TTT--
T ss_pred HHHHHhhccCCeECcCCcC
Confidence 3334444567799999986
No 141
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=29.45 E-value=26 Score=21.14 Aligned_cols=11 Identities=27% Similarity=0.815 Sum_probs=6.4
Q ss_pred EEecCCCCCCC
Q 004199 81 WICPFCFQRNH 91 (769)
Q Consensus 81 w~C~~C~~~N~ 91 (769)
|.|++|+....
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 78888887643
No 142
>PHA00626 hypothetical protein
Probab=29.44 E-value=48 Score=25.75 Aligned_cols=14 Identities=14% Similarity=0.377 Sum_probs=11.8
Q ss_pred CceEEecCCCCCCC
Q 004199 78 AKIWICPFCFQRNH 91 (769)
Q Consensus 78 ~~~w~C~~C~~~N~ 91 (769)
.+.++|+-||....
T Consensus 21 snrYkCkdCGY~ft 34 (59)
T PHA00626 21 SDDYVCCDCGYNDS 34 (59)
T ss_pred CcceEcCCCCCeec
Confidence 67899999998764
No 143
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=29.08 E-value=43 Score=23.01 Aligned_cols=29 Identities=21% Similarity=0.588 Sum_probs=17.1
Q ss_pred cCCCCCceecCc-cEEEcCCceE-----EecCCCC
Q 004199 60 RCRTCRSILNPF-SIVDFAAKIW-----ICPFCFQ 88 (769)
Q Consensus 60 rC~~C~aylNp~-~~~~~~~~~w-----~C~~C~~ 88 (769)
||..|+..|-+- ..+...++.| .|.-|+.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~ 35 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGK 35 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCC
Confidence 688888887774 3333334444 5666654
No 144
>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=29.04 E-value=1.1e+02 Score=29.46 Aligned_cols=76 Identities=16% Similarity=0.158 Sum_probs=44.9
Q ss_pred CccchhHHHHHHHHHhhccC---CC-----CCcEEEEEecCCCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHH
Q 004199 267 STRCTGTALSIAASLLGACV---PG-----SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFY 338 (769)
Q Consensus 267 ~~~~~G~Al~~A~~ll~~~~---~~-----~ggrI~~F~sg~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY 338 (769)
..+++|.||..|...+.... +. .-..|+++|+|-++.++. .+.+.+
T Consensus 77 GgT~l~~aL~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~~~~~~--------------------------~~~~~~ 130 (176)
T cd01464 77 GGTSMGAALELALDCIDRRVQRYRADQKGDWRPWVFLLTDGEPTDDLT--------------------------AAIERI 130 (176)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHhcccCcCCcCcEEEEEcCCCCCchHH--------------------------HHHHHH
Confidence 46899999999999986311 00 012699999997643321 011122
Q ss_pred HHHHHHHHhcCcEEEEEEecCCccChhhhhhhhhc
Q 004199 339 DALSKQLVHQGHVLDLFACALDQVGVAELKVAVEK 373 (769)
Q Consensus 339 ~~la~~~~~~~isvDlf~~~~~~~~l~~m~~l~~~ 373 (769)
+ .+...++.+..|..+. .++...|..++..
T Consensus 131 ~----~~~~~~~~i~~igiG~-~~~~~~L~~ia~~ 160 (176)
T cd01464 131 K----EARDSKGRIVACAVGP-KADLDTLKQITEG 160 (176)
T ss_pred H----hhcccCCcEEEEEecc-ccCHHHHHHHHCC
Confidence 2 2223356666666654 5777777777753
No 145
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=28.89 E-value=34 Score=26.64 Aligned_cols=25 Identities=24% Similarity=0.569 Sum_probs=19.6
Q ss_pred CCccCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
.+..|..|+.+.=| .-.|+.||+.+
T Consensus 25 ~l~~C~~cG~~~~~---------H~vc~~cG~Y~ 49 (55)
T TIGR01031 25 TLVVCPNCGEFKLP---------HRVCPSCGYYK 49 (55)
T ss_pred cceECCCCCCcccC---------eeECCccCeEC
Confidence 46889999997655 47899998765
No 146
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=28.67 E-value=2.2e+02 Score=32.25 Aligned_cols=45 Identities=20% Similarity=0.197 Sum_probs=29.8
Q ss_pred CcEEEEEEEcCcchhH-HHHHHHHHHHhcc--cCCCCceEEEEEECCeE
Q 004199 129 PPVFMFVVDTCIIEEE-MSFLKSALSQAID--LLPDNSLVGLITFGTLV 174 (769)
Q Consensus 129 ~p~~vFvID~s~~~~~-l~~~~~~l~~~l~--~lp~~~~VglITfd~~V 174 (769)
+| ++.+||.|+++.- -+....++..+|- .+-+|.++.++.||+.+
T Consensus 273 Gp-villlD~SGSM~G~~e~~AKAvalAl~~~alaenR~~~~~lF~s~~ 320 (437)
T COG2425 273 GP-VILLLDKSGSMSGFKEQWAKAVALALMRIALAENRDCYVILFDSEV 320 (437)
T ss_pred CC-EEEEEeCCCCcCCcHHHHHHHHHHHHHHHHHHhccceEEEEecccc
Confidence 44 5689999998754 2333334444443 35689999999999943
No 147
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=28.17 E-value=62 Score=34.51 Aligned_cols=28 Identities=36% Similarity=0.584 Sum_probs=25.6
Q ss_pred hHHHHHHHHHHHhcccCCCCceEEEEEE
Q 004199 143 EEMSFLKSALSQAIDLLPDNSLVGLITF 170 (769)
Q Consensus 143 ~~l~~~~~~l~~~l~~lp~~~~VglITf 170 (769)
.||+.+.++|.++++.|.++.|+++|||
T Consensus 218 dEL~~L~~~L~~a~~~L~~gGRl~VIsF 245 (314)
T COG0275 218 DELEELEEALEAALDLLKPGGRLAVISF 245 (314)
T ss_pred hHHHHHHHHHHHHHHhhCCCcEEEEEEe
Confidence 3599999999999999999999999985
No 148
>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=27.71 E-value=51 Score=23.47 Aligned_cols=27 Identities=26% Similarity=0.727 Sum_probs=18.3
Q ss_pred cCCCCCceecCccEEEc--CCceEEecCCCC
Q 004199 60 RCRTCRSILNPFSIVDF--AAKIWICPFCFQ 88 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~--~~~~w~C~~C~~ 88 (769)
-|..|++ ---|- +++ +...|+|+-|+.
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 3888877 23333 454 567899999975
No 149
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=27.65 E-value=30 Score=38.43 Aligned_cols=27 Identities=26% Similarity=0.704 Sum_probs=19.9
Q ss_pred ccCCCCCceecCccEEEcCCceE--EecCCCCCCCCCcC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIW--ICPFCFQRNHFPPH 95 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w--~C~~C~~~N~~p~~ 95 (769)
..|..|++ ..-+| +|+-|+..|.+-..
T Consensus 8 f~C~~CG~----------~s~KW~GkCp~Cg~Wns~vE~ 36 (456)
T COG1066 8 FVCQECGY----------VSPKWLGKCPACGAWNTLVEE 36 (456)
T ss_pred EEcccCCC----------CCccccccCCCCCCccceEEe
Confidence 56999987 23345 79999999987443
No 150
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=27.61 E-value=79 Score=29.78 Aligned_cols=65 Identities=17% Similarity=0.298 Sum_probs=36.5
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCCCCCCcCCCCCCCCCCCccccCCCccEEEecCCCCCCCCCCcEEEEEEEc
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPGPGEKSSVPPVFMFVVDT 138 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~p~~y~~~~~~~~~pEL~~~~~tvey~~~~~~~~~~~~p~~vFvID~ 138 (769)
.||.+|+.+.=| -+-.|+-|+....+- .+ .++ .+-++. .=|+-|..+.... ..+|..+-+|+.
T Consensus 30 ~kC~~CG~v~~P--------Pr~~Cp~C~~~~~~E-~v-els---~~G~V~--t~Tv~~~~~~~~~--~~~P~viaiV~l 92 (140)
T COG1545 30 TKCKKCGRVYFP--------PRAYCPKCGSETELE-WV-ELS---GEGKVE--TYTVVYVKPPGFS--LEEPYVIAIVEL 92 (140)
T ss_pred EEcCCCCeEEcC--------CcccCCCCCCCCceE-EE-EeC---CCeEEE--EEEEEeeCCCCcc--cCCCEEEEEEEe
Confidence 899999998777 356899999995320 11 000 011222 2334444443211 147777777776
Q ss_pred Cc
Q 004199 139 CI 140 (769)
Q Consensus 139 s~ 140 (769)
-.
T Consensus 93 ~~ 94 (140)
T COG1545 93 EE 94 (140)
T ss_pred CC
Confidence 54
No 151
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=27.13 E-value=76 Score=24.87 Aligned_cols=34 Identities=24% Similarity=0.571 Sum_probs=24.0
Q ss_pred CCccCCCCCceecCccEEEcCCceEEecCCCCCCC--CCcCCCCCC
Q 004199 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH--FPPHYASIT 100 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~--~p~~y~~~~ 100 (769)
.+-+|.+|+.|== +=.|+.||.... .|..|++.+
T Consensus 4 ~mr~C~~CgvYTL----------k~~CP~CG~~t~~~~P~rfSp~D 39 (56)
T PRK13130 4 KIRKCPKCGVYTL----------KEICPVCGGKTKNPHPPRFSPED 39 (56)
T ss_pred cceECCCCCCEEc----------cccCcCCCCCCCCCCCCCCCCCC
Confidence 4678999999732 467999997754 466676543
No 152
>PRK05580 primosome assembly protein PriA; Validated
Probab=27.11 E-value=2.1e+02 Score=34.49 Aligned_cols=35 Identities=23% Similarity=0.454 Sum_probs=21.1
Q ss_pred ccCCCCCcee-cCccE----EEcCCceEEecCCCCCCCCC
Q 004199 59 LRCRTCRSIL-NPFSI----VDFAAKIWICPFCFQRNHFP 93 (769)
Q Consensus 59 ~rC~~C~ayl-Np~~~----~~~~~~~w~C~~C~~~N~~p 93 (769)
+.|.+|+..+ .|.|. +....+.-+|..||..-.+|
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~ 421 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIP 421 (679)
T ss_pred eEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCC
Confidence 4555555442 33333 22346778999999887664
No 153
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.93 E-value=32 Score=22.19 Aligned_cols=22 Identities=27% Similarity=0.780 Sum_probs=11.9
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 88 (769)
..|.+|++.+.+ ..-.|+-||+
T Consensus 3 ~~Cp~Cg~~~~~--------~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP--------DAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc--------ccccChhhCC
Confidence 457777773321 2345666664
No 154
>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=26.91 E-value=30 Score=23.39 Aligned_cols=26 Identities=23% Similarity=0.551 Sum_probs=13.3
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
+.|..|++=.+- .++..++|+-|++.
T Consensus 3 p~Cp~C~se~~y-----~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 3 PKCPLCGSEYTY-----EDGELLVCPECGHE 28 (30)
T ss_dssp ---TTT-----E-----E-SSSEEETTTTEE
T ss_pred CCCCCCCCccee-----ccCCEEeCCccccc
Confidence 578888874333 34788999999863
No 155
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=26.76 E-value=61 Score=30.26 Aligned_cols=32 Identities=19% Similarity=0.430 Sum_probs=25.7
Q ss_pred CccCCCCCceecCccEEEcCCceE--EecCCCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIW--ICPFCFQRNHF 92 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w--~C~~C~~~N~~ 92 (769)
-+-|+.|+. |=..+...++.| +|.-||..-++
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 777776666776 89999998766
No 156
>PF14353 CpXC: CpXC protein
Probab=26.52 E-value=57 Score=30.02 Aligned_cols=34 Identities=15% Similarity=0.494 Sum_probs=22.6
Q ss_pred ccCCCCCcee--cCccEEEcC-------------CceEEecCCCCCCCC
Q 004199 59 LRCRTCRSIL--NPFSIVDFA-------------AKIWICPFCFQRNHF 92 (769)
Q Consensus 59 ~rC~~C~ayl--Np~~~~~~~-------------~~~w~C~~C~~~N~~ 92 (769)
+.|.+|+.-. .-|..++.. =..++|+-||+...+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceec
Confidence 5799998763 233333321 347999999999876
No 157
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=26.11 E-value=29 Score=22.13 Aligned_cols=14 Identities=36% Similarity=0.733 Sum_probs=11.8
Q ss_pred eEEecCCCCCCCCC
Q 004199 80 IWICPFCFQRNHFP 93 (769)
Q Consensus 80 ~w~C~~C~~~N~~p 93 (769)
.|.|+.|...|...
T Consensus 2 ~W~C~~C~~~N~~~ 15 (26)
T smart00547 2 DWECPACTFLNFAS 15 (26)
T ss_pred cccCCCCCCcChhh
Confidence 59999999999653
No 158
>PRK12722 transcriptional activator FlhC; Provisional
Probab=25.66 E-value=32 Score=34.03 Aligned_cols=29 Identities=14% Similarity=0.453 Sum_probs=20.8
Q ss_pred CCccCCCCCc-eecCccEEEcCCceEEecCCCC
Q 004199 57 APLRCRTCRS-ILNPFSIVDFAAKIWICPFCFQ 88 (769)
Q Consensus 57 ~p~rC~~C~a-ylNp~~~~~~~~~~w~C~~C~~ 88 (769)
...+|..|++ ||- ...+....++|++|+-
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 4688999987 331 2234467899999987
No 159
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=25.48 E-value=38 Score=23.79 Aligned_cols=24 Identities=33% Similarity=0.754 Sum_probs=12.9
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
.-||..|+.+.=| -.-.|+-|+..
T Consensus 11 ~~rC~~Cg~~~~p--------Pr~~Cp~C~s~ 34 (37)
T PF12172_consen 11 GQRCRDCGRVQFP--------PRPVCPHCGSD 34 (37)
T ss_dssp EEE-TTT--EEES----------SEETTTT--
T ss_pred EEEcCCCCCEecC--------CCcCCCCcCcc
Confidence 4689999998544 24788888754
No 160
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=25.43 E-value=37 Score=36.40 Aligned_cols=28 Identities=25% Similarity=0.672 Sum_probs=21.5
Q ss_pred CCccCCCCCceecCccEEEcCCceEEecCCCCCCCC
Q 004199 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~ 92 (769)
..-||.+|+= ....-.|.||-|+..-.+
T Consensus 353 ~~YRC~~CGF--------~a~~l~W~CPsC~~W~Ti 380 (389)
T COG2956 353 PRYRCQNCGF--------TAHTLYWHCPSCRAWETI 380 (389)
T ss_pred CCceecccCC--------cceeeeeeCCCccccccc
Confidence 5689999983 333457999999988765
No 161
>PF06707 DUF1194: Protein of unknown function (DUF1194); InterPro: IPR010607 This family consists of several hypothetical Rhizobiales specific proteins of around 270 residues in length. The function of this family is unknown.
Probab=25.40 E-value=7.1e+02 Score=25.12 Aligned_cols=97 Identities=25% Similarity=0.365 Sum_probs=56.4
Q ss_pred ccchhHHHHHHHHHhhccCCCCCcEEEEEecC--CCCCCCcccccCCCCCCcCCCCCCCCCCCcccchhHHHHHHHHHHH
Q 004199 268 TRCTGTALSIAASLLGACVPGSGARILAFVGG--PSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQL 345 (769)
Q Consensus 268 ~~~~G~Al~~A~~ll~~~~~~~ggrI~~F~sg--~pt~GpG~l~~~~~~~~~rs~~d~~~~~~~~~~~a~~fY~~la~~~ 345 (769)
.++.|.||..|..++... +..+.|-++=.|| +.|.|+.-+ +..-..+
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 389999999999999951 2235666666655 555553211 1112234
Q ss_pred HhcCcEEEEEEecCCcc----Chhhhhh--hhhccCceEEEeCCCCchhhHHHHHHHh
Q 004199 346 VHQGHVLDLFACALDQV----GVAELKV--AVEKTGGLVVLSDSFGHAVFKDSVRRVF 397 (769)
Q Consensus 346 ~~~~isvDlf~~~~~~~----~l~~m~~--l~~~TGG~v~~~~~f~~~~~~~~l~~~~ 397 (769)
...||+|+=+....... +|...-. +..-.|..+.....|. .|.+.++|-|
T Consensus 143 ~~~GitINgL~I~~~~~~~~~~L~~yy~~~VIgGpgAFV~~a~~~~--df~~AirrKL 198 (205)
T PF06707_consen 143 VAAGITINGLAILDDDPFGGADLDAYYRRCVIGGPGAFVETARGFE--DFAEAIRRKL 198 (205)
T ss_pred HHCCeEEeeeEecCCCCCccccHHHHHhhhcccCCCceEEEcCCHH--HHHHHHHHHH
Confidence 55799999998876554 4544322 2333333444444444 4666666544
No 162
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=24.70 E-value=34 Score=27.17 Aligned_cols=25 Identities=24% Similarity=0.685 Sum_probs=19.0
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCCCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~ 92 (769)
-|.+|+..++. ..=+|+.||...-.
T Consensus 6 AC~~Ck~l~~~--------d~e~CP~Cgs~~~t 30 (64)
T COG2093 6 ACKNCKRLTPE--------DTEICPVCGSTDLT 30 (64)
T ss_pred HHhhccccCCC--------CCccCCCCCCcccc
Confidence 49999987765 45689999987543
No 163
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.69 E-value=56 Score=34.55 Aligned_cols=28 Identities=21% Similarity=0.590 Sum_probs=20.1
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 88 (769)
--|.+|++-|- .....+..+|.|+-|..
T Consensus 245 ~pCprCG~~I~--~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 245 EPCLNCKTPIR--RVVVAGRSSHYCPHCQK 272 (272)
T ss_pred CcCCCCCCeeE--EEEECCCccEECcCCcC
Confidence 34999998762 22334678999999974
No 164
>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=24.03 E-value=27 Score=24.49 Aligned_cols=28 Identities=18% Similarity=0.304 Sum_probs=19.5
Q ss_pred CCCCCceecCccEEEcCCceEEecCCCC
Q 004199 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (769)
Q Consensus 61 C~~C~aylNp~~~~~~~~~~w~C~~C~~ 88 (769)
|.+|++-=.|.-+-...+....||-|+.
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 7889998889888888888889998874
No 165
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=23.92 E-value=16 Score=27.95 Aligned_cols=33 Identities=27% Similarity=0.511 Sum_probs=21.8
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~ 92 (769)
-+||..|.-.+---...- --.-+||-|...|.+
T Consensus 4 tiRC~~CnKlLa~a~~~~--yle~KCPrCK~vN~~ 36 (60)
T COG4416 4 TIRCAKCNKLLAEAEGQA--YLEKKCPRCKEVNEF 36 (60)
T ss_pred eeehHHHhHHHHhcccce--eeeecCCccceeeee
Confidence 479999987654321111 124689999999976
No 166
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=23.41 E-value=28 Score=23.92 Aligned_cols=12 Identities=42% Similarity=1.088 Sum_probs=6.9
Q ss_pred CCCCccCCCCCc
Q 004199 55 PYAPLRCRTCRS 66 (769)
Q Consensus 55 ~~~p~rC~~C~a 66 (769)
..+++||..|+.
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 167
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=22.94 E-value=60 Score=23.55 Aligned_cols=27 Identities=33% Similarity=0.752 Sum_probs=14.9
Q ss_pred CCCCCceecCccEEEc--CCceEEecCCCC
Q 004199 61 CRTCRSILNPFSIVDF--AAKIWICPFCFQ 88 (769)
Q Consensus 61 C~~C~aylNp~~~~~~--~~~~w~C~~C~~ 88 (769)
|..|++ -.-|..+++ +...|+|+-|+.
T Consensus 6 CP~CGG-~DrFri~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 6 CPICGG-KDRFRIFDDKDGRGTWICRQCGG 34 (40)
T ss_dssp -TTTT--TTTEEEETT----S-EEETTTTB
T ss_pred CCCCcC-ccccccCcCcccCCCEECCCCCC
Confidence 777877 444544553 467899999943
No 168
>PRK10220 hypothetical protein; Provisional
Probab=22.82 E-value=70 Score=28.51 Aligned_cols=28 Identities=25% Similarity=0.635 Sum_probs=19.6
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 90 (769)
.+.|.+|.+- |.-- ++..|+|+-|++.-
T Consensus 3 lP~CP~C~se---ytY~--d~~~~vCpeC~hEW 30 (111)
T PRK10220 3 LPHCPKCNSE---YTYE--DNGMYICPECAHEW 30 (111)
T ss_pred CCcCCCCCCc---ceEc--CCCeEECCcccCcC
Confidence 3668888862 2222 46789999999874
No 169
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.39 E-value=55 Score=30.32 Aligned_cols=25 Identities=28% Similarity=0.640 Sum_probs=19.1
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
.-|..|++ |..+ -.+.-.||.|++.
T Consensus 29 ~hCp~Cg~---PLF~---KdG~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGT---PLFR---KDGEVFCPVCGYR 53 (131)
T ss_pred hhCcccCC---ccee---eCCeEECCCCCce
Confidence 45999997 6666 2367999999964
No 170
>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=22.00 E-value=51 Score=27.76 Aligned_cols=30 Identities=23% Similarity=0.460 Sum_probs=17.4
Q ss_pred ccCCCCCceecCc----cEEE-----cCCceEEecCCCC
Q 004199 59 LRCRTCRSILNPF----SIVD-----FAAKIWICPFCFQ 88 (769)
Q Consensus 59 ~rC~~C~aylNp~----~~~~-----~~~~~w~C~~C~~ 88 (769)
.-|++|++++=|- +++. .+.-.|+|..|++
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 5699999997665 4455 3456799999984
No 171
>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=21.91 E-value=98 Score=28.18 Aligned_cols=31 Identities=26% Similarity=0.294 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhcccCCC---CceEEEEEECCeEE
Q 004199 145 MSFLKSALSQAIDLLPD---NSLVGLITFGTLVQ 175 (769)
Q Consensus 145 l~~~~~~l~~~l~~lp~---~~~VglITfd~~V~ 175 (769)
.+.++++|+.-+..-|. +.+|-+++||+.|-
T Consensus 112 Ae~vkDAi~Dyi~T~P~PT~~~~Vt~~~Fd~~V~ 145 (146)
T PF02905_consen 112 AECVKDAIRDYIMTRPQPTCNTQVTVCSFDDGVM 145 (146)
T ss_dssp HHHHHHHHHHHHCTS-TTGGGEEEEEEEEEEEE-
T ss_pred HHHHHHHHHHHhcCCCCCCcceEEEEEeCCCCCc
Confidence 56788999888877663 58999999998774
No 172
>PRK00420 hypothetical protein; Validated
Probab=21.88 E-value=66 Score=29.07 Aligned_cols=29 Identities=17% Similarity=0.324 Sum_probs=21.8
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~ 92 (769)
-.|..|+ .|+.++. ++.-.|+.||..-.+
T Consensus 24 ~~CP~Cg---~pLf~lk--~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCG---LPLFELK--DGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCC---CcceecC--CCceECCCCCCeeee
Confidence 5699999 4777763 468999999986544
No 173
>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=21.35 E-value=37 Score=33.35 Aligned_cols=29 Identities=28% Similarity=0.688 Sum_probs=10.5
Q ss_pred CCccCCCCCceecCccEEE-cCCceEEecCCCC
Q 004199 57 APLRCRTCRSILNPFSIVD-FAAKIWICPFCFQ 88 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~-~~~~~w~C~~C~~ 88 (769)
...+|.+|++ .|+.-. +....+.|+||+-
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 4688999987 232222 2257899999983
No 174
>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=21.33 E-value=65 Score=21.40 Aligned_cols=27 Identities=22% Similarity=0.754 Sum_probs=15.3
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 88 (769)
.|.+|+.++-.-.. .+...+.|+-|..
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 59999998544322 3557899999864
No 175
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=21.25 E-value=72 Score=22.98 Aligned_cols=28 Identities=29% Similarity=0.649 Sum_probs=18.3
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
.|.+|++-+.+... .+-..+.|+-|+-.
T Consensus 1 ~CP~C~~~l~~~~~--~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRL--GDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEE--CCEEEEECCCCCeE
Confidence 37788887666544 33567778877743
No 176
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=21.07 E-value=49 Score=40.41 Aligned_cols=26 Identities=23% Similarity=0.454 Sum_probs=21.3
Q ss_pred CCccCCCCCceecCccEEEcCCceEEecCCCCCCCC
Q 004199 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (769)
Q Consensus 57 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~~ 92 (769)
..-||.+|+.| +-.++|+.||..+..
T Consensus 624 ~~RKCPkCG~y----------Tlk~rCP~CG~~Te~ 649 (1095)
T TIGR00354 624 AIRKCPQCGKE----------SFWLKCPVCGELTEQ 649 (1095)
T ss_pred EEEECCCCCcc----------cccccCCCCCCcccc
Confidence 45799999997 357999999999754
No 177
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=21.01 E-value=57 Score=28.97 Aligned_cols=35 Identities=20% Similarity=0.373 Sum_probs=27.1
Q ss_pred ccCCCCCceecCc----cEEEcCCceEEecCCCCCCCCC
Q 004199 59 LRCRTCRSILNPF----SIVDFAAKIWICPFCFQRNHFP 93 (769)
Q Consensus 59 ~rC~~C~aylNp~----~~~~~~~~~w~C~~C~~~N~~p 93 (769)
--|++|.++|=|. +.+..+.-.|+|.-||..--+|
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p 95 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYP 95 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEec
Confidence 4599999986555 4555556799999999987665
No 178
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=20.95 E-value=47 Score=32.15 Aligned_cols=35 Identities=20% Similarity=0.625 Sum_probs=20.9
Q ss_pred CccCCCCCc------eecCccEEEcC------CceEEecCCCCCCCC
Q 004199 58 PLRCRTCRS------ILNPFSIVDFA------AKIWICPFCFQRNHF 92 (769)
Q Consensus 58 p~rC~~C~a------ylNp~~~~~~~------~~~w~C~~C~~~N~~ 92 (769)
-+.|.+|+- |||++-+.+-. +-.|+|.+|++.+.+
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 388999995 57888777643 447999999998865
No 179
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.47 E-value=55 Score=35.26 Aligned_cols=24 Identities=21% Similarity=0.665 Sum_probs=19.6
Q ss_pred ccCCCCCceecCccEEEcCCceEEecCCCCCCC
Q 004199 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (769)
Q Consensus 59 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~ 91 (769)
..|..|+. ..++.|.|+-||...+
T Consensus 310 ~~C~~cg~---------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 310 KTCPCCGH---------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred ccccccCC---------ccceeEECCCCCCeeh
Confidence 67999999 3468999999998743
No 180
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=20.36 E-value=51 Score=34.65 Aligned_cols=27 Identities=22% Similarity=0.613 Sum_probs=19.8
Q ss_pred cCCCCCceecCccEEEcCCceEEecCCCC
Q 004199 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (769)
Q Consensus 60 rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 88 (769)
-|.+|++.|--- ...+..+|+|+-|.+
T Consensus 247 pC~~CGt~I~k~--~~~gR~t~~CP~CQ~ 273 (273)
T COG0266 247 PCRRCGTPIEKI--KLGGRSTFYCPVCQK 273 (273)
T ss_pred CCCccCCEeEEE--EEcCCcCEeCCCCCC
Confidence 399999977542 233567899999974
No 181
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.31 E-value=3.2e+02 Score=31.74 Aligned_cols=18 Identities=17% Similarity=0.372 Sum_probs=14.1
Q ss_pred cCCceEEecCCCCCCCCC
Q 004199 76 FAAKIWICPFCFQRNHFP 93 (769)
Q Consensus 76 ~~~~~w~C~~C~~~N~~p 93 (769)
...+.-+|..||..-.+|
T Consensus 236 ~~~~~l~Ch~Cg~~~~~~ 253 (505)
T TIGR00595 236 KKEGKLRCHYCGYQEPIP 253 (505)
T ss_pred cCCCeEEcCCCcCcCCCC
Confidence 346688999999888775
No 182
>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=20.29 E-value=96 Score=33.34 Aligned_cols=27 Identities=33% Similarity=0.468 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHhcccCCCCceEEEEEE
Q 004199 144 EMSFLKSALSQAIDLLPDNSLVGLITF 170 (769)
Q Consensus 144 ~l~~~~~~l~~~l~~lp~~~~VglITf 170 (769)
||+.+...|..+.+.|.++.++++|||
T Consensus 215 EL~~L~~~L~~~~~~L~~gGrl~VISf 241 (305)
T TIGR00006 215 ELEELEEALQFAPNLLAPGGRLSIISF 241 (305)
T ss_pred hHHHHHHHHHHHHHHhcCCCEEEEEec
Confidence 489999999999999999999999985
No 183
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=20.27 E-value=55 Score=31.75 Aligned_cols=26 Identities=27% Similarity=0.721 Sum_probs=17.4
Q ss_pred CCceEEecCCCCCCCCCcCCCCCCCCCCCccccCCCc
Q 004199 77 AAKIWICPFCFQRNHFPPHYASITDDNLPAELFPQYT 113 (769)
Q Consensus 77 ~~~~w~C~~C~~~N~~p~~y~~~~~~~~~pEL~~~~~ 113 (769)
.|+.|+|+.||+.-. +.+||-+|-.+
T Consensus 131 ~~~~~vC~vCGy~~~-----------ge~P~~CPiCg 156 (166)
T COG1592 131 EGKVWVCPVCGYTHE-----------GEAPEVCPICG 156 (166)
T ss_pred cCCEEEcCCCCCccc-----------CCCCCcCCCCC
Confidence 355899999997743 14566665554
No 184
>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=20.24 E-value=37 Score=28.74 Aligned_cols=15 Identities=33% Similarity=0.961 Sum_probs=6.5
Q ss_pred ceEEecCCCCCCCCC
Q 004199 79 KIWICPFCFQRNHFP 93 (769)
Q Consensus 79 ~~w~C~~C~~~N~~p 93 (769)
+.+.|+||++.+.+-
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 689999999998863
No 185
>COG1773 Rubredoxin [Energy production and conversion]
Probab=20.20 E-value=50 Score=25.73 Aligned_cols=15 Identities=27% Similarity=0.698 Sum_probs=9.8
Q ss_pred EEcCCceEEecCCCC
Q 004199 74 VDFAAKIWICPFCFQ 88 (769)
Q Consensus 74 ~~~~~~~w~C~~C~~ 88 (769)
|.+---.|.|+.|+.
T Consensus 30 fedlPd~w~CP~Cg~ 44 (55)
T COG1773 30 FEDLPDDWVCPECGV 44 (55)
T ss_pred hhhCCCccCCCCCCC
Confidence 443345688888885
No 186
>PRK12366 replication factor A; Reviewed
Probab=20.18 E-value=71 Score=38.18 Aligned_cols=26 Identities=27% Similarity=0.631 Sum_probs=20.4
Q ss_pred CccCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 58 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
..+|..|+--+ ..+.+.|+|+-|+..
T Consensus 532 y~aCp~CnkKv------~~~~g~~~C~~c~~~ 557 (637)
T PRK12366 532 LYLCPNCRKRV------EEVDGEYICEFCGEV 557 (637)
T ss_pred EecccccCeEe------EcCCCcEECCCCCCC
Confidence 48999996644 345689999999988
No 187
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=20.01 E-value=33 Score=37.92 Aligned_cols=30 Identities=23% Similarity=0.419 Sum_probs=22.2
Q ss_pred CCCccCCCCCceecCccEEEcCCceEEecCCCCC
Q 004199 56 YAPLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (769)
Q Consensus 56 ~~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 89 (769)
|.---|.+|+.-++|--... ..|+|+ ||..
T Consensus 238 Yh~~~c~~C~~~~~~~~~~~---~~~~Cp-CG~~ 267 (374)
T TIGR00375 238 YHQTACEACGEPAVSEDAET---ACANCP-CGGR 267 (374)
T ss_pred cchhhhcccCCcCCchhhhh---cCCCCC-CCCc
Confidence 44567999998888753322 359999 9998
Done!