Query 012148
Match_columns 470
No_of_seqs 129 out of 745
Neff 7.7
Searched_HMMs 46136
Date Thu Mar 28 23:33:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012148.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012148hhsearch_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 6.7E-94 1.5E-98 788.0 43.2 452 2-468 1-465 (761)
2 KOG1986 Vesicle coat complex C 100.0 5.9E-85 1.3E-89 672.7 33.1 413 3-443 2-415 (745)
3 KOG1985 Vesicle coat complex C 100.0 2E-82 4.3E-87 663.2 25.5 401 6-469 166-585 (887)
4 COG5047 SEC23 Vesicle coat com 100.0 9.7E-82 2.1E-86 633.9 26.2 419 2-443 1-423 (755)
5 KOG1984 Vesicle coat complex C 100.0 2.8E-78 6.1E-83 632.8 28.5 407 6-469 283-709 (1007)
6 COG5028 Vesicle coat complex C 100.0 3.3E-70 7.2E-75 567.1 26.3 395 6-469 146-561 (861)
7 PTZ00395 Sec24-related protein 100.0 1.4E-65 3.1E-70 558.5 29.9 402 6-469 648-1258(1560)
8 cd01478 Sec23-like Sec23-like: 100.0 4.6E-57 9.9E-62 440.9 27.7 266 128-395 2-267 (267)
9 cd01468 trunk_domain trunk dom 100.0 4.1E-46 8.8E-51 360.3 23.7 227 127-394 1-234 (239)
10 cd01479 Sec24-like Sec24-like: 100.0 1E-45 2.2E-50 357.8 22.1 219 128-389 2-228 (244)
11 PF04811 Sec23_trunk: Sec23/Se 100.0 7.8E-45 1.7E-49 352.3 19.5 233 127-397 1-239 (243)
12 PF04810 zf-Sec23_Sec24: Sec23 99.6 5.2E-17 1.1E-21 111.7 2.3 40 57-96 1-40 (40)
13 cd01465 vWA_subgroup VWA subgr 98.6 3.5E-06 7.5E-11 76.5 17.4 159 131-385 2-164 (170)
14 PRK13685 hypothetical protein; 98.6 3.7E-06 8.1E-11 85.2 18.3 162 129-384 88-276 (326)
15 cd01451 vWA_Magnesium_chelatas 98.6 7.5E-06 1.6E-10 75.5 18.5 163 131-389 2-172 (178)
16 cd01456 vWA_ywmD_type VWA ywmD 98.5 4.3E-06 9.3E-11 78.9 16.1 169 128-378 19-196 (206)
17 cd01453 vWA_transcription_fact 98.5 4.3E-06 9.3E-11 77.6 15.6 153 131-384 5-168 (183)
18 cd01463 vWA_VGCC_like VWA Volt 98.5 9.3E-06 2E-10 75.6 17.2 166 128-384 12-189 (190)
19 cd01466 vWA_C3HC4_type VWA C3H 98.5 6.6E-06 1.4E-10 74.1 15.2 149 132-381 3-154 (155)
20 TIGR03436 acidobact_VWFA VWFA- 98.4 3.4E-05 7.4E-10 77.0 20.0 49 128-176 52-102 (296)
21 cd01467 vWA_BatA_type VWA BatA 98.3 4.1E-05 8.9E-10 70.3 17.3 157 130-384 3-177 (180)
22 cd01472 vWA_collagen von Wille 98.3 6.3E-05 1.4E-09 68.1 17.6 151 132-384 3-164 (164)
23 cd01470 vWA_complement_factors 98.3 4.2E-05 9E-10 71.7 16.8 168 132-385 3-191 (198)
24 cd01480 vWA_collagen_alpha_1-V 98.2 6.4E-05 1.4E-09 69.8 16.0 158 131-386 4-174 (186)
25 TIGR00868 hCaCC calcium-activa 98.1 0.00011 2.3E-09 82.4 17.8 155 128-384 303-463 (863)
26 cd01452 VWA_26S_proteasome_sub 98.1 0.00016 3.5E-09 67.1 15.8 145 131-374 5-161 (187)
27 cd01461 vWA_interalpha_trypsin 98.1 0.00035 7.7E-09 63.2 18.0 160 129-386 2-164 (171)
28 PF13519 VWA_2: von Willebrand 98.1 5.6E-05 1.2E-09 68.0 12.6 151 132-382 2-159 (172)
29 PF13768 VWA_3: von Willebrand 98.0 0.00021 4.5E-09 64.0 13.8 151 132-379 3-154 (155)
30 PF08033 Sec23_BS: Sec23/Sec24 97.9 4.6E-06 9.9E-11 69.0 2.3 53 407-469 1-62 (96)
31 cd01474 vWA_ATR ATR (Anthrax T 97.9 0.00048 1E-08 63.8 15.8 156 129-385 4-168 (185)
32 cd01475 vWA_Matrilin VWA_Matri 97.9 0.00061 1.3E-08 65.2 16.3 156 129-386 2-171 (224)
33 cd01471 vWA_micronemal_protein 97.8 0.00099 2.1E-08 61.6 16.1 44 132-175 3-52 (186)
34 cd01482 vWA_collagen_alphaI-XI 97.8 0.002 4.3E-08 58.3 17.6 44 132-175 3-51 (164)
35 cd01450 vWFA_subfamily_ECM Von 97.8 0.0012 2.7E-08 58.6 15.6 144 132-374 3-155 (161)
36 cd01469 vWA_integrins_alpha_su 97.8 0.0021 4.5E-08 59.1 17.2 156 132-385 3-172 (177)
37 cd01477 vWA_F09G8-8_type VWA F 97.6 0.0031 6.8E-08 59.0 16.3 48 129-176 19-77 (193)
38 TIGR02031 BchD-ChlD magnesium 97.6 0.0031 6.8E-08 68.9 18.7 176 128-387 406-586 (589)
39 smart00327 VWA von Willebrand 97.6 0.0063 1.4E-07 54.7 17.5 154 130-380 2-164 (177)
40 cd01481 vWA_collagen_alpha3-VI 97.6 0.0041 8.9E-08 56.6 16.0 44 132-175 3-51 (165)
41 TIGR03788 marine_srt_targ mari 97.5 0.011 2.3E-07 65.0 21.6 173 127-398 269-443 (596)
42 cd01476 VWA_integrin_invertebr 97.5 0.0052 1.1E-07 55.3 15.7 41 132-172 3-47 (163)
43 PF00092 VWA: von Willebrand f 97.5 0.0024 5.2E-08 57.8 13.0 44 132-175 2-50 (178)
44 PRK13406 bchD magnesium chelat 97.4 0.015 3.3E-07 63.3 19.8 172 128-390 400-576 (584)
45 TIGR02442 Cob-chelat-sub cobal 97.3 0.011 2.4E-07 65.3 18.4 161 128-381 464-632 (633)
46 cd00198 vWFA Von Willebrand fa 97.3 0.016 3.4E-07 50.6 16.2 147 131-374 2-155 (161)
47 cd01473 vWA_CTRP CTRP for CS 97.2 0.021 4.5E-07 53.3 15.9 45 132-176 3-53 (192)
48 PTZ00441 sporozoite surface pr 97.2 0.016 3.5E-07 62.1 16.6 165 128-386 41-218 (576)
49 COG1240 ChlD Mg-chelatase subu 97.2 0.021 4.5E-07 55.0 15.8 170 128-390 77-253 (261)
50 PF04056 Ssl1: Ssl1-like; Int 96.9 0.027 5.9E-07 52.5 13.6 90 268-393 79-169 (193)
51 cd01458 vWA_ku Ku70/Ku80 N-ter 96.7 0.072 1.6E-06 50.6 15.6 69 267-360 104-173 (218)
52 cd01454 vWA_norD_type norD typ 96.5 0.15 3.2E-06 46.5 15.6 43 131-173 2-48 (174)
53 cd01462 VWA_YIEM_type VWA YIEM 96.3 0.18 4E-06 44.6 14.6 43 132-174 3-48 (152)
54 TIGR00578 ku70 ATP-dependent D 95.2 0.41 8.9E-06 52.5 14.7 73 269-366 117-191 (584)
55 cd01464 vWA_subfamily VWA subf 93.7 0.12 2.5E-06 47.3 5.3 45 132-176 6-58 (176)
56 cd01460 vWA_midasin VWA_Midasi 93.1 8.4 0.00018 37.9 17.5 46 128-174 59-110 (266)
57 COG4245 TerY Uncharacterized p 91.1 0.42 9.2E-06 43.9 5.2 47 132-178 6-60 (207)
58 PF10058 DUF2296: Predicted in 84.8 0.59 1.3E-05 34.2 1.7 33 58-90 22-54 (54)
59 KOG2884 26S proteasome regulat 83.6 12 0.00027 35.3 10.1 85 269-384 85-176 (259)
60 TIGR01053 LSD1 zinc finger dom 83.4 1.1 2.4E-05 28.8 2.3 30 59-92 2-31 (31)
61 PRK00398 rpoP DNA-directed RNA 82.9 0.83 1.8E-05 32.1 1.7 29 59-91 4-32 (46)
62 KOG2807 RNA polymerase II tran 80.4 53 0.0012 33.0 13.7 74 269-376 143-217 (378)
63 TIGR00627 tfb4 transcription f 75.6 31 0.00066 34.2 10.7 86 268-383 118-209 (279)
64 PF09967 DUF2201: VWA-like dom 75.6 7.9 0.00017 33.5 5.9 41 133-175 2-44 (126)
65 smart00661 RPOL9 RNA polymeras 75.4 1.9 4.1E-05 30.8 1.7 33 60-94 2-34 (52)
66 PF03850 Tfb4: Transcription f 70.7 35 0.00076 33.8 9.9 88 269-386 116-210 (276)
67 smart00187 INB Integrin beta s 70.5 1.5E+02 0.0032 31.3 19.4 197 128-364 98-304 (423)
68 PF08271 TF_Zn_Ribbon: TFIIB z 69.1 5.7 0.00012 27.4 2.9 27 60-89 2-28 (43)
69 cd00350 rubredoxin_like Rubred 66.7 3.8 8.2E-05 26.6 1.5 23 60-88 3-25 (33)
70 PRK03954 ribonuclease P protei 66.5 3.5 7.6E-05 35.5 1.6 35 59-93 65-106 (121)
71 PF13719 zinc_ribbon_5: zinc-r 66.4 3.8 8.2E-05 27.4 1.4 33 58-90 2-35 (37)
72 PF09723 Zn-ribbon_8: Zinc rib 65.3 2.6 5.6E-05 29.0 0.5 30 59-89 6-35 (42)
73 COG5148 RPN10 26S proteasome r 64.5 30 0.00066 32.0 7.3 73 246-358 71-145 (243)
74 PRK12380 hydrogenase nickel in 63.1 4.3 9.3E-05 34.5 1.5 28 58-91 70-97 (113)
75 PF14803 Nudix_N_2: Nudix N-te 62.5 2.3 5E-05 28.0 -0.2 30 60-89 2-31 (34)
76 cd01457 vWA_ORF176_type VWA OR 62.4 10 0.00022 35.2 4.1 44 130-173 3-57 (199)
77 PF09082 DUF1922: Domain of un 62.3 4 8.6E-05 31.2 1.1 30 58-93 3-32 (68)
78 TIGR00100 hypA hydrogenase nic 62.3 4.6 9.9E-05 34.4 1.6 28 58-91 70-97 (115)
79 cd00730 rubredoxin Rubredoxin; 61.8 4.4 9.6E-05 29.1 1.2 29 60-88 3-42 (50)
80 PRK14890 putative Zn-ribbon RN 60.2 3.5 7.6E-05 30.6 0.4 22 58-89 36-57 (59)
81 TIGR02605 CxxC_CxxC_SSSS putat 59.0 4.2 9.1E-05 29.1 0.7 31 59-90 6-36 (52)
82 PF03731 Ku_N: Ku70/Ku80 N-ter 57.8 24 0.00052 33.3 5.9 65 268-357 104-172 (224)
83 PF10122 Mu-like_Com: Mu-like 57.7 4.7 0.0001 29.0 0.7 33 59-93 5-37 (51)
84 PF13240 zinc_ribbon_2: zinc-r 56.9 5.4 0.00012 23.8 0.8 21 60-88 1-21 (23)
85 PF08792 A2L_zn_ribbon: A2L zi 56.8 12 0.00026 24.5 2.4 29 58-90 3-31 (33)
86 KOG3799 Rab3 effector RIM1 and 56.5 5.6 0.00012 34.5 1.1 31 57-91 88-118 (169)
87 smart00834 CxxC_CXXC_SSSS Puta 55.6 4.9 0.00011 27.0 0.5 29 59-88 6-34 (41)
88 PF13717 zinc_ribbon_4: zinc-r 55.6 7.4 0.00016 25.9 1.4 31 59-89 3-34 (36)
89 PF09779 Ima1_N: Ima1 N-termin 55.2 9 0.00019 33.5 2.2 34 59-94 1-34 (131)
90 PF05762 VWA_CoxE: VWA domain 54.9 24 0.00052 33.5 5.3 44 128-174 55-100 (222)
91 PRK03681 hypA hydrogenase nick 54.7 7.2 0.00016 33.2 1.5 29 58-91 70-98 (114)
92 COG1198 PriA Primosomal protei 53.8 34 0.00074 38.5 6.9 106 58-180 444-571 (730)
93 PF07282 OrfB_Zn_ribbon: Putat 53.4 9.1 0.0002 29.1 1.8 28 59-90 29-56 (69)
94 PF02318 FYVE_2: FYVE-type zin 52.7 6.8 0.00015 33.5 1.1 32 59-90 72-104 (118)
95 PF00301 Rubredoxin: Rubredoxi 51.1 6.3 0.00014 28.0 0.5 30 60-89 3-43 (47)
96 PRK10997 yieM hypothetical pro 49.5 25 0.00054 37.7 4.9 52 129-180 323-377 (487)
97 smart00401 ZnF_GATA zinc finge 49.3 11 0.00023 27.3 1.5 32 58-89 3-34 (52)
98 COG1996 RPC10 DNA-directed RNA 49.3 8.9 0.00019 27.5 1.0 27 60-90 8-34 (49)
99 PF12773 DZR: Double zinc ribb 49.1 11 0.00023 26.7 1.4 32 57-93 11-42 (50)
100 PF06943 zf-LSD1: LSD1 zinc fi 48.5 14 0.0003 22.6 1.6 24 61-88 1-24 (25)
101 PRK00564 hypA hydrogenase nick 48.5 7.1 0.00015 33.4 0.5 29 58-91 71-99 (117)
102 smart00659 RPOLCX RNA polymera 48.1 14 0.00031 25.7 1.9 26 60-90 4-29 (44)
103 PRK00432 30S ribosomal protein 46.7 12 0.00026 26.9 1.4 25 59-89 21-46 (50)
104 COG1096 Predicted RNA-binding 46.3 11 0.00024 34.7 1.5 26 58-89 149-174 (188)
105 PF11781 RRN7: RNA polymerase 45.5 20 0.00043 23.9 2.2 26 59-89 9-34 (36)
106 PF12760 Zn_Tnp_IS1595: Transp 45.1 23 0.00051 24.7 2.7 27 59-88 19-45 (46)
107 PF07754 DUF1610: Domain of un 44.8 16 0.00034 22.1 1.5 24 61-88 1-24 (24)
108 TIGR02098 MJ0042_CXXC MJ0042 f 43.6 15 0.00032 24.4 1.4 31 59-89 3-34 (38)
109 PF00641 zf-RanBP: Zn-finger i 43.0 9.6 0.00021 24.0 0.4 14 79-92 3-16 (30)
110 COG1545 Predicted nucleic-acid 41.6 57 0.0012 28.8 5.2 61 59-141 30-95 (140)
111 PRK12286 rpmF 50S ribosomal pr 41.5 21 0.00045 26.5 2.0 26 57-91 26-51 (57)
112 PRK03824 hypA hydrogenase nick 41.3 16 0.00034 32.1 1.6 33 58-90 70-117 (135)
113 smart00132 LIM Zinc-binding do 40.6 21 0.00046 23.0 1.8 29 60-88 1-35 (39)
114 PRK00762 hypA hydrogenase nick 40.4 13 0.00028 32.1 0.9 33 58-91 70-103 (124)
115 PF01155 HypA: Hydrogenase exp 40.4 7.2 0.00016 33.1 -0.7 27 58-90 70-96 (113)
116 PF10571 UPF0547: Uncharacteri 40.0 14 0.0003 22.7 0.7 23 60-90 2-24 (26)
117 TIGR00311 aIF-2beta translatio 39.7 29 0.00062 30.4 2.9 31 59-92 98-130 (133)
118 PRK06393 rpoE DNA-directed RNA 39.4 17 0.00037 27.6 1.3 25 59-93 6-30 (64)
119 COG2956 Predicted N-acetylgluc 39.3 16 0.00034 36.9 1.4 29 57-93 353-381 (389)
120 TIGR01384 TFS_arch transcripti 38.8 19 0.00042 29.7 1.7 27 60-92 2-28 (104)
121 PF08274 PhnA_Zn_Ribbon: PhnA 38.6 16 0.00034 23.4 0.8 26 59-89 3-28 (30)
122 PHA00626 hypothetical protein 38.6 27 0.00059 25.6 2.1 29 61-91 3-34 (59)
123 COG0275 Predicted S-adenosylme 38.5 41 0.00088 33.7 4.1 29 143-171 218-246 (314)
124 COG3357 Predicted transcriptio 37.8 16 0.00035 29.5 1.0 36 57-96 57-92 (97)
125 PF02891 zf-MIZ: MIZ/SP-RING z 37.1 3.9 8.5E-05 29.3 -2.4 18 71-88 32-49 (50)
126 COG2023 RPR2 RNase P subunit R 36.2 19 0.00042 30.0 1.2 35 59-93 57-95 (105)
127 TIGR00686 phnA alkylphosphonat 35.2 32 0.00069 28.9 2.4 29 58-91 2-30 (109)
128 PF00320 GATA: GATA zinc finge 35.0 12 0.00026 24.8 -0.1 28 61-88 1-28 (36)
129 COG2051 RPS27A Ribosomal prote 34.7 31 0.00066 26.3 2.0 31 58-91 19-49 (67)
130 PF13894 zf-C2H2_4: C2H2-type 34.6 21 0.00046 20.2 0.9 11 81-91 1-11 (24)
131 PRK12722 transcriptional activ 33.2 20 0.00043 33.3 1.0 29 57-88 133-162 (187)
132 smart00778 Prim_Zn_Ribbon Zinc 33.1 39 0.00086 22.7 2.1 27 60-88 5-33 (37)
133 COG2888 Predicted Zn-ribbon RN 32.9 38 0.00082 25.2 2.2 28 57-88 8-35 (61)
134 PRK08351 DNA-directed RNA poly 32.8 28 0.0006 26.2 1.5 23 60-92 5-27 (61)
135 PRK08271 anaerobic ribonucleos 32.6 23 0.00049 39.2 1.4 26 57-90 565-590 (623)
136 PRK08270 anaerobic ribonucleos 32.6 22 0.00047 39.7 1.3 24 57-89 625-648 (656)
137 PF09297 zf-NADH-PPase: NADH p 32.1 41 0.00088 21.5 2.0 26 60-89 5-30 (32)
138 smart00547 ZnF_RBZ Zinc finger 30.5 22 0.00047 21.3 0.5 13 80-92 2-14 (26)
139 PF03604 DNA_RNApol_7kD: DNA d 30.4 20 0.00042 23.3 0.3 10 57-66 16-25 (32)
140 PF04032 Rpr2: RNAse P Rpr2/Rp 30.4 26 0.00056 27.6 1.1 30 59-88 47-85 (85)
141 PF14353 CpXC: CpXC protein 30.4 42 0.00091 28.8 2.5 14 80-93 38-51 (128)
142 PRK00420 hypothetical protein; 30.3 37 0.0008 28.8 2.0 29 59-92 24-52 (112)
143 PF05129 Elf1: Transcription e 30.2 19 0.00042 28.6 0.3 15 79-93 21-35 (81)
144 COG2425 Uncharacterized protei 29.9 2.3E+02 0.005 30.0 8.2 45 130-174 273-320 (437)
145 COG5415 Predicted integral mem 29.8 31 0.00068 32.4 1.6 37 58-94 192-228 (251)
146 KOG2846 Predicted membrane pro 29.6 28 0.0006 35.0 1.4 35 59-93 221-255 (328)
147 cd01455 vWA_F11C1-5a_type Von 29.4 4.7E+02 0.01 24.4 11.0 99 245-384 75-175 (191)
148 COG0675 Transposase and inacti 28.9 30 0.00065 34.4 1.5 24 59-91 310-333 (364)
149 PF05280 FlhC: Flagellar trans 28.6 20 0.00044 32.9 0.2 29 57-88 133-162 (175)
150 PF12257 DUF3608: Protein of u 28.2 1.5E+02 0.0032 29.5 6.1 63 271-361 205-272 (281)
151 cd00729 rubredoxin_SM Rubredox 28.2 31 0.00068 22.5 1.0 12 80-91 2-13 (34)
152 TIGR00006 S-adenosyl-methyltra 28.2 68 0.0015 32.3 3.8 28 144-171 215-242 (305)
153 COG1645 Uncharacterized Zn-fin 27.4 42 0.00092 29.2 1.9 25 59-89 29-53 (131)
154 PF03660 PHF5: PHF5-like prote 27.2 24 0.00051 29.3 0.3 41 59-99 28-74 (106)
155 PF15288 zf-CCHC_6: Zinc knuck 27.1 25 0.00054 24.1 0.4 9 59-67 2-10 (40)
156 PF13408 Zn_ribbon_recom: Reco 26.8 30 0.00065 24.9 0.8 31 57-88 4-34 (58)
157 PRK10220 hypothetical protein; 26.7 60 0.0013 27.3 2.6 29 58-91 3-31 (111)
158 cd02342 ZZ_UBA_plant Zinc fing 26.7 51 0.0011 22.9 1.8 22 59-87 1-22 (43)
159 PRK12860 transcriptional activ 26.6 33 0.00071 31.9 1.2 28 57-87 133-161 (189)
160 KOG2353 L-type voltage-depende 26.2 1E+02 0.0023 36.4 5.3 51 127-177 223-275 (1104)
161 COG4888 Uncharacterized Zn rib 26.2 32 0.00069 28.5 0.9 14 79-92 21-34 (104)
162 TIGR00354 polC DNA polymerase, 25.5 35 0.00075 39.2 1.3 26 57-92 624-649 (1095)
163 PF13597 NRDD: Anaerobic ribon 25.5 26 0.00056 38.2 0.3 25 57-90 490-514 (546)
164 cd01464 vWA_subfamily VWA subf 25.1 1.4E+02 0.003 26.8 5.1 77 267-374 77-161 (176)
165 PF01927 Mut7-C: Mut7-C RNAse 25.1 48 0.001 29.4 2.0 33 58-90 91-134 (147)
166 COG1592 Rubrerythrin [Energy p 25.0 39 0.00084 30.8 1.3 15 77-91 131-145 (166)
167 PF05907 DUF866: Eukaryotic pr 24.9 41 0.0009 30.4 1.5 35 58-92 30-76 (161)
168 KOG1296 Uncharacterized conser 24.6 34 0.00074 30.2 0.8 35 58-92 30-76 (161)
169 PF08273 Prim_Zn_Ribbon: Zinc- 24.5 49 0.0011 22.6 1.4 27 61-88 6-34 (40)
170 COG4867 Uncharacterized protei 24.2 7.1E+02 0.015 26.3 10.2 97 269-383 533-635 (652)
171 PRK00050 16S rRNA m(4)C1402 me 24.2 89 0.0019 31.3 3.8 28 144-171 211-238 (296)
172 COG1997 RPL43A Ribosomal prote 24.0 78 0.0017 25.5 2.7 31 57-91 34-64 (89)
173 COG1998 RPS31 Ribosomal protei 23.8 50 0.0011 23.7 1.4 27 58-88 19-45 (51)
174 PF13453 zf-TFIIB: Transcripti 23.5 52 0.0011 22.3 1.5 26 61-88 2-27 (41)
175 PRK14810 formamidopyrimidine-D 23.1 60 0.0013 32.0 2.4 27 59-88 245-272 (272)
176 PF00362 Integrin_beta: Integr 23.0 9.1E+02 0.02 25.5 16.3 197 128-363 101-306 (426)
177 cd00202 ZnF_GATA Zinc finger D 22.8 20 0.00044 26.1 -0.8 31 60-90 1-31 (54)
178 PF12874 zf-met: Zinc-finger o 22.8 50 0.0011 19.3 1.1 11 81-91 1-11 (25)
179 COG4874 Uncharacterized protei 22.6 2.5E+02 0.0053 27.3 6.2 58 332-397 53-124 (318)
180 PF09943 DUF2175: Uncharacteri 22.4 40 0.00087 28.0 0.8 12 79-90 1-12 (101)
181 TIGR01031 rpmF_bact ribosomal 22.0 57 0.0012 23.9 1.5 25 57-90 25-49 (55)
182 PRK09263 anaerobic ribonucleos 21.6 49 0.0011 37.3 1.6 30 57-90 640-669 (711)
183 PF02905 EBV-NA1: Epstein Barr 21.3 1.1E+02 0.0025 26.3 3.3 30 146-175 113-145 (146)
184 PF06827 zf-FPG_IleRS: Zinc fi 21.2 55 0.0012 20.4 1.1 27 60-88 3-29 (30)
185 COG1571 Predicted DNA-binding 21.0 46 0.001 34.8 1.1 55 30-91 314-378 (421)
186 PRK08579 anaerobic ribonucleos 20.9 46 0.001 36.9 1.2 26 57-90 567-592 (625)
187 PF02150 RNA_POL_M_15KD: RNA p 20.9 78 0.0017 20.8 1.8 30 60-92 3-32 (35)
188 PF05191 ADK_lid: Adenylate ki 20.8 44 0.00094 22.2 0.6 26 61-88 4-29 (36)
189 PF06677 Auto_anti-p27: Sjogre 20.7 73 0.0016 21.9 1.7 24 59-87 18-41 (41)
190 PRK12366 replication factor A; 20.7 65 0.0014 35.9 2.3 26 58-89 532-557 (637)
191 PRK07218 replication factor A; 20.6 42 0.00092 35.3 0.8 22 58-89 297-318 (423)
192 cd04476 RPA1_DBD_C RPA1_DBD_C: 20.6 71 0.0015 28.7 2.2 27 59-91 35-62 (166)
193 PRK14892 putative transcriptio 20.5 74 0.0016 26.4 2.0 34 57-91 20-53 (99)
194 PRK03988 translation initiatio 20.4 1.1E+02 0.0024 27.0 3.2 33 58-93 102-136 (138)
195 PRK12336 translation initiatio 20.3 93 0.002 29.2 2.9 33 59-94 99-133 (201)
196 PF11265 Med25_VWA: Mediator c 20.2 7.7E+02 0.017 23.6 13.3 105 246-380 91-204 (226)
No 1
>PLN00162 transport protein sec23; Provisional
Probab=100.00 E-value=6.7e-94 Score=788.04 Aligned_cols=452 Identities=64% Similarity=1.075 Sum_probs=400.8
Q ss_pred CCcccccCCCeeeecCCCCCCCHHHHhhCCCCeEEEEccCCCCCCCCCCCCCCCCCCccccCCCeeeCCCceEEcCCceE
Q 012148 2 TEFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRTCRSILNPFSIVDFAAKIW 81 (470)
Q Consensus 2 ~~~~~~~~~~~iR~T~~~~P~t~~~~~~~~iPlg~vv~P~~~~~~~~~~ip~v~~~~~RC~~C~aYiNp~~~~~~~g~~w 81 (470)
|||++.|+.++||+|||+||+++.++++++|||||+|+||++. +++|+++++|+||++|+|||||||+|+.+|++|
T Consensus 1 ~~~~~~e~~~gvR~s~n~~P~t~~~~~~~~iPlg~v~tPl~~~----~~vp~v~~~pvRC~~CraylNPf~~~d~~~~~W 76 (761)
T PLN00162 1 MDFAELEAIDGVRMSWNVWPSSKIEASKCVIPLAALYTPLKPL----PELPVLPYDPLRCRTCRAVLNPYCRVDFQAKIW 76 (761)
T ss_pred CchhhhcccCceEeeeecCCCCHHHHhcCCCCeEEEEecCCcC----CCCCcCCCCCCccCCCcCEECCceEEecCCCEE
Confidence 7999999999999999999999999999999999999999886 569999999999999999999999999999999
Q ss_pred EeCCCCCCCCCCccccCCCCCCCCcccCCCcceEEEeCCCCCCCCCCCCEEEEEEEcccchhhHHHHHHHHHHHhhcCCC
Q 012148 82 ICPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPGPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLPD 161 (470)
Q Consensus 82 ~C~~C~~~N~vp~~y~~~~~~~~~pEL~~~~~tvey~~~~~~~~~~~~p~~vFvID~S~~~~~~~~l~~~l~~~l~~lp~ 161 (470)
+||||++.|.+|++|..+++.++||||.++++||||.+++...+++.||+|+||||+|..+++++.++++|+++|+.||+
T Consensus 77 ~C~~C~~~N~~P~~Y~~~~~~~~p~EL~p~~~TvEY~~p~~~~~~~~pp~fvFvID~s~~~~~l~~lk~sl~~~L~~LP~ 156 (761)
T PLN00162 77 ICPFCFQRNHFPPHYSSISETNLPAELFPQYTTVEYTLPPGSGGAPSPPVFVFVVDTCMIEEELGALKSALLQAIALLPE 156 (761)
T ss_pred EccCCCCCCCCchHhcccCccCCChhhcCCceeEEEECCCCCCCCCCCcEEEEEEecchhHHHHHHHHHHHHHHHHhCCC
Confidence 99999999999999987777889999999999999999852234568999999999999999999999999999999999
Q ss_pred CceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHHHHhhcccCCCCCCCccccCccCCCCccccccceeecc
Q 012148 162 NSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAF 241 (470)
Q Consensus 162 ~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~ 241 (470)
+++|||||||+.||||+|+ .+. +++++||+|+++++.+++++++++.+.+..++....+.-.++++....++||+|++
T Consensus 157 ~a~VGlITF~s~V~~~~L~-~~~-~~~~~Vf~g~k~~t~~~l~~~l~l~~~~~~~~~~~~~~~~~~~~~p~~~~fLvpl~ 234 (761)
T PLN00162 157 NALVGLITFGTHVHVHELG-FSE-CSKSYVFRGNKEVSKDQILEQLGLGGKKRRPAGGGIAGARDGLSSSGVNRFLLPAS 234 (761)
T ss_pred CCEEEEEEECCEEEEEEcC-CCC-CcceEEecCCccCCHHHHHHHhccccccccccccccccccccccCCCccceeEEHH
Confidence 9999999999999999999 766 89999999999999999999988754211111000000001111114589999999
Q ss_pred chHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCC
Q 012148 242 DCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHK 321 (470)
Q Consensus 242 ~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~ 321 (470)
||+..|..+||+|++++|++++++|+.||+|+||++|..+|+.+..++||||++|++||||.|||+|+.++.++++|+|+
T Consensus 235 e~~~~i~~lLe~L~~~~~~~~~~~rp~r~tG~AL~vA~~lL~~~~~~~gGrI~~F~sgppT~GpG~v~~r~~~~~~rsh~ 314 (761)
T PLN00162 235 ECEFTLNSALEELQKDPWPVPPGHRPARCTGAALSVAAGLLGACVPGTGARIMAFVGGPCTEGPGAIVSKDLSEPIRSHK 314 (761)
T ss_pred HHHHHHHHHHHhhhccccccCCCCCCCccHHHHHHHHHHHHhhccCCCceEEEEEeCCCCCCCCceeecccccccccCcc
Confidence 99999999999999999988889999999999999999999988888999999999999999999999999999999999
Q ss_pred CCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccChhhchhhhcccCceEEEcCCCCchhhHHHHHHHHhc-c
Q 012148 322 DLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVFHS-G 400 (470)
Q Consensus 322 ~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~~~l~~-~ 400 (470)
+++++++++++++.+||++||++|+++||+||+|+++.+|+|+++|+.|++.|||.+++|++|+.+.|++++++++++ .
T Consensus 315 di~k~~~~~~~~a~~fY~~la~~~~~~gisvDlF~~s~dqvglaem~~l~~~TGG~v~~~~sF~~~~f~~~l~r~~~r~~ 394 (761)
T PLN00162 315 DLDKDAAPYYKKAVKFYEGLAKQLVAQGHVLDVFACSLDQVGVAEMKVAVERTGGLVVLAESFGHSVFKDSLRRVFERDG 394 (761)
T ss_pred ccccchhhhcchHHHHHHHHHHHHHHcCceEEEEEccccccCHHHHhhhHhhcCcEEEEeCCcChHHHHHHHHHHhcccc
Confidence 999998899999999999999999999999999999999999999999999999999999999999999999999953 3
Q ss_pred ccccceeeEEEEEecccccceeeeecCCeeeeEEEeCcee---cchhhhHh---------hhhhhcCCCccchhhccccc
Q 012148 401 DYDLGLSSKYGFMNFVLYFFLSRIADYPLPVLTIITPLYK---KYLLLAKL---------IYAYMHGADSLFQQDLSLSE 468 (470)
Q Consensus 401 ~~~~~~~~~~~lr~~~~~~~v~~r~S~gl~i~~~~G~~~~---~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~ 468 (470)
++++.+||+|+|| | |||+||+|.++|||++. ++....++ ...+..++|++|+..+++++
T Consensus 395 ~~~~~~gf~a~~~-------V--rtS~glkv~g~~G~~~s~~~~~~~vsd~~iG~g~T~~w~l~~l~~~~t~av~f~~~~ 465 (761)
T PLN00162 395 EGSLGLSFNGTFE-------V--NCSKDVKVQGAIGPCASLEKKGPSVSDTEIGEGGTTAWKLCGLDKKTSLAVFFEVAN 465 (761)
T ss_pred cccccccceeEEE-------E--EecCCeEEeeeEcCcccccccCCccccccccCCCCceeeecCcCcCCEEEEEEEEcc
Confidence 4567899999999 9 99999999999999973 32111121 22356889999999888764
No 2
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5.9e-85 Score=672.74 Aligned_cols=413 Identities=53% Similarity=0.948 Sum_probs=385.6
Q ss_pred CcccccCCCeeeecCCCCCCCHHHHhhCCCCeEEEEccCCCCCCCCCCCCCCCCCCccccCCCeeeCCCceEEcCCceEE
Q 012148 3 EFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRTCRSILNPFSIVDFAAKIWI 82 (470)
Q Consensus 3 ~~~~~~~~~~iR~T~~~~P~t~~~~~~~~iPlg~vv~P~~~~~~~~~~ip~v~~~~~RC~~C~aYiNp~~~~~~~g~~w~ 82 (470)
.++++++.+++|+||+.+|.++....++.+|++++++||.+. ..+|.+.|+|+||.+|+||+||||.++.+.+.|.
T Consensus 2 ~~~~~e~~dGvR~twnvwPs~~~~~~~~vvPla~lytPl~e~----~~~~~~~y~P~~C~~C~AvlNPyc~vd~~a~~W~ 77 (745)
T KOG1986|consen 2 FIEDIEEIDGVRFTWNVWPSTRAEASRTVVPLACLYTPLKER----PDLPPIQYDPLRCSKCGAVLNPYCSVDFRAKSWI 77 (745)
T ss_pred cccccccCCCcccccccCCCcccccccccccHHHhccccccC----CCCCccCCCCchhccchhhcCcceeecccCceEe
Confidence 466799999999999999999999999999999999999876 4578899999999999999999999999999999
Q ss_pred eCCCCCCCCCCccccCCCCCCCCcccCCCcceEEEeCCCCCCCCCCCCEEEEEEEcccchhhHHHHHHHHHHHhhcCCCC
Q 012148 83 CPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPGPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLPDN 162 (470)
Q Consensus 83 C~~C~~~N~vp~~y~~~~~~~~~pEL~~~~~tvey~~~~~~~~~~~~p~~vFvID~S~~~~~~~~l~~~l~~~l~~lp~~ 162 (470)
|+||.+.|.+|++|..++..|+|+||.|+++||||.++++.+ .||+|+||||++..++++++++++|+.+|+.||++
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 999999999999999999999999999999999999986555 69999999999999999999999999999999999
Q ss_pred ceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHHHHhhcccCCCCCCCccccCccCCCCccccccceeeccc
Q 012148 163 SLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFD 242 (470)
Q Consensus 163 ~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~ 242 (470)
++||||||++.||+|+++ ... +.+.+||.|+++++.+++.++++++..... +.+ . +....+||.|+++
T Consensus 155 alvGlItfg~~v~v~el~-~~~-~sk~~VF~G~ke~s~~q~~~~L~~~~~~~~-------~~~--~-~~~~~rFL~P~~~ 222 (745)
T KOG1986|consen 155 ALVGLITFGTMVQVHELG-FEE-CSKSYVFSGNKEYSAKQLLDLLGLSGGAGK-------GSE--N-QSASNRFLLPAQE 222 (745)
T ss_pred ceEEEEEecceEEEEEcC-CCc-ccceeEEeccccccHHHHHHHhcCCccccc-------CCc--c-cccchhhhccHHH
Confidence 999999999999999999 777 999999999999999999999987530000 000 0 0145789999999
Q ss_pred hHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCC
Q 012148 243 CEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKD 322 (470)
Q Consensus 243 ~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~ 322 (470)
|+..+.++|++|..++|++++++|+.||||+||.+|+.||+.|++++|+||++|++||||.|||.|++++.++++|+|++
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 CCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccChhhchhhhcccCceEEEcCCCCchhhHHHHHHHH-hccc
Q 012148 323 LDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF-HSGD 401 (470)
Q Consensus 323 ~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~~~l-~~~~ 401 (470)
++++++++++++.+||++||++++++|++||+|+++.+++|+++|.++++.|||.|.+.++|+.+.|+++++|++ ++..
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 4666
Q ss_pred cccceeeEEEEEecccccceeeeecCCeeeeEEEeCceecch
Q 012148 402 YDLGLSSKYGFMNFVLYFFLSRIADYPLPVLTIITPLYKKYL 443 (470)
Q Consensus 402 ~~~~~~~~~~lr~~~~~~~v~~r~S~gl~i~~~~G~~~~~~~ 443 (470)
+++.+||++.|+ | +||++++|.+.+||+..-+.
T Consensus 383 ~~l~~~fn~~le-------V--~tSkdlkI~g~IGp~~Sl~~ 415 (745)
T KOG1986|consen 383 GDLKMGFNGTLE-------V--KTSKDLKIQGVIGPCVSLNK 415 (745)
T ss_pred cchhhhcCceEE-------E--EecCCcEEEecccccccccC
Confidence 788999999999 9 99999999999999975433
No 3
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2e-82 Score=663.21 Aligned_cols=401 Identities=20% Similarity=0.348 Sum_probs=352.4
Q ss_pred cccCCCeeeecCCCCCCCHHHHhhCCCCeEEEEccCCCCCCCCCCCCCCCC-CCccccCCCeeeCCCceEEcCCceEEeC
Q 012148 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPY-APLRCRTCRSILNPFSIVDFAAKIWICP 84 (470)
Q Consensus 6 ~~~~~~~iR~T~~~~P~t~~~~~~~~iPlg~vv~P~~~~~~~~~~ip~v~~-~~~RC~~C~aYiNp~~~~~~~g~~w~C~ 84 (470)
-||+|+|+|+|+++||.+.+++++++||||++|+||++.. +..++|++.. .|+||++||+|||||+.|++.|++|+||
T Consensus 166 ~nc~p~y~RsTl~~iP~t~sLl~kskLPlglvv~Pf~~~~-d~~~~p~~~~~~IvRCr~CRtYiNPFV~fid~gr~WrCN 244 (887)
T KOG1985|consen 166 SNCSPSYVRSTLSAIPQTQSLLKKSKLPLGLVVHPFAHLD-DIDPLPVITSTLIVRCRRCRTYINPFVEFIDQGRRWRCN 244 (887)
T ss_pred cCCCHHHHHHHHHhCCccHHHHHhcCCCceEEEeeccccc-ccCCCCcccCCceeeehhhhhhcCCeEEecCCCceeeec
Confidence 5899999999999999999999999999999999999776 3356666554 7999999999999999999999999999
Q ss_pred CCCCCCCCCccccCC------CCCCCCcccCCCcceEEEeCCCCCC-CCCCCCEEEEEEEcccchhhHHH---HHHHHHH
Q 012148 85 FCFQRNHFPPHYASI------TDDNLPAELFPQYTTIEYEPPGPGE-KSSVPPVFMFVVDTCIIEEEMSF---LKSALSQ 154 (470)
Q Consensus 85 ~C~~~N~vp~~y~~~------~~~~~~pEL~~~~~tvey~~~~~~~-~~~~~p~~vFvID~S~~~~~~~~---l~~~l~~ 154 (470)
+|+..|++|.+|... .+...|||+. +++|||.+|.+|. +++.|++|||+||||.++.+.|+ ++++|+.
T Consensus 245 lC~~~NdvP~~f~~~~~t~~~~~~~~RpEl~--~s~vE~iAP~eYmlR~P~Pavy~FliDVS~~a~ksG~L~~~~~slL~ 322 (887)
T KOG1985|consen 245 LCGRVNDVPDDFDWDPLTGAYGDPYSRPELT--SSVVEFIAPSEYMLRPPQPAVYVFLIDVSISAIKSGYLETVARSLLE 322 (887)
T ss_pred hhhhhcCCcHHhhcCccccccCCcccCcccc--ceeEEEecCcccccCCCCCceEEEEEEeehHhhhhhHHHHHHHHHHH
Confidence 999999999988643 2345689995 9999999998887 67899999999999999999775 5899999
Q ss_pred HhhcCC--CCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHHHHhhcccCCCCCCCccccCccCCCCccc
Q 012148 155 AIDLLP--DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDT 232 (470)
Q Consensus 155 ~l~~lp--~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~ 232 (470)
.|+.|| ++++|||||||++||||++++ +...|+|++++ +++| |++| .
T Consensus 323 ~LD~lpgd~Rt~igfi~fDs~ihfy~~~~-~~~qp~mm~vs--------dl~d----------------~flp------~ 371 (887)
T KOG1985|consen 323 NLDALPGDPRTRIGFITFDSTIHFYSVQG-DLNQPQMMIVS--------DLDD----------------PFLP------M 371 (887)
T ss_pred hhhcCCCCCcceEEEEEeeceeeEEecCC-CcCCCceeeec--------cccc----------------cccC------C
Confidence 999999 679999999999999999994 33477776654 2222 2233 3
Q ss_pred cccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCceeecCC
Q 012148 233 IARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKN 312 (470)
Q Consensus 233 ~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~GG~Ii~F~~g~pt~GpG~l~~~~ 312 (470)
+++||||+++||+.|..+|++|+++ +..++..++|+|+||++|..+|+ ..||||++|.+++||.|.|+|+.||
T Consensus 372 pd~lLv~L~~ck~~i~~lL~~lp~~---F~~~~~t~~alGpALkaaf~li~----~~GGri~vf~s~lPnlG~G~L~~rE 444 (887)
T KOG1985|consen 372 PDSLLVPLKECKDLIETLLKTLPEM---FQDTRSTGSALGPALKAAFNLIG----STGGRISVFQSTLPNLGAGKLKPRE 444 (887)
T ss_pred chhheeeHHHHHHHHHHHHHHHHHH---HhhccCcccccCHHHHHHHHHHh----hcCCeEEEEeccCCCCCcccccccc
Confidence 3899999999999999999999998 67777789999999999999999 8999999999999999999999996
Q ss_pred CCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccChhhchhhhcccCceEEEcCCCCch-----
Q 012148 313 LSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHA----- 387 (470)
Q Consensus 313 ~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~----- 387 (470)
..+..+ .++ ...++.+++.|||++|.+|.+.+|+||+|+++.+|.|+|+|+.|++.|||.+|+|++|+..
T Consensus 445 dp~~~~----s~~-~~qlL~~~t~FYK~~a~~cs~~qI~VDlFl~s~qY~DlAsLs~LskySgG~~y~YP~f~~s~p~~~ 519 (887)
T KOG1985|consen 445 DPNVRS----SDE-DSQLLSPATDFYKDLALECSKSQICVDLFLFSEQYTDLASLSCLSKYSGGQVYYYPSFDGSNPHDV 519 (887)
T ss_pred cccccc----chh-hhhccCCCchHHHHHHHHhccCceEEEEEeecccccchhhhhccccccCceeEEccCCCCCCHHHH
Confidence 543322 223 3368899999999999999999999999999999999999999999999999999999987
Q ss_pred -hhHHHHHHHHhccccccceeeEEEEEecccccceeeeecCCeeeeEEEeCceecchhhhHhhhhhhcCCCccchhhccc
Q 012148 388 -VFKDSVRRVFHSGDYDLGLSSKYGFMNFVLYFFLSRIADYPLPVLTIITPLYKKYLLLAKLIYAYMHGADSLFQQDLSL 466 (470)
Q Consensus 388 -~~~~~l~~~l~~~~~~~~~~~~~~lr~~~~~~~v~~r~S~gl~i~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 466 (470)
+|.++|.|.| ++++||+|+|| | |||+|++++.+||||+.|+.||..+.+ +..|+++..++++
T Consensus 520 ~Kf~~el~r~L-----tr~~~feaVmR-------i--R~S~gl~~~~f~GnFF~RStDLla~~~---v~~D~sy~~qisi 582 (887)
T KOG1985|consen 520 LKFARELARYL-----TRKIGFEAVMR-------I--RCSTGLRMSSFFGNFFVRSTDLLALPN---VNPDQSYAFQISI 582 (887)
T ss_pred HHHHHHHHHHh-----hhhhhhheeEE-------e--eccccccccceecccccCcHHHhcccC---CCCCccceEEEEe
Confidence 4566666665 56799999999 9 999999999999999999999999964 9999999999999
Q ss_pred ccC
Q 012148 467 SEH 469 (470)
Q Consensus 467 ~~~ 469 (470)
+|.
T Consensus 583 Ees 585 (887)
T KOG1985|consen 583 EES 585 (887)
T ss_pred ehh
Confidence 884
No 4
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=100.00 E-value=9.7e-82 Score=633.86 Aligned_cols=419 Identities=43% Similarity=0.813 Sum_probs=388.5
Q ss_pred CCcccccCCCeeeecCCCCCCCHHHHhhCCCCeEEEEccCCCCCCCCCCCCCCCCCCccccC-CCeeeCCCceEEcCCce
Q 012148 2 TEFMDLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPYAPLRCRT-CRSILNPFSIVDFAAKI 80 (470)
Q Consensus 2 ~~~~~~~~~~~iR~T~~~~P~t~~~~~~~~iPlg~vv~P~~~~~~~~~~ip~v~~~~~RC~~-C~aYiNp~~~~~~~g~~ 80 (470)
|+|+.+|+.++||+||+++|.|+..+..+.+|++++|+||++. +.+++..++|+.|.. |+||+||||.++.+++.
T Consensus 1 m~fe~iee~dgir~twnvfpat~~da~~~~iPia~lY~Pl~e~----~~~~v~~yepv~C~~pC~avlnpyC~id~r~~~ 76 (755)
T COG5047 1 MNFEIIEENDGIRLTWNVFPATRGDATRTVIPIACLYTPLHED----DALTVNYYEPVKCTAPCKAVLNPYCHIDERNQS 76 (755)
T ss_pred CchhhhccccceEEEEecccCCccccccccccHHHhccccccc----cccCcccCCCceecccchhhcCcceeeccCCce
Confidence 8999999999999999999999999999999999999999886 568888899999999 99999999999999999
Q ss_pred EEeCCCCCCCCCCccccCCCCCCCCcccCCCcceEEEeCCCCCCCCCCCCEEEEEEEcccchhhHHHHHHHHHHHhhcCC
Q 012148 81 WICPFCFQRNHFPPHYASITDDNLPAELFPQYTTIEYEPPGPGEKSSVPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLP 160 (470)
Q Consensus 81 w~C~~C~~~N~vp~~y~~~~~~~~~pEL~~~~~tvey~~~~~~~~~~~~p~~vFvID~S~~~~~~~~l~~~l~~~l~~lp 160 (470)
|.|+||+..|.+|++|..+++.++|+||.||++|+||+++++.. .+|+|+||||+++..+++.+|+++|+..|..+|
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 99999999999999999999999999999999999999998876 799999999999999999999999999999999
Q ss_pred CCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHHHHhhcccCCCCCC--CccccCccCCCCcccccccee
Q 012148 161 DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPS--TGVIAGVRDGLSSDTIARFLV 238 (470)
Q Consensus 161 ~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~~~~~l~~~~~~~~--~~~~p~~~d~~~~~~~~~~lv 238 (470)
+++.||||||++.|++|+++ ... .++.+||+|.++||.+.+++++.++. ...+. ...+++.-. ....+|+.
T Consensus 154 peaLvglItygt~i~v~el~-ae~-~~r~~VF~g~~eyt~~~L~~ll~~~~-~~~~~~~es~is~~~~----~~~~rFl~ 226 (755)
T COG5047 154 PEALVGLITYGTSIQVHELN-AEN-HRRSYVFSGNKEYTKENLQELLALSK-PTKSGGFESKISGIGQ----FASSRFLL 226 (755)
T ss_pred ccceeeEEEecceeEEEecc-ccc-cCcceeecchHHHHHHHHHHHhcccC-CCCcchhhhhcccccc----cchhhhhc
Confidence 99999999999999999999 776 89999999999999999999987652 11110 011222110 13467999
Q ss_pred eccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCceeecCCCCCccc
Q 012148 239 PAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIR 318 (470)
Q Consensus 239 ~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r 318 (470)
|+++|+..+.++|++|.+++|++++++|+.||||+||.+|..||+.|+++.|+||++|++||||.|||.|++++.++++|
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 CCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccChhhchhhhcccCceEEEcCCCCchhhHHHHHHHH-
Q 012148 319 SHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF- 397 (470)
Q Consensus 319 ~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~~~l- 397 (470)
+|++++++++++.+++.+||++||++++++|.++|+|+.+.+|+|+.+|.+|+..|||.+.+.++|+.++|+++++|+|
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 hccccccceeeEEEEEecccccceeeeecCCeeeeEEEeCceecch
Q 012148 398 HSGDYDLGLSSKYGFMNFVLYFFLSRIADYPLPVLTIITPLYKKYL 443 (470)
Q Consensus 398 ~~~~~~~~~~~~~~lr~~~~~~~v~~r~S~gl~i~~~~G~~~~~~~ 443 (470)
++..+++.+||||.|+ | .|||+|+|++++|+...-+.
T Consensus 387 ~d~~g~l~~gfNa~m~-------V--~TsKnl~~~g~ig~a~~~~k 423 (755)
T COG5047 387 RDSEGYLKMGFNANME-------V--KTSKNLKIKGLIGHAVSVKK 423 (755)
T ss_pred cCcccchhhhhcccee-------E--eeccCceeeeeecceeeecc
Confidence 5666788999999999 9 99999999999999875443
No 5
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.8e-78 Score=632.80 Aligned_cols=407 Identities=19% Similarity=0.283 Sum_probs=360.9
Q ss_pred cccCCCeeeecCCCCCCCHHHHhhCCCCeEEEEccCCCCCCCCCCCCCCCC---CCccccCCCeeeCCCceEEcCCceEE
Q 012148 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPY---APLRCRTCRSILNPFSIVDFAAKIWI 82 (470)
Q Consensus 6 ~~~~~~~iR~T~~~~P~t~~~~~~~~iPlg~vv~P~~~~~~~~~~ip~v~~---~~~RC~~C~aYiNp~~~~~~~g~~w~ 82 (470)
.||+|+|||+|+|+||.|.++++.++||||++|+||+...+.|+++|+|+. +|+||+||+||+|||++|+++|++|+
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 699999999999999999999999999999999999999999999999986 69999999999999999999999999
Q ss_pred eCCCCCCCCCCccccCCCC-------CCCCcccCCCcceEEEeCCCCCC---CCCCCCEEEEEEEcccchhhHHH---HH
Q 012148 83 CPFCFQRNHFPPHYASITD-------DNLPAELFPQYTTIEYEPPGPGE---KSSVPPVFMFVVDTCIIEEEMSF---LK 149 (470)
Q Consensus 83 C~~C~~~N~vp~~y~~~~~-------~~~~pEL~~~~~tvey~~~~~~~---~~~~~p~~vFvID~S~~~~~~~~---l~ 149 (470)
||||+.+|++|++|++..+ .+.||||. .+||||++.+.|. +++.+|+|||+||||..+.+.|+ ++
T Consensus 363 Cn~C~~~n~vp~~yf~~L~~~grr~D~~erpEL~--~Gt~dfvatk~Y~~~~k~p~ppafvFmIDVSy~Ai~~G~~~a~c 440 (1007)
T KOG1984|consen 363 CNFCGSKNQVPDDYFNHLGPTGRRVDVEERPELC--LGTVDFVATKDYCRKTKPPKPPAFVFMIDVSYNAISNGAVKAAC 440 (1007)
T ss_pred ecCCCccccCChhhcccCCCcccccccccCchhc--ccccceeeehhhhhcCCCCCCceEEEEEEeehhhhhcchHHHHH
Confidence 9999999999999988632 34589995 8999999987764 36789999999999999999775 58
Q ss_pred HHHHHHhhcCC---CCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHHHHhhcccCCCCCCCccccCccC
Q 012148 150 SALSQAIDLLP---DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRD 226 (470)
Q Consensus 150 ~~l~~~l~~lp---~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~~~~~l~~~~~~~~~~~~p~~~d 226 (470)
++|++.|+.++ ++++|||||||++|||||++ +.+..|+|++++ ++++++ +|
T Consensus 441 e~ik~~l~~lp~~~p~~~Vgivtfd~tvhFfnl~-s~L~qp~mliVs--------dv~dvf----------------vP- 494 (1007)
T KOG1984|consen 441 EAIKSVLEDLPREEPNIRVGIVTFDKTVHFFNLS-SNLAQPQMLIVS--------DVDDVF----------------VP- 494 (1007)
T ss_pred HHHHHHHhhcCccCCceEEEEEEecceeEeeccC-ccccCceEEEee--------cccccc----------------cc-
Confidence 99999999998 36899999999999999999 888889999887 333322 22
Q ss_pred CCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCc
Q 012148 227 GLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPA 306 (470)
Q Consensus 227 ~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~GG~Ii~F~~g~pt~GpG 306 (470)
.+++++|+..|++..|+.+|++|+.+ +..++.++.++|+||++|..+|+. ..|||+++|++..||.|-|
T Consensus 495 -----f~~g~~V~~~es~~~i~~lLd~Ip~m---f~~sk~pes~~g~alqaa~lalk~---~~gGKl~vF~s~Lpt~g~g 563 (1007)
T KOG1984|consen 495 -----FLDGLFVNPNESRKVIELLLDSIPTM---FQDSKIPESVFGSALQAAKLALKA---ADGGKLFVFHSVLPTAGAG 563 (1007)
T ss_pred -----cccCeeccchHHHHHHHHHHHHhhhh---hccCCCCchhHHHHHHHHHHHHhc---cCCceEEEEecccccccCc
Confidence 45889999999999999999999998 677788999999999999999984 2299999999999999988
Q ss_pred -eeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccChhhchhhhcccCceEEEcCCCC
Q 012148 307 -AIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFG 385 (470)
Q Consensus 307 -~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~ 385 (470)
++..|++.. +.++++|+ ++|.++.++|++||++|++.|||||||+++..++|+|+++.+++.|||.+|+|..|.
T Consensus 564 ~kl~~r~D~~----l~~t~kek-~l~~pq~~~y~~LA~e~v~~g~svDlF~t~~ayvDvAtlg~v~~~TgG~vy~Y~~F~ 638 (1007)
T KOG1984|consen 564 GKLSNRDDRR----LIGTDKEK-NLLQPQDKTYTTLAKEFVESGCSVDLFLTPNAYVDVATLGVVPALTGGQVYKYYPFQ 638 (1007)
T ss_pred ccccccchhh----hhcccchh-hccCcchhHHHHHHHHHHHhCceEEEEEcccceeeeeeecccccccCceeEEecchh
Confidence 887766543 44678887 799999999999999999999999999999999999999999999999999999999
Q ss_pred chhhHHHHHHHHhccccccceeeEEEEEecccccceeeeecCCeeeeEEEeCceecchhhhHhhhhhhcCCCccchhhcc
Q 012148 386 HAVFKDSVRRVFHSGDYDLGLSSKYGFMNFVLYFFLSRIADYPLPVLTIITPLYKKYLLLAKLIYAYMHGADSLFQQDLS 465 (470)
Q Consensus 386 ~~~~~~~l~~~l~~~~~~~~~~~~~~lr~~~~~~~v~~r~S~gl~i~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 465 (470)
..++...|.+.|++. .+++.||+|+|| | |||+||++.+|||++..++.-..++ +..+.|.++.+++.
T Consensus 639 a~~D~~rl~nDL~~~-vtk~~gf~a~mr-------v--RtStGirv~~f~Gnf~~~~~tDiel---a~lD~dkt~~v~fk 705 (1007)
T KOG1984|consen 639 ALTDGPRLLNDLVRN-VTKKQGFDAVMR-------V--RTSTGIRVQDFYGNFLMRNPTDIEL---AALDCDKTLTVEFK 705 (1007)
T ss_pred hcccHHHHHHHHHHh-cccceeeeeEEE-------E--eecCceeeeeeechhhhcCCCCccc---cccccCceeEEEEe
Confidence 987766666666432 467899999999 9 9999999999999999999875566 46889999999988
Q ss_pred cccC
Q 012148 466 LSEH 469 (470)
Q Consensus 466 ~~~~ 469 (470)
.++.
T Consensus 706 hDdk 709 (1007)
T KOG1984|consen 706 HDDK 709 (1007)
T ss_pred cccc
Confidence 8763
No 6
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=100.00 E-value=3.3e-70 Score=567.12 Aligned_cols=395 Identities=19% Similarity=0.338 Sum_probs=336.3
Q ss_pred cccCCCeeeecCCCCCCCHHHHhhCCCCeEEEEccCCCCCCCCCCCCCCCC-CCccccCCCeeeCCCceEEcCCceEEeC
Q 012148 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILPY-APLRCRTCRSILNPFSIVDFAAKIWICP 84 (470)
Q Consensus 6 ~~~~~~~iR~T~~~~P~t~~~~~~~~iPlg~vv~P~~~~~~~~~~ip~v~~-~~~RC~~C~aYiNp~~~~~~~g~~w~C~ 84 (470)
.||+|+|+|+|++++|.+.+++++++||||++|+||.+..+++..+|++.. .|+||++||+|+|||.+|+++|++|+||
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 689999999999999999999999999999999999998876667777654 4899999999999999999999999999
Q ss_pred CCCCCCCCCccccCCC-------CCCCCcccCCCcceEEEeCCCCCC-CCCCCCEEEEEEEcccchhhHHHH---HHHHH
Q 012148 85 FCFQRNHFPPHYASIT-------DDNLPAELFPQYTTIEYEPPGPGE-KSSVPPVFMFVVDTCIIEEEMSFL---KSALS 153 (470)
Q Consensus 85 ~C~~~N~vp~~y~~~~-------~~~~~pEL~~~~~tvey~~~~~~~-~~~~~p~~vFvID~S~~~~~~~~l---~~~l~ 153 (470)
+|+.+|++|..+.... +...|+||. ++++||.++.++. +.+.||+|||+||||.++.+.|++ .++|+
T Consensus 226 iC~~kN~vp~~~~~~~~~~~~r~d~~~r~El~--~~vvdf~ap~~Y~~~~p~P~~yvFlIDVS~~a~~~g~~~a~~r~Il 303 (861)
T COG5028 226 ICRSKNDVPEGFDNPSGPNDPRSDRYSRPELK--SGVVDFLAPKEYSLRQPPPPVYVFLIDVSFEAIKNGLVKAAIRAIL 303 (861)
T ss_pred eccccccCcccccCcCCCCCccccccccchhh--ceeeEEecccceeeccCCCCEEEEEEEeehHhhhcchHHHHHHHHH
Confidence 9999999998876321 134578996 8999999998875 344699999999999999997765 56777
Q ss_pred HHhhcCC---CCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHHHHhhcccCCCCCCCccccCccCCCCc
Q 012148 154 QAIDLLP---DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSS 230 (470)
Q Consensus 154 ~~l~~lp---~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~~~~~l~~~~~~~~~~~~p~~~d~~~~ 230 (470)
+.|+.+| +++||+||-||+.|||++++ .+. -.+++++. + +..||+| +
T Consensus 304 ~~l~~~~~~dpr~kIaii~fD~sl~ffk~s-~d~-~~~~~~vs-----------------d-------ld~pFlP--f-- 353 (861)
T COG5028 304 ENLDQIPNFDPRTKIAIICFDSSLHFFKLS-PDL-DEQMLIVS-----------------D-------LDEPFLP--F-- 353 (861)
T ss_pred hhccCCCCCCCcceEEEEEEcceeeEEecC-CCC-ccceeeec-----------------c-------ccccccc--C--
Confidence 7777775 58999999999999999998 432 01222221 1 1145555 1
Q ss_pred cccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCCCCceeec
Q 012148 231 DTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGARILAFVGGPSTEGPAAIVS 310 (470)
Q Consensus 231 ~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~GG~Ii~F~~g~pt~GpG~l~~ 310 (470)
+-..|++|+.+++..++.||++++.+ +..++.++.|+|.||++|..|++ .+||||++|.++.||.|.|+|.-
T Consensus 354 -~s~~fv~pl~~~k~~~etLl~~~~~I---f~d~~~pk~~~G~aLk~a~~l~g----~~GGkii~~~stlPn~G~Gkl~~ 425 (861)
T COG5028 354 -PSGLFVLPLKSCKQIIETLLDRVPRI---FQDNKSPKNALGPALKAAKSLIG----GTGGKIIVFLSTLPNMGIGKLQL 425 (861)
T ss_pred -CcchhcccHHHHHHHHHHHHHHhhhh---hcccCCCccccCHHHHHHHHHhh----ccCceEEEEeecCCCcccccccc
Confidence 23689999999998888899999887 56678899999999999999998 89999999999999999999987
Q ss_pred CCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccChhhchhhhcccCceEEEcCCCCchh--
Q 012148 311 KNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAV-- 388 (470)
Q Consensus 311 ~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~~-- 388 (470)
|++ +|. .++.....||+++|.+|.+.||+||+|+++.+++|++|++.|++.|||.+++|+.|+..+
T Consensus 426 r~d-----------~e~-~ll~c~d~fYk~~a~e~~k~gIsvd~Flt~~~yidvaTls~l~~~T~G~~~~Yp~f~~~~~~ 493 (861)
T COG5028 426 RED-----------KES-SLLSCKDSFYKEFAIECSKVGISVDLFLTSEDYIDVATLSHLCRYTGGQTYFYPNFSATRPN 493 (861)
T ss_pred ccc-----------chh-hhccccchHHHHHHHHHHHhcceEEEEeccccccchhhhcchhhccCcceEEcCCcccCCch
Confidence 763 333 378889999999999999999999999999999999999999999999999999999987
Q ss_pred ----hHHHHHHHHhccccccceeeEEEEEecccccceeeeecCCeeeeEEEeCceecchhhhHhhhhhhcCCCccchhhc
Q 012148 389 ----FKDSVRRVFHSGDYDLGLSSKYGFMNFVLYFFLSRIADYPLPVLTIITPLYKKYLLLAKLIYAYMHGADSLFQQDL 464 (470)
Q Consensus 389 ----~~~~l~~~l~~~~~~~~~~~~~~lr~~~~~~~v~~r~S~gl~i~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 464 (470)
+..+|-+.+ .++.||+++|| | |||+|++++++|||++.|+.|+-.. +.-..|.+.-..+
T Consensus 494 d~~kl~~dL~~~l-----s~~~gy~~~~r-------v--R~S~glr~s~fyGnf~~rs~dl~~F---~tm~rd~Sl~~~~ 556 (861)
T COG5028 494 DATKLANDLVSHL-----SMEIGYEAVMR-------V--RCSTGLRVSSFYGNFFNRSSDLCAF---STMPRDTSLLVEF 556 (861)
T ss_pred hHHHHHHHHHHhh-----hhhhhhheeeE-------e--eccCceehhhhhccccccCcccccc---cccCCCceEEEEE
Confidence 455544443 56789999999 9 9999999999999999999976554 5678899999999
Q ss_pred ccccC
Q 012148 465 SLSEH 469 (470)
Q Consensus 465 ~~~~~ 469 (470)
+++|.
T Consensus 557 sid~~ 561 (861)
T COG5028 557 SIDEK 561 (861)
T ss_pred Eeccc
Confidence 98874
No 7
>PTZ00395 Sec24-related protein; Provisional
Probab=100.00 E-value=1.4e-65 Score=558.47 Aligned_cols=402 Identities=18% Similarity=0.219 Sum_probs=313.3
Q ss_pred cccCCCeeeecCCCCCCCHHHHhhCCCCeEEEEccCCCCCCCCCCCCCCC-----------CCCccccCCCeeeCCCceE
Q 012148 6 DLEAQDGVRMPWNVIPGTKQEASNCVVPVSAIYTPIKAFPVNNNSMPILP-----------YAPLRCRTCRSILNPFSIV 74 (470)
Q Consensus 6 ~~~~~~~iR~T~~~~P~t~~~~~~~~iPlg~vv~P~~~~~~~~~~ip~v~-----------~~~~RC~~C~aYiNp~~~~ 74 (470)
.+|+|++||+|||.||.+.++++.+.||||++|+||+...++ ++||.++ .+|+||.+|+||+|+++.+
T Consensus 648 gn~dP~~~r~tmY~iP~~~~~~~~~~iP~gi~v~Pfa~~~~~-e~~~~~~~~~~~~d~~~~~~~~rc~~c~~y~~~~~~~ 726 (1560)
T PTZ00395 648 GKADPRFLKSTLYQIPLFSETLKLSQIPFGIIVNPFACLNEG-EGIDKIDMKDIINDKEENIEILRCPKCLGYLHATILE 726 (1560)
T ss_pred CCCChhhhhhhhhcCcchHHHHHhcCCCceeecchhhhcCCC-CCCcccchhhcccchhhccceeecchhHhhhcchhee
Confidence 689999999999999999999999999999999999998776 4677654 2689999999999999999
Q ss_pred EcCCceEEeCCCCCCCCCC-----------------------------------------ccccCCCC----------C-
Q 012148 75 DFAAKIWICPFCFQRNHFP-----------------------------------------PHYASITD----------D- 102 (470)
Q Consensus 75 ~~~g~~w~C~~C~~~N~vp-----------------------------------------~~y~~~~~----------~- 102 (470)
+-. .++.|+||.+.+.+. +.|+...+ .
T Consensus 727 ~~~-~~~~c~~c~~~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 805 (1560)
T PTZ00395 727 DIS-SSVQCVFCDTDFLINENVLFDIFQYNEKIGHKESDHNEHGNSLSPLLKGSVDIIIPPIYYHNVNKFKLTYTYLNKN 805 (1560)
T ss_pred ccc-ceEEEEecCCcchhhHHHHHHHHHHhhhhccccccccccccccchhhcCceeEEccchhhccCCccceeeehhhcc
Confidence 876 799999999988872 22221000 0
Q ss_pred -CC-------------------------------C-cccCC--------------------CcceEE----Ee-------
Q 012148 103 -NL-------------------------------P-AELFP--------------------QYTTIE----YE------- 118 (470)
Q Consensus 103 -~~-------------------------------~-pEL~~--------------------~~~tve----y~------- 118 (470)
++ - ..+.. .+.|++ |.
T Consensus 806 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 885 (1560)
T PTZ00395 806 INQTAFMITNKIMSFTKHISNSLVANDSKGGNKATSASAFGDSGDANFLAGGGYTNYGGAGGYNTYDNQSGYNNHDVVNN 885 (1560)
T ss_pred hhhhhhhhhhhhhhhhhhhcchheecccccccccchhhhccccccccccccccccccccccccccccccccccccccccc
Confidence 00 0 00000 000000 10
Q ss_pred ------------------------------CC-----------CC-------------C-C-CCCCCCEEEEEEEcccch
Q 012148 119 ------------------------------PP-----------GP-------------G-E-KSSVPPVFMFVVDTCIIE 142 (470)
Q Consensus 119 ------------------------------~~-----------~~-------------~-~-~~~~~p~~vFvID~S~~~ 142 (470)
+. ++ + + +-+.||+|+||||||..+
T Consensus 886 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~PP~YvFLIDVS~~A 965 (1560)
T PTZ00395 886 RGGSGAGNHLYGKDHDVQNFDNVMDNANFTIHDMKNLICEKNGEPDSAKIRRNSFLAKYPQVKNMLPPYFVFVVECSYNA 965 (1560)
T ss_pred ccccCcCcccccCcccccchhhhccCCceeeecchhhhhcccCCchhhhhhccchhhccccccCCCCCEEEEEEECCHHH
Confidence 00 00 0 0 235899999999999999
Q ss_pred hhHHH---HHHHHHHHhhcCC-CCceEEEEEECCeEEEEEcCCCCC-------------CCCceeeecCCcccCHHHHHH
Q 012148 143 EEMSF---LKSALSQAIDLLP-DNSLVGLITFGTLVQVHELGGFGQ-------------IIPKTYVFKGSKDVSKDQLLE 205 (470)
Q Consensus 143 ~~~~~---l~~~l~~~l~~lp-~~~~VglITfd~~V~~y~l~~~~~-------------~~~~~~v~~g~~~~t~~~i~~ 205 (470)
++.|+ ++++|+++|+.++ +++||||||||+.||||+|+ +.. ..|+|+|
T Consensus 966 VkSGLl~tacesIK~sLDsL~dpRTRVGIITFDSsLHFYNLk-s~l~~~~~~~~~~~~l~qPQMLV-------------- 1030 (1560)
T PTZ00395 966 IYNNITYTILEGIRYAVQNVKCPQTKIAIITFNSSIYFYHCK-GGKGVSGEEGDGGGGSGNHQVIV-------------- 1030 (1560)
T ss_pred HhhChHHHHHHHHHHHHhcCCCCCcEEEEEEecCcEEEEecC-cccccccccccccccCCCceEEe--------------
Confidence 99875 5899999999997 57999999999999999998 431 2344444
Q ss_pred HhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhcc
Q 012148 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (470)
Q Consensus 206 ~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 285 (470)
++++.|+|-|.+.+++||++.|+++.|+.+|+.|+++ +........|+|+||++|..+|+
T Consensus 1031 ---------------VSDLDDPFLPlP~ddLLVnL~ESRevIe~LLDkLPem---Ft~t~~~esCLGSALqAA~~aLk-- 1090 (1560)
T PTZ00395 1031 ---------------MSDVDDPFLPLPLEDLFFGCVEEIDKINTLIDTIKSV---STTMQSYGSCGNSALKIAMDMLK-- 1090 (1560)
T ss_pred ---------------ecCCccCcCCCCccCeeechHHHHHHHHHHHHHHHHH---hhccCCCcccHHHHHHHHHHHHH--
Confidence 4445555544455899999999999999999999986 45556678999999999999998
Q ss_pred CCCC--CcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccC
Q 012148 286 VPGS--GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVG 363 (470)
Q Consensus 286 ~~~~--GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~ 363 (470)
.. ||||++|++++|+.|||+|+.++. ..+++ .++.++.+||++||.+|++++|+||||+++..++|
T Consensus 1091 --~~GGGGKIiVF~SSLPniGpGaLK~Re~---------~~KEk-~Ll~pqd~FYK~LA~ECsk~qISVDLFLfSsqYvD 1158 (1560)
T PTZ00395 1091 --ERNGLGSICMFYTTTPNCGIGAIKELKK---------DLQEN-FLEVKQKIFYDSLLLDLYAFNISVDIFIISSNNVR 1158 (1560)
T ss_pred --hcCCCceEEEEEcCCCCCCCCccccccc---------ccccc-cccccchHHHHHHHHHHHhcCCceEEEEccCcccc
Confidence 44 499999999999999999986531 12444 46788899999999999999999999999998876
Q ss_pred --hhhchhhhcccCceEEEcCCCCchhhHHHHHHHHhcccccc-ceeeEEEEEecccccceeeeecCCeeeeEEE--eCc
Q 012148 364 --VAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVFHSGDYDL-GLSSKYGFMNFVLYFFLSRIADYPLPVLTII--TPL 438 (470)
Q Consensus 364 --l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~~~l~~~~~~~-~~~~~~~lr~~~~~~~v~~r~S~gl~i~~~~--G~~ 438 (470)
+++|+.|++.|||.+|+|+.|+..++...|..-+.+. .++ .+||+|+|| | |||+||+|+++| |++
T Consensus 1159 VDVATLg~Lsr~TGGqlyyYPnFna~rD~~KL~~DL~r~-LTre~iGyEAVMR-------V--RCS~GLrVs~fyG~Gnn 1228 (1560)
T PTZ00395 1159 VCVPSLQYVAQNTGGKILFVENFLWQKDYKEIYMNIMDT-LTSEDIAYCCELK-------L--RYSHHMSVKKLFCCNNN 1228 (1560)
T ss_pred cccccccchhcccceeEEEeCCCcccccHHHHHHHHHHH-hhccceeeEEEEE-------E--ECCCCeEEEEEeccCCc
Confidence 7999999999999999999999876554444433221 122 479999999 9 999999999999 445
Q ss_pred e--ecchhhhHhhhhhhcCCCccchhhcccccC
Q 012148 439 Y--KKYLLLAKLIYAYMHGADSLFQQDLSLSEH 469 (470)
Q Consensus 439 ~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 469 (470)
+ .++.|++.| |.+++|++|.++|+++|.
T Consensus 1229 F~s~rStDLLaL---P~Id~DqSfaVeLk~DEk 1258 (1560)
T PTZ00395 1229 FNSIISVDTIKI---PKIRHDQTFAFLLNYSDI 1258 (1560)
T ss_pred cccccccccccc---cccCCCceEEEEEEeccc
Confidence 4 456666665 579999999999999874
No 8
>cd01478 Sec23-like Sec23-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 23 is very similar to Sec24. The Sec23 and Sec24
Probab=100.00 E-value=4.6e-57 Score=440.85 Aligned_cols=266 Identities=56% Similarity=0.944 Sum_probs=239.7
Q ss_pred CCCEEEEEEEcccchhhHHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHHHHh
Q 012148 128 VPPVFMFVVDTCIIEEEMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQL 207 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~~~~~l~~~l~~~l~~lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~~~~ 207 (470)
.||+|+||||+|.++++++.++++|+++|+.||++++|||||||+.||||+|+ .+. +++.+||.|+++++.+++++++
T Consensus 2 ~pp~~vFviDvs~~~~el~~l~~sl~~~L~~lP~~a~VGlITfd~~V~~~~L~-~~~-~~~~~vf~g~~~~~~~~~~~~l 79 (267)
T cd01478 2 SPPVFLFVVDTCMDEEELDALKESLIMSLSLLPPNALVGLITFGTMVQVHELG-FEE-CSKSYVFRGNKDYTAKQIQDML 79 (267)
T ss_pred CCCEEEEEEECccCHHHHHHHHHHHHHHHHhCCCCCEEEEEEECCEEEEEEcC-CCc-CceeeeccCCccCCHHHHHHHh
Confidence 58999999999999999999999999999999999999999999999999999 766 9999999999999999999998
Q ss_pred hcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhccCC
Q 012148 208 NFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVP 287 (470)
Q Consensus 208 ~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~ 287 (470)
++.+..-.....+.++++|++.|.+.++||+|++||++.|..+|++|+++.|++.+++++.||+|+||++|..+|+.+.+
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 76431100000111223444433455799999999999999999999999998888999999999999999999998777
Q ss_pred CCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccChhhc
Q 012148 288 GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAEL 367 (470)
Q Consensus 288 ~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l~~l 367 (470)
+.||||++|++|+||.|||+|+.|+.++++|+|++++++++++++++.+||++||++|+++||+||+|+++.+|+|+++|
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 89999999999999999999999999999999999999988899999999999999999999999999999999999999
Q ss_pred hhhhcccCceEEEcCCCCchhhHHHHHH
Q 012148 368 KVAVEKTGGLVVLSDSFGHAVFKDSVRR 395 (470)
Q Consensus 368 ~~l~~~TGG~v~~y~~f~~~~~~~~l~~ 395 (470)
+.|++.|||.+++|++|+.+.|+++++|
T Consensus 240 ~~l~~~TGG~v~~~~~f~~~~f~~s~~~ 267 (267)
T cd01478 240 KVLVNSTGGHVVLSDSFTTSIFKQSFQR 267 (267)
T ss_pred HHHHHhcCcEEEEeCCcchHHHHHHhcC
Confidence 9999999999999999999999988764
No 9
>cd01468 trunk_domain trunk domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface. Some members of this family possess a partial MIDAS motif that is a characteristic feature of most vWA domain proteins.
Probab=100.00 E-value=4.1e-46 Score=360.27 Aligned_cols=227 Identities=41% Similarity=0.640 Sum_probs=194.7
Q ss_pred CCCCEEEEEEEcccch---hhHHHHHHHHHHHhhcCC--CCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHH
Q 012148 127 SVPPVFMFVVDTCIIE---EEMSFLKSALSQAIDLLP--DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (470)
Q Consensus 127 ~~~p~~vFvID~S~~~---~~~~~l~~~l~~~l~~lp--~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~ 201 (470)
|+||+|+||||+|.++ ..++.++++|+++|+.|| ++++|||||||+.||||+++ .....++++|+++.++
T Consensus 1 p~pp~~vFvID~s~~ai~~~~l~~~~~sl~~~l~~lp~~~~~~igiITf~~~V~~~~~~-~~~~~~~~~v~~dl~d---- 75 (239)
T cd01468 1 PQPPVFVFVIDVSYEAIKEGLLQALKESLLASLDLLPGDPRARVGLITYDSTVHFYNLS-SDLAQPKMYVVSDLKD---- 75 (239)
T ss_pred CCCCEEEEEEEcchHhccccHHHHHHHHHHHHHHhCCCCCCcEEEEEEeCCeEEEEECC-CCCCCCeEEEeCCCcc----
Confidence 3699999999999995 446778999999999999 99999999999999999999 5543577888764322
Q ss_pred HHHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHH
Q 012148 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (470)
Q Consensus 202 ~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~l 281 (470)
|++| ...++++++.|+++.|.++|++|+++.+.. .+.++.||+|+||++|..+
T Consensus 76 --------------------~f~p------~~~~~l~~~~e~~~~i~~~l~~l~~~~~~~-~~~~~~~~~G~Al~~A~~l 128 (239)
T cd01468 76 --------------------VFLP------LPDRFLVPLSECKKVIHDLLEQLPPMFWPV-PTHRPERCLGPALQAAFLL 128 (239)
T ss_pred --------------------CcCC------CcCceeeeHHHHHHHHHHHHHhhhhhcccc-CCCCCcccHHHHHHHHHHH
Confidence 1222 346899999999999999999999874322 2678899999999999999
Q ss_pred HhccCCCC--CcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccC
Q 012148 282 LGACVPGS--GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACAL 359 (470)
Q Consensus 282 l~~~~~~~--GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~ 359 (470)
|+ .. ||||++|++|+||.|||+|+.++.++++|+| ++ +++++++.+||++||++|+++||+||+|+++.
T Consensus 129 l~----~~~~gGkI~~f~sg~pt~GpG~l~~~~~~~~~~~~----~e-~~~~~~a~~fY~~la~~~~~~~isvdlF~~~~ 199 (239)
T cd01468 129 LK----GTFAGGRIIVFQGGLPTVGPGKLKSREDKEPIRSH----DE-AQLLKPATKFYKSLAKECVKSGICVDLFAFSL 199 (239)
T ss_pred Hh----hcCCCceEEEEECCCCCCCCCccccCcccccCCCc----cc-hhcccccHHHHHHHHHHHHHcCeEEEEEeccc
Confidence 99 55 9999999999999999999999888888775 23 37899999999999999999999999999999
Q ss_pred CccChhhchhhhcccCceEEEcCCCCchhhHHHHH
Q 012148 360 DQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVR 394 (470)
Q Consensus 360 ~~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~ 394 (470)
+++|+++|++|++.|||.+++|++|+..++.+.+.
T Consensus 200 ~~~dl~~l~~l~~~TGG~v~~y~~f~~~~~~~~~~ 234 (239)
T cd01468 200 DYVDVATLKQLAKSTGGQVYLYDSFQAPNDGSKFK 234 (239)
T ss_pred cccCHHHhhhhhhcCCceEEEeCCCCCcccHHHHH
Confidence 99999999999999999999999996654444443
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=1e-45 Score=357.77 Aligned_cols=219 Identities=24% Similarity=0.330 Sum_probs=188.1
Q ss_pred CCCEEEEEEEcccchhh---HHHHHHHHHHHhhcCCCC---ceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHH
Q 012148 128 VPPVFMFVVDTCIIEEE---MSFLKSALSQAIDLLPDN---SLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~~---~~~l~~~l~~~l~~lp~~---~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~ 201 (470)
.||+|+||||+|..+++ ++.++++|+++|+.+|++ ++|||||||+.||||+++ ++...+++++++
T Consensus 2 ~pp~~~FvIDvs~~a~~~g~~~~~~~si~~~L~~lp~~~~~~~VgiITfd~~v~~y~l~-~~~~~~q~~vv~-------- 72 (244)
T cd01479 2 QPAVYVFLIDVSYNAIKSGLLATACEALLSNLDNLPGDDPRTRVGFITFDSTLHFFNLK-SSLEQPQMMVVS-------- 72 (244)
T ss_pred CCCEEEEEEEccHHHHhhChHHHHHHHHHHHHHhcCCCCCCeEEEEEEECCeEEEEECC-CCCCCCeEEEee--------
Confidence 68999999999999997 556799999999999977 999999999999999999 655466766654
Q ss_pred HHHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHH
Q 012148 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (470)
Q Consensus 202 ~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~l 281 (470)
++++ |++| ..++||++++|+++.|.++|++|+.. +.++.++.+|+|+||++|..+
T Consensus 73 dl~d----------------~f~P------~~~~~lv~l~e~~~~i~~lL~~L~~~---~~~~~~~~~c~G~Al~~A~~l 127 (244)
T cd01479 73 DLDD----------------PFLP------LPDGLLVNLKESRQVIEDLLDQIPEM---FQDTKETESALGPALQAAFLL 127 (244)
T ss_pred Cccc----------------ccCC------CCcceeecHHHHHHHHHHHHHHHHHH---HhcCCCCcccHHHHHHHHHHH
Confidence 1211 2222 34789999999999999999999764 567788899999999999999
Q ss_pred HhccCCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCc
Q 012148 282 LGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (470)
Q Consensus 282 l~~~~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~ 361 (470)
|+ +.||||++|++|+||.|||+|+.++.++ .+.+ ++|+ ++++++.+||+++|.+|+++||+||+|+++.++
T Consensus 128 L~----~~GGkIi~f~s~~pt~GpG~l~~~~~~~-~~~~---~~e~-~~~~p~~~fY~~la~~~~~~~isvDlF~~~~~~ 198 (244)
T cd01479 128 LK----ETGGKIIVFQSSLPTLGAGKLKSREDPK-LLST---DKEK-QLLQPQTDFYKKLALECVKSQISVDLFLFSNQY 198 (244)
T ss_pred HH----hcCCEEEEEeCCCCCcCCcccccCcccc-ccCc---hhhh-hhcCcchHHHHHHHHHHHHcCeEEEEEEccCcc
Confidence 99 8999999999999999999999987544 3333 2444 688999999999999999999999999999999
Q ss_pred cChhhchhhhcccCceEEEcC--CCCchhh
Q 012148 362 VGVAELKVAVEKTGGLVVLSD--SFGHAVF 389 (470)
Q Consensus 362 ~~l~~l~~l~~~TGG~v~~y~--~f~~~~~ 389 (470)
+|+++|+.|++.|||.+++|+ +|+..++
T Consensus 199 ~dla~l~~l~~~TGG~v~~y~~~~~~~~~d 228 (244)
T cd01479 199 VDVATLGCLSRLTGGQVYYYPSFNFSAPND 228 (244)
T ss_pred cChhhhhhhhhhcCceEEEECCccCCchhh
Confidence 999999999999999999999 6665543
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=7.8e-45 Score=352.33 Aligned_cols=233 Identities=32% Similarity=0.506 Sum_probs=176.9
Q ss_pred CCCCEEEEEEEcccchhh---HHHHHHHHHHHhhcCC--CCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHH
Q 012148 127 SVPPVFMFVVDTCIIEEE---MSFLKSALSQAIDLLP--DNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (470)
Q Consensus 127 ~~~p~~vFvID~S~~~~~---~~~l~~~l~~~l~~lp--~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~ 201 (470)
|+||+|+||||+|.++++ ++.++++|+++|+.+| +++||||||||++||||+++ .+...+++++++
T Consensus 1 P~pp~y~FvID~s~~av~~g~~~~~~~sl~~~l~~l~~~~~~~vgiitfd~~V~~y~l~-~~~~~~~~~v~~-------- 71 (243)
T PF04811_consen 1 PQPPVYVFVIDVSYEAVQSGLLQSLIESLKSALDSLPGDERTRVGIITFDSSVHFYNLS-SSLSQPQMIVVS-------- 71 (243)
T ss_dssp -S--EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTSSTSTT-EEEEEEESSSEEEEETT-TTSSSTEEEEEH--------
T ss_pred CCCCEEEEEEECchhhhhccHHHHHHHHHHHHHHhccCCCCcEEEEEEeCCEEEEEECC-CCcCCCcccchH--------
Confidence 369999999999999666 5567999999999999 99999999999999999999 554466776664
Q ss_pred HHHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHH
Q 012148 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (470)
Q Consensus 202 ~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~l 281 (470)
++++.+ +| ..++|++++.++++.|.++|++|++. +....+.++.||+|+||++|..+
T Consensus 72 dl~~~~----------------~p------~~~~llv~~~e~~~~i~~ll~~L~~~-~~~~~~~~~~~c~G~Al~~A~~l 128 (243)
T PF04811_consen 72 DLDDPF----------------IP------LPDGLLVPLSECRDAIEELLESLPSI-FPETAGKRPERCLGSALSAALSL 128 (243)
T ss_dssp HTTSHH----------------SS------TSSSSSEETTTCHHHHHHHHHHHHHH-STT-TTB-----HHHHHHHHHHH
T ss_pred HHhhcc----------------cC------CcccEEEEhHHhHHHHHHHHHHhhhh-cccccccCccccHHHHHHHHHHH
Confidence 443332 22 23889999999999999999999874 22223477899999999999999
Q ss_pred HhccCCCCCcEEEEEecCCCCCCC-ceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCC
Q 012148 282 LGACVPGSGARILAFVGGPSTEGP-AAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (470)
Q Consensus 282 l~~~~~~~GG~Ii~F~~g~pt~Gp-G~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~ 360 (470)
|+.. ..||||++|++|+||.|| |++..++.. .++++++++..++.++.+||++||++|+++||+||+|+++.+
T Consensus 129 l~~~--~~gGkI~~F~s~~pt~G~Gg~l~~~~~~----~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~ 202 (243)
T PF04811_consen 129 LSSR--NTGGKILVFTSGPPTYGPGGSLKKREDS----SHYDTEKEKALLLPPANEFYKKLAEECSKQGISVDLFVFSSD 202 (243)
T ss_dssp HHHH--TS-EEEEEEESS---SSSTTSS-SBTTS----CCCCHCTTHHCHSHSSSHHHHHHHHHHHHCTEEEEEEEECSS
T ss_pred Hhcc--ccCCEEEEEeccCCCCCCCceecccccc----cccccccchhhhccccchHHHHHHHHHHhcCCEEEEEeecCC
Confidence 9831 389999999999999999 677666433 456777776678889999999999999999999999999999
Q ss_pred ccChhhchhhhcccCceEEEcCCCCchhhHHHHHHHH
Q 012148 361 QVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVF 397 (470)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~~~l 397 (470)
++|+++|+.|++.|||.+++|++|+.+++...|++.|
T Consensus 203 ~~~l~tl~~l~~~TGG~l~~y~~f~~~~~~~~l~~dl 239 (243)
T PF04811_consen 203 YVDLATLGPLARYTGGSLYYYPNFNAERDGEKLRQDL 239 (243)
T ss_dssp --SHHHHTHHHHCTT-EEEEETTTTCHHHHHHHHHHH
T ss_pred CCCcHhHHHHHHhCceeEEEeCCCCCchhHHHHHHHH
Confidence 9999999999999999999999999655444444433
No 12
>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=99.65 E-value=5.2e-17 Score=111.70 Aligned_cols=40 Identities=55% Similarity=1.250 Sum_probs=29.0
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCCCCCccc
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHY 96 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp~~y 96 (470)
+|+||++|+||||||++++.++++|+|+||++.|.+|++|
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 4799999999999999999999999999999999999887
No 13
>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=98.59 E-value=3.5e-06 Score=76.46 Aligned_cols=159 Identities=15% Similarity=0.182 Sum_probs=108.8
Q ss_pred EEEEEEEcccchhh--HHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEE-cCCCCCCCCceeeecCCcccCHHHHHHHh
Q 012148 131 VFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHE-LGGFGQIIPKTYVFKGSKDVSKDQLLEQL 207 (470)
Q Consensus 131 ~~vFvID~S~~~~~--~~~l~~~l~~~l~~lp~~~~VglITfd~~V~~y~-l~~~~~~~~~~~v~~g~~~~t~~~i~~~~ 207 (470)
.++|++|+|.+... +..+++++...+..++++.+|++|+|++..+..- .. .
T Consensus 2 ~~~~vlD~S~SM~~~~~~~~k~a~~~~~~~l~~~~~v~li~f~~~~~~~~~~~-~------------------------- 55 (170)
T cd01465 2 NLVFVIDRSGSMDGPKLPLVKSALKLLVDQLRPDDRLAIVTYDGAAETVLPAT-P------------------------- 55 (170)
T ss_pred cEEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEecCCccEEecCc-c-------------------------
Confidence 37899999998654 4567888888999999889999999997644321 00 0
Q ss_pred hcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhccCC
Q 012148 208 NFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVP 287 (470)
Q Consensus 208 ~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~ 287 (470)
......+...|+.+.. ...+.++.||..|...+.....
T Consensus 56 ---------------------------------~~~~~~l~~~l~~~~~---------~g~T~~~~al~~a~~~~~~~~~ 93 (170)
T cd01465 56 ---------------------------------VRDKAAILAAIDRLTA---------GGSTAGGAGIQLGYQEAQKHFV 93 (170)
T ss_pred ---------------------------------cchHHHHHHHHHcCCC---------CCCCCHHHHHHHHHHHHHhhcC
Confidence 0011234455554432 1234578999999888763221
Q ss_pred CC-CcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccChhh
Q 012148 288 GS-GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAE 366 (470)
Q Consensus 288 ~~-GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l~~ 366 (470)
.. -.+|++|+.|.++.|+.. .+-+.+...++.+.++.|+.+.+. +..+...
T Consensus 94 ~~~~~~ivl~TDG~~~~~~~~---------------------------~~~~~~~~~~~~~~~v~i~~i~~g-~~~~~~~ 145 (170)
T cd01465 94 PGGVNRILLATDGDFNVGETD---------------------------PDELARLVAQKRESGITLSTLGFG-DNYNEDL 145 (170)
T ss_pred CCCeeEEEEEeCCCCCCCCCC---------------------------HHHHHHHHHHhhcCCeEEEEEEeC-CCcCHHH
Confidence 11 267999999988776411 112344555667789999999887 6788999
Q ss_pred chhhhcccCceEEEcCCCC
Q 012148 367 LKVAVEKTGGLVVLSDSFG 385 (470)
Q Consensus 367 l~~l~~~TGG~v~~y~~f~ 385 (470)
|..++..++|..++-++..
T Consensus 146 l~~ia~~~~g~~~~~~~~~ 164 (170)
T cd01465 146 MEAIADAGNGNTAYIDNLA 164 (170)
T ss_pred HHHHHhcCCceEEEeCCHH
Confidence 9999999999988766543
No 14
>PRK13685 hypothetical protein; Provisional
Probab=98.56 E-value=3.7e-06 Score=85.17 Aligned_cols=162 Identities=20% Similarity=0.187 Sum_probs=111.7
Q ss_pred CCEEEEEEEcccchh-------hHHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHH
Q 012148 129 PPVFMFVVDTCIIEE-------EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (470)
Q Consensus 129 ~p~~vFvID~S~~~~-------~~~~l~~~l~~~l~~lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~ 201 (470)
+..++||||+|.+.. .+...+++++..++.++++.+||+|+|++..++. .
T Consensus 88 ~~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l~~~d~vglv~Fa~~a~~~--~--------------------- 144 (326)
T PRK13685 88 RAVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELTPGINLGLIAFAGTATVL--V--------------------- 144 (326)
T ss_pred CceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhCCCCCeEEEEEEcCceeec--C---------------------
Confidence 457899999999864 3667899999999999888999999999774421 0
Q ss_pred HHHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHH
Q 012148 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (470)
Q Consensus 202 ~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~l 281 (470)
|....++.+...|+.+... ...+.|.|+..|...
T Consensus 145 -------------------------------------p~t~d~~~l~~~l~~l~~~---------~~T~~g~al~~A~~~ 178 (326)
T PRK13685 145 -------------------------------------SPTTNREATKNAIDKLQLA---------DRTATGEAIFTALQA 178 (326)
T ss_pred -------------------------------------CCCCCHHHHHHHHHhCCCC---------CCcchHHHHHHHHHH
Confidence 0011234677777776531 235678899888887
Q ss_pred Hhcc-------CCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEE
Q 012148 282 LGAC-------VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDL 354 (470)
Q Consensus 282 l~~~-------~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdl 354 (470)
+... .....++|++++.|-.+.|..... . .. . .+.++.+.+.||.|..
T Consensus 179 l~~~~~~~~~~~~~~~~~IILlTDG~~~~~~~~~~---------------~------~~--~--~~aa~~a~~~gi~i~~ 233 (326)
T PRK13685 179 IATVGAVIGGGDTPPPARIVLMSDGKETVPTNPDN---------------P------RG--A--YTAARTAKDQGVPIST 233 (326)
T ss_pred HHhhhcccccccCCCCCEEEEEcCCCCCCCCCCCC---------------c------cc--H--HHHHHHHHHcCCeEEE
Confidence 7521 112347899999998766531100 0 00 0 1356667788999999
Q ss_pred eeccCC-------------ccChhhchhhhcccCceEEEcCCC
Q 012148 355 FACALD-------------QVGVAELKVAVEKTGGLVVLSDSF 384 (470)
Q Consensus 355 F~~s~~-------------~~~l~~l~~l~~~TGG~v~~y~~f 384 (470)
+.++.+ ..|-..|..+++.|||+.|+.++-
T Consensus 234 Ig~G~~~g~~~~~g~~~~~~~d~~~L~~iA~~tgG~~~~~~~~ 276 (326)
T PRK13685 234 ISFGTPYGSVEINGQRQPVPVDDESLKKIAQLSGGEFYTAASL 276 (326)
T ss_pred EEECCCCCCcCcCCceeeecCCHHHHHHHHHhcCCEEEEcCCH
Confidence 987764 257789999999999988887653
No 15
>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=98.55 E-value=7.5e-06 Score=75.46 Aligned_cols=163 Identities=19% Similarity=0.128 Sum_probs=107.5
Q ss_pred EEEEEEEcccchh---hHHHHHHHHHHHhhc-CCCCceEEEEEECCe-EEEEEcCCCCCCCCceeeecCCcccCHHHHHH
Q 012148 131 VFMFVVDTCIIEE---EMSFLKSALSQAIDL-LPDNSLVGLITFGTL-VQVHELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (470)
Q Consensus 131 ~~vFvID~S~~~~---~~~~l~~~l~~~l~~-lp~~~~VglITfd~~-V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~~ 205 (470)
.++|+||+|.+.. .+..+++++...+.. ++++.+||+|+|++. .++. +. .
T Consensus 2 ~v~lvlD~SgSM~~~~rl~~ak~a~~~~~~~~~~~~d~v~lv~F~~~~~~~~-~~-~----------------------- 56 (178)
T cd01451 2 LVIFVVDASGSMAARHRMAAAKGAVLSLLRDAYQRRDKVALIAFRGTEAEVL-LP-P----------------------- 56 (178)
T ss_pred eEEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCceEE-eC-C-----------------------
Confidence 3689999999865 456678887777754 567889999999854 2211 01 0
Q ss_pred HhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhcc
Q 012148 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (470)
Q Consensus 206 ~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 285 (470)
......+...|+.++. .....++.||..|...++..
T Consensus 57 -----------------------------------t~~~~~~~~~l~~l~~---------~G~T~l~~aL~~a~~~l~~~ 92 (178)
T cd01451 57 -----------------------------------TRSVELAKRRLARLPT---------GGGTPLAAGLLAAYELAAEQ 92 (178)
T ss_pred -----------------------------------CCCHHHHHHHHHhCCC---------CCCCcHHHHHHHHHHHHHHH
Confidence 0011234445555432 13467899999999887211
Q ss_pred CCCCC--cEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHH-HHHHHHHHhcCeEEEEeeccCCcc
Q 012148 286 VPGSG--ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFY-DALSKQLVHQGHVLDLFACALDQV 362 (470)
Q Consensus 286 ~~~~G--G~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY-~~la~~~~~~gisvdlF~~s~~~~ 362 (470)
....+ ..|++++.|.++.|.... ..- ..+++++.+.||.+..+.......
T Consensus 93 ~~~~~~~~~ivliTDG~~~~g~~~~---------------------------~~~~~~~~~~l~~~gi~v~~I~~~~~~~ 145 (178)
T cd01451 93 ARDPGQRPLIVVITDGRANVGPDPT---------------------------ADRALAAARKLRARGISALVIDTEGRPV 145 (178)
T ss_pred hcCCCCceEEEEECCCCCCCCCCch---------------------------hHHHHHHHHHHHhcCCcEEEEeCCCCcc
Confidence 11222 578888889887763100 011 467788888898886665555556
Q ss_pred ChhhchhhhcccCceEEEcCCCCchhh
Q 012148 363 GVAELKVAVEKTGGLVVLSDSFGHAVF 389 (470)
Q Consensus 363 ~l~~l~~l~~~TGG~v~~y~~f~~~~~ 389 (470)
+-..|..|++.|||+.++.++.+...|
T Consensus 146 ~~~~l~~iA~~tgG~~~~~~d~~~~~~ 172 (178)
T cd01451 146 RRGLAKDLARALGGQYVRLPDLSADAI 172 (178)
T ss_pred CccHHHHHHHHcCCeEEEcCcCCHHHH
Confidence 778899999999999999998886544
No 16
>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=98.51 E-value=4.3e-06 Score=78.92 Aligned_cols=169 Identities=24% Similarity=0.293 Sum_probs=105.8
Q ss_pred CCCEEEEEEEcccchh--------hHHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccC
Q 012148 128 VPPVFMFVVDTCIIEE--------EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVS 199 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~--------~~~~l~~~l~~~l~~lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t 199 (470)
.+..++||||+|.+.. .+..+++++...++.++++.+||+++|++.+.-. . . . + .+++
T Consensus 19 ~~~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~l~~~~~v~lv~F~~~~~~~--~-~---~-~-~~~p------ 84 (206)
T cd01456 19 LPPNVAIVLDNSGSMREVDGGGETRLDNAKAALDETANALPDGTRLGLWTFSGDGDNP--L-D---V-R-VLVP------ 84 (206)
T ss_pred CCCcEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHhCCCCceEEEEEecCCCCCC--c-c---c-c-cccc------
Confidence 5788999999999875 3567899999999999989999999999854210 0 0 0 0 0000
Q ss_pred HHHHHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHH
Q 012148 200 KDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAA 279 (470)
Q Consensus 200 ~~~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~ 279 (470)
-.+ +. .....+. ...+..+.+.|+.|.. . .....++.||..|.
T Consensus 85 -----------------------~~~--~~-~~~~~~~---~~~~~~l~~~i~~i~~-----~---~G~T~l~~aL~~a~ 127 (206)
T cd01456 85 -----------------------KGC--LT-APVNGFP---SAQRSALDAALNSLQT-----P---TGWTPLAAALAEAA 127 (206)
T ss_pred -----------------------ccc--cc-cccCCCC---cccHHHHHHHHHhhcC-----C---CCcChHHHHHHHHH
Confidence 000 00 0000000 0134567777777651 1 12467899999999
Q ss_pred HHHhccCCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHH-HhcCeEEEEeecc
Q 012148 280 SLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQL-VHQGHVLDLFACA 358 (470)
Q Consensus 280 ~ll~~~~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~-~~~gisvdlF~~s 358 (470)
.++. ...-..|++++.|.++.|... .+..++++... ...+|.|+.+.+.
T Consensus 128 ~~l~---~~~~~~iillTDG~~~~~~~~---------------------------~~~~~~~~~~~~~~~~i~i~~igiG 177 (206)
T cd01456 128 AYVD---PGRVNVVVLITDGEDTCGPDP---------------------------CEVARELAKRRTPAPPIKVNVIDFG 177 (206)
T ss_pred HHhC---CCCcceEEEEcCCCccCCCCH---------------------------HHHHHHHHHhcCCCCCceEEEEEec
Confidence 8874 133368999999977655300 01112222211 2258999999886
Q ss_pred CCccChhhchhhhcccCceE
Q 012148 359 LDQVGVAELKVAVEKTGGLV 378 (470)
Q Consensus 359 ~~~~~l~~l~~l~~~TGG~v 378 (470)
.+ .+...|..++..|||..
T Consensus 178 ~~-~~~~~l~~iA~~tgG~~ 196 (206)
T cd01456 178 GD-ADRAELEAIAEATGGTY 196 (206)
T ss_pred Cc-ccHHHHHHHHHhcCCeE
Confidence 54 67889999999999988
No 17
>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=98.51 E-value=4.3e-06 Score=77.64 Aligned_cols=153 Identities=13% Similarity=0.053 Sum_probs=98.4
Q ss_pred EEEEEEEcccchh-------hHHHHHHHHHHHhhcC---CCCceEEEEEE-CCeEEEEEcCCCCCCCCceeeecCCcccC
Q 012148 131 VFMFVVDTCIIEE-------EMSFLKSALSQAIDLL---PDNSLVGLITF-GTLVQVHELGGFGQIIPKTYVFKGSKDVS 199 (470)
Q Consensus 131 ~~vFvID~S~~~~-------~~~~l~~~l~~~l~~l---p~~~~VglITf-d~~V~~y~l~~~~~~~~~~~v~~g~~~~t 199 (470)
..+++||+|.+.. .+...+..+...++.+ .+..+||||+| +..-++- .
T Consensus 5 ~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~a~~~--~------------------- 63 (183)
T cd01453 5 HLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKL--T------------------- 63 (183)
T ss_pred EEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCccEEE--E-------------------
Confidence 4799999999865 3666788887777654 35679999999 4432221 1
Q ss_pred HHHHHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHH
Q 012148 200 KDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAA 279 (470)
Q Consensus 200 ~~~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~ 279 (470)
|+....+.+...|+.+ + .+ .....++.||..|.
T Consensus 64 ---------------------------------------PlT~D~~~~~~~L~~~--~---~~---~G~t~l~~aL~~A~ 96 (183)
T cd01453 64 ---------------------------------------DLTGNPRKHIQALKTA--R---EC---SGEPSLQNGLEMAL 96 (183)
T ss_pred ---------------------------------------CCCCCHHHHHHHhhcc--c---CC---CCchhHHHHHHHHH
Confidence 1111111334444433 1 01 12367999999999
Q ss_pred HHHhccCCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccC
Q 012148 280 SLLGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACAL 359 (470)
Q Consensus 280 ~ll~~~~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~ 359 (470)
..|+..-....++|++++++.-+.+| .-+.++++++.+.||-|++..+..
T Consensus 97 ~~l~~~~~~~~~~iiil~sd~~~~~~------------------------------~~~~~~~~~l~~~~I~v~~IgiG~ 146 (183)
T cd01453 97 ESLKHMPSHGSREVLIIFSSLSTCDP------------------------------GNIYETIDKLKKENIRVSVIGLSA 146 (183)
T ss_pred HHHhcCCccCceEEEEEEcCCCcCCh------------------------------hhHHHHHHHHHHcCcEEEEEEech
Confidence 99963111224678888775211111 012457888989999999998853
Q ss_pred CccChhhchhhhcccCceEEEcCCC
Q 012148 360 DQVGVAELKVAVEKTGGLVVLSDSF 384 (470)
Q Consensus 360 ~~~~l~~l~~l~~~TGG~v~~y~~f 384 (470)
+...|..+|+.|||+.|.-.+-
T Consensus 147 ---~~~~L~~ia~~tgG~~~~~~~~ 168 (183)
T cd01453 147 ---EMHICKEICKATNGTYKVILDE 168 (183)
T ss_pred ---HHHHHHHHHHHhCCeeEeeCCH
Confidence 4678999999999998876553
No 18
>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=9.3e-06 Score=75.61 Aligned_cols=166 Identities=16% Similarity=0.149 Sum_probs=104.9
Q ss_pred CCCEEEEEEEcccchh--hHHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEE-cCCCCCCCCceeeecCCcccCHHHHH
Q 012148 128 VPPVFMFVVDTCIIEE--EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHE-LGGFGQIIPKTYVFKGSKDVSKDQLL 204 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~--~~~~l~~~l~~~l~~lp~~~~VglITfd~~V~~y~-l~~~~~~~~~~~v~~g~~~~t~~~i~ 204 (470)
.|-.++||||+|.+.. .+..++++++..++.++++.+||||+|++.++..- +. ..
T Consensus 12 ~p~~vv~llD~SgSM~~~~l~~ak~~~~~ll~~l~~~d~v~lv~F~~~~~~~~~~~-~~--------------------- 69 (190)
T cd01463 12 SPKDIVILLDVSGSMTGQRLHLAKQTVSSILDTLSDNDFFNIITFSNEVNPVVPCF-ND--------------------- 69 (190)
T ss_pred CCceEEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCCCEEEEEEeCCCeeEEeeec-cc---------------------
Confidence 4678999999999864 35667899999999999999999999999877542 11 00
Q ss_pred HHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhc
Q 012148 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (470)
Q Consensus 205 ~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~ 284 (470)
.++....+....+...|+.|+.. ....++.||..|...+..
T Consensus 70 ------------------------------~~~~~~~~~~~~~~~~l~~l~~~---------G~T~~~~al~~a~~~l~~ 110 (190)
T cd01463 70 ------------------------------TLVQATTSNKKVLKEALDMLEAK---------GIANYTKALEFAFSLLLK 110 (190)
T ss_pred ------------------------------ceEecCHHHHHHHHHHHhhCCCC---------CcchHHHHHHHHHHHHHH
Confidence 00000011233455555555421 235688999999988873
Q ss_pred cC--------CCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHH-HHHhcCeEEEEe
Q 012148 285 CV--------PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSK-QLVHQGHVLDLF 355 (470)
Q Consensus 285 ~~--------~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~-~~~~~gisvdlF 355 (470)
.. ......|++++.|.++.+.- ...++.. .....++.|..|
T Consensus 111 ~~~~~~~~~~~~~~~~iillTDG~~~~~~~------------------------------~~~~~~~~~~~~~~v~i~ti 160 (190)
T cd01463 111 NLQSNHSGSRSQCNQAIMLITDGVPENYKE------------------------------IFDKYNWDKNSEIPVRVFTY 160 (190)
T ss_pred hhhcccccccCCceeEEEEEeCCCCCcHhH------------------------------HHHHhcccccCCCcEEEEEE
Confidence 10 11224688899987653210 0111110 011124666666
Q ss_pred eccCCccChhhchhhhcccCceEEEcCCC
Q 012148 356 ACALDQVGVAELKVAVEKTGGLVVLSDSF 384 (470)
Q Consensus 356 ~~s~~~~~l~~l~~l~~~TGG~v~~y~~f 384 (470)
.++.+..+...|..|+..+||..++.++.
T Consensus 161 giG~~~~d~~~L~~lA~~~~G~~~~i~~~ 189 (190)
T cd01463 161 LIGREVTDRREIQWMACENKGYYSHIQSL 189 (190)
T ss_pred ecCCccccchHHHHHHhhcCCeEEEcccC
Confidence 66555568889999999999999988764
No 19
>cd01466 vWA_C3HC4_type VWA C3HC4-type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most,
Probab=98.46 E-value=6.6e-06 Score=74.11 Aligned_cols=149 Identities=19% Similarity=0.193 Sum_probs=101.2
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHHHHhhc
Q 012148 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNF 209 (470)
Q Consensus 132 ~vFvID~S~~~~~--~~~l~~~l~~~l~~lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~~~~~l 209 (470)
.+|+||+|.+... +..+++++...++.|+++.+||||+|++..+.+. . .. ..+
T Consensus 3 v~~vlD~S~SM~~~rl~~ak~a~~~l~~~l~~~~~~~li~F~~~~~~~~-~-~~-------------~~~---------- 57 (155)
T cd01466 3 LVAVLDVSGSMAGDKLQLVKHALRFVISSLGDADRLSIVTFSTSAKRLS-P-LR-------------RMT---------- 57 (155)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcceEEEEEecCCccccC-C-Cc-------------ccC----------
Confidence 5799999998653 5678899999999999989999999998754321 0 00 000
Q ss_pred ccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhccC-CC
Q 012148 210 FIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACV-PG 288 (470)
Q Consensus 210 ~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~-~~ 288 (470)
...+..+.++++.+.. ....+++.||..|..++.... ..
T Consensus 58 -------------------------------~~~~~~~~~~i~~~~~---------~g~T~~~~al~~a~~~~~~~~~~~ 97 (155)
T cd01466 58 -------------------------------AKGKRSAKRVVDGLQA---------GGGTNVVGGLKKALKVLGDRRQKN 97 (155)
T ss_pred -------------------------------HHHHHHHHHHHHhccC---------CCCccHHHHHHHHHHHHhhcccCC
Confidence 0123355666666532 234679999999999986321 12
Q ss_pred CCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccChhhch
Q 012148 289 SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELK 368 (470)
Q Consensus 289 ~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l~~l~ 368 (470)
....|++++.|.++.|... .++.+.++.|..+.++. ..+..+|.
T Consensus 98 ~~~~iillTDG~~~~~~~~-----------------------------------~~~~~~~v~v~~igig~-~~~~~~l~ 141 (155)
T cd01466 98 PVASIMLLSDGQDNHGAVV-----------------------------------LRADNAPIPIHTFGLGA-SHDPALLA 141 (155)
T ss_pred CceEEEEEcCCCCCcchhh-----------------------------------hcccCCCceEEEEecCC-CCCHHHHH
Confidence 3468999999987765100 00123577788777753 46888999
Q ss_pred hhhcccCceEEEc
Q 012148 369 VAVEKTGGLVVLS 381 (470)
Q Consensus 369 ~l~~~TGG~v~~y 381 (470)
.|+..|||+.++.
T Consensus 142 ~iA~~t~G~~~~~ 154 (155)
T cd01466 142 FIAEITGGTFSYV 154 (155)
T ss_pred HHHhccCceEEEe
Confidence 9999999998864
No 20
>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain. Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196.
Probab=98.39 E-value=3.4e-05 Score=76.95 Aligned_cols=49 Identities=22% Similarity=0.265 Sum_probs=40.0
Q ss_pred CCCEEEEEEEcccchhh-HHHHHHHHHHHhhc-CCCCceEEEEEECCeEEE
Q 012148 128 VPPVFMFVVDTCIIEEE-MSFLKSALSQAIDL-LPDNSLVGLITFGTLVQV 176 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~~-~~~l~~~l~~~l~~-lp~~~~VglITfd~~V~~ 176 (470)
.|...+|+||+|.+... +..+++++...++. ++++.+||||+|++.++.
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 47899999999997654 45567888888876 788999999999987764
No 21
>cd01467 vWA_BatA_type VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=98.32 E-value=4.1e-05 Score=70.25 Aligned_cols=157 Identities=18% Similarity=0.195 Sum_probs=100.5
Q ss_pred CEEEEEEEcccchh--------hHHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHH
Q 012148 130 PVFMFVVDTCIIEE--------EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKD 201 (470)
Q Consensus 130 p~~vFvID~S~~~~--------~~~~l~~~l~~~l~~lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~ 201 (470)
.-++|+||+|.+.. .+..+++.+...+... ++.+||+|+|+..++..- .
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 35799999998753 2455677776666654 477999999987654220 0
Q ss_pred HHHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHH
Q 012148 202 QLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASL 281 (470)
Q Consensus 202 ~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~l 281 (470)
+...+..+.++|+.|... .. .....++.||..|..+
T Consensus 60 --------------------------------------~~~~~~~~~~~l~~l~~~---~~---~g~T~l~~al~~a~~~ 95 (180)
T cd01467 60 --------------------------------------LTLDRESLKELLEDIKIG---LA---GQGTAIGDAIGLAIKR 95 (180)
T ss_pred --------------------------------------CCccHHHHHHHHHHhhhc---cc---CCCCcHHHHHHHHHHH
Confidence 000122344555555421 01 1235688899999988
Q ss_pred HhccCCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCC-
Q 012148 282 LGACVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD- 360 (470)
Q Consensus 282 l~~~~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~- 360 (470)
+... ......|++++.|.++.|+ . .+ .+.++.+.+.||.|+.+.+...
T Consensus 96 l~~~-~~~~~~iiliTDG~~~~g~--~-----------------------~~-----~~~~~~~~~~gi~i~~i~ig~~~ 144 (180)
T cd01467 96 LKNS-EAKERVIVLLTDGENNAGE--I-----------------------DP-----ATAAELAKNKGVRIYTIGVGKSG 144 (180)
T ss_pred HHhc-CCCCCEEEEEeCCCCCCCC--C-----------------------CH-----HHHHHHHHHCCCEEEEEEecCCC
Confidence 8631 1234678888888766542 0 00 1223445578999998877652
Q ss_pred ---------ccChhhchhhhcccCceEEEcCCC
Q 012148 361 ---------QVGVAELKVAVEKTGGLVVLSDSF 384 (470)
Q Consensus 361 ---------~~~l~~l~~l~~~TGG~v~~y~~f 384 (470)
..+...|..|+..|||..++..+-
T Consensus 145 ~~~~~~~~~~~~~~~l~~la~~tgG~~~~~~~~ 177 (180)
T cd01467 145 SGPKPDGSTILDEDSLVEIADKTGGRIFRALDG 177 (180)
T ss_pred CCcCCCCcccCCHHHHHHHHHhcCCEEEEecCc
Confidence 367888999999999999987653
No 22
>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.
Probab=98.29 E-value=6.3e-05 Score=68.14 Aligned_cols=151 Identities=17% Similarity=0.183 Sum_probs=93.9
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcCC---CCceEEEEEECCeEEEEE-cCCCCCCCCceeeecCCcccCHHHHHH
Q 012148 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVHE-LGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (470)
Q Consensus 132 ~vFvID~S~~~~~--~~~l~~~l~~~l~~lp---~~~~VglITfd~~V~~y~-l~~~~~~~~~~~v~~g~~~~t~~~i~~ 205 (470)
.+|+||+|.+... +..++++++..++.+. ++.++|+|+|++..+..- +. .
T Consensus 3 vv~vlD~SgSm~~~~~~~~k~~~~~~~~~l~~~~~~~~~giv~Fs~~~~~~~~~~-~----------------------- 58 (164)
T cd01472 3 IVFLVDGSESIGLSNFNLVKDFVKRVVERLDIGPDGVRVGVVQYSDDPRTEFYLN-T----------------------- 58 (164)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHhhcccCCCCeEEEEEEEcCceeEEEecC-C-----------------------
Confidence 5899999987654 4557788888877764 568999999998765421 11 0
Q ss_pred HhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhcc
Q 012148 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (470)
Q Consensus 206 ~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 285 (470)
......+.+.|+.++.. +..+.+|.||..|...+...
T Consensus 59 -----------------------------------~~~~~~~~~~l~~l~~~--------~g~T~~~~al~~a~~~l~~~ 95 (164)
T cd01472 59 -----------------------------------YRSKDDVLEAVKNLRYI--------GGGTNTGKALKYVRENLFTE 95 (164)
T ss_pred -----------------------------------CCCHHHHHHHHHhCcCC--------CCCchHHHHHHHHHHHhCCc
Confidence 00122455566665431 22367999999999987631
Q ss_pred ----CCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCc
Q 012148 286 ----VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (470)
Q Consensus 286 ----~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~ 361 (470)
.+.....|++++.|.++.+ . ...+..+.+.||.+..+... .
T Consensus 96 ~~~~~~~~~~~iiliTDG~~~~~-------------------------~--------~~~~~~l~~~gv~i~~ig~g--~ 140 (164)
T cd01472 96 ASGSREGVPKVLVVITDGKSQDD-------------------------V--------EEPAVELKQAGIEVFAVGVK--N 140 (164)
T ss_pred ccCCCCCCCEEEEEEcCCCCCch-------------------------H--------HHHHHHHHHCCCEEEEEECC--c
Confidence 1233445677777732211 0 11223455577765555443 3
Q ss_pred cChhhchhhhcccCc-eEEEcCCC
Q 012148 362 VGVAELKVAVEKTGG-LVVLSDSF 384 (470)
Q Consensus 362 ~~l~~l~~l~~~TGG-~v~~y~~f 384 (470)
.+...|..++..++| .++.+.+|
T Consensus 141 ~~~~~L~~ia~~~~~~~~~~~~~~ 164 (164)
T cd01472 141 ADEEELKQIASDPKELYVFNVADF 164 (164)
T ss_pred CCHHHHHHHHCCCchheEEeccCC
Confidence 499999999999987 66665543
No 23
>cd01470 vWA_complement_factors Complement factors B and C2 are two critical proteases for complement activation. They both contain three CCP or Sushi domains, a trypsin-type serine protease domain and a single VWA domain with a conserved metal ion dependent adhesion site referred commonly as the MIDAS motif. Orthologues of these molecules are found from echinoderms to chordates. During complement activation, the CCP domains are cleaved off, resulting in the formation of an active protease that cleaves and activates complement C3. Complement C2 is in the classical pathway and complement B is in the alternative pathway. The interaction of C2 with C4 and of factor B with C3b are both dependent on Mg2+ binding sites within the VWA domains and the VWA domain of factor B has been shown to mediate the binding of C3. This is consistent with the common inferred function of VWA domains as magnesium-dependent protein interaction domains.
Probab=98.29 E-value=4.2e-05 Score=71.68 Aligned_cols=168 Identities=14% Similarity=0.087 Sum_probs=99.3
Q ss_pred EEEEEEcccchh--hHHHHHHHHHHHhhcCC---CCceEEEEEECCeEEEE-EcCCCCCCCCceeeecCCcccCHHHHHH
Q 012148 132 FMFVVDTCIIEE--EMSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (470)
Q Consensus 132 ~vFvID~S~~~~--~~~~l~~~l~~~l~~lp---~~~~VglITfd~~V~~y-~l~~~~~~~~~~~v~~g~~~~t~~~i~~ 205 (470)
++||||+|.+.. .+..+++++...++.|+ .+.+||+|+|++..+.. .+. ...
T Consensus 3 i~~vlD~SgSM~~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~~~~~~~~-~~~--------------------- 60 (198)
T cd01470 3 IYIALDASDSIGEEDFDEAKNAIKTLIEKISSYEVSPRYEIISYASDPKEIVSIR-DFN--------------------- 60 (198)
T ss_pred EEEEEECCCCccHHHHHHHHHHHHHHHHHccccCCCceEEEEEecCCceEEEecc-cCC---------------------
Confidence 689999999864 35668889998888875 36899999999886532 222 100
Q ss_pred HhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhcc
Q 012148 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (470)
Q Consensus 206 ~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 285 (470)
...+..+...|+.+.... ........++.||..|...+...
T Consensus 61 -----------------------------------~~~~~~~~~~l~~~~~~~----~~~~ggT~~~~Al~~~~~~l~~~ 101 (198)
T cd01470 61 -----------------------------------SNDADDVIKRLEDFNYDD----HGDKTGTNTAAALKKVYERMALE 101 (198)
T ss_pred -----------------------------------CCCHHHHHHHHHhCCccc----ccCccchhHHHHHHHHHHHHHHH
Confidence 001223445555554321 11123456788888877655310
Q ss_pred C-CC------CCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHH------HHHhcCeEE
Q 012148 286 V-PG------SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSK------QLVHQGHVL 352 (470)
Q Consensus 286 ~-~~------~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~------~~~~~gisv 352 (470)
. .. .--.|++++.|.++.|... ....+.++++.. .+...+|.|
T Consensus 102 ~~~~~~~~~~~~~~iillTDG~~~~g~~~------------------------~~~~~~~~~~~~~~~~~~~~~~~~v~i 157 (198)
T cd01470 102 KVRNKEAFNETRHVIILFTDGKSNMGGSP------------------------LPTVDKIKNLVYKNNKSDNPREDYLDV 157 (198)
T ss_pred HhcCccchhhcceEEEEEcCCCcCCCCCh------------------------hHHHHHHHHHHhcccccccchhcceeE
Confidence 0 00 1124788999988876210 001112222211 123456666
Q ss_pred EEeeccCCccChhhchhhhcccCc--eEEEcCCCC
Q 012148 353 DLFACALDQVGVAELKVAVEKTGG--LVVLSDSFG 385 (470)
Q Consensus 353 dlF~~s~~~~~l~~l~~l~~~TGG--~v~~y~~f~ 385 (470)
..+.... .++-.+|..++..||| .+|...+|+
T Consensus 158 ~~iGvG~-~~~~~~L~~iA~~~~g~~~~f~~~~~~ 191 (198)
T cd01470 158 YVFGVGD-DVNKEELNDLASKKDNERHFFKLKDYE 191 (198)
T ss_pred EEEecCc-ccCHHHHHHHhcCCCCCceEEEeCCHH
Confidence 6665533 5789999999999999 477777664
No 24
>cd01480 vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=98.21 E-value=6.4e-05 Score=69.81 Aligned_cols=158 Identities=15% Similarity=0.132 Sum_probs=97.9
Q ss_pred EEEEEEEcccchhh--HHHHHHHHHHHhhcC---------CCCceEEEEEECCeEEEE-EcCCCCCCCCceeeecCCccc
Q 012148 131 VFMFVVDTCIIEEE--MSFLKSALSQAIDLL---------PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDV 198 (470)
Q Consensus 131 ~~vFvID~S~~~~~--~~~l~~~l~~~l~~l---------p~~~~VglITfd~~V~~y-~l~~~~~~~~~~~v~~g~~~~ 198 (470)
-.+|+||.|.+... ++..++.++..++.+ +++.+||+|+|++..++. .+. .
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 46899999998653 445566666666665 456899999999775432 111 0
Q ss_pred CHHHHHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHH
Q 012148 199 SKDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIA 278 (470)
Q Consensus 199 t~~~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A 278 (470)
. ...+..+.+.|++++.. .....+|.||..|
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 01234566777766431 1246799999999
Q ss_pred HHHHhc-cCCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeec
Q 012148 279 ASLLGA-CVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFAC 357 (470)
Q Consensus 279 ~~ll~~-~~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~ 357 (470)
...+.. ........|++++.|.++.++ + .-..+.+..+.+.||.+-.+..
T Consensus 98 ~~~l~~~~~~~~~~~iillTDG~~~~~~--------------------~---------~~~~~~~~~~~~~gi~i~~vgi 148 (186)
T cd01480 98 TEQLLEGSHQKENKFLLVITDGHSDGSP--------------------D---------GGIEKAVNEADHLGIKIFFVAV 148 (186)
T ss_pred HHHHhccCCCCCceEEEEEeCCCcCCCc--------------------c---------hhHHHHHHHHHHCCCEEEEEec
Confidence 988863 122333566777777542111 0 0113455667788887665555
Q ss_pred cCCccChhhchhhhcccCceEEEcCCCCc
Q 012148 358 ALDQVGVAELKVAVEKTGGLVVLSDSFGH 386 (470)
Q Consensus 358 s~~~~~l~~l~~l~~~TGG~v~~y~~f~~ 386 (470)
.. .+...|..++...+|. |+-++|..
T Consensus 149 g~--~~~~~L~~IA~~~~~~-~~~~~~~~ 174 (186)
T cd01480 149 GS--QNEEPLSRIACDGKSA-LYRENFAE 174 (186)
T ss_pred Cc--cchHHHHHHHcCCcch-hhhcchhh
Confidence 33 7888899999877775 55555543
No 25
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=98.11 E-value=0.00011 Score=82.36 Aligned_cols=155 Identities=15% Similarity=0.206 Sum_probs=102.3
Q ss_pred CCCEEEEEEEcccchh---hHHHHHHHHHHHh-hcCCCCceEEEEEECCeEEEEE-cCCCCCCCCceeeecCCcccCHHH
Q 012148 128 VPPVFMFVVDTCIIEE---EMSFLKSALSQAI-DLLPDNSLVGLITFGTLVQVHE-LGGFGQIIPKTYVFKGSKDVSKDQ 202 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~---~~~~l~~~l~~~l-~~lp~~~~VglITfd~~V~~y~-l~~~~~~~~~~~v~~g~~~~t~~~ 202 (470)
.+..+++|||+|.+.. .+..++++++..+ +.++++.+||||+|++..++.. +. .
T Consensus 303 ~~r~VVLVLDvSGSM~g~dRL~~lkqAA~~fL~~~l~~~DrVGLVtFsssA~vl~pLt-~-------------------- 361 (863)
T TIGR00868 303 RQRIVCLVLDKSGSMTVEDRLKRMNQAAKLFLLQTVEKGSWVGMVTFDSAAYIKNELI-Q-------------------- 361 (863)
T ss_pred CCceEEEEEECCccccccCHHHHHHHHHHHHHHHhCCCCCEEEEEEECCceeEeeccc-c--------------------
Confidence 3456999999999864 3666788877665 4578889999999999865431 11 0
Q ss_pred HHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHH
Q 012148 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (470)
Q Consensus 203 i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll 282 (470)
+.+ ......++..|+.. + ....+++.||..|..+|
T Consensus 362 -------------------------------------Its-~~dr~aL~~~L~~~----A---~GGT~I~~GL~~Alq~L 396 (863)
T TIGR00868 362 -------------------------------------ITS-SAERDALTANLPTA----A---SGGTSICSGLKAAFQVI 396 (863)
T ss_pred -------------------------------------CCc-HHHHHHHHHhhccc----c---CCCCcHHHHHHHHHHHH
Confidence 000 00112222233211 1 23578999999999998
Q ss_pred hccC-CCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCc
Q 012148 283 GACV-PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (470)
Q Consensus 283 ~~~~-~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~ 361 (470)
.... ...+..|++++.|.++.+ ..+...+.+.||.|..+.++.+.
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 7422 235678888888753211 12344556789999999887653
Q ss_pred cChhhchhhhcccCceEEEcCCC
Q 012148 362 VGVAELKVAVEKTGGLVVLSDSF 384 (470)
Q Consensus 362 ~~l~~l~~l~~~TGG~v~~y~~f 384 (470)
-..|..||+.|||..|+..+-
T Consensus 443 --d~~L~~IA~~TGG~~f~asd~ 463 (863)
T TIGR00868 443 --AKELEELSDMTGGLRFYASDQ 463 (863)
T ss_pred --HHHHHHHHHhcCCEEEEeCCH
Confidence 356899999999999998753
No 26
>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=98.09 E-value=0.00016 Score=67.14 Aligned_cols=145 Identities=21% Similarity=0.202 Sum_probs=92.6
Q ss_pred EEEEEEEcccchhh-------HHHHHHHHHHHh----hcCCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccC
Q 012148 131 VFMFVVDTCIIEEE-------MSFLKSALSQAI----DLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVS 199 (470)
Q Consensus 131 ~~vFvID~S~~~~~-------~~~l~~~l~~~l----~~lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t 199 (470)
+.+++||+|....+ +...++++...+ +..| ..+||||+|..... |-+
T Consensus 5 a~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np-~~~vGlv~fag~~a-~v~-------------------- 62 (187)
T cd01452 5 ATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNP-ENNVGLMTMAGNSP-EVL-------------------- 62 (187)
T ss_pred EEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCC-CccEEEEEecCCce-EEE--------------------
Confidence 57999999988544 555666666553 5555 55999999986311 111
Q ss_pred HHHHHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHH
Q 012148 200 KDQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAA 279 (470)
Q Consensus 200 ~~~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~ 279 (470)
+|+......+...|+.+.. .+...+|.||+.|.
T Consensus 63 --------------------------------------~plT~D~~~~~~~L~~i~~---------~g~~~l~~AL~~A~ 95 (187)
T cd01452 63 --------------------------------------VTLTNDQGKILSKLHDVQP---------KGKANFITGIQIAQ 95 (187)
T ss_pred --------------------------------------ECCCCCHHHHHHHHHhCCC---------CCcchHHHHHHHHH
Confidence 1111123356666665532 13356999999999
Q ss_pred HHHhccCCC-CCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeecc
Q 012148 280 SLLGACVPG-SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACA 358 (470)
Q Consensus 280 ~ll~~~~~~-~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s 358 (470)
..|+..-.. ...||++|++++-+.=+ .+ ..++++++.++||.||+..++
T Consensus 96 ~~L~~~~~~~~~~rivi~v~S~~~~d~-----------------------------~~-i~~~~~~lkk~~I~v~vI~~G 145 (187)
T cd01452 96 LALKHRQNKNQKQRIVAFVGSPIEEDE-----------------------------KD-LVKLAKRLKKNNVSVDIINFG 145 (187)
T ss_pred HHHhcCCCcCCcceEEEEEecCCcCCH-----------------------------HH-HHHHHHHHHHcCCeEEEEEeC
Confidence 998742212 33599999987521110 12 237899999999999999987
Q ss_pred CCccChhhchhhhccc
Q 012148 359 LDQVGVAELKVAVEKT 374 (470)
Q Consensus 359 ~~~~~l~~l~~l~~~T 374 (470)
...-+..-+..+.+..
T Consensus 146 ~~~~~~~~l~~~~~~~ 161 (187)
T cd01452 146 EIDDNTEKLTAFIDAV 161 (187)
T ss_pred CCCCCHHHHHHHHHHh
Confidence 7655555565555544
No 27
>cd01461 vWA_interalpha_trypsin_inhibitor vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to the extracellular matrix by binding to hyaluronic acid. The heavy chains carry the VWA domain with a conserved MIDAS motif. Although the exact role of the VWA domains remains unknown, it has been speculated to be involved in mediating protein-protein interactions with the components of the extracellular matrix.
Probab=98.09 E-value=0.00035 Score=63.16 Aligned_cols=160 Identities=21% Similarity=0.210 Sum_probs=101.0
Q ss_pred CCEEEEEEEcccchhh--HHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHHHH
Q 012148 129 PPVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQ 206 (470)
Q Consensus 129 ~p~~vFvID~S~~~~~--~~~l~~~l~~~l~~lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~~~ 206 (470)
|.-++||+|+|.+... +..+++++...+..+++..+|++++|++.++.+- . ..
T Consensus 2 ~~~v~~vlD~S~SM~~~~~~~~~~al~~~l~~l~~~~~~~l~~Fs~~~~~~~-~--~~---------------------- 56 (171)
T cd01461 2 PKEVVFVIDTSGSMSGTKIEQTKEALLTALKDLPPGDYFNIIGFSDTVEEFS-P--SS---------------------- 56 (171)
T ss_pred CceEEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEeCCCceeec-C--cc----------------------
Confidence 5668999999998743 5567889988899999888999999998765431 1 00
Q ss_pred hhcccCCCCCCCccccCccCCCCccccccceeecc-chHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhcc
Q 012148 207 LNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAF-DCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (470)
Q Consensus 207 ~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~-~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 285 (470)
.+.+ +....+.+.|+.+.. .....+..||..|...+..
T Consensus 57 -------------------------------~~~~~~~~~~~~~~l~~~~~---------~g~T~l~~al~~a~~~l~~- 95 (171)
T cd01461 57 -------------------------------VSATAENVAAAIEYVNRLQA---------LGGTNMNDALEAALELLNS- 95 (171)
T ss_pred -------------------------------eeCCHHHHHHHHHHHHhcCC---------CCCcCHHHHHHHHHHhhcc-
Confidence 0000 011122333444322 1234578899888887752
Q ss_pred CCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccChh
Q 012148 286 VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVA 365 (470)
Q Consensus 286 ~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l~ 365 (470)
.......|++|+.|.++. ..+.+ +..+++.+.++.|..+.++. ..+-.
T Consensus 96 ~~~~~~~iillTDG~~~~------------------------------~~~~~-~~~~~~~~~~i~i~~i~~g~-~~~~~ 143 (171)
T cd01461 96 SPGSVPQIILLTDGEVTN------------------------------ESQIL-KNVREALSGRIRLFTFGIGS-DVNTY 143 (171)
T ss_pred CCCCccEEEEEeCCCCCC------------------------------HHHHH-HHHHHhcCCCceEEEEEeCC-ccCHH
Confidence 113346677777775210 01233 33444444578777776643 46778
Q ss_pred hchhhhcccCceEEEcCCCCc
Q 012148 366 ELKVAVEKTGGLVVLSDSFGH 386 (470)
Q Consensus 366 ~l~~l~~~TGG~v~~y~~f~~ 386 (470)
.|..++..|||..++..+-.+
T Consensus 144 ~l~~ia~~~gG~~~~~~~~~~ 164 (171)
T cd01461 144 LLERLAREGRGIARRIYETDD 164 (171)
T ss_pred HHHHHHHcCCCeEEEecChHH
Confidence 899999999999998887654
No 28
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=98.08 E-value=5.6e-05 Score=67.96 Aligned_cols=151 Identities=22% Similarity=0.216 Sum_probs=95.0
Q ss_pred EEEEEEcccchhh-------HHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHH
Q 012148 132 FMFVVDTCIIEEE-------MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (470)
Q Consensus 132 ~vFvID~S~~~~~-------~~~l~~~l~~~l~~lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~ 204 (470)
++||||+|.+... ...+++++...++.+| +.+|||++|+...+..- .
T Consensus 2 vv~v~D~SgSM~~~~~~~~~~~~~~~~~~~~~~~~~-~~~v~l~~f~~~~~~~~-~------------------------ 55 (172)
T PF13519_consen 2 VVFVLDNSGSMNGYDGNRTRIDQAKDALNELLANLP-GDRVGLVSFSDSSRTLS-P------------------------ 55 (172)
T ss_dssp EEEEEE-SGGGGTTTSSS-HHHHHHHHHHHHHHHHT-TSEEEEEEESTSCEEEE-E------------------------
T ss_pred EEEEEECCcccCCCCCCCcHHHHHHHHHHHHHHHCC-CCEEEEEEecccccccc-c------------------------
Confidence 6899999998654 4567888888888887 44999999997532110 0
Q ss_pred HHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhc
Q 012148 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (470)
Q Consensus 205 ~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~ 284 (470)
+...+..+.+.++++.... ......+++.|+..|..++..
T Consensus 56 -----------------------------------~t~~~~~~~~~l~~~~~~~-----~~~~~t~~~~al~~a~~~~~~ 95 (172)
T PF13519_consen 56 -----------------------------------LTSDKDELKNALNKLSPQG-----MPGGGTNLYDALQEAAKMLAS 95 (172)
T ss_dssp -----------------------------------EESSHHHHHHHHHTHHHHG-------SSS--HHHHHHHHHHHHHC
T ss_pred -----------------------------------ccccHHHHHHHhhcccccc-----cCccCCcHHHHHHHHHHHHHh
Confidence 0112234455555544210 112336788999999999873
Q ss_pred cCCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccCh
Q 012148 285 CVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGV 364 (470)
Q Consensus 285 ~~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l 364 (470)
. ......|++|+.|.++ . .. .+.++.+.+.+|.+..+.+..+...-
T Consensus 96 ~-~~~~~~iv~iTDG~~~-----------------------~--~~--------~~~~~~~~~~~i~i~~v~~~~~~~~~ 141 (172)
T PF13519_consen 96 S-DNRRRAIVLITDGEDN-----------------------S--SD--------IEAAKALKQQGITIYTVGIGSDSDAN 141 (172)
T ss_dssp --SSEEEEEEEEES-TTH-----------------------C--HH--------HHHHHHHHCTTEEEEEEEES-TT-EH
T ss_pred C-CCCceEEEEecCCCCC-----------------------c--ch--------hHHHHHHHHcCCeEEEEEECCCccHH
Confidence 1 1233566666666432 0 00 12677788999999999888776656
Q ss_pred hhchhhhcccCceEEEcC
Q 012148 365 AELKVAVEKTGGLVVLSD 382 (470)
Q Consensus 365 ~~l~~l~~~TGG~v~~y~ 382 (470)
..|..+++.|||..+...
T Consensus 142 ~~l~~la~~tgG~~~~~~ 159 (172)
T PF13519_consen 142 EFLQRLAEATGGRYFHVD 159 (172)
T ss_dssp HHHHHHHHHTEEEEEEE-
T ss_pred HHHHHHHHhcCCEEEEec
Confidence 789999999999988874
No 29
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=97.96 E-value=0.00021 Score=64.00 Aligned_cols=151 Identities=20% Similarity=0.211 Sum_probs=96.0
Q ss_pred EEEEEEcccchhhH-HHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHHHHhhcc
Q 012148 132 FMFVVDTCIIEEEM-SFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLLEQLNFF 210 (470)
Q Consensus 132 ~vFvID~S~~~~~~-~~l~~~l~~~l~~lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~~~~~l~ 210 (470)
.+||||+|.+.... ..++++|+.+++.|+++.++.||+|++.+..+.-. . ... .
T Consensus 3 vvilvD~S~Sm~g~~~~~k~al~~~l~~L~~~d~fnii~f~~~~~~~~~~---~-------------------~~~---~ 57 (155)
T PF13768_consen 3 VVILVDTSGSMSGEKELVKDALRAILRSLPPGDRFNIIAFGSSVRPLFPG---L-------------------VPA---T 57 (155)
T ss_pred EEEEEeCCCCCCCcHHHHHHHHHHHHHhCCCCCEEEEEEeCCEeeEcchh---H-------------------HHH---h
Confidence 68999999986543 67899999999999999999999999987655311 0 000 0
Q ss_pred cCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhccCCCCC
Q 012148 211 IKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSG 290 (470)
Q Consensus 211 ~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~G 290 (470)
.+..+...+.|+.+... .....+..||..|...+. ....-
T Consensus 58 ------------------------------~~~~~~a~~~I~~~~~~--------~G~t~l~~aL~~a~~~~~--~~~~~ 97 (155)
T PF13768_consen 58 ------------------------------EENRQEALQWIKSLEAN--------SGGTDLLAALRAALALLQ--RPGCV 97 (155)
T ss_pred ------------------------------HHHHHHHHHHHHHhccc--------CCCccHHHHHHHHHHhcc--cCCCc
Confidence 01122333444444321 234668899999988752 12455
Q ss_pred cEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccChhhchhh
Q 012148 291 ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVA 370 (470)
Q Consensus 291 G~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l~~l~~l 370 (470)
-.|++++.|.|+.++ ....+.+. +. ...+.++.|.+.. ..+-..|..|
T Consensus 98 ~~IilltDG~~~~~~-----------------------------~~i~~~v~-~~-~~~~~i~~~~~g~-~~~~~~L~~L 145 (155)
T PF13768_consen 98 RAIILLTDGQPVSGE-----------------------------EEILDLVR-RA-RGHIRIFTFGIGS-DADADFLREL 145 (155)
T ss_pred cEEEEEEeccCCCCH-----------------------------HHHHHHHH-hc-CCCceEEEEEECC-hhHHHHHHHH
Confidence 678888888653322 11222222 11 1456677776644 4667889999
Q ss_pred hcccCceEE
Q 012148 371 VEKTGGLVV 379 (470)
Q Consensus 371 ~~~TGG~v~ 379 (470)
++.|||..+
T Consensus 146 A~~~~G~~~ 154 (155)
T PF13768_consen 146 ARATGGSFH 154 (155)
T ss_pred HHcCCCEEE
Confidence 999999865
No 30
>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=97.94 E-value=4.6e-06 Score=69.04 Aligned_cols=53 Identities=13% Similarity=0.098 Sum_probs=41.7
Q ss_pred eeEEEEEecccccceeeeecCCeeeeEEEeCceecc---------hhhhHhhhhhhcCCCccchhhcccccC
Q 012148 407 SSKYGFMNFVLYFFLSRIADYPLPVLTIITPLYKKY---------LLLAKLIYAYMHGADSLFQQDLSLSEH 469 (470)
Q Consensus 407 ~~~~~lr~~~~~~~v~~r~S~gl~i~~~~G~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~ 469 (470)
||+|+|| | |||+||+|++++||+..++ .++.. ...+..++|++|+..++++|.
T Consensus 1 g~~~~l~-------v--r~S~gl~v~~~~G~~~~~~~~s~~~~g~~~~~~-~~~~~l~~~~s~~~~~~~~~~ 62 (96)
T PF08033_consen 1 GFNAVLR-------V--RCSKGLKVSGVIGPCFNRSSVSDNEIGEGDTTR-WKLPSLDPDTSFAFEFEIDED 62 (96)
T ss_dssp EEEEEEE-------E--EE-TTEEEEEEESSSEESSTBESSECSBSSCSE-EEEEEEETT--EEEEEEESSB
T ss_pred CceEEEE-------E--EECCCeEEEEEEcCccccccccceeeccCCccE-EEecccCCCCEEEEEEEECCC
Confidence 7999999 9 9999999999999999997 44411 334679999999999998764
No 31
>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax. ATR is the cellular receptor for the anthrax protective antigen and facilitates entry of the toxin into cells. The VWA domain in ATR contains the toxin binding site and mediates interaction with protective antigen. The binding is mediated by divalent cations that binds to the MIDAS motif. These proteins are a family of vertebrate ECM receptors expressed by endothelial cells.
Probab=97.92 E-value=0.00048 Score=63.79 Aligned_cols=156 Identities=17% Similarity=0.100 Sum_probs=88.9
Q ss_pred CCEEEEEEEcccchhhH-HHHHHHHHHHhhcC-CCCceEEEEEECCeEEEE-EcCCCCCCCCceeeecCCcccCHHHHHH
Q 012148 129 PPVFMFVVDTCIIEEEM-SFLKSALSQAIDLL-PDNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (470)
Q Consensus 129 ~p~~vFvID~S~~~~~~-~~l~~~l~~~l~~l-p~~~~VglITfd~~V~~y-~l~~~~~~~~~~~v~~g~~~~t~~~i~~ 205 (470)
+.-++|+||.|.+.... ....+.++..++.+ .++.|||+|+|++..+.. .+. .
T Consensus 4 ~~Dvv~llD~SgSm~~~~~~~~~~~~~l~~~~~~~~~rvglv~Fs~~~~~~~~l~-~----------------------- 59 (185)
T cd01474 4 HFDLYFVLDKSGSVAANWIEIYDFVEQLVDRFNSPGLRFSFITFSTRATKILPLT-D----------------------- 59 (185)
T ss_pred ceeEEEEEeCcCchhhhHHHHHHHHHHHHHHcCCCCcEEEEEEecCCceEEEecc-c-----------------------
Confidence 45689999999986542 11234444444443 356999999999775432 111 0
Q ss_pred HhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhcc
Q 012148 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (470)
Q Consensus 206 ~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 285 (470)
....+...++.|... .+ ...+.+|.||..|...+...
T Consensus 60 -------------------------------------~~~~~~~~l~~l~~~---~~---~g~T~~~~aL~~a~~~l~~~ 96 (185)
T cd01474 60 -------------------------------------DSSAIIKGLEVLKKV---TP---SGQTYIHEGLENANEQIFNR 96 (185)
T ss_pred -------------------------------------cHHHHHHHHHHHhcc---CC---CCCCcHHHHHHHHHHHHHhh
Confidence 001233344444432 11 23578999999998776310
Q ss_pred CCCCCc-----EEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCC
Q 012148 286 VPGSGA-----RILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (470)
Q Consensus 286 ~~~~GG-----~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~ 360 (470)
..|| .|++++.|.++...+. .+ ...++.+.+.|+.|..+.. .
T Consensus 97 --~~~~r~~~~~villTDG~~~~~~~~------------------------~~-----~~~a~~l~~~gv~i~~vgv--~ 143 (185)
T cd01474 97 --NGGGRETVSVIIALTDGQLLLNGHK------------------------YP-----EHEAKLSRKLGAIVYCVGV--T 143 (185)
T ss_pred --ccCCCCCCeEEEEEcCCCcCCCCCc------------------------ch-----HHHHHHHHHcCCEEEEEee--c
Confidence 2233 3777787865311000 00 1234566678886655554 5
Q ss_pred ccChhhchhhhcccCceEE-EcCCCC
Q 012148 361 QVGVAELKVAVEKTGGLVV-LSDSFG 385 (470)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~-~y~~f~ 385 (470)
..+..+|..++..++ .+| ...+|+
T Consensus 144 ~~~~~~L~~iA~~~~-~~f~~~~~~~ 168 (185)
T cd01474 144 DFLKSQLINIADSKE-YVFPVTSGFQ 168 (185)
T ss_pred hhhHHHHHHHhCCCC-eeEecCccHH
Confidence 678889999998774 455 344565
No 32
>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
Probab=97.88 E-value=0.00061 Score=65.19 Aligned_cols=156 Identities=22% Similarity=0.332 Sum_probs=96.4
Q ss_pred CCEEEEEEEcccchh--hHHHHHHHHHHHhhcC---CCCceEEEEEECCeEEEEE-cCCCCCCCCceeeecCCcccCHHH
Q 012148 129 PPVFMFVVDTCIIEE--EMSFLKSALSQAIDLL---PDNSLVGLITFGTLVQVHE-LGGFGQIIPKTYVFKGSKDVSKDQ 202 (470)
Q Consensus 129 ~p~~vFvID~S~~~~--~~~~l~~~l~~~l~~l---p~~~~VglITfd~~V~~y~-l~~~~~~~~~~~v~~g~~~~t~~~ 202 (470)
+.-.+|+||.|.+.. +++.+++.++..++.+ |+.+|||+|+|++.+++.- +. .
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 4566788888887776 4578999999998865431 11 0
Q ss_pred HHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHH
Q 012148 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (470)
Q Consensus 203 i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll 282 (470)
...+..+...|+.+... .....+|.||..|...+
T Consensus 61 --------------------------------------~~~~~~l~~~i~~i~~~--------~~~t~tg~AL~~a~~~~ 94 (224)
T cd01475 61 --------------------------------------FKSKADLKRAVRRMEYL--------ETGTMTGLAIQYAMNNA 94 (224)
T ss_pred --------------------------------------cCCHHHHHHHHHhCcCC--------CCCChHHHHHHHHHHHh
Confidence 00122455666665432 12346889998887642
Q ss_pred -hcc---CCCC---CcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEe
Q 012148 283 -GAC---VPGS---GARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLF 355 (470)
Q Consensus 283 -~~~---~~~~---GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF 355 (470)
... .+.. -..|++|+.|.++. -.++.++++.+.||.| |
T Consensus 95 ~~~~~g~r~~~~~~~kvvillTDG~s~~---------------------------------~~~~~a~~lk~~gv~i--~ 139 (224)
T cd01475 95 FSEAEGARPGSERVPRVGIVVTDGRPQD---------------------------------DVSEVAAKARALGIEM--F 139 (224)
T ss_pred CChhcCCCCCCCCCCeEEEEEcCCCCcc---------------------------------cHHHHHHHHHHCCcEE--E
Confidence 210 1111 12356777664210 0235677777888755 4
Q ss_pred eccCCccChhhchhhhcccC-ceEEEcCCCCc
Q 012148 356 ACALDQVGVAELKVAVEKTG-GLVVLSDSFGH 386 (470)
Q Consensus 356 ~~s~~~~~l~~l~~l~~~TG-G~v~~y~~f~~ 386 (470)
+..-...+..+|..++..++ +.++.-++|+.
T Consensus 140 ~VgvG~~~~~~L~~ias~~~~~~~f~~~~~~~ 171 (224)
T cd01475 140 AVGVGRADEEELREIASEPLADHVFYVEDFST 171 (224)
T ss_pred EEeCCcCCHHHHHHHhCCCcHhcEEEeCCHHH
Confidence 44444568889999998765 46777777764
No 33
>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=97.82 E-value=0.00099 Score=61.56 Aligned_cols=44 Identities=20% Similarity=0.181 Sum_probs=35.4
Q ss_pred EEEEEEcccchhh---HHHHHHHHHHHhhcCC---CCceEEEEEECCeEE
Q 012148 132 FMFVVDTCIIEEE---MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQ 175 (470)
Q Consensus 132 ~vFvID~S~~~~~---~~~l~~~l~~~l~~lp---~~~~VglITfd~~V~ 175 (470)
++|+||.|.+... +..+++.+...++.++ ++.+||+|+|++..+
T Consensus 3 v~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~ 52 (186)
T cd01471 3 LYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAK 52 (186)
T ss_pred EEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCce
Confidence 6899999998654 4557888888887764 678999999998765
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=0.002 Score=58.34 Aligned_cols=44 Identities=25% Similarity=0.472 Sum_probs=34.1
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcC---CCCceEEEEEECCeEE
Q 012148 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLL---PDNSLVGLITFGTLVQ 175 (470)
Q Consensus 132 ~vFvID~S~~~~~--~~~l~~~l~~~l~~l---p~~~~VglITfd~~V~ 175 (470)
.+|++|.|.+... ...+++.++..+..+ +++.+||+|+|++..+
T Consensus 3 v~~vlD~S~Sm~~~~~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~~ 51 (164)
T cd01482 3 IVFLVDGSWSIGRSNFNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDPR 51 (164)
T ss_pred EEEEEeCCCCcChhhHHHHHHHHHHHHhheeeCCCceEEEEEEECCCee
Confidence 6899999998754 455677777777655 4679999999998754
No 35
>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=97.78 E-value=0.0012 Score=58.57 Aligned_cols=144 Identities=19% Similarity=0.175 Sum_probs=94.4
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcCC---CCceEEEEEECCeEEEE-EcCCCCCCCCceeeecCCcccCHHHHHH
Q 012148 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (470)
Q Consensus 132 ~vFvID~S~~~~~--~~~l~~~l~~~l~~lp---~~~~VglITfd~~V~~y-~l~~~~~~~~~~~v~~g~~~~t~~~i~~ 205 (470)
++|++|+|.+... ...+++.+...+..+. ++.++++++|++..... ++. .
T Consensus 3 i~~llD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~~~~~~~-~----------------------- 58 (161)
T cd01450 3 IVFLLDGSESVGPENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVRVEFSLN-D----------------------- 58 (161)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCceEEEECC-C-----------------------
Confidence 5799999998654 5667888888777665 47899999999754322 111 0
Q ss_pred HhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhcc
Q 012148 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGAC 285 (470)
Q Consensus 206 ~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~ 285 (470)
. . ....+.+.++.+... .. ..+.++.||..|...+...
T Consensus 59 -----------------------------~-----~-~~~~~~~~i~~~~~~---~~----~~t~~~~al~~a~~~~~~~ 96 (161)
T cd01450 59 -----------------------------Y-----K-SKDDLLKAVKNLKYL---GG----GGTNTGKALQYALEQLFSE 96 (161)
T ss_pred -----------------------------C-----C-CHHHHHHHHHhcccC---CC----CCccHHHHHHHHHHHhccc
Confidence 0 0 122455555554321 11 3467899999999887632
Q ss_pred C---CCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCcc
Q 012148 286 V---PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (470)
Q Consensus 286 ~---~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~ 362 (470)
. ...-..|++|+.|.++.++ -..++.+++.+.++.|..+..+. .
T Consensus 97 ~~~~~~~~~~iiliTDG~~~~~~-------------------------------~~~~~~~~~~~~~v~v~~i~~g~--~ 143 (161)
T cd01450 97 SNARENVPKVIIVLTDGRSDDGG-------------------------------DPKEAAAKLKDEGIKVFVVGVGP--A 143 (161)
T ss_pred ccccCCCCeEEEEECCCCCCCCc-------------------------------chHHHHHHHHHCCCEEEEEeccc--c
Confidence 1 2344578888888765542 11355666667788888777655 6
Q ss_pred Chhhchhhhccc
Q 012148 363 GVAELKVAVEKT 374 (470)
Q Consensus 363 ~l~~l~~l~~~T 374 (470)
+...|..++..+
T Consensus 144 ~~~~l~~la~~~ 155 (161)
T cd01450 144 DEEELREIASCP 155 (161)
T ss_pred CHHHHHHHhCCC
Confidence 888899999888
No 36
>cd01469 vWA_integrins_alpha_subunit Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration. Integrins consist of an alpha and a beta sub-unit. Each sub-unit has a large extracellular portion, a single transmembrane segment and a short cytoplasmic domain. The N-terminal domains of the alpha and beta subunits associate to form the integrin headpiece, which contains the ligand binding site, whereas the C-terminal segments traverse the plasma membrane and mediate interaction with the cytoskeleton and with signalling proteins.The VWA domains present in the alpha subunits of integrins seem to be a chordate specific radiation of the gene family being found only in vertebrates. They mediate protein-protein interactions.
Probab=97.76 E-value=0.0021 Score=59.13 Aligned_cols=156 Identities=16% Similarity=0.159 Sum_probs=95.8
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcCC---CCceEEEEEECCeEEEE-EcCCCCCCCCceeeecCCcccCHHHHHH
Q 012148 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP---DNSLVGLITFGTLVQVH-ELGGFGQIIPKTYVFKGSKDVSKDQLLE 205 (470)
Q Consensus 132 ~vFvID~S~~~~~--~~~l~~~l~~~l~~lp---~~~~VglITfd~~V~~y-~l~~~~~~~~~~~v~~g~~~~t~~~i~~ 205 (470)
++|+||.|.+... ...+++.++..++.+. +++|||+|+|++..++. ++. .
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 6899999998643 5567777887777664 57899999999886543 222 0
Q ss_pred HhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHh-c
Q 012148 206 QLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG-A 284 (470)
Q Consensus 206 ~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~-~ 284 (470)
+ .....+..+++.++.. . ..+.+|.||..|...+- .
T Consensus 59 ------------------------------~-----~~~~~~~~~i~~~~~~----~----g~T~~~~AL~~a~~~l~~~ 95 (177)
T cd01469 59 ------------------------------Y-----RTKEEPLSLVKHISQL----L----GLTNTATAIQYVVTELFSE 95 (177)
T ss_pred ------------------------------c-----CCHHHHHHHHHhCccC----C----CCccHHHHHHHHHHHhcCc
Confidence 0 0111344455555432 1 23678999999987652 1
Q ss_pred ---cCCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCc
Q 012148 285 ---CVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQ 361 (470)
Q Consensus 285 ---~~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~ 361 (470)
..+..-..+++++.|..+.|+ . . +..++.+.+.||.|-.+......
T Consensus 96 ~~g~R~~~~kv~illTDG~~~~~~------------------------~------~-~~~~~~~k~~gv~v~~Vgvg~~~ 144 (177)
T cd01469 96 SNGARKDATKVLVVITDGESHDDP------------------------L------L-KDVIPQAEREGIIRYAIGVGGHF 144 (177)
T ss_pred ccCCCCCCCeEEEEEeCCCCCCcc------------------------c------c-HHHHHHHHHCCcEEEEEEecccc
Confidence 011122347777777654331 0 0 23455666788866666554432
Q ss_pred ---cChhhchhhhcccCc-eEEEcCCCC
Q 012148 362 ---VGVAELKVAVEKTGG-LVVLSDSFG 385 (470)
Q Consensus 362 ---~~l~~l~~l~~~TGG-~v~~y~~f~ 385 (470)
.+..+|..++..+++ .+|..++|+
T Consensus 145 ~~~~~~~~L~~ias~p~~~h~f~~~~~~ 172 (177)
T cd01469 145 QRENSREELKTIASKPPEEHFFNVTDFA 172 (177)
T ss_pred cccccHHHHHHHhcCCcHHhEEEecCHH
Confidence 346888899988764 677777775
No 37
>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=97.63 E-value=0.0031 Score=59.01 Aligned_cols=48 Identities=23% Similarity=0.283 Sum_probs=35.7
Q ss_pred CCEEEEEEEcccchh--hHHHHHHHHHHHhhcC---------CCCceEEEEEECCeEEE
Q 012148 129 PPVFMFVVDTCIIEE--EMSFLKSALSQAIDLL---------PDNSLVGLITFGTLVQV 176 (470)
Q Consensus 129 ~p~~vFvID~S~~~~--~~~~l~~~l~~~l~~l---------p~~~~VglITfd~~V~~ 176 (470)
..=.||+||.|.+.. +++.+++.++..+..+ |+.+|||+|+|++..++
T Consensus 19 ~~DivfvlD~S~Sm~~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a~~ 77 (193)
T cd01477 19 WLDIVFVVDNSKGMTQGGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNATV 77 (193)
T ss_pred eeeEEEEEeCCCCcchhhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCceEE
Confidence 455899999999854 4566777777665543 44689999999988654
No 38
>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=97.63 E-value=0.0031 Score=68.95 Aligned_cols=176 Identities=16% Similarity=0.063 Sum_probs=113.2
Q ss_pred CCCEEEEEEEcccchhh--HHHHHHHHHHHhhc-CCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHH
Q 012148 128 VPPVFMFVVDTCIIEEE--MSFLKSALSQAIDL-LPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~~--~~~l~~~l~~~l~~-lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~ 204 (470)
....++||||+|.+... +..++.++...+.. +.+..+||+|+|+....-+-+. .
T Consensus 406 ~~~~v~fvvD~SGSM~~~rl~~aK~av~~Ll~~~~~~~D~v~Li~F~~~~a~~~lp-~---------------------- 462 (589)
T TIGR02031 406 SGRLLIFVVDASGSAAVARMSEAKGAVELLLGEAYVHRDQVSLIAFRGTAAEVLLP-P---------------------- 462 (589)
T ss_pred cCceEEEEEECCCCCChHHHHHHHHHHHHHHHhhccCCCEEEEEEECCCCceEECC-C----------------------
Confidence 35678999999998743 56678888887765 3456699999997543111111 0
Q ss_pred HHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhc
Q 012148 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (470)
Q Consensus 205 ~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~ 284 (470)
......+...|+.|+. .....++.||..|...+..
T Consensus 463 ------------------------------------t~~~~~~~~~L~~l~~---------gGgTpL~~gL~~A~~~~~~ 497 (589)
T TIGR02031 463 ------------------------------------SRSVEQAKRRLDVLPG---------GGGTPLAAGLAAAFQTALQ 497 (589)
T ss_pred ------------------------------------CCCHHHHHHHHhcCCC---------CCCCcHHHHHHHHHHHHHH
Confidence 0011233445555532 1235688999999988864
Q ss_pred cCCCCCc--EEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCcc
Q 012148 285 CVPGSGA--RILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (470)
Q Consensus 285 ~~~~~GG--~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~ 362 (470)
.... ++ .|++++.|.+|.|-+..... .+ .-..+..+-...++.++.+.||.+-+.-+...+.
T Consensus 498 ~~~~-~~~~~ivllTDG~~nv~~~~~~~~--------------~~-~~~~~~~~~~~~~a~~~~~~gi~~~vid~~~~~~ 561 (589)
T TIGR02031 498 ARSS-GGTPTIVLITDGRGNIPLDGDPES--------------IK-ADREQAAEEALALARKIREAGMPALVIDTAMRFV 561 (589)
T ss_pred hccc-CCceEEEEECCCCCCCCCCccccc--------------cc-ccchhHHHHHHHHHHHHHhcCCeEEEEeCCCCCc
Confidence 2222 33 69999999999875311000 00 0012233444677999999998766666655666
Q ss_pred ChhhchhhhcccCceEEEcCCCCch
Q 012148 363 GVAELKVAVEKTGGLVVLSDSFGHA 387 (470)
Q Consensus 363 ~l~~l~~l~~~TGG~v~~y~~f~~~ 387 (470)
....+..|++..||..|+.++-+.+
T Consensus 562 ~~~~~~~lA~~~~g~y~~l~~~~a~ 586 (589)
T TIGR02031 562 STGFAQKLARKMGAHYIYLPNATAA 586 (589)
T ss_pred cchHHHHHHHhcCCcEEeCCCCChh
Confidence 6667889999999999999887654
No 39
>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=97.59 E-value=0.0063 Score=54.74 Aligned_cols=154 Identities=21% Similarity=0.162 Sum_probs=98.2
Q ss_pred CEEEEEEEcccchhh--HHHHHHHHHHHhhcCCC---CceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHH
Q 012148 130 PVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPD---NSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (470)
Q Consensus 130 p~~vFvID~S~~~~~--~~~l~~~l~~~l~~lp~---~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~ 204 (470)
..++|+||+|.+... +..+++.+...+..+.. +.+||+++|++..+.+.-- .
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 357899999998732 45567777777777764 8999999999854332100 0
Q ss_pred HHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhc
Q 012148 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (470)
Q Consensus 205 ~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~ 284 (470)
.....+.+...++.+... ......++.||..|...+..
T Consensus 59 -----------------------------------~~~~~~~~~~~i~~~~~~-------~~~~~~~~~al~~~~~~~~~ 96 (177)
T smart00327 59 -----------------------------------DSRSKDALLEALASLSYK-------LGGGTNLGAALQYALENLFS 96 (177)
T ss_pred -----------------------------------ccCCHHHHHHHHHhcCCC-------CCCCchHHHHHHHHHHHhcC
Confidence 001122455666655421 12235578888888887642
Q ss_pred cCCC----CCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCC
Q 012148 285 CVPG----SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (470)
Q Consensus 285 ~~~~----~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~ 360 (470)
.... ..-.|++|+.|.++.+ +.+.+...++.+.+|.+..+.+...
T Consensus 97 ~~~~~~~~~~~~iviitDg~~~~~-------------------------------~~~~~~~~~~~~~~i~i~~i~~~~~ 145 (177)
T smart00327 97 KSAGSRRGAPKVLILITDGESNDG-------------------------------GDLLKAAKELKRSGVKVFVVGVGND 145 (177)
T ss_pred cCCCCCCCCCeEEEEEcCCCCCCC-------------------------------ccHHHHHHHHHHCCCEEEEEEccCc
Confidence 1111 1336777777765433 1335677777788888888877654
Q ss_pred ccChhhchhhhcccCceEEE
Q 012148 361 QVGVAELKVAVEKTGGLVVL 380 (470)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~~ 380 (470)
. +-..+..++..++|...+
T Consensus 146 ~-~~~~l~~~~~~~~~~~~~ 164 (177)
T smart00327 146 V-DEEELKKLASAPGGVYVF 164 (177)
T ss_pred c-CHHHHHHHhCCCcceEEe
Confidence 3 788899999999887655
No 40
>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=97.58 E-value=0.0041 Score=56.65 Aligned_cols=44 Identities=14% Similarity=0.291 Sum_probs=34.8
Q ss_pred EEEEEEcccchh--hHHHHHHHHHHHhhcCC---CCceEEEEEECCeEE
Q 012148 132 FMFVVDTCIIEE--EMSFLKSALSQAIDLLP---DNSLVGLITFGTLVQ 175 (470)
Q Consensus 132 ~vFvID~S~~~~--~~~~l~~~l~~~l~~lp---~~~~VglITfd~~V~ 175 (470)
.+|+||.|.+-. +.+.+++-++..++.++ +.+|||+|+|++..+
T Consensus 3 ivfllD~S~Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~ 51 (165)
T cd01481 3 IVFLIDGSDNVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPR 51 (165)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCee
Confidence 589999998754 45567777888777764 679999999998764
No 41
>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=97.54 E-value=0.011 Score=65.00 Aligned_cols=173 Identities=17% Similarity=0.137 Sum_probs=103.9
Q ss_pred CCCCEEEEEEEcccchh--hHHHHHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHHH
Q 012148 127 SVPPVFMFVVDTCIIEE--EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQLL 204 (470)
Q Consensus 127 ~~~p~~vFvID~S~~~~--~~~~l~~~l~~~l~~lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i~ 204 (470)
..+..++||||+|.+.. ....+++++..+|..|+++.+++||+|++.++.+.-. . . ..+
T Consensus 269 ~~p~~vvfvlD~SgSM~g~~i~~ak~al~~~l~~L~~~d~~~ii~F~~~~~~~~~~---~-~----------~~~----- 329 (596)
T TIGR03788 269 VLPRELVFVIDTSGSMAGESIEQAKSALLLALDQLRPGDRFNIIQFDSDVTLLFPV---P-V----------PAT----- 329 (596)
T ss_pred CCCceEEEEEECCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEECCcceEeccc---c-c----------cCC-----
Confidence 34567999999999864 3566889999999999999999999999987754211 0 0 000
Q ss_pred HHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhc
Q 012148 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (470)
Q Consensus 205 ~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~ 284 (470)
.+....+...++.|... ....+..||..|+.....
T Consensus 330 ------------------------------------~~~~~~a~~~i~~l~a~---------GgT~l~~aL~~a~~~~~~ 364 (596)
T TIGR03788 330 ------------------------------------AHNLARARQFVAGLQAD---------GGTEMAGALSAALRDDGP 364 (596)
T ss_pred ------------------------------------HHHHHHHHHHHhhCCCC---------CCccHHHHHHHHHHhhcc
Confidence 01112334445544321 235688888888876431
Q ss_pred cCCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccCh
Q 012148 285 CVPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGV 364 (470)
Q Consensus 285 ~~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l 364 (470)
.....-.+|++++.|..+ . + .+..+.+.. ...++.+..|.++. ..+-
T Consensus 365 ~~~~~~~~iillTDG~~~----~------------------~--------~~~~~~~~~--~~~~~ri~tvGiG~-~~n~ 411 (596)
T TIGR03788 365 ESSGALRQVVFLTDGAVG----N------------------E--------DALFQLIRT--KLGDSRLFTVGIGS-APNS 411 (596)
T ss_pred cCCCceeEEEEEeCCCCC----C------------------H--------HHHHHHHHH--hcCCceEEEEEeCC-CcCH
Confidence 111122468888888420 0 0 112222321 22356666666644 3677
Q ss_pred hhchhhhcccCceEEEcCCCCchhhHHHHHHHHh
Q 012148 365 AELKVAVEKTGGLVVLSDSFGHAVFKDSVRRVFH 398 (470)
Q Consensus 365 ~~l~~l~~~TGG~v~~y~~f~~~~~~~~l~~~l~ 398 (470)
..|..|++.+||..++..+-+ .....+.+++.
T Consensus 412 ~lL~~lA~~g~G~~~~i~~~~--~~~~~~~~~l~ 443 (596)
T TIGR03788 412 YFMRKAAQFGRGSFTFIGSTD--EVQRKMSQLFA 443 (596)
T ss_pred HHHHHHHHcCCCEEEECCCHH--HHHHHHHHHHH
Confidence 889999999999877765432 23444455553
No 42
>cd01476 VWA_integrin_invertebrates VWA_integrin (invertebrates): Integrins are a family of cell surface receptors that have diverse functions in cell-cell and cell-extracellular matrix interactions. Because of their involvement in many biologically important adhesion processes, integrins are conserved across a wide range of multicellular animals. Integrins from invertebrates have been identified from six phyla. There are no data to date to suggest any immunological functions for the invertebrate integrins. The members of this sub-group have the conserved MIDAS motif that is charateristic of this domain suggesting the involvement of the integrins in the recognition and binding of multi-ligands.
Probab=97.51 E-value=0.0052 Score=55.29 Aligned_cols=41 Identities=22% Similarity=0.332 Sum_probs=30.8
Q ss_pred EEEEEEcccchhh-HHHHHHHHHHHhhcCC---CCceEEEEEECC
Q 012148 132 FMFVVDTCIIEEE-MSFLKSALSQAIDLLP---DNSLVGLITFGT 172 (470)
Q Consensus 132 ~vFvID~S~~~~~-~~~l~~~l~~~l~~lp---~~~~VglITfd~ 172 (470)
++|++|+|.+... ....++.++..+..+. +..+||+|+|++
T Consensus 3 v~~llD~S~Sm~~~~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~~ 47 (163)
T cd01476 3 LLFVLDSSGSVRGKFEKYKKYIERIVEGLEIGPTATRVALITYSG 47 (163)
T ss_pred EEEEEeCCcchhhhHHHHHHHHHHHHHhcCCCCCCcEEEEEEEcC
Confidence 6899999987644 3345666777776664 479999999998
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=97.47 E-value=0.0024 Score=57.78 Aligned_cols=44 Identities=25% Similarity=0.346 Sum_probs=35.0
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcC---CCCceEEEEEECCeEE
Q 012148 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLL---PDNSLVGLITFGTLVQ 175 (470)
Q Consensus 132 ~vFvID~S~~~~~--~~~l~~~l~~~l~~l---p~~~~VglITfd~~V~ 175 (470)
.+|+||.|.+... ...+++.+...++.+ ++..|||+|+|++..+
T Consensus 2 ivflvD~S~sm~~~~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~ 50 (178)
T PF00092_consen 2 IVFLVDTSGSMSGDNFEKAKQFVKSIISRLSISNNGTRVGIVTFSDSAR 50 (178)
T ss_dssp EEEEEE-STTSCHHHHHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEE
T ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHHhhhccccccccceeeeecccc
Confidence 5899999998765 556788888888754 5789999999998876
No 44
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=97.38 E-value=0.015 Score=63.31 Aligned_cols=172 Identities=13% Similarity=0.085 Sum_probs=108.9
Q ss_pred CCCEEEEEEEcccchh--hHHHHHHHHHHHhhc-CCCCceEEEEEECCe-EEEEEcCCCCCCCCceeeecCCcccCHHHH
Q 012148 128 VPPVFMFVVDTCIIEE--EMSFLKSALSQAIDL-LPDNSLVGLITFGTL-VQVHELGGFGQIIPKTYVFKGSKDVSKDQL 203 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~--~~~~l~~~l~~~l~~-lp~~~~VglITfd~~-V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i 203 (470)
.+-.++||||+|.+.. .+..+|.++...|.. +.+.-+|++|+|+.. ..+ -+.
T Consensus 400 ~~~~vvfvvD~SGSM~~~rl~~aK~a~~~ll~~ay~~rD~v~lI~F~g~~a~~-~lp----------------------- 455 (584)
T PRK13406 400 SETTTIFVVDASGSAALHRLAEAKGAVELLLAEAYVRRDQVALVAFRGRGAEL-LLP----------------------- 455 (584)
T ss_pred CCccEEEEEECCCCCcHhHHHHHHHHHHHHHHhhcCCCCEEEEEEECCCceeE-EcC-----------------------
Confidence 4678999999999873 355678888887754 466779999999754 221 111
Q ss_pred HHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHh
Q 012148 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG 283 (470)
Q Consensus 204 ~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~ 283 (470)
...+...+...|+.|+. .....++.||..|..++.
T Consensus 456 ------------------------------------pT~~~~~~~~~L~~l~~---------gGgTpL~~gL~~A~~~l~ 490 (584)
T PRK13406 456 ------------------------------------PTRSLVRAKRSLAGLPG---------GGGTPLAAGLDAAAALAL 490 (584)
T ss_pred ------------------------------------CCcCHHHHHHHHhcCCC---------CCCChHHHHHHHHHHHHH
Confidence 00112234445554432 134678899999988876
Q ss_pred ccCC-CCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCcc
Q 012148 284 ACVP-GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQV 362 (470)
Q Consensus 284 ~~~~-~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~ 362 (470)
.... ..--.|++++.|-+|.|-+.-..+. .... +- ..++..+.+.||.+-++-+....
T Consensus 491 ~~~~~~~~~~iVLlTDG~~n~~~~~~~~~~----------------~~~~---~~-~~~a~~~~~~gi~~~vId~g~~~- 549 (584)
T PRK13406 491 QVRRKGMTPTVVLLTDGRANIARDGTAGRA----------------QAEE---DA-LAAARALRAAGLPALVIDTSPRP- 549 (584)
T ss_pred HhccCCCceEEEEEeCCCCCCCcccccccc----------------chhh---HH-HHHHHHHHhcCCeEEEEecCCCC-
Confidence 3221 2235788899999888753211110 0000 11 35577888888876655554333
Q ss_pred ChhhchhhhcccCceEEEcCCCCchhhH
Q 012148 363 GVAELKVAVEKTGGLVVLSDSFGHAVFK 390 (470)
Q Consensus 363 ~l~~l~~l~~~TGG~v~~y~~f~~~~~~ 390 (470)
...+..|++.+||..|..+.-+.+...
T Consensus 550 -~~~~~~LA~~~gg~y~~l~~~~a~~~~ 576 (584)
T PRK13406 550 -QPQARALAEAMGARYLPLPRADAGRLS 576 (584)
T ss_pred -cHHHHHHHHhcCCeEEECCCCCHHHHH
Confidence 345789999999999999999876543
No 45
>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=97.33 E-value=0.011 Score=65.31 Aligned_cols=161 Identities=18% Similarity=0.139 Sum_probs=101.8
Q ss_pred CCCEEEEEEEcccchh---hHHHHHHHHHHHhhc-CCCCceEEEEEECCe-EEEEEcCCCCCCCCceeeecCCcccCHHH
Q 012148 128 VPPVFMFVVDTCIIEE---EMSFLKSALSQAIDL-LPDNSLVGLITFGTL-VQVHELGGFGQIIPKTYVFKGSKDVSKDQ 202 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~---~~~~l~~~l~~~l~~-lp~~~~VglITfd~~-V~~y~l~~~~~~~~~~~v~~g~~~~t~~~ 202 (470)
....++|+||+|.+.. .+..++.++...+.. .....+||+|+|+.. ..+. +.
T Consensus 464 ~~~~vv~vvD~SgSM~~~~rl~~ak~a~~~ll~~a~~~~D~v~lI~F~g~~a~~~-~p---------------------- 520 (633)
T TIGR02442 464 AGNLVIFVVDASGSMAARGRMAAAKGAVLSLLRDAYQKRDKVALITFRGEEAEVL-LP---------------------- 520 (633)
T ss_pred CCceEEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCceEE-cC----------------------
Confidence 3568899999999874 345567777666643 456789999999743 2111 00
Q ss_pred HHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHH
Q 012148 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (470)
Q Consensus 203 i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll 282 (470)
.......+...|+.++. .....++.||..|..++
T Consensus 521 -------------------------------------~t~~~~~~~~~L~~l~~---------gG~Tpl~~aL~~A~~~l 554 (633)
T TIGR02442 521 -------------------------------------PTSSVELAARRLEELPT---------GGRTPLAAGLLKAAEVL 554 (633)
T ss_pred -------------------------------------CCCCHHHHHHHHHhCCC---------CCCCCHHHHHHHHHHHH
Confidence 01112234455555542 12356789999998887
Q ss_pred hcc---CCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccC
Q 012148 283 GAC---VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACAL 359 (470)
Q Consensus 283 ~~~---~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~ 359 (470)
... ....-+.|++++.|.+|.|.+. .. +..+ -..++.++.+.||-+.++-...
T Consensus 555 ~~~~~~~~~~~~~vvliTDG~~n~~~~~---~~--------------------~~~~-~~~~a~~l~~~~i~~~vIdt~~ 610 (633)
T TIGR02442 555 SNELLRDDDGRPLLVVITDGRANVADGG---EP--------------------PTDD-ARTIAAKLAARGILFVVIDTES 610 (633)
T ss_pred HHhhccCCCCceEEEEECCCCCCCCCCC---CC--------------------hHHH-HHHHHHHHHhcCCeEEEEeCCC
Confidence 721 1224467999999998876210 00 0011 1456777777787666555545
Q ss_pred CccChhhchhhhcccCceEEEc
Q 012148 360 DQVGVAELKVAVEKTGGLVVLS 381 (470)
Q Consensus 360 ~~~~l~~l~~l~~~TGG~v~~y 381 (470)
..++...+..|++.+||..|..
T Consensus 611 ~~~~~~~~~~lA~~~gg~y~~l 632 (633)
T TIGR02442 611 GFVRLGLAEDLARALGGEYVRL 632 (633)
T ss_pred CCcchhHHHHHHHhhCCeEEec
Confidence 6677788999999999998864
No 46
>cd00198 vWFA Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.
Probab=97.33 E-value=0.016 Score=50.60 Aligned_cols=147 Identities=24% Similarity=0.321 Sum_probs=92.5
Q ss_pred EEEEEEEcccch--hhHHHHHHHHHHHhhcCCC---CceEEEEEECCeEEEEE-cCCCCCCCCceeeecCCcccCHHHHH
Q 012148 131 VFMFVVDTCIIE--EEMSFLKSALSQAIDLLPD---NSLVGLITFGTLVQVHE-LGGFGQIIPKTYVFKGSKDVSKDQLL 204 (470)
Q Consensus 131 ~~vFvID~S~~~--~~~~~l~~~l~~~l~~lp~---~~~VglITfd~~V~~y~-l~~~~~~~~~~~v~~g~~~~t~~~i~ 204 (470)
.++|+||+|.+. .....+++.+...+..++. ..+++++.|+...+.+- +. .
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 3456678888888888875 78999999997433221 10 0
Q ss_pred HHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhc
Q 012148 205 EQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGA 284 (470)
Q Consensus 205 ~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~ 284 (470)
. ...+.+...++.+.. .......+..|+..|...+..
T Consensus 59 -------------------------------~-----~~~~~~~~~~~~~~~-------~~~~~t~~~~al~~~~~~~~~ 95 (161)
T cd00198 59 -------------------------------D-----TDKADLLEAIDALKK-------GLGGGTNIGAALRLALELLKS 95 (161)
T ss_pred -------------------------------c-----CCHHHHHHHHHhccc-------CCCCCccHHHHHHHHHHHhcc
Confidence 0 012244555555432 112335577889888888763
Q ss_pred c-CCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccC
Q 012148 285 C-VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVG 363 (470)
Q Consensus 285 ~-~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~ 363 (470)
. .......|++|+.|.++.++ .-..+..+++.+.++.+.++.++. ..+
T Consensus 96 ~~~~~~~~~lvvitDg~~~~~~------------------------------~~~~~~~~~~~~~~v~v~~v~~g~-~~~ 144 (161)
T cd00198 96 AKRPNARRVIILLTDGEPNDGP------------------------------ELLAEAARELRKLGITVYTIGIGD-DAN 144 (161)
T ss_pred cCCCCCceEEEEEeCCCCCCCc------------------------------chhHHHHHHHHHcCCEEEEEEcCC-CCC
Confidence 2 12346678888887654432 001235556666799998887765 345
Q ss_pred hhhchhhhccc
Q 012148 364 VAELKVAVEKT 374 (470)
Q Consensus 364 l~~l~~l~~~T 374 (470)
-..+..++..|
T Consensus 145 ~~~l~~l~~~~ 155 (161)
T cd00198 145 EDELKEIADKT 155 (161)
T ss_pred HHHHHHHhccc
Confidence 66777788777
No 47
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=97.17 E-value=0.021 Score=53.35 Aligned_cols=45 Identities=16% Similarity=0.155 Sum_probs=34.0
Q ss_pred EEEEEEcccchhhH--H-HHHHHHHHHhhcC---CCCceEEEEEECCeEEE
Q 012148 132 FMFVVDTCIIEEEM--S-FLKSALSQAIDLL---PDNSLVGLITFGTLVQV 176 (470)
Q Consensus 132 ~vFvID~S~~~~~~--~-~l~~~l~~~l~~l---p~~~~VglITfd~~V~~ 176 (470)
++|+||.|.+..+. . .+++.++..++.+ ++++|||+|+|++..++
T Consensus 3 i~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~~ 53 (192)
T cd01473 3 LTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNRD 53 (192)
T ss_pred EEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCcee
Confidence 58999999987553 2 3566777777665 46799999999987654
No 48
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=97.16 E-value=0.016 Score=62.09 Aligned_cols=165 Identities=12% Similarity=0.040 Sum_probs=94.9
Q ss_pred CCCEEEEEEEcccchhhH---HHHHHHHHHHhhcC---CCCceEEEEEECCeEE-EEEcCCCCCCCCceeeecCCcccCH
Q 012148 128 VPPVFMFVVDTCIIEEEM---SFLKSALSQAIDLL---PDNSLVGLITFGTLVQ-VHELGGFGQIIPKTYVFKGSKDVSK 200 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~~~---~~l~~~l~~~l~~l---p~~~~VglITfd~~V~-~y~l~~~~~~~~~~~v~~g~~~~t~ 200 (470)
...-++|+||+|.+...- ..++..++.++..+ ++.++||+++|++..+ ++.+. ... ..
T Consensus 41 ~~lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~r~vfpL~-s~~------------s~-- 105 (576)
T PTZ00441 41 EEVDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNTTELIRLG-SGA------------SK-- 105 (576)
T ss_pred CCceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCceEEEecC-CCc------------cc--
Confidence 356789999999987542 44566677766666 3568999999998754 33333 110 00
Q ss_pred HHHHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHH
Q 012148 201 DQLLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAAS 280 (470)
Q Consensus 201 ~~i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ 280 (470)
.+..+...|.+|.... .. .....+|.||..|..
T Consensus 106 ------------------------------------------Dk~~aL~~I~sL~~~~--~p---gGgTnig~AL~~Aae 138 (576)
T PTZ00441 106 ------------------------------------------DKEQALIIVKSLRKTY--LP---YGKTNMTDALLEVRK 138 (576)
T ss_pred ------------------------------------------cHHHHHHHHHHHHhhc--cC---CCCccHHHHHHHHHH
Confidence 0112233333332210 01 123568899988877
Q ss_pred HHhcc--CCCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeecc
Q 012148 281 LLGAC--VPGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACA 358 (470)
Q Consensus 281 ll~~~--~~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s 358 (470)
.+... ....-+.||+|+.|.++.+ + +. .+.++++.+.||-|-++..+
T Consensus 139 ~L~sr~~R~nvpKVVILLTDG~sns~---------------------~---------dv-leaAq~LR~~GVeI~vIGVG 187 (576)
T PTZ00441 139 HLNDRVNRENAIQLVILMTDGIPNSK---------------------Y---------RA-LEESRKLKDRNVKLAVIGIG 187 (576)
T ss_pred HHhhcccccCCceEEEEEecCCCCCc---------------------c---------cH-HHHHHHHHHCCCEEEEEEeC
Confidence 76521 1122367888888764211 0 00 13456777788866666553
Q ss_pred CCccChhhchhhh----cccCceEEEcCCCCc
Q 012148 359 LDQVGVAELKVAV----EKTGGLVVLSDSFGH 386 (470)
Q Consensus 359 ~~~~~l~~l~~l~----~~TGG~v~~y~~f~~ 386 (470)
. ..+...+..++ ..++|.+|...+|+.
T Consensus 188 ~-g~n~e~LrlIAgC~p~~g~c~~Y~vadf~e 218 (576)
T PTZ00441 188 Q-GINHQFNRLLAGCRPREGKCKFYSDADWEE 218 (576)
T ss_pred C-CcCHHHHHHHhccCCCCCCCceEEeCCHHH
Confidence 3 45665565566 335568888888864
No 49
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=97.16 E-value=0.021 Score=55.00 Aligned_cols=170 Identities=16% Similarity=0.103 Sum_probs=108.4
Q ss_pred CCCEEEEEEEcccchhh---HHHHHHHHHHHhhc-CCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHH
Q 012148 128 VPPVFMFVVDTCIIEEE---MSFLKSALSQAIDL-LPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQL 203 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~~---~~~l~~~l~~~l~~-lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i 203 (470)
...-+|||||.|.+... ...++-++.+.|.. -...-+|++|+|... .
T Consensus 77 ~g~lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~dAYq~RdkvavI~F~G~--------~--------------------- 127 (261)
T COG1240 77 AGNLIVFVVDASGSMAARRRMAAAKGAALSLLRDAYQRRDKVAVIAFRGE--------K--------------------- 127 (261)
T ss_pred cCCcEEEEEeCcccchhHHHHHHHHHHHHHHHHHHHHccceEEEEEecCC--------c---------------------
Confidence 35679999999998654 34455555555543 334579999998622 0
Q ss_pred HHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHh
Q 012148 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG 283 (470)
Q Consensus 204 ~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~ 283 (470)
..+++|...+-+.+.+.|+.|+.- + ..=+..||..|..++.
T Consensus 128 ------------------------------A~lll~pT~sv~~~~~~L~~l~~G------G---~TPL~~aL~~a~ev~~ 168 (261)
T COG1240 128 ------------------------------AELLLPPTSSVELAERALERLPTG------G---KTPLADALRQAYEVLA 168 (261)
T ss_pred ------------------------------ceEEeCCcccHHHHHHHHHhCCCC------C---CCchHHHHHHHHHHHH
Confidence 012223333344667777777531 1 2347899999999988
Q ss_pred ccCC---CCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCC
Q 012148 284 ACVP---GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALD 360 (470)
Q Consensus 284 ~~~~---~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~ 360 (470)
.+.. ..--.+++.+.|.||.+.+.= .... -...+.++...|+-+=+.=+-..
T Consensus 169 r~~r~~p~~~~~~vviTDGr~n~~~~~~---------------------~~~e----~~~~a~~~~~~g~~~lvid~e~~ 223 (261)
T COG1240 169 REKRRGPDRRPVMVVITDGRANVPIPLG---------------------PKAE----TLEAASKLRLRGIQLLVIDTEGS 223 (261)
T ss_pred HhhccCCCcceEEEEEeCCccCCCCCCc---------------------hHHH----HHHHHHHHhhcCCcEEEEecCCc
Confidence 4331 234578889999988775221 0001 12345556666664444444455
Q ss_pred ccChhhchhhhcccCceEEEcCCCCchhhH
Q 012148 361 QVGVAELKVAVEKTGGLVVLSDSFGHAVFK 390 (470)
Q Consensus 361 ~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~ 390 (470)
++.+.-...||...||..++.++.+.....
T Consensus 224 ~~~~g~~~~iA~~~Gg~~~~L~~l~~~~i~ 253 (261)
T COG1240 224 EVRLGLAEEIARASGGEYYHLDDLSDDSIV 253 (261)
T ss_pred cccccHHHHHHHHhCCeEEecccccchHHH
Confidence 677888889999999999999999987543
No 50
>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=96.89 E-value=0.027 Score=52.48 Aligned_cols=90 Identities=22% Similarity=0.279 Sum_probs=60.2
Q ss_pred ccchhHHHHHHHHHHhccCCCCCc-EEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHH
Q 012148 268 TRCTGTALSIAASLLGACVPGSGA-RILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLV 346 (470)
Q Consensus 268 ~~~~G~AL~~A~~ll~~~~~~~GG-~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~ 346 (470)
.-++-.||+.|...|+.. +..|. .|+++.++.-|.-||. . .+..+.+.
T Consensus 79 ~~SLqN~Le~A~~~L~~~-p~~~srEIlvi~gSl~t~Dp~d-----------------------------i-~~ti~~l~ 127 (193)
T PF04056_consen 79 EPSLQNGLEMARSSLKHM-PSHGSREILVIFGSLTTCDPGD-----------------------------I-HETIESLK 127 (193)
T ss_pred ChhHHHHHHHHHHHHhhC-ccccceEEEEEEeecccCCchh-----------------------------H-HHHHHHHH
Confidence 356788999999998742 23444 4555555554444432 2 26788899
Q ss_pred hcCeEEEEeeccCCccChhhchhhhcccCceEEEcCCCCchhhHHHH
Q 012148 347 HQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVFKDSV 393 (470)
Q Consensus 347 ~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~~~~~~l 393 (470)
+.+|-|++..++. ++.....+|+.|||.... -.++..|++.+
T Consensus 128 ~~~IrvsvI~laa---Ev~I~k~i~~~T~G~y~V--~lde~H~~~lL 169 (193)
T PF04056_consen 128 KENIRVSVISLAA---EVYICKKICKETGGTYGV--ILDEDHFKELL 169 (193)
T ss_pred HcCCEEEEEEEhH---HHHHHHHHHHhhCCEEEE--ecCHHHHHHHH
Confidence 9999999998865 677899999999994332 33334444433
No 51
>cd01458 vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.
Probab=96.71 E-value=0.072 Score=50.63 Aligned_cols=69 Identities=20% Similarity=0.214 Sum_probs=46.0
Q ss_pred CccchhHHHHHHHHHHhccCC-CCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHH
Q 012148 267 STRCTGTALSIAASLLGACVP-GSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQL 345 (470)
Q Consensus 267 ~~~~~G~AL~~A~~ll~~~~~-~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~ 345 (470)
....++.||.+|..++..+.+ ...-+|++|+.|--..|. + .....-+.+++.++
T Consensus 104 ~~~~l~~aL~~a~~~~~~~~~~~~~k~IvL~TDg~~p~~~--------------------~-----~~~~~~~~~~a~~l 158 (218)
T cd01458 104 GQVSLSDALWVCLDLFSKGKKKKSHKRIFLFTNNDDPHGG--------------------D-----SIKDSQAAVKAEDL 158 (218)
T ss_pred CCccHHHHHHHHHHHHHhccccccccEEEEECCCCCCCCC--------------------C-----HHHHHHHHHHHHHH
Confidence 457799999999999985222 234579999987432221 0 01123356788999
Q ss_pred HhcCeEEEEeeccCC
Q 012148 346 VHQGHVLDLFACALD 360 (470)
Q Consensus 346 ~~~gisvdlF~~s~~ 360 (470)
.+.||.+.+|....+
T Consensus 159 ~~~gI~i~~i~i~~~ 173 (218)
T cd01458 159 KDKGIELELFPLSSP 173 (218)
T ss_pred HhCCcEEEEEecCCC
Confidence 999999999876443
No 52
>cd01454 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial denitrification has been established as NO3- ------ NO2- ------ NO ------- N2O --------- N2. This reaction generally occurs under oxygen limiting conditions. Genetic and biochemical studies have shown that the first srep of the biochemical pathway is catalyzed by periplasmic nitrate reductases. This family is widely present in proteobacteria and firmicutes. This version of the domain is also present in some archaeal members. The function of the vWA domain in this sub-group is not known. Members of this subgroup have a conserved MIDAS motif.
Probab=96.50 E-value=0.15 Score=46.48 Aligned_cols=43 Identities=14% Similarity=0.095 Sum_probs=33.8
Q ss_pred EEEEEEEcccchhh---HHHHHHHHHHHhhcCCC-CceEEEEEECCe
Q 012148 131 VFMFVVDTCIIEEE---MSFLKSALSQAIDLLPD-NSLVGLITFGTL 173 (470)
Q Consensus 131 ~~vFvID~S~~~~~---~~~l~~~l~~~l~~lp~-~~~VglITfd~~ 173 (470)
+++|+||+|.+... +..+++++...++.+.+ +.++|+++|++.
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 57899999998643 56677777777776764 789999999876
No 53
>cd01462 VWA_YIEM_type VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=96.28 E-value=0.18 Score=44.60 Aligned_cols=43 Identities=16% Similarity=0.098 Sum_probs=31.0
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcCC-CCceEEEEEECCeE
Q 012148 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP-DNSLVGLITFGTLV 174 (470)
Q Consensus 132 ~vFvID~S~~~~~--~~~l~~~l~~~l~~lp-~~~~VglITfd~~V 174 (470)
++|+||+|.+... ....+..+...+..+. ++.+|++|+|++..
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 3344555555555554 47799999999883
No 54
>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=95.24 E-value=0.41 Score=52.48 Aligned_cols=73 Identities=18% Similarity=0.197 Sum_probs=44.7
Q ss_pred cchhHHHHHHHHHHhccCCCCCc-EEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHh
Q 012148 269 RCTGTALSIAASLLGACVPGSGA-RILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVH 347 (470)
Q Consensus 269 ~~~G~AL~~A~~ll~~~~~~~GG-~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~ 347 (470)
..+..||.+|..++..+..+.+. ||++||+----.+. ++ .. .+-=...|..+..
T Consensus 117 ~~l~daL~~~~~~f~~~~~k~~~kRI~lfTd~D~P~~~------------------~~---~~----~~~a~~~a~dl~~ 171 (584)
T TIGR00578 117 YSLSEVLWVCANLFSDVQFRMSHKRIMLFTNEDNPHGN------------------DS---AK----ASRARTKAGDLRD 171 (584)
T ss_pred CcHHHHHHHHHHHHHhcchhhcCcEEEEECCCCCCCCC------------------ch---hH----HHHHHHHHHHHHh
Confidence 47899999999999854445554 59999974211110 00 00 0011235788889
Q ss_pred cCeEEEEeecc-CCccChhh
Q 012148 348 QGHVLDLFACA-LDQVGVAE 366 (470)
Q Consensus 348 ~gisvdlF~~s-~~~~~l~~ 366 (470)
.||.+++|..+ .+.+|...
T Consensus 172 ~gi~ielf~l~~~~~Fd~s~ 191 (584)
T TIGR00578 172 TGIFLDLMHLKKPGGFDISL 191 (584)
T ss_pred cCeEEEEEecCCCCCCChhh
Confidence 99999999654 23355553
No 55
>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=93.71 E-value=0.12 Score=47.30 Aligned_cols=45 Identities=20% Similarity=0.264 Sum_probs=34.8
Q ss_pred EEEEEEcccchhh--HHHHHHHHHHHhhcCC------CCceEEEEEECCeEEE
Q 012148 132 FMFVVDTCIIEEE--MSFLKSALSQAIDLLP------DNSLVGLITFGTLVQV 176 (470)
Q Consensus 132 ~vFvID~S~~~~~--~~~l~~~l~~~l~~lp------~~~~VglITfd~~V~~ 176 (470)
++|+||+|.+... ...++++++..++.+. ++.+||+|+|++..+.
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 5899999998643 4567888888887774 3579999999987553
No 56
>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=93.15 E-value=8.4 Score=37.91 Aligned_cols=46 Identities=22% Similarity=0.236 Sum_probs=34.0
Q ss_pred CCCEEEEEEEcccchhhHHH------HHHHHHHHhhcCCCCceEEEEEECCeE
Q 012148 128 VPPVFMFVVDTCIIEEEMSF------LKSALSQAIDLLPDNSLVGLITFGTLV 174 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~~~~~------l~~~l~~~l~~lp~~~~VglITfd~~V 174 (470)
...-++++||.|.+..+... .+..|..+++.++ .-+||++.|+..+
T Consensus 59 r~~qIvlaID~S~SM~~~~~~~~aleak~lIs~al~~Le-~g~vgVv~Fg~~~ 110 (266)
T cd01460 59 RDYQILIAIDDSKSMSENNSKKLALESLCLVSKALTLLE-VGQLGVCSFGEDV 110 (266)
T ss_pred cCceEEEEEecchhcccccccccHHHHHHHHHHHHHhCc-CCcEEEEEeCCCc
Confidence 57889999999998755221 3445666666666 4699999999875
No 57
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=91.08 E-value=0.42 Score=43.94 Aligned_cols=47 Identities=23% Similarity=0.321 Sum_probs=36.3
Q ss_pred EEEEEEcccchh--hHHHHHHHHHHHhhcCC------CCceEEEEEECCeEEEEE
Q 012148 132 FMFVVDTCIIEE--EMSFLKSALSQAIDLLP------DNSLVGLITFGTLVQVHE 178 (470)
Q Consensus 132 ~vFvID~S~~~~--~~~~l~~~l~~~l~~lp------~~~~VglITfd~~V~~y~ 178 (470)
.+|++|+|.+.. ..+.+..+|+.+++.|. +.+.++|||||..++.|.
T Consensus 6 ~~lllDtSgSM~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~~a~~~~ 60 (207)
T COG4245 6 CYLLLDTSGSMIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGPARVIQ 60 (207)
T ss_pred EEEEEecCcccccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecCcceEEe
Confidence 458899998754 46778888888887774 357999999998777663
No 58
>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=84.80 E-value=0.59 Score=34.24 Aligned_cols=33 Identities=27% Similarity=0.507 Sum_probs=24.4
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
++-|++|++----+-+-+...-+|+|+.|++.|
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 456999998644443555555699999999876
No 59
>KOG2884 consensus 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=83.58 E-value=12 Score=35.30 Aligned_cols=85 Identities=21% Similarity=0.210 Sum_probs=56.5
Q ss_pred cchhHHHHHHHHHHhccCCCCC--cEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHH
Q 012148 269 RCTGTALSIAASLLGACVPGSG--ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLV 346 (470)
Q Consensus 269 ~~~G~AL~~A~~ll~~~~~~~G--G~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~ 346 (470)
--++.+|++|.-.|+. ..+.+ -||++|.++|-. +. .+-.-++|+++.
T Consensus 85 ~~~~~~i~iA~lalkh-Rqnk~~~~riVvFvGSpi~---------------------e~---------ekeLv~~akrlk 133 (259)
T KOG2884|consen 85 ANFMTGIQIAQLALKH-RQNKNQKQRIVVFVGSPIE---------------------ES---------EKELVKLAKRLK 133 (259)
T ss_pred ccHHHHHHHHHHHHHh-hcCCCcceEEEEEecCcch---------------------hh---------HHHHHHHHHHHH
Confidence 4488999999988882 33444 799999998721 01 123458999999
Q ss_pred hcCeEEEEeeccCCccChhhchhhhcccCce-----EEEcCCC
Q 012148 347 HQGHVLDLFACALDQVGVAELKVAVEKTGGL-----VVLSDSF 384 (470)
Q Consensus 347 ~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~-----v~~y~~f 384 (470)
+++|+||+..+.-..-+-.-+......++|. +...+.-
T Consensus 134 k~~Vaidii~FGE~~~~~e~l~~fida~N~~~~gshlv~Vppg 176 (259)
T KOG2884|consen 134 KNKVAIDIINFGEAENNTEKLFEFIDALNGKGDGSHLVSVPPG 176 (259)
T ss_pred hcCeeEEEEEeccccccHHHHHHHHHHhcCCCCCceEEEeCCC
Confidence 9999999999876555533344444444443 5555543
No 60
>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=83.41 E-value=1.1 Score=28.81 Aligned_cols=30 Identities=27% Similarity=0.483 Sum_probs=23.0
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~v 92 (470)
++|..|+.-+.- -.+..+++|..|...|.+
T Consensus 2 ~~C~~C~t~L~y----P~gA~~vrCs~C~~vt~v 31 (31)
T TIGR01053 2 VVCGGCRTLLMY----PRGASSVRCALCQTVNLV 31 (31)
T ss_pred cCcCCCCcEeec----CCCCCeEECCCCCeEecC
Confidence 579999987642 255689999999988753
No 61
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.87 E-value=0.83 Score=32.12 Aligned_cols=29 Identities=24% Similarity=0.506 Sum_probs=20.5
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
.+|.+|++-+. +++....++|+.||....
T Consensus 4 y~C~~CG~~~~----~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVE----LDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEE----ECCCCCceECCCCCCeEE
Confidence 68999999543 233333799999997654
No 62
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=80.39 E-value=53 Score=32.97 Aligned_cols=74 Identities=24% Similarity=0.260 Sum_probs=49.3
Q ss_pred cchhHHHHHHHHHHhccCCCCC-cEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHHHh
Q 012148 269 RCTGTALSIAASLLGACVPGSG-ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQLVH 347 (470)
Q Consensus 269 ~~~G~AL~~A~~ll~~~~~~~G-G~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~ 347 (470)
-++-.||+.|...|+.. +..+ =.|++..++..|.-||.+ | +.-+.+.+
T Consensus 143 fSLqNaLe~a~~~Lk~~-p~H~sREVLii~sslsT~DPgdi-----------------------------~-~tI~~lk~ 191 (378)
T KOG2807|consen 143 FSLQNALELAREVLKHM-PGHVSREVLIIFSSLSTCDPGDI-----------------------------Y-ETIDKLKA 191 (378)
T ss_pred hHHHHHHHHHHHHhcCC-CcccceEEEEEEeeecccCcccH-----------------------------H-HHHHHHHh
Confidence 34567888888888721 1222 345666666666666544 3 34456677
Q ss_pred cCeEEEEeeccCCccChhhchhhhcccCc
Q 012148 348 QGHVLDLFACALDQVGVAELKVAVEKTGG 376 (470)
Q Consensus 348 ~gisvdlF~~s~~~~~l~~l~~l~~~TGG 376 (470)
..|-|.+.-.+. ++..-..||+.|||
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 888899887755 56677889999999
No 63
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.62 E-value=31 Score=34.24 Aligned_cols=86 Identities=19% Similarity=0.088 Sum_probs=57.4
Q ss_pred ccchhHHHHHHHHHHhccC------CCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHH
Q 012148 268 TRCTGTALSIAASLLGACV------PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDAL 341 (470)
Q Consensus 268 ~~~~G~AL~~A~~ll~~~~------~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~l 341 (470)
...+..||..|+..+.... ...-+||+++..++ +. ..+..=+.+.
T Consensus 118 ~s~lagals~ALcyinr~~~~~~~~~~~~~RIlii~~s~-----------~~------------------~~qYi~~mn~ 168 (279)
T TIGR00627 118 RTVLAGALSDALGYINRSEQSETASEKLKSRILVISITP-----------DM------------------ALQYIPLMNC 168 (279)
T ss_pred cccchhHHHhhhhhhcccccccccCcCCcceEEEEECCC-----------Cc------------------hHHHHHHHHH
Confidence 3456778888887765321 13358899987752 00 0111223488
Q ss_pred HHHHHhcCeEEEEeeccCCccChhhchhhhcccCceEEEcCC
Q 012148 342 SKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDS 383 (470)
Q Consensus 342 a~~~~~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~v~~y~~ 383 (470)
...+.+.+|.||++..+.+ -+..-+..++..|||.-....+
T Consensus 169 Ifaaqk~~I~Idv~~L~~e-~~~~~lqQa~~~TgG~Y~~~~~ 209 (279)
T TIGR00627 169 IFSAQKQNIPIDVVSIGGD-FTSGFLQQAADITGGSYLHVKK 209 (279)
T ss_pred HHHHHHcCceEEEEEeCCc-cccHHHHHHHHHhCCEEeccCC
Confidence 8899999999999988543 4577899999999995444443
No 64
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=75.56 E-value=7.9 Score=33.47 Aligned_cols=41 Identities=22% Similarity=0.230 Sum_probs=30.4
Q ss_pred EEEEEcccchh--hHHHHHHHHHHHhhcCCCCceEEEEEECCeEE
Q 012148 133 MFVVDTCIIEE--EMSFLKSALSQAIDLLPDNSLVGLITFGTLVQ 175 (470)
Q Consensus 133 vFvID~S~~~~--~~~~l~~~l~~~l~~lp~~~~VglITfd~~V~ 175 (470)
+++||+|.+.. ++..+...+...++.. +.+|-+|.||..|+
T Consensus 2 ~vaiDtSGSis~~~l~~fl~ev~~i~~~~--~~~v~vi~~D~~v~ 44 (126)
T PF09967_consen 2 VVAIDTSGSISDEELRRFLSEVAGILRRF--PAEVHVIQFDAEVQ 44 (126)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHHhC--CCCEEEEEECCEee
Confidence 68999999753 4555566666666666 45699999998876
No 65
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=75.44 E-value=1.9 Score=30.82 Aligned_cols=33 Identities=18% Similarity=0.413 Sum_probs=22.4
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCCCCCCCc
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp~ 94 (470)
.|..|+..+-+- -..+++.|.|+-||..-.+.+
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCCeEECCC
Confidence 489999966332 122235899999998766543
No 66
>PF03850 Tfb4: Transcription factor Tfb4; InterPro: IPR004600 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p34 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0000439 core TFIIH complex
Probab=70.66 E-value=35 Score=33.77 Aligned_cols=88 Identities=18% Similarity=0.097 Sum_probs=59.9
Q ss_pred cchhHHHHHHHHHHhccC-------CCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHH
Q 012148 269 RCTGTALSIAASLLGACV-------PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDAL 341 (470)
Q Consensus 269 ~~~G~AL~~A~~ll~~~~-------~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~l 341 (470)
..+..||..|+--+.... ....+||+++.++-+. . ..+.-=+.+.
T Consensus 116 s~LagALS~ALCyINR~~~~~~~~~~~~~~RILv~~s~s~d-----------------------~-----~~QYi~~MN~ 167 (276)
T PF03850_consen 116 SLLAGALSMALCYINRISRESPSGGTSLKSRILVIVSGSPD-----------------------S-----SSQYIPLMNC 167 (276)
T ss_pred hhhHHHHHHHHHHHhhhhhcccCCCCCcCccEEEEEecCCC-----------------------c-----cHHHHHHHHH
Confidence 567788888877766431 1345799996332110 0 1112234567
Q ss_pred HHHHHhcCeEEEEeeccCCccChhhchhhhcccCceEEEcCCCCc
Q 012148 342 SKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSFGH 386 (470)
Q Consensus 342 a~~~~~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~ 386 (470)
...+.+.+|.+|++.... -+-.-|.+.+..|||.-+..+....
T Consensus 168 iFaAqk~~v~IDv~~L~~--~~s~fLqQa~d~T~G~y~~~~~~~~ 210 (276)
T PF03850_consen 168 IFAAQKQKVPIDVCKLGG--KDSTFLQQASDITGGIYLKVSKPEG 210 (276)
T ss_pred HHHHhcCCceeEEEEecC--CchHHHHHHHHHhCceeeccCcccc
Confidence 888889999999999866 4666789999999998888777543
No 67
>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=70.55 E-value=1.5e+02 Score=31.27 Aligned_cols=197 Identities=13% Similarity=0.091 Sum_probs=104.3
Q ss_pred CCCEEEEEEEcccchhh----HHHHHHHHHHHhhcCCCCceEEEEEEC-CeEEEEEcCCCCCCCCceeeecCCcccCHHH
Q 012148 128 VPPVFMFVVDTCIIEEE----MSFLKSALSQAIDLLPDNSLVGLITFG-TLVQVHELGGFGQIIPKTYVFKGSKDVSKDQ 202 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~~----~~~l~~~l~~~l~~lp~~~~VglITfd-~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~ 202 (470)
.|-=..|+.|+|.+..+ +..+...|...|..+..+.|+||=+|= +.|.=|-.. . .++
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 34557899999998765 334566777778888899999998874 333322111 0 111
Q ss_pred HHHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHH
Q 012148 203 LLEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLL 282 (470)
Q Consensus 203 i~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll 282 (470)
+..-.. . ..+.+. |+-. =+-.+++.+......+.+....-. .+...|...+-+-+++|+--=
T Consensus 160 l~~PC~--~--------~~~~c~---p~f~-f~~~L~LT~~~~~F~~~V~~~~iS----gN~D~PEgG~DAimQaaVC~~ 221 (423)
T smart00187 160 LENPCP--N--------YNLTCE---PPYG-FKHVLSLTDDTDEFNEEVKKQRIS----GNLDAPEGGFDAIMQAAVCTE 221 (423)
T ss_pred hcCCCc--C--------CCCCcC---CCcc-eeeeccCCCCHHHHHHHHhhceee----cCCcCCcccHHHHHHHHhhcc
Confidence 111000 0 000010 0001 123466676666666666654321 233345555667777774210
Q ss_pred hccCCCCCcEEEEEecCCCC--CCCceeecCCCCCcccCCCCCC---CCCCCccchhHHHHHHHHHHHHhcCeEEEEeec
Q 012148 283 GACVPGSGARILAFVGGPST--EGPAAIVSKNLSEPIRSHKDLD---KDSAPHYHKAVKFYDALSKQLVHQGHVLDLFAC 357 (470)
Q Consensus 283 ~~~~~~~GG~Ii~F~~g~pt--~GpG~l~~~~~~~~~r~~~~~~---~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~ 357 (470)
+-.-+...-|+++|.+-.+. -|-|+|..--..+..+-|-+-+ .....+--| --.+|++++.+++|- =+|+.
T Consensus 222 ~IGWR~~a~rllv~~TDa~fH~AGDGkLaGIv~PNDg~CHL~~~g~Yt~s~~~DYP---Si~ql~~kL~e~nI~-~IFAV 297 (423)
T smart00187 222 QIGWREDARRLLVFSTDAGFHFAGDGKLAGIVQPNDGQCHLDNNGEYTMSTTQDYP---SIGQLNQKLAENNIN-PIFAV 297 (423)
T ss_pred ccccCCCceEEEEEEcCCCccccCCcceeeEecCCCCcceeCCCCCcCccCcCCCC---CHHHHHHHHHhcCce-EEEEE
Confidence 10012334589999886554 6888876644333333332211 000001111 245788999999985 47877
Q ss_pred cCCccCh
Q 012148 358 ALDQVGV 364 (470)
Q Consensus 358 s~~~~~l 364 (470)
...+.++
T Consensus 298 T~~~~~~ 304 (423)
T smart00187 298 TKKQVSL 304 (423)
T ss_pred cccchhH
Confidence 7776555
No 68
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=69.06 E-value=5.7 Score=27.36 Aligned_cols=27 Identities=26% Similarity=0.502 Sum_probs=20.5
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
+|..|++-- ..+|.....++|.-||..
T Consensus 2 ~Cp~Cg~~~---~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE---IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE---EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc---eEEcCCCCeEECCCCCCE
Confidence 699999933 567777778999999964
No 69
>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=66.67 E-value=3.8 Score=26.63 Aligned_cols=23 Identities=30% Similarity=0.836 Sum_probs=14.8
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
+|..|+=...+-. .-|+|+.||.
T Consensus 3 ~C~~CGy~y~~~~------~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGEE------APWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCCc------CCCcCcCCCC
Confidence 5777774434322 4688888886
No 70
>PRK03954 ribonuclease P protein component 4; Validated
Probab=66.45 E-value=3.5 Score=35.45 Aligned_cols=35 Identities=23% Similarity=0.425 Sum_probs=24.9
Q ss_pred ccccCCCeeeCCC----ceEEcCC---ceEEeCCCCCCCCCC
Q 012148 59 LRCRTCRSILNPF----SIVDFAA---KIWICPFCFQRNHFP 93 (470)
Q Consensus 59 ~RC~~C~aYiNp~----~~~~~~g---~~w~C~~C~~~N~vp 93 (470)
.-|++|.+|+=|- +++..++ -.++|..||+....|
T Consensus 65 ~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~P 106 (121)
T PRK03954 65 RYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRYP 106 (121)
T ss_pred HHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEeec
Confidence 4599999998663 3444332 245999999988876
No 71
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=66.41 E-value=3.8 Score=27.42 Aligned_cols=33 Identities=15% Similarity=0.324 Sum_probs=24.0
Q ss_pred CccccCCCeeeCCC-ceEEcCCceEEeCCCCCCC
Q 012148 58 PLRCRTCRSILNPF-SIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 58 ~~RC~~C~aYiNp~-~~~~~~g~~w~C~~C~~~N 90 (470)
.++|.+|++-.+-= .++...|++.+|+-|++.-
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 36899998876544 3455667889999998754
No 72
>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=65.26 E-value=2.6 Score=29.04 Aligned_cols=30 Identities=20% Similarity=0.437 Sum_probs=24.3
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
-||..|+....-+....+ .....|+-||..
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 479999988877777766 568999999973
No 73
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=64.54 E-value=30 Score=31.98 Aligned_cols=73 Identities=25% Similarity=0.327 Sum_probs=49.2
Q ss_pred HHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhccCCCCC--cEEEEEecCCCCCCCceeecCCCCCcccCCCCC
Q 012148 246 TLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSG--ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDL 323 (470)
Q Consensus 246 ~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~G--G~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~ 323 (470)
+|...|..++-. ..--.+.+|+.|..+|+. ..+.| .||++|.++|-.
T Consensus 71 kilt~lhd~~~~---------g~a~~~~~lqiaql~lkh-R~nk~q~qriVaFvgSpi~--------------------- 119 (243)
T COG5148 71 KILTFLHDIRLH---------GGADIMRCLQIAQLILKH-RDNKGQRQRIVAFVGSPIQ--------------------- 119 (243)
T ss_pred HHHHHhcccccc---------CcchHHHHHHHHHHHHhc-ccCCccceEEEEEecCccc---------------------
Confidence 566666555421 122378899999988873 33455 799999998621
Q ss_pred CCCCCCccchhHHHHHHHHHHHHhcCeEEEEeecc
Q 012148 324 DKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACA 358 (470)
Q Consensus 324 ~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s 358 (470)
++ .+-.-.+|+++.++++++|+.-++
T Consensus 120 es---------edeLirlak~lkknnVAidii~fG 145 (243)
T COG5148 120 ES---------EDELIRLAKQLKKNNVAIDIIFFG 145 (243)
T ss_pred cc---------HHHHHHHHHHHHhcCeeEEEEehh
Confidence 11 122346899999999999998764
No 74
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=63.08 E-value=4.3 Score=34.52 Aligned_cols=28 Identities=21% Similarity=0.561 Sum_probs=19.9
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
..||..|+.. |......|.|+-||..+.
T Consensus 70 ~~~C~~Cg~~------~~~~~~~~~CP~Cgs~~~ 97 (113)
T PRK12380 70 QAWCWDCSQV------VEIHQHDAQCPHCHGERL 97 (113)
T ss_pred EEEcccCCCE------EecCCcCccCcCCCCCCc
Confidence 4899999953 333335688999997653
No 75
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=62.52 E-value=2.3 Score=27.99 Aligned_cols=30 Identities=20% Similarity=0.270 Sum_probs=15.1
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
-|..|++-+..-.--.++..+|+|.-||..
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 388888876544433345568999999864
No 76
>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=62.45 E-value=10 Score=35.23 Aligned_cols=44 Identities=9% Similarity=0.021 Sum_probs=31.6
Q ss_pred CEEEEEEEcccchhh---------HHHHHHHHHHHhhcCC--CCceEEEEEECCe
Q 012148 130 PVFMFVVDTCIIEEE---------MSFLKSALSQAIDLLP--DNSLVGLITFGTL 173 (470)
Q Consensus 130 p~~vFvID~S~~~~~---------~~~l~~~l~~~l~~lp--~~~~VglITfd~~ 173 (470)
.-++|+||.|.+... .+.+++++...+..+. +...+++++|++.
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 358999999998753 4667777777766543 3456888888655
No 77
>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=62.34 E-value=4 Score=31.25 Aligned_cols=30 Identities=27% Similarity=0.461 Sum_probs=19.8
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp 93 (470)
+.|| +|+.|+ --+++.++-+| .||....+.
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 5899 799976 23466688999 999887764
No 78
>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=62.33 E-value=4.6 Score=34.43 Aligned_cols=28 Identities=21% Similarity=0.635 Sum_probs=20.4
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
-.||.+|+....+ ....|.|+-||..+.
T Consensus 70 ~~~C~~Cg~~~~~------~~~~~~CP~Cgs~~~ 97 (115)
T TIGR00100 70 ECECEDCSEEVSP------EIDLYRCPKCHGIML 97 (115)
T ss_pred EEEcccCCCEEec------CCcCccCcCCcCCCc
Confidence 4899999964433 233689999998763
No 79
>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=61.81 E-value=4.4 Score=29.15 Aligned_cols=29 Identities=31% Similarity=0.824 Sum_probs=18.3
Q ss_pred cccCCCeeeCCC-----------ceEEcCCceEEeCCCCC
Q 012148 60 RCRTCRSILNPF-----------SIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 60 RC~~C~aYiNp~-----------~~~~~~g~~w~C~~C~~ 88 (470)
+|..|+=..+|- +.|++--..|+|+.|+.
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCC
Confidence 677888666654 23333334689999985
No 80
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=60.20 E-value=3.5 Score=30.59 Aligned_cols=22 Identities=32% Similarity=0.801 Sum_probs=14.3
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
|.||.+||- .++.|+|+-||..
T Consensus 36 I~RC~~CRk----------~~~~Y~CP~CGF~ 57 (59)
T PRK14890 36 IYRCEKCRK----------QSNPYTCPKCGFE 57 (59)
T ss_pred EeechhHHh----------cCCceECCCCCCc
Confidence 566666664 2456778888764
No 81
>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=58.98 E-value=4.2 Score=29.11 Aligned_cols=31 Identities=19% Similarity=0.460 Sum_probs=21.7
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
-||.+|+....-+....+ .....|+-||..+
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~~ 36 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-DPLATCPECGGEK 36 (52)
T ss_pred EEeCCCCCEeEEEEecCC-CCCCCCCCCCCCc
Confidence 479999986665544443 3568899999744
No 82
>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=57.79 E-value=24 Score=33.26 Aligned_cols=65 Identities=26% Similarity=0.452 Sum_probs=36.6
Q ss_pred ccchhHHHHHHHHHHhc--cCCC-CCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHH-HHH
Q 012148 268 TRCTGTALSIAASLLGA--CVPG-SGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDA-LSK 343 (470)
Q Consensus 268 ~~~~G~AL~~A~~ll~~--~~~~-~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~-la~ 343 (470)
...+..||.+|..++.. +... ..-||++||..- +| +. +.+. . . .-.++ .++
T Consensus 104 ~~~l~~al~v~~~~~~~~~~~~k~~~krI~l~Td~d---~p--------------~~--~~~~--~-~---~~~~~l~~~ 158 (224)
T PF03731_consen 104 EGDLSDALWVASDMFRERTCKKKKNKKRIFLFTDND---GP--------------HE--DDDE--L-E---RIIQKLKAK 158 (224)
T ss_dssp ---HHHHHHHHHHHHHCHCTTS-ECEEEEEEEES-S---ST--------------TT---CCC--H-H---HHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHHHHhhcccCCCcEEEEEeCCC---CC--------------CC--CHHH--H-H---HHHHhhccc
Confidence 35688999999999984 3333 345777777642 11 00 0110 1 1 11122 277
Q ss_pred HHHhcCeEEEEeec
Q 012148 344 QLVHQGHVLDLFAC 357 (470)
Q Consensus 344 ~~~~~gisvdlF~~ 357 (470)
.+...+|.+++|..
T Consensus 159 Dl~~~~i~~~~~~l 172 (224)
T PF03731_consen 159 DLQDNGIEIELFFL 172 (224)
T ss_dssp HHHHHTEEEEEEEC
T ss_pred cchhcCcceeEeec
Confidence 78899999999977
No 83
>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=57.74 E-value=4.7 Score=28.99 Aligned_cols=33 Identities=30% Similarity=0.531 Sum_probs=23.4
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp 93 (470)
+||.+|+-.+--.-.+. .-.-+|+=|++.|.+-
T Consensus 5 iRC~~CnklLa~~g~~~--~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVI--ELEIKCPRCKTINHVR 37 (51)
T ss_pred eeccchhHHHhhhcCcc--EEEEECCCCCccceEe
Confidence 89999987665432221 1358999999999873
No 84
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=56.89 E-value=5.4 Score=23.77 Aligned_cols=21 Identities=24% Similarity=0.605 Sum_probs=12.3
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
+|.+|++-+..-.+| |+-||+
T Consensus 1 ~Cp~CG~~~~~~~~f--------C~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKF--------CPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcc--------hhhhCC
Confidence 477777755443332 666765
No 85
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=56.84 E-value=12 Score=24.46 Aligned_cols=29 Identities=24% Similarity=0.428 Sum_probs=19.8
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
+.+|..|++-. -+........|.+|+...
T Consensus 3 ~~~C~~C~~~~----i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNG----IVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCe----EEEecCCeEEcccCCcEe
Confidence 46899999855 221223489999999754
No 86
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.51 E-value=5.6 Score=34.48 Aligned_cols=31 Identities=19% Similarity=0.597 Sum_probs=22.5
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
.+--|.+|++-+..-. +.-.|.||+|...-+
T Consensus 88 q~r~CARCGGrv~lrs----NKv~wvcnlc~k~q~ 118 (169)
T KOG3799|consen 88 QTRFCARCGGRVSLRS----NKVMWVCNLCRKQQE 118 (169)
T ss_pred hhhHHHhcCCeeeecc----CceEEeccCCcHHHH
Confidence 4566899999776543 234899999997654
No 87
>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=55.61 E-value=4.9 Score=27.02 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=21.1
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
-||..|+..........+ +....|+-||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 479999987665555433 56788999987
No 88
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=55.56 E-value=7.4 Score=25.87 Aligned_cols=31 Identities=13% Similarity=0.281 Sum_probs=20.8
Q ss_pred ccccCCCeeeCCC-ceEEcCCceEEeCCCCCC
Q 012148 59 LRCRTCRSILNPF-SIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 59 ~RC~~C~aYiNp~-~~~~~~g~~w~C~~C~~~ 89 (470)
++|.+|++-.+-= -++-..|.+.+|.-|++.
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 5788888765543 234455678888888864
No 89
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=55.22 E-value=9 Score=33.46 Aligned_cols=34 Identities=29% Similarity=0.539 Sum_probs=23.7
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCCCCCCc
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp~ 94 (470)
++|.-|+..- -...+.....|.|+-|+..|-+..
T Consensus 1 v~C~fC~~~s--~~~~~~~~~~w~C~~C~q~N~f~e 34 (131)
T PF09779_consen 1 VNCWFCGQNS--KVPYDNRNSNWTCPHCEQYNGFDE 34 (131)
T ss_pred CeeccCCCCC--CCCCCCCCCeeECCCCCCccCccc
Confidence 4788888752 333344444699999999998753
No 90
>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=54.88 E-value=24 Score=33.55 Aligned_cols=44 Identities=16% Similarity=0.163 Sum_probs=28.3
Q ss_pred CCC-EEEEEEEcccchhhH-HHHHHHHHHHhhcCCCCceEEEEEECCeE
Q 012148 128 VPP-VFMFVVDTCIIEEEM-SFLKSALSQAIDLLPDNSLVGLITFGTLV 174 (470)
Q Consensus 128 ~~p-~~vFvID~S~~~~~~-~~l~~~l~~~l~~lp~~~~VglITfd~~V 174 (470)
..| .+|+++|+|.+.... ..+...+..+....+ ++.++.|++.+
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 899999999988773 334444443334444 67777787653
No 91
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=54.69 E-value=7.2 Score=33.19 Aligned_cols=29 Identities=21% Similarity=0.575 Sum_probs=19.3
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
..||..|+.+...- ....|.|+-||..+.
T Consensus 70 ~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~~~ 98 (114)
T PRK03681 70 ECWCETCQQYVTLL-----TQRVRRCPQCHGDML 98 (114)
T ss_pred EEEcccCCCeeecC-----CccCCcCcCcCCCCc
Confidence 48999999643221 112488999997653
No 92
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=53.76 E-value=34 Score=38.54 Aligned_cols=106 Identities=18% Similarity=0.255 Sum_probs=63.8
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCCCCCccccCCCCCCCCcccCCCcc--eEEEeCCC------CC-CCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHYASITDDNLPAELFPQYT--TIEYEPPG------PG-EKSSV 128 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp~~y~~~~~~~~~pEL~~~~~--tvey~~~~------~~-~~~~~ 128 (470)
+.+|.+|-++ +.+....+.-+|-.||+.-.+|.. +|+++ .+.|.... +- ..-|.
T Consensus 444 v~~Cp~Cd~~----lt~H~~~~~L~CH~Cg~~~~~p~~-------------Cp~Cgs~~L~~~G~GterieeeL~~~FP~ 506 (730)
T COG1198 444 IAECPNCDSP----LTLHKATGQLRCHYCGYQEPIPQS-------------CPECGSEHLRAVGPGTERIEEELKRLFPG 506 (730)
T ss_pred cccCCCCCcc----eEEecCCCeeEeCCCCCCCCCCCC-------------CCCCCCCeeEEecccHHHHHHHHHHHCCC
Confidence 6777777765 345566689999999999776632 22332 23333211 00 01246
Q ss_pred CCEEEEEEEcccchhhHHHHHHHHHH----------Hh---hcCCCCceEEEEEECCeEEEEEcC
Q 012148 129 PPVFMFVVDTCIIEEEMSFLKSALSQ----------AI---DLLPDNSLVGLITFGTLVQVHELG 180 (470)
Q Consensus 129 ~p~~vFvID~S~~~~~~~~l~~~l~~----------~l---~~lp~~~~VglITfd~~V~~y~l~ 180 (470)
.+++.|--|++.....+..+...+.. +| ...|.-++||++-=|..+..-|+.
T Consensus 507 ~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfR 571 (730)
T COG1198 507 ARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFR 571 (730)
T ss_pred CcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcc
Confidence 78888888888876655443222211 00 124566899999888887777766
No 93
>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=53.38 E-value=9.1 Score=29.07 Aligned_cols=28 Identities=18% Similarity=0.459 Sum_probs=22.0
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
-.|..|+...-. ...++.|+|+-||..-
T Consensus 29 q~C~~CG~~~~~----~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 29 QTCPRCGHRNKK----RRSGRVFTCPNCGFEM 56 (69)
T ss_pred cCccCccccccc----ccccceEEcCCCCCEE
Confidence 559999987666 4557899999999763
No 94
>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=52.71 E-value=6.8 Score=33.46 Aligned_cols=32 Identities=22% Similarity=0.517 Sum_probs=25.4
Q ss_pred ccccCCCeeeCCCceEEc-CCceEEeCCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDF-AAKIWICPFCFQRN 90 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~-~g~~w~C~~C~~~N 90 (470)
..|..|+-.+..-|.... ....|.|.+|....
T Consensus 72 ~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k~r 104 (118)
T PF02318_consen 72 RVCVDCKHRVCKKCGVYSKKEPIWLCKVCQKQR 104 (118)
T ss_dssp EEETTTTEEEETTSEEETSSSCCEEEHHHHHHH
T ss_pred CcCCcCCccccCccCCcCCCCCCEEChhhHHHH
Confidence 678888888888888864 45799999997643
No 95
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=51.13 E-value=6.3 Score=27.96 Aligned_cols=30 Identities=23% Similarity=0.679 Sum_probs=14.6
Q ss_pred cccCCCeeeCCCce-----------EEcCCceEEeCCCCCC
Q 012148 60 RCRTCRSILNPFSI-----------VDFAAKIWICPFCFQR 89 (470)
Q Consensus 60 RC~~C~aYiNp~~~-----------~~~~g~~w~C~~C~~~ 89 (470)
+|..|+-..+|--. |++--..|+|+.|+..
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 46666655544432 2222335888888753
No 96
>PRK10997 yieM hypothetical protein; Provisional
Probab=49.49 E-value=25 Score=37.66 Aligned_cols=52 Identities=25% Similarity=0.144 Sum_probs=34.6
Q ss_pred CCEEEEEEEcccchh-hHHHHHHHHHHHhh--cCCCCceEEEEEECCeEEEEEcC
Q 012148 129 PPVFMFVVDTCIIEE-EMSFLKSALSQAID--LLPDNSLVGLITFGTLVQVHELG 180 (470)
Q Consensus 129 ~p~~vFvID~S~~~~-~~~~l~~~l~~~l~--~lp~~~~VglITfd~~V~~y~l~ 180 (470)
.--++++||+|.+.. .-.....++..+|- .+.++-++++|.|++.+.-|.+.
T Consensus 323 kGpiII~VDtSGSM~G~ke~~AkalAaAL~~iAl~q~dr~~li~Fs~~i~~~~l~ 377 (487)
T PRK10997 323 RGPFIVCVDTSGSMGGFNEQCAKAFCLALMRIALAENRRCYIMLFSTEVVTYELT 377 (487)
T ss_pred CCcEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHhcCCCEEEEEecCCceeeccC
Confidence 345889999999875 11222234333433 34577899999999988777655
No 97
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=49.32 E-value=11 Score=27.32 Aligned_cols=32 Identities=16% Similarity=0.271 Sum_probs=27.2
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
+.+|.+|++--.|..+-...|..-.||-|+-.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~ 34 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLY 34 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHH
Confidence 46899999999998888777778999999953
No 98
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=49.28 E-value=8.9 Score=27.46 Aligned_cols=27 Identities=26% Similarity=0.632 Sum_probs=15.2
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
+|.+|++-+ ..+.......|+-||+.-
T Consensus 8 ~C~~Cg~~~----~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 8 KCARCGREV----ELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EhhhcCCee----ehhhccCceeCCCCCcEE
Confidence 566666655 333334456677776543
No 99
>PF12773 DZR: Double zinc ribbon
Probab=49.09 E-value=11 Score=26.71 Aligned_cols=32 Identities=25% Similarity=0.330 Sum_probs=24.3
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp 93 (470)
+-..|.+|++-+. ......++|+-|++.+...
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCcCC
Confidence 4578999999887 3445689999999987643
No 100
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=48.52 E-value=14 Score=22.62 Aligned_cols=24 Identities=29% Similarity=0.620 Sum_probs=14.8
Q ss_pred ccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 61 C~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
|.+|+..+. .-.+...++|..|++
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 566776553 224456788888864
No 101
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.47 E-value=7.1 Score=33.36 Aligned_cols=29 Identities=28% Similarity=0.730 Sum_probs=18.5
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
..||..|+.+..+- ....+.|+-||..+.
T Consensus 71 ~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~~~ 99 (117)
T PRK00564 71 ELECKDCSHVFKPN-----ALDYGVCEKCHSKNV 99 (117)
T ss_pred EEEhhhCCCccccC-----CccCCcCcCCCCCce
Confidence 48999999443221 112345999998764
No 102
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=48.11 E-value=14 Score=25.74 Aligned_cols=26 Identities=19% Similarity=0.259 Sum_probs=15.1
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
+|.+|++-+..- .+..-+|+-||+.-
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~rI 29 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGYRI 29 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCceE
Confidence 577777754432 23457777777543
No 103
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=46.68 E-value=12 Score=26.88 Aligned_cols=25 Identities=24% Similarity=0.549 Sum_probs=17.8
Q ss_pred ccccCCCe-eeCCCceEEcCCceEEeCCCCCC
Q 012148 59 LRCRTCRS-ILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 59 ~RC~~C~a-YiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
..|.+|++ ++-+ . ...|.|.-|+..
T Consensus 21 ~fCP~Cg~~~m~~----~--~~r~~C~~Cgyt 46 (50)
T PRK00432 21 KFCPRCGSGFMAE----H--LDRWHCGKCGYT 46 (50)
T ss_pred CcCcCCCcchhec----c--CCcEECCCcCCE
Confidence 46999998 4433 2 257999999853
No 104
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=46.33 E-value=11 Score=34.75 Aligned_cols=26 Identities=31% Similarity=0.651 Sum_probs=20.8
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
-.||.+|++-|=. .+++.+|+-||..
T Consensus 149 ~A~CsrC~~~L~~------~~~~l~Cp~Cg~t 174 (188)
T COG1096 149 YARCSRCRAPLVK------KGNMLKCPNCGNT 174 (188)
T ss_pred EEEccCCCcceEE------cCcEEECCCCCCE
Confidence 3899999996533 5679999999963
No 105
>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=45.54 E-value=20 Score=23.89 Aligned_cols=26 Identities=23% Similarity=0.467 Sum_probs=19.5
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
.+|..|++. +...++ ..|.|.-||+.
T Consensus 9 ~~C~~C~~~---~~~~~d--G~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSR---WFYSDD--GFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCe---EeEccC--CEEEhhhCceE
Confidence 569999998 444433 48999999975
No 106
>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=45.15 E-value=23 Score=24.68 Aligned_cols=27 Identities=19% Similarity=0.414 Sum_probs=18.9
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
+.|.+|++- -+..+.. .+.|.|.-|++
T Consensus 19 ~~CP~Cg~~--~~~~~~~-~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLKT-RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeCC-CCeEECCCCCC
Confidence 569999987 2233322 46899999985
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=44.84 E-value=16 Score=22.10 Aligned_cols=24 Identities=29% Similarity=0.618 Sum_probs=16.9
Q ss_pred ccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 61 C~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
|.+|+.-|-|.-+ +..|.|+-||.
T Consensus 1 C~sC~~~i~~r~~----~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQ----AVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCccc----CceEeCCCCCC
Confidence 6778777766543 45799998874
No 108
>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=43.65 E-value=15 Score=24.39 Aligned_cols=31 Identities=16% Similarity=0.366 Sum_probs=15.0
Q ss_pred ccccCCCeeeCCC-ceEEcCCceEEeCCCCCC
Q 012148 59 LRCRTCRSILNPF-SIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 59 ~RC~~C~aYiNp~-~~~~~~g~~w~C~~C~~~ 89 (470)
++|.+|++-..-- -.+...+...+|+-|++.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 4567776632111 112223446677777653
No 109
>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=43.03 E-value=9.6 Score=23.97 Aligned_cols=14 Identities=36% Similarity=0.688 Sum_probs=12.1
Q ss_pred ceEEeCCCCCCCCC
Q 012148 79 KIWICPFCFQRNHF 92 (470)
Q Consensus 79 ~~w~C~~C~~~N~v 92 (470)
+.|.|..|...|..
T Consensus 3 g~W~C~~C~~~N~~ 16 (30)
T PF00641_consen 3 GDWKCPSCTFMNPA 16 (30)
T ss_dssp SSEEETTTTEEEES
T ss_pred cCccCCCCcCCchH
Confidence 37999999999974
No 110
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=41.59 E-value=57 Score=28.76 Aligned_cols=61 Identities=21% Similarity=0.292 Sum_probs=36.2
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCCCCCCccccCCCCCCCCcccCCCcce-----EEEeCCCCCCCCCCCCEEE
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHYASITDDNLPAELFPQYTT-----IEYEPPGPGEKSSVPPVFM 133 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp~~y~~~~~~~~~pEL~~~~~t-----vey~~~~~~~~~~~~p~~v 133 (470)
.||.+|+.+.=|= +-.|+-|+..+++.. -|+. ..+. +.|..+.. ....+|.++
T Consensus 30 ~kC~~CG~v~~PP--------r~~Cp~C~~~~~~E~-----------vels-~~G~V~t~Tv~~~~~~~--~~~~~P~vi 87 (140)
T COG1545 30 TKCKKCGRVYFPP--------RAYCPKCGSETELEW-----------VELS-GEGKVETYTVVYVKPPG--FSLEEPYVI 87 (140)
T ss_pred EEcCCCCeEEcCC--------cccCCCCCCCCceEE-----------EEeC-CCeEEEEEEEEeeCCCC--cccCCCEEE
Confidence 8999999976552 467999998863221 1342 2333 34443321 112478888
Q ss_pred EEEEcccc
Q 012148 134 FVVDTCII 141 (470)
Q Consensus 134 FvID~S~~ 141 (470)
-+|++-..
T Consensus 88 aiV~l~~~ 95 (140)
T COG1545 88 AIVELEEG 95 (140)
T ss_pred EEEEeCCC
Confidence 88887643
No 111
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=41.50 E-value=21 Score=26.47 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=20.2
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
.+..|..|+.+.=| .-.|..||+.+.
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 45889999997654 578999997654
No 112
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.32 E-value=16 Score=32.09 Aligned_cols=33 Identities=24% Similarity=0.421 Sum_probs=20.1
Q ss_pred CccccCCCeeeCCCc-------------eEEcC--CceEEeCCCCCCC
Q 012148 58 PLRCRTCRSILNPFS-------------IVDFA--AKIWICPFCFQRN 90 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~-------------~~~~~--g~~w~C~~C~~~N 90 (470)
..||..|+.....-- .+.+. ...|.|+-||..+
T Consensus 70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 489999996544320 01110 3468899999765
No 113
>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=40.63 E-value=21 Score=22.99 Aligned_cols=29 Identities=21% Similarity=0.588 Sum_probs=17.3
Q ss_pred cccCCCeeeCCC-ceEEcCCceE-----EeCCCCC
Q 012148 60 RCRTCRSILNPF-SIVDFAAKIW-----ICPFCFQ 88 (470)
Q Consensus 60 RC~~C~aYiNp~-~~~~~~g~~w-----~C~~C~~ 88 (470)
||.+|+-.|-+- ..+...++.| .|.-|+.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~ 35 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGK 35 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCC
Confidence 688888888774 3333334444 5666653
No 114
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.41 E-value=13 Score=32.15 Aligned_cols=33 Identities=21% Similarity=0.399 Sum_probs=19.7
Q ss_pred CccccCCCeeeCCC-ceEEcCCceEEeCCCCCCCC
Q 012148 58 PLRCRTCRSILNPF-SIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 58 ~~RC~~C~aYiNp~-~~~~~~g~~w~C~~C~~~N~ 91 (470)
..|| .|+.+..+- ...+.-...|.|+-||..+.
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~ 103 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRA 103 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCCCCCC
Confidence 4899 999765432 11111111378999997664
No 115
>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=40.37 E-value=7.2 Score=33.08 Aligned_cols=27 Identities=30% Similarity=0.627 Sum_probs=17.5
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
..||..|+.-..+- ...+.|+.||..+
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 48999999854432 3347799999876
No 116
>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=40.04 E-value=14 Score=22.73 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=15.8
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
+|..|++-|+- ..-.|+.||+..
T Consensus 2 ~CP~C~~~V~~--------~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPE--------SAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchh--------hcCcCCCCCCCC
Confidence 58888887632 245788888754
No 117
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=39.65 E-value=29 Score=30.44 Aligned_cols=31 Identities=19% Similarity=0.477 Sum_probs=25.8
Q ss_pred ccccCCCeeeCCCceEEcCCceE--EeCCCCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIW--ICPFCFQRNHF 92 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w--~C~~C~~~N~v 92 (470)
+-|..|+. |=..+...++.| +|.-||..-+|
T Consensus 98 VlC~~C~s---PdT~l~k~~r~~~l~C~ACGa~~~v 130 (133)
T TIGR00311 98 VICRECNR---PDTRIIKEGRVSLLKCEACGAKAPL 130 (133)
T ss_pred EECCCCCC---CCcEEEEeCCeEEEecccCCCCCcc
Confidence 78999997 777787777776 89999988766
No 118
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=39.44 E-value=17 Score=27.57 Aligned_cols=25 Identities=20% Similarity=0.549 Sum_probs=17.7
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp 93 (470)
.-|++|+.... + . +|+.||..+..+
T Consensus 6 ~AC~~C~~i~~-------~-~--~Cp~Cgs~~~S~ 30 (64)
T PRK06393 6 RACKKCKRLTP-------E-K--TCPVHGDEKTTT 30 (64)
T ss_pred hhHhhCCcccC-------C-C--cCCCCCCCcCCc
Confidence 34999998662 1 1 899999975443
No 119
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=39.26 E-value=16 Score=36.92 Aligned_cols=29 Identities=24% Similarity=0.642 Sum_probs=21.8
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp 93 (470)
..-||.+|+- ....-.|.|+-|+..-.+-
T Consensus 353 ~~YRC~~CGF--------~a~~l~W~CPsC~~W~Tik 381 (389)
T COG2956 353 PRYRCQNCGF--------TAHTLYWHCPSCRAWETIK 381 (389)
T ss_pred CCceecccCC--------cceeeeeeCCCcccccccC
Confidence 4689999983 3334589999999887654
No 120
>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=38.81 E-value=19 Score=29.71 Aligned_cols=27 Identities=26% Similarity=0.725 Sum_probs=21.3
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~v 92 (470)
.|.+|++.|.|- +..|.|+-|+.....
T Consensus 2 fC~~Cg~~l~~~------~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPK------NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccC------CCeEECcCCCCcccc
Confidence 599999999652 348999999987553
No 121
>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=38.64 E-value=16 Score=23.38 Aligned_cols=26 Identities=23% Similarity=0.551 Sum_probs=13.2
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
+.|..|++=-+- .+|..|+|+-|++.
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 678888874332 34678999999864
No 122
>PHA00626 hypothetical protein
Probab=38.64 E-value=27 Score=25.64 Aligned_cols=29 Identities=17% Similarity=0.274 Sum_probs=17.8
Q ss_pred ccCCCe---eeCCCceEEcCCceEEeCCCCCCCC
Q 012148 61 CRTCRS---ILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 61 C~~C~a---YiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
|.+|++ +-+..|+- ..+.|+|+-||....
T Consensus 3 CP~CGS~~Ivrcg~cr~--~snrYkCkdCGY~ft 34 (59)
T PHA00626 3 CPKCGSGNIAKEKTMRG--WSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCceeeeeceecc--cCcceEcCCCCCeec
Confidence 666665 22333322 246899999998765
No 123
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=38.48 E-value=41 Score=33.70 Aligned_cols=29 Identities=34% Similarity=0.548 Sum_probs=25.8
Q ss_pred hhHHHHHHHHHHHhhcCCCCceEEEEEEC
Q 012148 143 EEMSFLKSALSQAIDLLPDNSLVGLITFG 171 (470)
Q Consensus 143 ~~~~~l~~~l~~~l~~lp~~~~VglITfd 171 (470)
.|++.+.++|.++++.|.++.|+++|||-
T Consensus 218 dEL~~L~~~L~~a~~~L~~gGRl~VIsFH 246 (314)
T COG0275 218 DELEELEEALEAALDLLKPGGRLAVISFH 246 (314)
T ss_pred hHHHHHHHHHHHHHHhhCCCcEEEEEEec
Confidence 46888999999999999999999999874
No 124
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=37.76 E-value=16 Score=29.54 Aligned_cols=36 Identities=25% Similarity=0.511 Sum_probs=24.2
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCCCCCccc
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPPHY 96 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp~~y 96 (470)
.|+||++||--.++ -++ +.--.|+-|+..-.-++.|
T Consensus 57 ~Pa~CkkCGfef~~-~~i---k~pSRCP~CKSE~Ie~prF 92 (97)
T COG3357 57 RPARCKKCGFEFRD-DKI---KKPSRCPKCKSEWIEEPRF 92 (97)
T ss_pred cChhhcccCccccc-ccc---CCcccCCcchhhcccCCce
Confidence 58999999976555 222 2346799999776555443
No 125
>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=37.06 E-value=3.9 Score=29.33 Aligned_cols=18 Identities=28% Similarity=0.744 Sum_probs=7.3
Q ss_pred CceEEcCCceEEeCCCCC
Q 012148 71 FSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 71 ~~~~~~~g~~w~C~~C~~ 88 (470)
|.......+.|+|++|++
T Consensus 32 fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 32 FLESNQRTPKWKCPICNK 49 (50)
T ss_dssp HHHHHHHS---B-TTT--
T ss_pred HHHHhhccCCeECcCCcC
Confidence 333334456799999986
No 126
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=36.15 E-value=19 Score=30.01 Aligned_cols=35 Identities=20% Similarity=0.373 Sum_probs=26.4
Q ss_pred ccccCCCeeeCCC----ceEEcCCceEEeCCCCCCCCCC
Q 012148 59 LRCRTCRSILNPF----SIVDFAAKIWICPFCFQRNHFP 93 (470)
Q Consensus 59 ~RC~~C~aYiNp~----~~~~~~g~~w~C~~C~~~N~vp 93 (470)
--|++|.+.+=|. +++..+.-.|+|.-||+.-..|
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 4599999976555 4455455689999999987765
No 127
>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=35.19 E-value=32 Score=28.86 Aligned_cols=29 Identities=24% Similarity=0.572 Sum_probs=19.7
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
.|.|.+|.+- |. . .+|..|+|+-|++.-.
T Consensus 2 lp~CP~C~se---yt-Y-~dg~~~iCpeC~~EW~ 30 (109)
T TIGR00686 2 LPPCPKCNSE---YT-Y-HDGTQLICPSCLYEWN 30 (109)
T ss_pred CCcCCcCCCc---ce-E-ecCCeeECcccccccc
Confidence 3678888762 22 2 2456899999997643
No 128
>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=35.01 E-value=12 Score=24.81 Aligned_cols=28 Identities=18% Similarity=0.304 Sum_probs=19.7
Q ss_pred ccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 61 C~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
|.+|++==.|..+-.+.|....||-|+.
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 7889998889988888887789999874
No 129
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=34.71 E-value=31 Score=26.32 Aligned_cols=31 Identities=16% Similarity=0.443 Sum_probs=22.5
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
-++|..|+- --+.|.......+|..||..=-
T Consensus 19 ~VkCpdC~N---~q~vFshast~V~C~~CG~~l~ 49 (67)
T COG2051 19 RVKCPDCGN---EQVVFSHASTVVTCLICGTTLA 49 (67)
T ss_pred EEECCCCCC---EEEEeccCceEEEecccccEEE
Confidence 488999984 4455556667899999996543
No 130
>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=34.62 E-value=21 Score=20.17 Aligned_cols=11 Identities=27% Similarity=0.815 Sum_probs=6.7
Q ss_pred EEeCCCCCCCC
Q 012148 81 WICPFCFQRNH 91 (470)
Q Consensus 81 w~C~~C~~~N~ 91 (470)
|.|++|+....
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 78999987654
No 131
>PRK12722 transcriptional activator FlhC; Provisional
Probab=33.22 E-value=20 Score=33.27 Aligned_cols=29 Identities=14% Similarity=0.438 Sum_probs=20.6
Q ss_pred CCccccCCCe-eeCCCceEEcCCceEEeCCCCC
Q 012148 57 APLRCRTCRS-ILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 57 ~~~RC~~C~a-YiNp~~~~~~~g~~w~C~~C~~ 88 (470)
...+|.+|++ ||-.. .+....++|++|.-
T Consensus 133 ~l~~C~~Cgg~fv~~~---~e~~~~f~CplC~~ 162 (187)
T PRK12722 133 QLSSCNCCGGHFVTHA---HDPVGSFVCGLCQP 162 (187)
T ss_pred eeccCCCCCCCeeccc---cccCCCCcCCCCCC
Confidence 4789999987 44222 23346899999996
No 132
>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=33.06 E-value=39 Score=22.67 Aligned_cols=27 Identities=26% Similarity=0.727 Sum_probs=17.3
Q ss_pred cccCCCeeeCCCceEEc--CCceEEeCCCCC
Q 012148 60 RCRTCRSILNPFSIVDF--AAKIWICPFCFQ 88 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~--~g~~w~C~~C~~ 88 (470)
-|..|++ ---|- +++ +...|.|+-|+.
T Consensus 5 pCP~CGG-~DrFr-~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 5 PCPNCGG-SDRFR-FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CCCCCCC-ccccc-cccCCCCcCEEeCCCCC
Confidence 3788877 22222 444 346899999985
No 133
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=32.90 E-value=38 Score=25.25 Aligned_cols=28 Identities=29% Similarity=0.613 Sum_probs=18.9
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
.+++|.+|+.-|-|--+ +-+|.|+-||.
T Consensus 8 ~~~~CtSCg~~i~p~e~----~v~F~CPnCGe 35 (61)
T COG2888 8 DPPVCTSCGREIAPGET----AVKFPCPNCGE 35 (61)
T ss_pred CCceeccCCCEeccCCc----eeEeeCCCCCc
Confidence 36788888887766443 34677777773
No 134
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=32.79 E-value=28 Score=26.19 Aligned_cols=23 Identities=35% Similarity=0.792 Sum_probs=16.5
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~v 92 (470)
-|++|+..+. .. +|+.||...-.
T Consensus 5 AC~~C~~i~~--------~~--~CP~Cgs~~~T 27 (61)
T PRK08351 5 ACRHCHYITT--------ED--RCPVCGSRDLS 27 (61)
T ss_pred hhhhCCcccC--------CC--cCCCCcCCccc
Confidence 4999998762 11 69999987643
No 135
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=32.61 E-value=23 Score=39.22 Aligned_cols=26 Identities=23% Similarity=0.447 Sum_probs=20.1
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
.+-+|..|+. + ..|..|.|+-||..+
T Consensus 565 ~~~iC~~CG~-~-------~~g~~~~CP~CGs~~ 590 (623)
T PRK08271 565 KITICNDCHH-I-------DKRTGKRCPICGSEN 590 (623)
T ss_pred CCccCCCCCC-c-------CCCCCcCCcCCCCcc
Confidence 5789999994 3 245679999999755
No 136
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=32.59 E-value=22 Score=39.68 Aligned_cols=24 Identities=21% Similarity=0.356 Sum_probs=18.9
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
..-+|..|+ |+ .|..|.|+-||..
T Consensus 625 ~~~~C~~CG-~~--------~g~~~~CP~CG~~ 648 (656)
T PRK08270 625 TFSICPKHG-YL--------SGEHEFCPKCGEE 648 (656)
T ss_pred CCcccCCCC-Cc--------CCCCCCCcCCcCc
Confidence 578999999 44 3668999999944
No 137
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=32.08 E-value=41 Score=21.47 Aligned_cols=26 Identities=19% Similarity=0.341 Sum_probs=14.0
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
.|.+|++= +....+|..-+|+-|+..
T Consensus 5 fC~~CG~~----t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAP----TKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--B----EEE-SSSS-EEESSSS-E
T ss_pred ccCcCCcc----ccCCCCcCEeECCCCcCE
Confidence 58888873 345566778889888853
No 138
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=30.47 E-value=22 Score=21.33 Aligned_cols=13 Identities=38% Similarity=0.779 Sum_probs=11.3
Q ss_pred eEEeCCCCCCCCC
Q 012148 80 IWICPFCFQRNHF 92 (470)
Q Consensus 80 ~w~C~~C~~~N~v 92 (470)
.|.|..|+..|..
T Consensus 2 ~W~C~~C~~~N~~ 14 (26)
T smart00547 2 DWECPACTFLNFA 14 (26)
T ss_pred cccCCCCCCcChh
Confidence 5999999999864
No 139
>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=30.42 E-value=20 Score=23.29 Aligned_cols=10 Identities=40% Similarity=1.185 Sum_probs=4.9
Q ss_pred CCccccCCCe
Q 012148 57 APLRCRTCRS 66 (470)
Q Consensus 57 ~~~RC~~C~a 66 (470)
+++||..|+.
T Consensus 16 ~~irC~~CG~ 25 (32)
T PF03604_consen 16 DPIRCPECGH 25 (32)
T ss_dssp STSSBSSSS-
T ss_pred CcEECCcCCC
Confidence 4455555554
No 140
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=30.40 E-value=26 Score=27.61 Aligned_cols=30 Identities=23% Similarity=0.460 Sum_probs=16.7
Q ss_pred ccccCCCeeeCCC----ceEE-----cCCceEEeCCCCC
Q 012148 59 LRCRTCRSILNPF----SIVD-----FAAKIWICPFCFQ 88 (470)
Q Consensus 59 ~RC~~C~aYiNp~----~~~~-----~~g~~w~C~~C~~ 88 (470)
.-|++|++++=|- .++. ...-.|+|..||+
T Consensus 47 ~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 47 TICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp TB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred ccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 5699999987665 3344 2334899999984
No 141
>PF14353 CpXC: CpXC protein
Probab=30.39 E-value=42 Score=28.81 Aligned_cols=14 Identities=21% Similarity=0.636 Sum_probs=11.8
Q ss_pred eEEeCCCCCCCCCC
Q 012148 80 IWICPFCFQRNHFP 93 (470)
Q Consensus 80 ~w~C~~C~~~N~vp 93 (470)
.++|+-||+...++
T Consensus 38 ~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 38 SFTCPSCGHKFRLE 51 (128)
T ss_pred EEECCCCCCceecC
Confidence 89999999888764
No 142
>PRK00420 hypothetical protein; Validated
Probab=30.32 E-value=37 Score=28.83 Aligned_cols=29 Identities=17% Similarity=0.281 Sum_probs=22.0
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~v 92 (470)
-.|..|+ .|+.++ .+ +...|+.||..-.+
T Consensus 24 ~~CP~Cg---~pLf~l-k~-g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCG---LPLFEL-KD-GEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCC---Ccceec-CC-CceECCCCCCeeee
Confidence 5699999 588877 33 37999999986554
No 143
>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=30.22 E-value=19 Score=28.65 Aligned_cols=15 Identities=33% Similarity=0.961 Sum_probs=6.5
Q ss_pred ceEEeCCCCCCCCCC
Q 012148 79 KIWICPFCFQRNHFP 93 (470)
Q Consensus 79 ~~w~C~~C~~~N~vp 93 (470)
..|.|+||++.+.+.
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 579999999999864
No 144
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=29.90 E-value=2.3e+02 Score=30.01 Aligned_cols=45 Identities=18% Similarity=0.149 Sum_probs=29.0
Q ss_pred CEEEEEEEcccchhhHH-HHHHHHHHHhh--cCCCCceEEEEEECCeE
Q 012148 130 PVFMFVVDTCIIEEEMS-FLKSALSQAID--LLPDNSLVGLITFGTLV 174 (470)
Q Consensus 130 p~~vFvID~S~~~~~~~-~l~~~l~~~l~--~lp~~~~VglITfd~~V 174 (470)
.-++.+||.|.+..-.. ....++..+|- .+-++.++.++.||+.+
T Consensus 273 GpvilllD~SGSM~G~~e~~AKAvalAl~~~alaenR~~~~~lF~s~~ 320 (437)
T COG2425 273 GPVILLLDKSGSMSGFKEQWAKAVALALMRIALAENRDCYVILFDSEV 320 (437)
T ss_pred CCEEEEEeCCCCcCCcHHHHHHHHHHHHHHHHHHhccceEEEEecccc
Confidence 44678999999864322 22224433332 35678899999999843
No 145
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=29.76 E-value=31 Score=32.35 Aligned_cols=37 Identities=22% Similarity=0.505 Sum_probs=24.7
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCCCCCc
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFPP 94 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp~ 94 (470)
-+.|+.|.-=-+.+.--...-..|+|.+|++.|..+.
T Consensus 192 alIC~~C~hhngl~~~~ek~~~efiC~~Cn~~n~~~~ 228 (251)
T COG5415 192 ALICPQCHHHNGLYRLAEKPIIEFICPHCNHKNDEVK 228 (251)
T ss_pred hhccccccccccccccccccchheecccchhhcCccc
Confidence 3668888654444433333445799999999997654
No 146
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=29.62 E-value=28 Score=35.01 Aligned_cols=35 Identities=20% Similarity=0.383 Sum_probs=24.9
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHFP 93 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~vp 93 (470)
+.|+.|+.==+.+-.=+..--.|.|.+|++.|.-.
T Consensus 221 LIC~~C~~HNGla~~ee~~yi~F~C~~Cn~LN~~~ 255 (328)
T KOG2846|consen 221 LICSQCHHHNGLARKEEYEYITFRCPHCNALNPAK 255 (328)
T ss_pred hcchhhccccCcCChhhcCceEEECccccccCCCc
Confidence 66999987655444433334589999999999743
No 147
>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=29.44 E-value=4.7e+02 Score=24.38 Aligned_cols=99 Identities=12% Similarity=-0.057 Sum_probs=59.0
Q ss_pred HHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHhccCCCCCc-EEEEEecCCCCCCCceeecCCCCCcccCCCCC
Q 012148 245 FTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLGACVPGSGA-RILAFVGGPSTEGPAAIVSKNLSEPIRSHKDL 323 (470)
Q Consensus 245 ~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~~~~~~~GG-~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~ 323 (470)
..+..+|+...-- .. + ..|..||..|+.-|.... .... -||+++.|--|.|- +
T Consensus 75 ~~l~~~l~~~q~g---~a-g----~~TadAi~~av~rl~~~~-~a~~kvvILLTDG~n~~~~--i--------------- 128 (191)
T cd01455 75 ETLKMMHAHSQFC---WS-G----DHTVEATEFAIKELAAKE-DFDEAIVIVLSDANLERYG--I--------------- 128 (191)
T ss_pred HHHHHHHHhcccC---cc-C----ccHHHHHHHHHHHHHhcC-cCCCcEEEEEeCCCcCCCC--C---------------
Confidence 4677777765421 11 1 223388988888875111 2234 45555555432220 1
Q ss_pred CCCCCCccchhHHHHHHH-HHHHHhcCeEEEEeeccCCccChhhchhhhcccCceEEEcCCC
Q 012148 324 DKDSAPHYHKAVKFYDAL-SKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDSF 384 (470)
Q Consensus 324 ~~~~~~~~~~~~~fY~~l-a~~~~~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~v~~y~~f 384 (470)
.| .+. ++.+.+.||-|..+..+. .|-.++..+++.|||+-|...+-
T Consensus 129 --------~P-----~~aAa~lA~~~gV~iytIgiG~--~d~~~l~~iA~~tgG~~F~A~d~ 175 (191)
T cd01455 129 --------QP-----KKLADALAREPNVNAFVIFIGS--LSDEADQLQRELPAGKAFVCMDT 175 (191)
T ss_pred --------Ch-----HHHHHHHHHhCCCEEEEEEecC--CCHHHHHHHHhCCCCcEEEeCCH
Confidence 12 233 355567888877766644 36677889999999999988765
No 148
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=28.87 E-value=30 Score=34.40 Aligned_cols=24 Identities=21% Similarity=0.665 Sum_probs=19.1
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
..|..|+. ..++.|.|+-||....
T Consensus 310 ~~C~~cg~---------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 310 KTCPCCGH---------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred ccccccCC---------ccceeEECCCCCCeeh
Confidence 67999998 3357899999998654
No 149
>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=28.61 E-value=20 Score=32.89 Aligned_cols=29 Identities=24% Similarity=0.668 Sum_probs=10.7
Q ss_pred CCccccCCCe-eeCCCceEEcCCceEEeCCCCC
Q 012148 57 APLRCRTCRS-ILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 57 ~~~RC~~C~a-YiNp~~~~~~~g~~w~C~~C~~ 88 (470)
...+|.+|++ |+... .+....++|+||+-
T Consensus 133 ~l~~C~~C~~~fv~~~---~~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 133 QLAPCRRCGGHFVTHA---HDPRHSFVCPFCQP 162 (175)
T ss_dssp EEEE-TTT--EEEEES---S--SS----TT---
T ss_pred cccCCCCCCCCeECcC---CCCCcCcCCCCCCC
Confidence 3689999986 44321 12246899999993
No 150
>PF12257 DUF3608: Protein of unknown function (DUF3608); InterPro: IPR022046 This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with PF00610 from PFAM.
Probab=28.20 E-value=1.5e+02 Score=29.50 Aligned_cols=63 Identities=14% Similarity=0.230 Sum_probs=43.6
Q ss_pred hhHHHHHHHHHHhccC-----CCCCcEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHHHHHHHHH
Q 012148 271 TGTALSIAASLLGACV-----PGSGARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFYDALSKQL 345 (470)
Q Consensus 271 ~G~AL~~A~~ll~~~~-----~~~GG~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY~~la~~~ 345 (470)
+--||..|+..+.... ..+|-.|++-+.|. |-. .-..+..+...+++
T Consensus 205 iLEaINlaln~~~~~~idRdl~rTG~~iivITpG~-----Gvf-----------------------~Vd~~ll~~T~~rl 256 (281)
T PF12257_consen 205 ILEAINLALNQFDKHYIDRDLRRTGQSIIVITPGT-----GVF-----------------------EVDYDLLRLTTQRL 256 (281)
T ss_pred HHHHHHHHhhhcccccccCcccccCceEEEEcCCC-----ceE-----------------------EECHHHHHHHHHHH
Confidence 4467888877776432 24677777766653 333 22246678889999
Q ss_pred HhcCeEEEEeeccCCc
Q 012148 346 VHQGHVLDLFACALDQ 361 (470)
Q Consensus 346 ~~~gisvdlF~~s~~~ 361 (470)
...||++|+.+.+..-
T Consensus 257 ~~~gi~~DlIcL~~~P 272 (281)
T PF12257_consen 257 LDNGIGIDLICLSKPP 272 (281)
T ss_pred HhcCccEEEEEcCCCC
Confidence 9999999999987653
No 151
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=28.18 E-value=31 Score=22.55 Aligned_cols=12 Identities=33% Similarity=1.204 Sum_probs=9.8
Q ss_pred eEEeCCCCCCCC
Q 012148 80 IWICPFCFQRNH 91 (470)
Q Consensus 80 ~w~C~~C~~~N~ 91 (470)
.|+|..||..-.
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 699999997643
No 152
>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=28.17 E-value=68 Score=32.25 Aligned_cols=28 Identities=32% Similarity=0.434 Sum_probs=24.0
Q ss_pred hHHHHHHHHHHHhhcCCCCceEEEEEEC
Q 012148 144 EMSFLKSALSQAIDLLPDNSLVGLITFG 171 (470)
Q Consensus 144 ~~~~l~~~l~~~l~~lp~~~~VglITfd 171 (470)
|++.|...|..+.+.|.++.|+++|||-
T Consensus 215 EL~~L~~~L~~~~~~L~~gGrl~VISfH 242 (305)
T TIGR00006 215 ELEELEEALQFAPNLLAPGGRLSIISFH 242 (305)
T ss_pred hHHHHHHHHHHHHHHhcCCCEEEEEecC
Confidence 4667888999999999999999999874
No 153
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=27.39 E-value=42 Score=29.23 Aligned_cols=25 Identities=28% Similarity=0.623 Sum_probs=19.2
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
--|..|++ |..+ .+| .-.|+.|++.
T Consensus 29 ~hCp~Cg~---PLF~--KdG-~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGT---PLFR--KDG-EVFCPVCGYR 53 (131)
T ss_pred hhCcccCC---ccee--eCC-eEECCCCCce
Confidence 45999997 6666 445 7999999953
No 154
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=27.16 E-value=24 Score=29.34 Aligned_cols=41 Identities=22% Similarity=0.380 Sum_probs=18.3
Q ss_pred ccccCCCeeeCCCceEE------cCCceEEeCCCCCCCCCCccccCC
Q 012148 59 LRCRTCRSILNPFSIVD------FAAKIWICPFCFQRNHFPPHYASI 99 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~------~~g~~w~C~~C~~~N~vp~~y~~~ 99 (470)
-||.-|-+|+.|...+- .+...-+|-+||....+.++||+.
T Consensus 28 GkCpiCDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~~g~sdAYYC~ 74 (106)
T PF03660_consen 28 GKCPICDSYVRPCTKVRICDECSFGSLQGRCIICGSGPGVSDAYYCW 74 (106)
T ss_dssp T--TTT-------EE-EEEHHHHTSSTTSB-TTTSSSB--EE-EE-H
T ss_pred CcccccCCccCCcceEEECCcCCCCCcCceEEEecCCCCcccceehh
Confidence 68999999999965542 244567899999777777788763
No 155
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=27.13 E-value=25 Score=24.06 Aligned_cols=9 Identities=22% Similarity=1.176 Sum_probs=7.4
Q ss_pred ccccCCCee
Q 012148 59 LRCRTCRSI 67 (470)
Q Consensus 59 ~RC~~C~aY 67 (470)
+||.+|++|
T Consensus 2 ~kC~~CG~~ 10 (40)
T PF15288_consen 2 VKCKNCGAF 10 (40)
T ss_pred ccccccccc
Confidence 589999985
No 156
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=26.83 E-value=30 Score=24.86 Aligned_cols=31 Identities=19% Similarity=0.284 Sum_probs=20.7
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
+.++|..|+..+...- .......|.|.-+..
T Consensus 4 g~l~C~~CG~~m~~~~-~~~~~~yy~C~~~~~ 34 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRRK-RKGKYRYYRCSNRRR 34 (58)
T ss_pred CcEEcccCCcEeEEEE-CCCCceEEEcCCCcC
Confidence 3589999999887743 223336788776653
No 157
>PRK10220 hypothetical protein; Provisional
Probab=26.73 E-value=60 Score=27.30 Aligned_cols=29 Identities=24% Similarity=0.575 Sum_probs=19.7
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
.|.|.+|.+- | .. .+|..|+|+-|+++-.
T Consensus 3 lP~CP~C~se---y-tY-~d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 3 LPHCPKCNSE---Y-TY-EDNGMYICPECAHEWN 31 (111)
T ss_pred CCcCCCCCCc---c-eE-cCCCeEECCcccCcCC
Confidence 3678888762 1 12 3456899999997654
No 158
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=26.69 E-value=51 Score=22.95 Aligned_cols=22 Identities=14% Similarity=0.356 Sum_probs=15.0
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCF 87 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~ 87 (470)
+.|..|+- .|.. |.+|+|..|.
T Consensus 1 I~CDgCg~--~PI~-----G~RykC~~C~ 22 (43)
T cd02342 1 IQCDGCGV--LPIT-----GPRYKSKVKE 22 (43)
T ss_pred CCCCCCCC--Cccc-----ccceEeCCCC
Confidence 46788873 3332 6789999885
No 159
>PRK12860 transcriptional activator FlhC; Provisional
Probab=26.56 E-value=33 Score=31.91 Aligned_cols=28 Identities=18% Similarity=0.509 Sum_probs=20.2
Q ss_pred CCccccCCCe-eeCCCceEEcCCceEEeCCCC
Q 012148 57 APLRCRTCRS-ILNPFSIVDFAAKIWICPFCF 87 (470)
Q Consensus 57 ~~~RC~~C~a-YiNp~~~~~~~g~~w~C~~C~ 87 (470)
...+|..|++ ||-. ..+....++|++|.
T Consensus 133 ~l~~C~~Cgg~fv~~---~~e~~~~f~CplC~ 161 (189)
T PRK12860 133 QLARCCRCGGKFVTH---AHDLRHNFVCGLCQ 161 (189)
T ss_pred eeccCCCCCCCeecc---ccccCCCCcCCCCC
Confidence 4799999987 4422 22445689999999
No 160
>KOG2353 consensus L-type voltage-dependent Ca2+ channel, alpha2/delta subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=26.22 E-value=1e+02 Score=36.44 Aligned_cols=51 Identities=22% Similarity=0.389 Sum_probs=42.9
Q ss_pred CCCCEEEEEEEcccchhh--HHHHHHHHHHHhhcCCCCceEEEEEECCeEEEE
Q 012148 127 SVPPVFMFVVDTCIIEEE--MSFLKSALSQAIDLLPDNSLVGLITFGTLVQVH 177 (470)
Q Consensus 127 ~~~p~~vFvID~S~~~~~--~~~l~~~l~~~l~~lp~~~~VglITfd~~V~~y 177 (470)
..+--.+|++|+|.+... +...+..+.++|+.|.++..|-++||++.++.-
T Consensus 223 t~pKdiviLlD~SgSm~g~~~~lak~tv~~iLdtLs~~Dfvni~tf~~~~~~v 275 (1104)
T KOG2353|consen 223 TSPKDIVILLDVSGSMSGLRLDLAKQTVNEILDTLSDNDFVNILTFNSEVNPV 275 (1104)
T ss_pred CCccceEEEEeccccccchhhHHHHHHHHHHHHhcccCCeEEEEeeccccCcc
Confidence 357789999999997543 566799999999999999999999999886644
No 161
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=26.17 E-value=32 Score=28.45 Aligned_cols=14 Identities=29% Similarity=0.605 Sum_probs=12.1
Q ss_pred ceEEeCCCCCCCCC
Q 012148 79 KIWICPFCFQRNHF 92 (470)
Q Consensus 79 ~~w~C~~C~~~N~v 92 (470)
++|+|++||+.+.+
T Consensus 21 k~FtCp~Cghe~vs 34 (104)
T COG4888 21 KTFTCPRCGHEKVS 34 (104)
T ss_pred ceEecCccCCeeee
Confidence 68999999998864
No 162
>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=25.55 E-value=35 Score=39.18 Aligned_cols=26 Identities=23% Similarity=0.454 Sum_probs=21.1
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~v 92 (470)
+.-||.+|+.| .-+++|+.||..+..
T Consensus 624 ~~RKCPkCG~y----------Tlk~rCP~CG~~Te~ 649 (1095)
T TIGR00354 624 AIRKCPQCGKE----------SFWLKCPVCGELTEQ 649 (1095)
T ss_pred EEEECCCCCcc----------cccccCCCCCCcccc
Confidence 46899999997 246999999998754
No 163
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=25.46 E-value=26 Score=38.25 Aligned_cols=25 Identities=24% Similarity=0.240 Sum_probs=12.4
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
.+.+|..|+- ..+ ..|+|+.||..|
T Consensus 490 ~~~~C~~CG~--------~~~-~~~~CP~CGs~~ 514 (546)
T PF13597_consen 490 PIDICPDCGY--------IGG-EGDKCPKCGSEN 514 (546)
T ss_dssp -EEEETTT-----------S---EEE-CCC----
T ss_pred CcccccCCCc--------CCC-CCCCCCCCCCcc
Confidence 5688999984 123 389999999987
No 164
>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=25.15 E-value=1.4e+02 Score=26.76 Aligned_cols=77 Identities=17% Similarity=0.200 Sum_probs=44.5
Q ss_pred CccchhHHHHHHHHHHhccCCC-----CC---cEEEEEecCCCCCCCceeecCCCCCcccCCCCCCCCCCCccchhHHHH
Q 012148 267 STRCTGTALSIAASLLGACVPG-----SG---ARILAFVGGPSTEGPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKFY 338 (470)
Q Consensus 267 ~~~~~G~AL~~A~~ll~~~~~~-----~G---G~Ii~F~~g~pt~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~fY 338 (470)
..+.++.||..|...+...... .+ ..|++++.|.|+.++. ...+.+
T Consensus 77 GgT~l~~aL~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~~~~~~--------------------------~~~~~~ 130 (176)
T cd01464 77 GGTSMGAALELALDCIDRRVQRYRADQKGDWRPWVFLLTDGEPTDDLT--------------------------AAIERI 130 (176)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHhcccCcCCcCcEEEEEcCCCCCchHH--------------------------HHHHHH
Confidence 4578999999999988631100 01 2688888887643210 011222
Q ss_pred HHHHHHHHhcCeEEEEeeccCCccChhhchhhhccc
Q 012148 339 DALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKT 374 (470)
Q Consensus 339 ~~la~~~~~~gisvdlF~~s~~~~~l~~l~~l~~~T 374 (470)
+ .+.+.++.+..|..+. .++...|..++..+
T Consensus 131 ~----~~~~~~~~i~~igiG~-~~~~~~L~~ia~~~ 161 (176)
T cd01464 131 K----EARDSKGRIVACAVGP-KADLDTLKQITEGV 161 (176)
T ss_pred H----hhcccCCcEEEEEecc-ccCHHHHHHHHCCC
Confidence 2 2333466666666654 57777777777533
No 165
>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=25.08 E-value=48 Score=29.35 Aligned_cols=33 Identities=30% Similarity=0.598 Sum_probs=22.5
Q ss_pred CccccCCCeeeCCCceE-----------EcCCceEEeCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIV-----------DFAAKIWICPFCFQRN 90 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~-----------~~~g~~w~C~~C~~~N 90 (470)
..||..|.+-+-+-.+- .....-|.|+-||+.-
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 48999999965443221 1124589999999765
No 166
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=25.00 E-value=39 Score=30.77 Aligned_cols=15 Identities=33% Similarity=1.094 Sum_probs=11.7
Q ss_pred CCceEEeCCCCCCCC
Q 012148 77 AAKIWICPFCFQRNH 91 (470)
Q Consensus 77 ~g~~w~C~~C~~~N~ 91 (470)
.|+.|+|+.||+.-.
T Consensus 131 ~~~~~vC~vCGy~~~ 145 (166)
T COG1592 131 EGKVWVCPVCGYTHE 145 (166)
T ss_pred cCCEEEcCCCCCccc
Confidence 355899999997654
No 167
>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=24.90 E-value=41 Score=30.43 Aligned_cols=35 Identities=20% Similarity=0.633 Sum_probs=20.9
Q ss_pred CccccCCCe------eeCCCceEEcCC------ceEEeCCCCCCCCC
Q 012148 58 PLRCRTCRS------ILNPFSIVDFAA------KIWICPFCFQRNHF 92 (470)
Q Consensus 58 ~~RC~~C~a------YiNp~~~~~~~g------~~w~C~~C~~~N~v 92 (470)
-+.|.+|+- |||++-+.+..| =.|+|.+|++.+.+
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 378999985 688887776533 27999999988775
No 168
>KOG1296 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.58 E-value=34 Score=30.25 Aligned_cols=35 Identities=23% Similarity=0.582 Sum_probs=26.7
Q ss_pred CccccCCCe------eeCCCceEEcCCc------eEEeCCCCCCCCC
Q 012148 58 PLRCRTCRS------ILNPFSIVDFAAK------IWICPFCFQRNHF 92 (470)
Q Consensus 58 ~~RC~~C~a------YiNp~~~~~~~g~------~w~C~~C~~~N~v 92 (470)
-..|.+||- ||+-+-.+...|. ..+|-||+..|.+
T Consensus 30 kLkCtnCgE~~dkw~~I~l~E~~~~pg~Rgta~~v~KCK~C~Rensv 76 (161)
T KOG1296|consen 30 KLKCTNCGELSDKWQYITLNEEVAMPGSRGTASFVMKCKFCSRENSV 76 (161)
T ss_pred EeccccccccCCceEEEEeeeeecCCCCcchhhHhhhhhhhcccCcE
Confidence 588999984 6777666665542 4689999999986
No 169
>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=24.54 E-value=49 Score=22.64 Aligned_cols=27 Identities=33% Similarity=0.752 Sum_probs=14.0
Q ss_pred ccCCCeeeCCCceEEc--CCceEEeCCCCC
Q 012148 61 CRTCRSILNPFSIVDF--AAKIWICPFCFQ 88 (470)
Q Consensus 61 C~~C~aYiNp~~~~~~--~g~~w~C~~C~~ 88 (470)
|..|++ -.-|..|++ ++..|.|+-|+.
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 777777 333443544 345899999953
No 170
>COG4867 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=24.20 E-value=7.1e+02 Score=26.31 Aligned_cols=97 Identities=18% Similarity=0.165 Sum_probs=62.5
Q ss_pred cchhHHHHHHHHHHhccCCCCCcEEEEEecCCCCC----CCceeecCCCCCcccCCCCCCCCCCCccchhHHH--HHHHH
Q 012148 269 RCTGTALSIAASLLGACVPGSGARILAFVGGPSTE----GPAAIVSKNLSEPIRSHKDLDKDSAPHYHKAVKF--YDALS 342 (470)
Q Consensus 269 ~~~G~AL~~A~~ll~~~~~~~GG~Ii~F~~g~pt~----GpG~l~~~~~~~~~r~~~~~~~~~~~~~~~~~~f--Y~~la 342 (470)
..+.-||..|..+++... .---.|++.+.|-||- |.|.+...+ +.+ .|-.-| .+. -
T Consensus 533 TNlhhaL~LA~r~l~Rh~-~~~~~il~vTDGePtAhle~~DG~~~~f~--------yp~--------DP~t~~~Tvr~-~ 594 (652)
T COG4867 533 TNLHHALALAGRHLRRHA-GAQPVVLVVTDGEPTAHLEDGDGTSVFFD--------YPP--------DPRTIAHTVRG-F 594 (652)
T ss_pred cchHHHHHHHHHHHHhCc-ccCceEEEEeCCCccccccCCCCceEecC--------CCC--------ChhHHHHHHHH-H
Confidence 446678888888887422 2345788999998872 445433221 111 121111 112 2
Q ss_pred HHHHhcCeEEEEeeccCCccChhhchhhhcccCceEEEcCC
Q 012148 343 KQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVLSDS 383 (470)
Q Consensus 343 ~~~~~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~v~~y~~ 383 (470)
..|.+.|+-+.+|....+.-=..-+..+++.++|+++.-+.
T Consensus 595 d~~~r~G~q~t~FrLg~DpgL~~Fv~qva~rv~G~vv~pdl 635 (652)
T COG4867 595 DDMARLGAQVTIFRLGSDPGLARFIDQVARRVQGRVVVPDL 635 (652)
T ss_pred HHHHhccceeeEEeecCCHhHHHHHHHHHHHhCCeEEecCc
Confidence 45788999999999988764445578899999999987544
No 171
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=24.18 E-value=89 Score=31.27 Aligned_cols=28 Identities=36% Similarity=0.530 Sum_probs=23.8
Q ss_pred hHHHHHHHHHHHhhcCCCCceEEEEEEC
Q 012148 144 EMSFLKSALSQAIDLLPDNSLVGLITFG 171 (470)
Q Consensus 144 ~~~~l~~~l~~~l~~lp~~~~VglITfd 171 (470)
|++.|...|.++.+.|.++.++++|||-
T Consensus 211 El~~L~~~L~~~~~~L~~gGrl~visfH 238 (296)
T PRK00050 211 ELEELERALEAALDLLKPGGRLAVISFH 238 (296)
T ss_pred hHHHHHHHHHHHHHHhcCCCEEEEEecC
Confidence 3667788888888999999999999885
No 172
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=23.95 E-value=78 Score=25.55 Aligned_cols=31 Identities=23% Similarity=0.328 Sum_probs=22.5
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
+...|..|+.= -.+-... ..|+|.-||..-.
T Consensus 34 ~~~~Cp~C~~~---~VkR~a~-GIW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRT---TVKRIAT-GIWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCc---ceeeecc-CeEEcCCCCCeec
Confidence 56789999873 4444443 5999999997765
No 173
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=23.77 E-value=50 Score=23.67 Aligned_cols=27 Identities=22% Similarity=0.438 Sum_probs=17.5
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
-..|.+|++ .-|+- +...+|.|.=||.
T Consensus 19 ~~~CPrCG~--gvfmA--~H~dR~~CGkCgy 45 (51)
T COG1998 19 NRFCPRCGP--GVFMA--DHKDRWACGKCGY 45 (51)
T ss_pred cccCCCCCC--cchhh--hcCceeEeccccc
Confidence 467999994 11222 2234899999985
No 174
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=23.46 E-value=52 Score=22.25 Aligned_cols=26 Identities=31% Similarity=0.695 Sum_probs=16.2
Q ss_pred ccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 61 C~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
|.+|+.-|.+... .+-..+.|+-|+-
T Consensus 2 CP~C~~~l~~~~~--~~~~id~C~~C~G 27 (41)
T PF13453_consen 2 CPRCGTELEPVRL--GDVEIDVCPSCGG 27 (41)
T ss_pred cCCCCcccceEEE--CCEEEEECCCCCe
Confidence 7777776665543 2335677777763
No 175
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.14 E-value=60 Score=31.98 Aligned_cols=27 Identities=22% Similarity=0.540 Sum_probs=18.8
Q ss_pred ccccCCCeeeCCCceEE-cCCceEEeCCCCC
Q 012148 59 LRCRTCRSILNPFSIVD-FAAKIWICPFCFQ 88 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~-~~g~~w~C~~C~~ 88 (470)
--|.+|++-| -+.. .+...|.|+-|..
T Consensus 245 ~pCprCG~~I---~~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 245 EPCLNCKTPI---RRVVVAGRSSHYCPHCQK 272 (272)
T ss_pred CcCCCCCCee---EEEEECCCccEECcCCcC
Confidence 3499999866 3332 3456999999963
No 176
>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=23.02 E-value=9.1e+02 Score=25.49 Aligned_cols=197 Identities=12% Similarity=0.088 Sum_probs=95.0
Q ss_pred CCCEEEEEEEcccchhh-HHH---HHHHHHHHhhcCCCCceEEEEEECCeEEEEEcCCCCCCCCceeeecCCcccCHHHH
Q 012148 128 VPPVFMFVVDTCIIEEE-MSF---LKSALSQAIDLLPDNSLVGLITFGTLVQVHELGGFGQIIPKTYVFKGSKDVSKDQL 203 (470)
Q Consensus 128 ~~p~~vFvID~S~~~~~-~~~---l~~~l~~~l~~lp~~~~VglITfd~~V~~y~l~~~~~~~~~~~v~~g~~~~t~~~i 203 (470)
.|-=..|++|+|.+..+ +.. +...|...|..+..+.|+||=+|-.+.- .-+. . .+.+.+
T Consensus 101 yPvDLYyLmDlS~Sm~ddl~~l~~lg~~l~~~~~~it~~~~~GfGsfvdK~~-~P~~-~---------------~~p~~l 163 (426)
T PF00362_consen 101 YPVDLYYLMDLSYSMKDDLENLKSLGQDLAEEMRNITSNFRLGFGSFVDKPV-MPFV-S---------------TTPEKL 163 (426)
T ss_dssp --EEEEEEEE-SGGGHHHHHHHCCCCHHHHHHHHTT-SSEEEEEEEESSSSS-TTTS-T----------------SSHCH
T ss_pred cceeEEEEeechhhhhhhHHHHHHHHHHHHHHHHhcCccceEechhhccccc-CCcc-c---------------CChhhh
Confidence 34567899999998654 443 3567888888999999999988854311 0000 0 001111
Q ss_pred HHHhhcccCCCCCCCccccCccCCCCccccccceeeccchHHHHHHHHHhccCCCCCCCCCCCCccchhHHHHHHHHHHh
Q 012148 204 LEQLNFFIKKPKPSTGVIAGVRDGLSSDTIARFLVPAFDCEFTLNSVLEELQKDPWPVPPDQRSTRCTGTALSIAASLLG 283 (470)
Q Consensus 204 ~~~~~l~~~~~~~~~~~~p~~~d~~~~~~~~~~lv~~~~~~~~i~~lL~~L~~~~~~~~~~~~~~~~~G~AL~~A~~ll~ 283 (470)
.... .. ..+.+.-++ . -+-.+++.+........+....- . .+-..|...+=+-+++|+--=.
T Consensus 164 ~~pc--~~--------~~~~c~~~~---~-f~~~l~Lt~~~~~F~~~v~~~~i-s---~n~D~PEgg~dal~Qa~vC~~~ 225 (426)
T PF00362_consen 164 KNPC--PS--------KNPNCQPPF---S-FRHVLSLTDDITEFNEEVNKQKI-S---GNLDAPEGGLDALMQAAVCQEE 225 (426)
T ss_dssp HSTS--CC--------TTS--B------S-EEEEEEEES-HHHHHHHHHTS---B-----SSSSBSHHHHHHHHHH-HHH
T ss_pred cCcc--cc--------cCCCCCCCe---e-eEEeecccchHHHHHHhhhhccc-c---CCCCCCccccchheeeeecccc
Confidence 1111 00 000011001 1 23446677666666666665321 1 2233455566667777653211
Q ss_pred ccCCCCCcEEEEEecCCC--CCCCceeecCCCCCcccCCCCCCCCCCCccc---hhHHHHHHHHHHHHhcCeEEEEeecc
Q 012148 284 ACVPGSGARILAFVGGPS--TEGPAAIVSKNLSEPIRSHKDLDKDSAPHYH---KAVKFYDALSKQLVHQGHVLDLFACA 358 (470)
Q Consensus 284 ~~~~~~GG~Ii~F~~g~p--t~GpG~l~~~~~~~~~r~~~~~~~~~~~~~~---~~~~fY~~la~~~~~~gisvdlF~~s 358 (470)
-.-.+..-||++|++-.+ .-|-|++..--..+..+-|-+ .+. .|.. ....-..+|.+.+.+++|. =+|+..
T Consensus 226 igWr~~a~~llv~~TD~~fH~agDg~l~gi~~pnd~~Chl~--~~~-~y~~~~~~DYPSv~ql~~~l~e~~i~-~IFAVt 301 (426)
T PF00362_consen 226 IGWRNEARRLLVFSTDAGFHFAGDGKLAGIVKPNDGKCHLD--DNG-MYTASTEQDYPSVGQLVRKLSENNIN-PIFAVT 301 (426)
T ss_dssp HT--STSEEEEEEEESS-B--TTGGGGGT--S---SS--BS--TTS-BBGGGGCS----HHHHHHHHHHTTEE-EEEEEE
T ss_pred cCcccCceEEEEEEcCCccccccccccceeeecCCCceEEC--CCC-cccccccccCCCHHHHHHHHHHcCCE-EEEEEc
Confidence 111244578999887544 478888877554444444432 221 1211 1234467888899998885 477776
Q ss_pred CCccC
Q 012148 359 LDQVG 363 (470)
Q Consensus 359 ~~~~~ 363 (470)
....+
T Consensus 302 ~~~~~ 306 (426)
T PF00362_consen 302 KDVYS 306 (426)
T ss_dssp GGGHH
T ss_pred hhhhh
Confidence 66544
No 177
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=22.79 E-value=20 Score=26.14 Aligned_cols=31 Identities=16% Similarity=0.277 Sum_probs=25.1
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
.|.+|++--.|..+-...+..-.||-|+..-
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~ 31 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYW 31 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHH
Confidence 3899999888888887767788999999543
No 178
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=22.76 E-value=50 Score=19.26 Aligned_cols=11 Identities=18% Similarity=0.640 Sum_probs=8.0
Q ss_pred EEeCCCCCCCC
Q 012148 81 WICPFCFQRNH 91 (470)
Q Consensus 81 w~C~~C~~~N~ 91 (470)
|.|.+|+..-.
T Consensus 1 ~~C~~C~~~f~ 11 (25)
T PF12874_consen 1 FYCDICNKSFS 11 (25)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCCcC
Confidence 78888886543
No 179
>COG4874 Uncharacterized protein conserved in bacteria containing a pentein-type domain [Function unknown]
Probab=22.61 E-value=2.5e+02 Score=27.29 Aligned_cols=58 Identities=14% Similarity=0.139 Sum_probs=41.3
Q ss_pred chhHHHHHHHHHHHHhcCeEEEEe-----------eccCCccChhhchhhhcccCceEEEcCCCCchhh---HHHHHHHH
Q 012148 332 HKAVKFYDALSKQLVHQGHVLDLF-----------ACALDQVGVAELKVAVEKTGGLVVLSDSFGHAVF---KDSVRRVF 397 (470)
Q Consensus 332 ~~~~~fY~~la~~~~~~gisvdlF-----------~~s~~~~~l~~l~~l~~~TGG~v~~y~~f~~~~~---~~~l~~~l 397 (470)
..+-.=+..+.+.+.+.||-|.+| ++++.+ .+..-||.|++|+-|...+- .+++...|
T Consensus 53 q~A~~Ef~amve~L~~~GvdV~ifddtg~~~TPDsvFPNNW--------FSTh~~g~v~LyPM~~~nRRlER~~~lid~l 124 (318)
T COG4874 53 QRAMSEFNAMVEGLRQAGVDVVIFDDTGQGETPDSVFPNNW--------FSTHEAGEVFLYPMACANRRLERPEALIDTL 124 (318)
T ss_pred HHHHHHHHHHHHHHHhcCceEEEeecCCCCCCCcccCCCcc--------cccCcCCeEEEeeccCccccccchHHHHHHH
Confidence 344556778999999999988888 333332 36678999999999988642 44555555
No 180
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=22.40 E-value=40 Score=27.98 Aligned_cols=12 Identities=33% Similarity=0.741 Sum_probs=9.4
Q ss_pred ceEEeCCCCCCC
Q 012148 79 KIWICPFCFQRN 90 (470)
Q Consensus 79 ~~w~C~~C~~~N 90 (470)
.+|+|-+||..-
T Consensus 1 ~kWkC~iCg~~I 12 (101)
T PF09943_consen 1 KKWKCYICGKPI 12 (101)
T ss_pred CceEEEecCCee
Confidence 379999999544
No 181
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=22.00 E-value=57 Score=23.90 Aligned_cols=25 Identities=24% Similarity=0.569 Sum_probs=18.5
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
.+..|..|+.+.=| ...|..||+.+
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 45889999996433 57888888655
No 182
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.58 E-value=49 Score=37.31 Aligned_cols=30 Identities=20% Similarity=0.363 Sum_probs=20.0
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
..-+|..|+ | ..-.+. .++.|.|+-||..+
T Consensus 640 ~~~~C~~CG-~-~Ge~~~--~~~~~~CP~CG~~~ 669 (711)
T PRK09263 640 PIDECYECG-F-TGEFEC--TEKGFTCPKCGNHD 669 (711)
T ss_pred CCcccCCCC-C-CccccC--CCCCCcCcCCCCCC
Confidence 568999999 4 221212 23459999999776
No 183
>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=21.27 E-value=1.1e+02 Score=26.27 Aligned_cols=30 Identities=27% Similarity=0.311 Sum_probs=21.5
Q ss_pred HHHHHHHHHHhhcCCC---CceEEEEEECCeEE
Q 012148 146 SFLKSALSQAIDLLPD---NSLVGLITFGTLVQ 175 (470)
Q Consensus 146 ~~l~~~l~~~l~~lp~---~~~VglITfd~~V~ 175 (470)
+.++++|+.-+..-|. +++|.+++||+.|-
T Consensus 113 e~vkDAi~Dyi~T~P~PT~~~~Vt~~~Fd~~V~ 145 (146)
T PF02905_consen 113 ECVKDAIRDYIMTRPQPTCNTQVTVCSFDDGVM 145 (146)
T ss_dssp HHHHHHHHHHHCTS-TTGGGEEEEEEEEEEEE-
T ss_pred HHHHHHHHHHhcCCCCCCcceEEEEEeCCCCCc
Confidence 3467888877766653 57999999997764
No 184
>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=21.24 E-value=55 Score=20.44 Aligned_cols=27 Identities=22% Similarity=0.754 Sum_probs=15.0
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
.|.+|+.++-.... .+...+.|+-|..
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 59999998654433 3345789998864
No 185
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.98 E-value=46 Score=34.80 Aligned_cols=55 Identities=13% Similarity=0.184 Sum_probs=33.9
Q ss_pred CCCCeEEEEccCCCCCCCCCCCCC--------CCC--CCccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 30 CVVPVSAIYTPIKAFPVNNNSMPI--------LPY--APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 30 ~~iPlg~vv~P~~~~~~~~~~ip~--------v~~--~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
..|.-|-.|++.....++ .+-+ ..+ .-++|.+|++-+...=+ +-|+|.=||+.-.
T Consensus 314 ~~L~pGD~i~~~G~~~~~--~~n~ek~~v~~l~~~~~~~p~Cp~Cg~~m~S~G~-----~g~rC~kCg~~~~ 378 (421)
T COG1571 314 RKLIPGDEITVYGSVKPG--TLNLEKFQVLKLARYERVNPVCPRCGGRMKSAGR-----NGFRCKKCGTRAR 378 (421)
T ss_pred HhcCCCCEEEEecCcccc--ceeEEEEEEEEeeeeEEcCCCCCccCCchhhcCC-----CCcccccccccCC
Confidence 446777777776543221 1111 011 35899999997665422 2699999998755
No 186
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.95 E-value=46 Score=36.88 Aligned_cols=26 Identities=23% Similarity=0.424 Sum_probs=20.0
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRN 90 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N 90 (470)
...+|..|+.-+ .|..|.|+.||..+
T Consensus 567 ~~~~C~~CG~~~--------~g~~~~CP~CGs~~ 592 (625)
T PRK08579 567 AITVCNKCGRST--------TGLYTRCPRCGSED 592 (625)
T ss_pred CCccCCCCCCcc--------CCCCCcCcCCCCch
Confidence 578999999822 35579999999753
No 187
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=20.93 E-value=78 Score=20.83 Aligned_cols=30 Identities=23% Similarity=0.533 Sum_probs=19.3
Q ss_pred cccCCCeeeCCCceEEcCCceEEeCCCCCCCCC
Q 012148 60 RCRTCRSILNPFSIVDFAAKIWICPFCFQRNHF 92 (470)
Q Consensus 60 RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~v 92 (470)
-|..|+..|=| +-+..++. .|.-|+..-++
T Consensus 3 FCp~C~nlL~p--~~~~~~~~-~C~~C~Y~~~~ 32 (35)
T PF02150_consen 3 FCPECGNLLYP--KEDKEKRV-ACRTCGYEEPI 32 (35)
T ss_dssp BETTTTSBEEE--EEETTTTE-EESSSS-EEE-
T ss_pred eCCCCCccceE--cCCCccCc-CCCCCCCccCC
Confidence 48899988844 44444445 89999976543
No 188
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=20.83 E-value=44 Score=22.24 Aligned_cols=26 Identities=19% Similarity=0.257 Sum_probs=12.2
Q ss_pred ccCCCeeeCCCceEEcCCceEEeCCCCC
Q 012148 61 CRTCRSILNPFSIVDFAAKIWICPFCFQ 88 (470)
Q Consensus 61 C~~C~aYiNp~~~~~~~g~~w~C~~C~~ 88 (470)
|..|++..|-...- .....+|-.||.
T Consensus 4 C~~Cg~~Yh~~~~p--P~~~~~Cd~cg~ 29 (36)
T PF05191_consen 4 CPKCGRIYHIEFNP--PKVEGVCDNCGG 29 (36)
T ss_dssp ETTTTEEEETTTB----SSTTBCTTTTE
T ss_pred cCCCCCccccccCC--CCCCCccCCCCC
Confidence 55566655544332 223355555553
No 189
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=20.69 E-value=73 Score=21.89 Aligned_cols=24 Identities=25% Similarity=0.492 Sum_probs=17.2
Q ss_pred ccccCCCeeeCCCceEEcCCceEEeCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIWICPFCF 87 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w~C~~C~ 87 (470)
-.|..|+ .|.++ +.+| +-.|..|+
T Consensus 18 ~~Cp~C~---~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCG---TPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred CccCCCC---CeeEE-ecCC-CEECCCCC
Confidence 3588895 67787 3444 68899995
No 190
>PRK12366 replication factor A; Reviewed
Probab=20.67 E-value=65 Score=35.88 Aligned_cols=26 Identities=27% Similarity=0.631 Sum_probs=19.8
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
..+|..|+--+ ..+.+.|.|.-|+..
T Consensus 532 y~aCp~CnkKv------~~~~g~~~C~~c~~~ 557 (637)
T PRK12366 532 LYLCPNCRKRV------EEVDGEYICEFCGEV 557 (637)
T ss_pred EecccccCeEe------EcCCCcEECCCCCCC
Confidence 58999996643 234568999999977
No 191
>PRK07218 replication factor A; Provisional
Probab=20.57 E-value=42 Score=35.31 Aligned_cols=22 Identities=18% Similarity=0.283 Sum_probs=18.0
Q ss_pred CccccCCCeeeCCCceEEcCCceEEeCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKIWICPFCFQR 89 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~ 89 (470)
+-||..|+=-+ .+|.|+.||..
T Consensus 297 i~rCP~C~r~v----------~~~~C~~hG~v 318 (423)
T PRK07218 297 IERCPECGRVI----------QKGQCRSHGAV 318 (423)
T ss_pred eecCcCccccc----------cCCcCCCCCCc
Confidence 68999998766 24999999965
No 192
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=20.56 E-value=71 Score=28.67 Aligned_cols=27 Identities=19% Similarity=0.342 Sum_probs=19.0
Q ss_pred ccccCCCeeeCCCceEEcCC-ceEEeCCCCCCCC
Q 012148 59 LRCRTCRSILNPFSIVDFAA-KIWICPFCFQRNH 91 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g-~~w~C~~C~~~N~ 91 (470)
..|..|+-= +...+ +.|.|.-|+....
T Consensus 35 ~aC~~C~kk------v~~~~~~~~~C~~C~~~~~ 62 (166)
T cd04476 35 PACPGCNKK------VVEEGNGTYRCEKCNKSVP 62 (166)
T ss_pred ccccccCcc------cEeCCCCcEECCCCCCcCC
Confidence 668888663 33333 6899999998764
No 193
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.49 E-value=74 Score=26.39 Aligned_cols=34 Identities=15% Similarity=0.265 Sum_probs=25.0
Q ss_pred CCccccCCCeeeCCCceEEcCCceEEeCCCCCCCC
Q 012148 57 APLRCRTCRSILNPFSIVDFAAKIWICPFCFQRNH 91 (470)
Q Consensus 57 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~~C~~~N~ 91 (470)
....|.+|++. .--+.++.+...-.|..||....
T Consensus 20 t~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 20 KIFECPRCGKV-SISVKIKKNIAIITCGNCGLYTE 53 (99)
T ss_pred cEeECCCCCCe-EeeeecCCCcceEECCCCCCccC
Confidence 35889999963 44455666666899999998765
No 194
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=20.39 E-value=1.1e+02 Score=27.00 Aligned_cols=33 Identities=21% Similarity=0.357 Sum_probs=26.0
Q ss_pred CccccCCCeeeCCCceEEcCCce--EEeCCCCCCCCCC
Q 012148 58 PLRCRTCRSILNPFSIVDFAAKI--WICPFCFQRNHFP 93 (470)
Q Consensus 58 ~~RC~~C~aYiNp~~~~~~~g~~--w~C~~C~~~N~vp 93 (470)
=+.|..|++ |=..+...++. -+|.-||..-.+.
T Consensus 102 yVlC~~C~s---pdT~l~k~~r~~~l~C~ACGa~~~V~ 136 (138)
T PRK03988 102 YVICPECGS---PDTKLIKEGRIWVLKCEACGAETPVK 136 (138)
T ss_pred cEECCCCCC---CCcEEEEcCCeEEEEcccCCCCCcCC
Confidence 388999997 77777766664 5799999988774
No 195
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=20.34 E-value=93 Score=29.23 Aligned_cols=33 Identities=15% Similarity=0.330 Sum_probs=26.3
Q ss_pred ccccCCCeeeCCCceEEcCCceE--EeCCCCCCCCCCc
Q 012148 59 LRCRTCRSILNPFSIVDFAAKIW--ICPFCFQRNHFPP 94 (470)
Q Consensus 59 ~RC~~C~aYiNp~~~~~~~g~~w--~C~~C~~~N~vp~ 94 (470)
+.|..|+. |=..+...++.| +|.-||..-.+..
T Consensus 99 V~C~~C~~---pdT~l~k~~~~~~l~C~aCGa~~~v~~ 133 (201)
T PRK12336 99 VICSECGL---PDTRLVKEDRVLMLRCDACGAHRPVKK 133 (201)
T ss_pred EECCCCCC---CCcEEEEcCCeEEEEcccCCCCccccc
Confidence 88999997 777777666654 7999999988753
No 196
>PF11265 Med25_VWA: Mediator complex subunit 25 von Willebrand factor type A; InterPro: IPR021419 The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex [].
Probab=20.24 E-value=7.7e+02 Score=23.64 Aligned_cols=105 Identities=13% Similarity=0.109 Sum_probs=62.8
Q ss_pred HHHHHHHhccCCCCCCCCCCCCccc-hhHHHHHHHHHHhccC---CCCC-----cEEEEEecCCCCCCCceeecCCCCCc
Q 012148 246 TLNSVLEELQKDPWPVPPDQRSTRC-TGTALSIAASLLGACV---PGSG-----ARILAFVGGPSTEGPAAIVSKNLSEP 316 (470)
Q Consensus 246 ~i~~lL~~L~~~~~~~~~~~~~~~~-~G~AL~~A~~ll~~~~---~~~G-----G~Ii~F~~g~pt~GpG~l~~~~~~~~ 316 (470)
.+...|++|+-.. +.-..++ ...+|..|+.++.... ...+ =+.|+.++++|..=| ..
T Consensus 91 ~fl~~L~~I~f~G-----GG~e~~a~iaEGLa~AL~~fd~~~~~r~~~~~~~~~khcILI~nSpP~~~p----~~----- 156 (226)
T PF11265_consen 91 KFLQWLDAIQFSG-----GGFESCAAIAEGLAEALQCFDDFKQMRQQQQQTDVQKHCILICNSPPYRLP----VN----- 156 (226)
T ss_pred HHHHHHHccCcCC-----CCcccchhHHHHHHHHHHHhcchhhhccccCcccccceEEEEeCCCCcccc----cc-----
Confidence 5667777776542 2222233 6677888887776211 1111 245666667764333 11
Q ss_pred ccCCCCCCCCCCCccchhHHHHHHHHHHHHhcCeEEEEeeccCCccChhhchhhhcccCceEEE
Q 012148 317 IRSHKDLDKDSAPHYHKAVKFYDALSKQLVHQGHVLDLFACALDQVGVAELKVAVEKTGGLVVL 380 (470)
Q Consensus 317 ~r~~~~~~~~~~~~~~~~~~fY~~la~~~~~~gisvdlF~~s~~~~~l~~l~~l~~~TGG~v~~ 380 (470)
+..++ ....+++++..+.+++|.+.++.= --+..+..|-+..+|....
T Consensus 157 ---------~~~~~---~~~~~d~la~~~~~~~I~LSiisP----rklP~l~~Lfeka~~~~~~ 204 (226)
T PF11265_consen 157 ---------ECPQY---SGKTCDQLAVLISERNISLSIISP----RKLPSLRSLFEKAKGNPRA 204 (226)
T ss_pred ---------CCCcc---cCCCHHHHHHHHHhcCceEEEEcC----ccCHHHHHHHHhcCCCccc
Confidence 11111 224678999999999999998742 3567788888888877665
Done!